{ "sibils_version": "v5.0.5.8", "success": true, "error": "", "collection": "medline", "ndocs": 10, "original_query": "Rhinolophus and Pangolin", "transformed_query": { "query": { "bool": { "must": [ { "bool": { "should": [ { "multi_match": { "query": "Rhinolophus", "fields": [ "title", "abstract", "keywords", "mesh_terms", "sup_mesh_terms", "chemicals" ] } }, { "term": { "annotations.all": "ncbitaxon_full|49442|Rhinolophus" } }, { "term": { "annotations.all": "mesh|D002685|Chiroptera" } }, { "term": { "annotations.all": "covocorganism|SP_20|Rhinolophus macrotis" } }, { "term": { "annotations.all": "ott|756634|Rhinolophus" } } ] } }, { "multi_match": { "query": "and", "fields": [ "title", "abstract", "keywords", "mesh_terms", "sup_mesh_terms", "chemicals" ] } }, { "bool": { "should": [ { "multi_match": { "query": "Pangolin", "fields": [ "title", "abstract", "keywords", "mesh_terms", "sup_mesh_terms", "chemicals" ] } }, { "term": { "annotations.all": "ott|644247|Manis" } }, { "term": { "annotations.all": "covocorganism|SP_14|Manidae" } }, { "term": { "annotations.all": "mesh|D000086642|Pangolins" } } ] } } ] } } }, "elastic_output": { "took": 14, "timed_out": false, "_shards": { "total": 1, "successful": 1, "skipped": 0, "failed": 0 }, "hits": { "total": { "value": 154, "relation": "eq" }, "max_score": 150.63004, "hits": [ { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "35700806", "_score": 150.63004, "_source": { "title": "Variation in synonymous nucleotide composition among genomes of sarbecoviruses and consequences for the origin of COVID-19.", "abstract": "The subgenus Sarbecovirus includes two human viruses, SARS-CoV and SARS-CoV-2, respectively responsible for the SARS epidemic and COVID-19 pandemic, as well as many bat viruses and two pangolin viruses. Here, the synonymous nucleotide composition (SNC) of Sarbecovirus genomes was analysed by examining third codon-positions, dinucleotides, and degenerate codons. The results show evidence for the eight following groups: (i) SARS-CoV related coronaviruses (SCoVrC including many bat viruses from China), (ii) SARS-CoV-2 related coronaviruses (SCoV2rC; including five bat viruses from Cambodia, Thailand and Yunnan), (iii) pangolin sarbecoviruses, (iv) three bat sarbecoviruses showing evidence of recombination between SCoVrC and SCoV2rC genomes, (v) two highly divergent bat sarbecoviruses from Yunnan, (vi) the bat sarbecovirus from Japan, (vii) the bat sarbecovirus from Bulgaria, and (viii) the bat sarbecovirus from Kenya. All these groups can be diagnosed by specific nucleotide compositional features except the one concerned by recombination between SCoVrC and SCoV2rC. In particular, SCoV2rC genomes have less cytosines and more uracils at third codon-positions than other sarbecoviruses, whereas the genomes of pangolin sarbecoviruses show more adenines at third codon-positions. I suggest that taxonomic differences in the imbalanced nucleotide pools available in host cells during viral replication can explain the eight groups of SNC here detected among Sarbecovirus genomes. A related effect due to hibernating bats and their latitudinal distribution is also discussed. I conclude that the two independent host switches from Rhinolophus bats to pangolins resulted in convergent mutational constraints and that SARS-CoV-2 emerged directly from a horseshoe bat sarbecovirus.", "coi_statement": "", "journal": "Gene", "authors": [ "Hassanin Alexandre" ], "affiliations": [ "Institut de Syst\u00e9matique, \u00c9volution, Biodiversit\u00e9 (ISYEB), Sorbonne Universit\u00e9, CNRS, EPHE, MNHN, UA, Paris, France. Electronic address: alexandre.hassanin@mnhn.fr." ], "pubyear": "2022", "publication_date": "2022-08-15", "entrez_date": "2022-06-14", "pmid": "35700806", "mesh_terms": [ "D000818:Animals", "D000086382:COVID-19", "D002681:China", "D002685:Chiroptera", "D016679:Genome, Viral", "D006801:Humans", "D009711:Nucleotides", "D058873:Pandemics", "D000086642:Pangolins", "D010802:Phylogeny", "D045473:Severe acute respiratory syndrome-related coronavirus", "D000086402:SARS-CoV-2" ], "sup_mesh_terms": [], "chemicals": [ "RN 0, D009711:Nucleotides" ], "publication_types": [ "Journal Article" ], "keywords": [ "Intermediate host", "Manis javanica", "RdRp selection", "Recombination", "Reservoir host", "Synonymous mutations" ], "pmcid": "PMC9200079", "doi": "10.1016/j.gene.2022.146641", "medline_ta": "Gene", "docid": "35700806", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1140.json.gz", "annotations": { "title": [ "mesh|D016678|Genome", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "agrovoc|c_3224|genomes", "agrovoc|c_4ad07701|COVID-19", "chebi|CHEBI:36976|nucleotide" ], "all": [ "mesh|D016678|Genome", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "agrovoc|c_3224|genomes", "agrovoc|c_4ad07701|COVID-19", "chebi|CHEBI:36976|nucleotide", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_full|10239|Viruses", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_viruses|10239|Viruses", "mesh|D000086382|COVID-19", "covocorganism|SP_4|Chiroptera", "covocconceptualentities|CE_22|epidemics", "covocorganism|SP_6|COVID-19", "agrovoc|c_8262|viruses", "covocorganism|SP_14|Manidae", "mdd|1000718|Homo_sapiens", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|10239|Viruses", "covocbiomed|BMV_163|viruses", "agrovoc|c_8262|viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D000086642|Pangolins", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_163|viruses", "covocorganism|SP_21|SARS-CoV", "ncbitaxon_models|9606|Homo sapiens", "agrovoc|c_8262|viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_163|viruses", "agrovoc|c_4ad07701|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|644247|Manis", "pubchemmesh|439693|Pentostatin", "mesh|D014780|Viruses", "ncbitaxon_viruses|2509511|Sarbecovirus", "ott|770315|Homo sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D014780|Viruses", "ncbitaxon_viruses|10239|Viruses", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_11|Homo sapiens", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D014780|Viruses", "covocconceptualentities|CE_54|Pandemics", "ncbitaxon_viruses|10239|Viruses", "ncbitaxon_full|10239|Viruses", "chebi|CHEBI:47885|dinucleotide", "mesh|D003062|Codon", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D003062|Codon", "agrovoc|c_3224|genomes", "agrovoc|c_37477|codons", "pubchemmesh|20831824|(4R,4aR,7aR,12bS)-9-methoxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one;2,3-dihydroxybutanedioic acid", "chebi|CHEBI:36976|nucleotide", "mesh|D016678|Genome", "ncbitaxon_viruses|2509511|Sarbecovirus", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_163|viruses", "covocbiomed|BMV_34|coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D007630|Kenya", "ncbitaxon_full|2509511|Sarbecovirus", "mesh|D002031|Bulgaria", "agrovoc|c_1145|Bulgaria", "mesh|D014780|Viruses", "covocorganism|SP_4|Chiroptera", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D017934|Coronavirus", "ncbitaxon_full|2509511|Sarbecovirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_14|Manidae", "covocorganism|SP_4|Chiroptera", "mesh|D002160|Cambodia", "agrovoc|c_3224|genomes", "ncbitaxon_viruses|10239|Viruses", "covocorganism|SP_4|Chiroptera", "agrovoc|c_6475|recombination", "mesh|D014780|Viruses", "mesh|D016678|Genome", "ncbitaxon_full|73171|Bulgaria", "ncbitaxon_full|10239|Viruses", "mesh|D000086642|Pangolins", "ncbitaxon_viruses|2509511|Sarbecovirus", "ncbitaxon_models|227859|Human SARS coronavirus", "covocbiomed|BMV_119|recombination", "ncbitaxon_viruses|10239|Viruses", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D007564|Japan", "mesh|D013785|Thailand", "covocorganism|SP_4|Chiroptera", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_21|SARS-CoV", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "agrovoc|c_8262|viruses", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_full|10239|Viruses", "ott|644247|Manis", "covocbiomed|BMV_163|viruses", "ncbitaxon_viruses|2509511|Sarbecovirus", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_viruses|2509511|Sarbecovirus", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_4|Chiroptera", "mesh|D017934|Coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocgeographicloc|LOC_3|China", "agrovoc|c_8262|viruses", "pubchemmesh|439693|Pentostatin", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocbiomed|BMV_119|recombination", "chebi|CHEBI:36976|nucleotide", "agrovoc|c_6475|recombination", "agrovoc|c_3224|genomes", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D016678|Genome", "pubchemmesh|190|Adenine", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "agrovoc|c_3224|genomes", "mesh|D016678|Genome", "mesh|D003062|Codon", "mesh|D003062|Codon", "pubchemmesh|20831824|(4R,4aR,7aR,12bS)-9-methoxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one;2,3-dihydroxybutanedioic acid", "pubchemmesh|20831824|(4R,4aR,7aR,12bS)-9-methoxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one;2,3-dihydroxybutanedioic acid", "mesh|D000086642|Pangolins", "pubchemmesh|1174|Uracil", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "agrovoc|c_35087|viral replication", "ncbitaxon_viruses|2509511|Sarbecovirus", "ncbitaxon_full|2509511|Sarbecovirus", "mesh|D016678|Genome", "covocconceptualentities|CE_37|host", "go_bp|GO:0019058|viral life cycle", "chebi|CHEBI:36976|nucleotide", "covocbiomed|BMV_162|Virus Replication", "covocbiomed|BMV_64|host cell", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "agrovoc|c_3224|genomes", "ott|574724|Chiroptera", "covocconceptualentities|CE_19|distribution", "covocorganism|SP_4|Chiroptera", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|3068538|Horseshoe bat sarbecovirus", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_4|Chiroptera", "ott|574724|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D000086642|Pangolins", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|49442|Rhinolophus", "covocconceptualentities|CE_37|host", "covocorganism|SP_14|Manidae", "mesh|D002685|Chiroptera", "agrovoc|c_5793|Pholidota", "agrovoc|c_1820|constraints", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D002685|Chiroptera", "ncbitaxon_full|3068538|Horseshoe bat sarbecovirus", "ott|756634|Rhinolophus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_4|Chiroptera", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_20|Rhinolophus macrotis", "ror|01dadvw90|\"Institut de Syst\u00e9matique", "ror|02feahw73|Centre National de la Recherche Scientifique", "ror|04daj8721|\"France", "ror|011abem59|\"\u00c9volution", "ror|03wkt5x30|Mus\u00e9um national d'Histoire naturelle", "ror|03wkt5x30|Mus\u00e9um national d'Histoire naturelle", "ror|04byv8g40|\"Biodiversit\u00e9", "ror|046b3cj80|\u00c9cole Pratique des Hautes \u00c9tudes", "ror|02en5vm52|Sorbonne Universit\u00e9", "mesh|D000818|Animals", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "covocgeographicloc|LOC_3|China", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "mesh|D009711|Nucleotides", "agrovoc|c_5259|nucleotides", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "agrovoc|c_31878c8d|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_viruses|694009|Severe acute respiratory syndrome-related coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "ncbitaxon_full|694009|Severe acute respiratory syndrome-related coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_5|Coronavirus", "ncit|C85064|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D009711|Nucleotides", "agrovoc|c_5259|nucleotides", "covocconceptualentities|CE_44|intermediate host", "mesh|D000086642|Pangolins", "ncbitaxon_full|9974|Manis javanica", "ott|644245|Manis javanica", "covocproteinsgenomes|PG_26|RNA-dependent RNA polymerase", "covocbiomed|BMV_119|recombination", "agrovoc|c_6475|recombination", "envo|ENVO_00000025|reservoir", "covocconceptualentities|CE_37|host", "robiext|RO_e000051|reservoir host", "mesh|D000069456|Silent Mutation", "covocbiomed|BMV_95|Mutation" ], "abstract": [ "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_full|10239|Viruses", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_viruses|10239|Viruses", "mesh|D000086382|COVID-19", "covocorganism|SP_4|Chiroptera", "covocconceptualentities|CE_22|epidemics", "covocorganism|SP_6|COVID-19", "agrovoc|c_8262|viruses", "covocorganism|SP_14|Manidae", "mdd|1000718|Homo_sapiens", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|10239|Viruses", "covocbiomed|BMV_163|viruses", "agrovoc|c_8262|viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D000086642|Pangolins", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_163|viruses", "covocorganism|SP_21|SARS-CoV", "ncbitaxon_models|9606|Homo sapiens", "agrovoc|c_8262|viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_163|viruses", "agrovoc|c_4ad07701|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|644247|Manis", "pubchemmesh|439693|Pentostatin", "mesh|D014780|Viruses", "ncbitaxon_viruses|2509511|Sarbecovirus", "ott|770315|Homo sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D014780|Viruses", "ncbitaxon_viruses|10239|Viruses", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_11|Homo sapiens", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D014780|Viruses", "covocconceptualentities|CE_54|Pandemics", "ncbitaxon_viruses|10239|Viruses", "ncbitaxon_full|10239|Viruses", "chebi|CHEBI:47885|dinucleotide", "mesh|D003062|Codon", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D003062|Codon", "agrovoc|c_3224|genomes", "agrovoc|c_37477|codons", "pubchemmesh|20831824|(4R,4aR,7aR,12bS)-9-methoxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one;2,3-dihydroxybutanedioic acid", "chebi|CHEBI:36976|nucleotide", "mesh|D016678|Genome", "ncbitaxon_viruses|2509511|Sarbecovirus", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_163|viruses", "covocbiomed|BMV_34|coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D007630|Kenya", "ncbitaxon_full|2509511|Sarbecovirus", "mesh|D002031|Bulgaria", "agrovoc|c_1145|Bulgaria", "mesh|D014780|Viruses", "covocorganism|SP_4|Chiroptera", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D017934|Coronavirus", "ncbitaxon_full|2509511|Sarbecovirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_14|Manidae", "covocorganism|SP_4|Chiroptera", "mesh|D002160|Cambodia", "agrovoc|c_3224|genomes", "ncbitaxon_viruses|10239|Viruses", "covocorganism|SP_4|Chiroptera", "agrovoc|c_6475|recombination", "mesh|D014780|Viruses", "mesh|D016678|Genome", "ncbitaxon_full|73171|Bulgaria", "ncbitaxon_full|10239|Viruses", "mesh|D000086642|Pangolins", "ncbitaxon_viruses|2509511|Sarbecovirus", "ncbitaxon_models|227859|Human SARS coronavirus", "covocbiomed|BMV_119|recombination", "ncbitaxon_viruses|10239|Viruses", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D007564|Japan", "mesh|D013785|Thailand", "covocorganism|SP_4|Chiroptera", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_21|SARS-CoV", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "agrovoc|c_8262|viruses", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_full|10239|Viruses", "ott|644247|Manis", "covocbiomed|BMV_163|viruses", "ncbitaxon_viruses|2509511|Sarbecovirus", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_viruses|2509511|Sarbecovirus", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_4|Chiroptera", "mesh|D017934|Coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocgeographicloc|LOC_3|China", "agrovoc|c_8262|viruses", "pubchemmesh|439693|Pentostatin", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocbiomed|BMV_119|recombination", "chebi|CHEBI:36976|nucleotide", "agrovoc|c_6475|recombination", "agrovoc|c_3224|genomes", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D016678|Genome", "pubchemmesh|190|Adenine", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "agrovoc|c_3224|genomes", "mesh|D016678|Genome", "mesh|D003062|Codon", "mesh|D003062|Codon", "pubchemmesh|20831824|(4R,4aR,7aR,12bS)-9-methoxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one;2,3-dihydroxybutanedioic acid", "pubchemmesh|20831824|(4R,4aR,7aR,12bS)-9-methoxy-3-methyl-1,2,4,4a,5,6,7a,13-octahydro-4,12-methanobenzofuro[3,2-e]isoquinolin-7-one;2,3-dihydroxybutanedioic acid", "mesh|D000086642|Pangolins", "pubchemmesh|1174|Uracil", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "agrovoc|c_35087|viral replication", "ncbitaxon_viruses|2509511|Sarbecovirus", "ncbitaxon_full|2509511|Sarbecovirus", "mesh|D016678|Genome", "covocconceptualentities|CE_37|host", "go_bp|GO:0019058|viral life cycle", "chebi|CHEBI:36976|nucleotide", "covocbiomed|BMV_162|Virus Replication", "covocbiomed|BMV_64|host cell", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "agrovoc|c_3224|genomes", "ott|574724|Chiroptera", "covocconceptualentities|CE_19|distribution", "covocorganism|SP_4|Chiroptera", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|3068538|Horseshoe bat sarbecovirus", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_4|Chiroptera", "ott|574724|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D000086642|Pangolins", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|49442|Rhinolophus", "covocconceptualentities|CE_37|host", "covocorganism|SP_14|Manidae", "mesh|D002685|Chiroptera", "agrovoc|c_5793|Pholidota", "agrovoc|c_1820|constraints", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D002685|Chiroptera", "ncbitaxon_full|3068538|Horseshoe bat sarbecovirus", "ott|756634|Rhinolophus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_4|Chiroptera", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_20|Rhinolophus macrotis" ], "affiliations": [ "ror|01dadvw90|\"Institut de Syst\u00e9matique", "ror|02feahw73|Centre National de la Recherche Scientifique", "ror|04daj8721|\"France", "ror|011abem59|\"\u00c9volution", "ror|03wkt5x30|Mus\u00e9um national d'Histoire naturelle", "ror|03wkt5x30|Mus\u00e9um national d'Histoire naturelle", "ror|04byv8g40|\"Biodiversit\u00e9", "ror|046b3cj80|\u00c9cole Pratique des Hautes \u00c9tudes", "ror|02en5vm52|Sorbonne Universit\u00e9" ], "mesh_terms": [ "mesh|D000818|Animals", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "covocgeographicloc|LOC_3|China", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "mesh|D009711|Nucleotides", "agrovoc|c_5259|nucleotides", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "agrovoc|c_31878c8d|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_viruses|694009|Severe acute respiratory syndrome-related coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "ncbitaxon_full|694009|Severe acute respiratory syndrome-related coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_5|Coronavirus", "ncit|C85064|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin" ], "chemicals": [ "mesh|D009711|Nucleotides", "agrovoc|c_5259|nucleotides" ], "keywords": [ "covocconceptualentities|CE_44|intermediate host", "mesh|D000086642|Pangolins", "ncbitaxon_full|9974|Manis javanica", "ott|644245|Manis javanica", "covocproteinsgenomes|PG_26|RNA-dependent RNA polymerase", "covocbiomed|BMV_119|recombination", "agrovoc|c_6475|recombination", "envo|ENVO_00000025|reservoir", "covocconceptualentities|CE_37|host", "robiext|RO_e000051|reservoir host", "mesh|D000069456|Silent Mutation", "covocbiomed|BMV_95|Mutation" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "32637954", "_score": 148.34071, "_source": { "title": "Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2.", "abstract": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates infection of cells expressing angiotensin-converting enzyme 2 (ACE2). ACE2 is also the viral receptor of SARS-CoV (SARS-CoV-1), a related coronavirus that emerged in 2002-2003. Horseshoe bats (genus Rhinolophus ) are presumed to be the original reservoir of both viruses, and a SARS-like coronavirus, RaTG13, closely related SARS-CoV-2, has been isolated from one horseshoe-bat species. Here we characterize the ability of S-protein receptor-binding domains (RBDs) of SARS-CoV-1, SARS-CoV-2, and RaTG13 to bind a range of ACE2 orthologs. We observed that the SARS-CoV-2 RBD bound human, pangolin, and horseshoe bat ( R. macrotis) ACE2 more efficiently than the SARS-CoV-1 or RaTG13 RBD. Only the RaTG13 RBD bound rodent ACE2 orthologs efficiently. Five mutations drawn from ACE2 orthologs of nine Rhinolophus species enhanced human ACE2 binding to the SARS-CoV-2 RBD and neutralization of SARS-CoV-2 by an immunoadhesin form of human ACE2 (ACE2-Fc). Two of these mutations impaired neutralization of SARS-CoV-1. An ACE2-Fc variant bearing all five mutations neutralized SARS-CoV-2 five-fold more efficiently than human ACE2-Fc. These data narrow the potential SARS-CoV-2 reservoir, suggest that SARS-CoV-1 and -2 originate from distinct bat species, and identify a more potently neutralizing form of ACE2-Fc.", "coi_statement": "", "journal": "bioRxiv : the preprint server for biology", "authors": [ "Mou Huihui", "Quinlan Brian D", "Peng Haiyong", "Guo Yan", "Peng Shoujiao", "Zhang Lizhou", "Davis-Gardner Meredith E", "Gardner Matthew R", "Crynen Gogce", "Voo Zhi Xiang", "Bailey Charles C", "Alpert Michael D", "Rader Christoph", "Choe Hyeryun", "Farzan Michael" ], "affiliations": [ "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Emmune, Inc., Juno Beach, FL 33408, USA.", "Emmune, Inc., Juno Beach, FL 33408, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA." ], "pubyear": "2020", "publication_date": "2020-06-30", "entrez_date": "2020-07-09", "pmid": "32637954", "mesh_terms": [], "sup_mesh_terms": [], "chemicals": [], "publication_types": [ "Preprint", "Journal Article" ], "keywords": [], "pmcid": "PMC7337384", "doi": "10.1101/2020.06.29.178459", "medline_ta": "bioRxiv", "docid": "32637954", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1040.json.gz", "annotations": { "title": [ "uniprot_swissprot|Q5EGZ1|Ace2", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_95|Mutation", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q5EGZ1|Ace2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "nextprot|NX_Q9BYF1|ACE2", 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Cuba Astronomical Observatory", "ror|0231an742|Jiangmen Underground Neutrino Observatory", "ror|02anj9s22|Mt. Cuba Astronomical Observatory", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute" ], "abstract": [ "agrovoc|c_365a18ab|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_34|coronavirus", "covocproteinsgenomes|PG_2|ACE2", "covocproteinsgenomes|PG_29|Spike glycoprotein", "psimi|MI:1115|spike", "ncit|C85064|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_37|infection", "nextprot|NX_Q9BYF1|ACE2", "uniprot_swissprot|Q5EGZ1|Ace2", "mesh|D000085962|Angiotensin-Converting Enzyme 2", "nextprot|NX_Q9BYF1|ACE2", "uniprot_swissprot|P19704|hss", "ncbitaxon_models|227859|Human SARS coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D000086402|SARS-CoV-2", "pubchemmesh|439693|Pentostatin", "ncit|C128320|Infection", "mesh|D000086402|SARS-CoV-2", "psimi|MI:0501|enzyme", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_36006|angiotensin", "covocbiomed|BMV_77|infection", "ncbitaxon_models|227859|Human SARS coronavirus", "chebi|CHEBI:48433|angiotensin", "uniprot_swissprot|Q5EGZ1|Ace2", "covocorganism|SP_6|COVID-19", "flopo|FLOPO_0900001|inflorescence type spike", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "nextprot|NX_Q9BYF1|ACE2", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_21|SARS-CoV", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_21|SARS-CoV", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "uniprot_swissprot|Q5EGZ1|Ace2", "ncbitaxon_full|10239|Viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|49442|Rhinolophus", "covocorganism|SP_5|Coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|694009|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_viruses|694009|Severe acute respiratory syndrome-related coronavirus", "mesh|D002685|Chiroptera", "mesh|D014780|Viruses", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "agrovoc|c_8262|viruses", "ott|756634|Rhinolophus", "envo|ENVO_00000025|reservoir", "covocorganism|SP_20|Rhinolophus macrotis", "covocbiomed|BMV_163|viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_viruses|10239|Viruses", "ott|635025|Rhinolophidae", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D002685|Chiroptera", "covocbiomed|BMV_34|coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_21|SARS-CoV", "psimi|MI:0462|bind", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ppiptm|PPI:2|bind", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "go_mf|GO:0005488|binding", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_P04004|VTN", "nextprot|NX_Q9BYF1|ACE2", "ppiptm|PPI:2|bind", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "uniprot_swissprot|P22458|VTN", "pubchemmesh|439693|Pentostatin", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "covocorganism|SP_14|Manidae", "covocproteinsgenomes|PG_27|SARS-CoV-2 RBD", "ott|665410|Rhinolophus macrotis", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_4|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D002685|Chiroptera", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D000086642|Pangolins", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ott|770315|Homo sapiens", "covocproteinsgenomes|PG_2|ACE2", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "mdd|1000718|Homo_sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "covocorganism|SP_21|SARS-CoV", "ott|644247|Manis", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_full|92650|Macrotis", "ott|864593|Rodentia", "covocproteinsgenomes|PG_2|ACE2", "uniprot_swissprot|Q5EGZ1|Ace2", "mesh|D012377|Rodentia", "nextprot|NX_Q9BYF1|ACE2", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "mdd|1000718|Homo_sapiens", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q5EGZ1|Ace2", "ott|770315|Homo sapiens", "covocproteinsgenomes|PG_27|SARS-CoV-2 RBD", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q5EGZ1|Ace2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "go_mf|GO:0005488|binding", "covocproteinsgenomes|PG_2|ACE2", "covocorganism|SP_11|Homo sapiens", "uniprot_swissprot|Q5EGZ1|Ace2", "pubchemmesh|439693|Pentostatin", "ncbitaxon_models|227859|Human SARS coronavirus", "nextprot|NX_Q9BYF1|ACE2", "ncbitaxon_models|9606|Homo sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "ott|770315|Homo sapiens", "covocbiomed|BMV_95|Mutation", "nextprot|NX_Q9BYF1|ACE2", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "mesh|D002685|Chiroptera", "pubchemmesh|439693|Pentostatin", "covocproteinsgenomes|PG_2|ACE2", "covocorganism|SP_11|Homo sapiens", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "ott|756634|Rhinolophus", "ncbitaxon_models|9606|Homo sapiens", "ppiptm|PPI:2|bind", "mdd|1000718|Homo_sapiens", "nextprot|NX_Q9BYF1|ACE2", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "nextprot|NX_Q9BYF1|ACE2", "uniprot_swissprot|Q5EGZ1|Ace2", "agrovoc|c_5151|neutralization", "ncbitaxon_full|49442|Rhinolophus", "pubchemmesh|439693|Pentostatin", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_21|SARS-CoV", "covocbiomed|BMV_95|Mutation", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "agrovoc|c_5151|neutralization", "ncbitaxon_models|227859|Human SARS coronavirus", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "mdd|1000718|Homo_sapiens", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "covocbiomed|BMV_95|Mutation", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "psimi|MI:1241|variant", "ott|770315|Homo sapiens", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "covocorganism|SP_21|SARS-CoV", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "uniprot_swissprot|Q8CIQ8|Sars", "pubchemmesh|439693|Pentostatin", "ncbitaxon_models|227859|Human SARS coronavirus", "envo|ENVO_00000025|reservoir", "uniprot_swissprot|Q5EGZ1|Ace2", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "nextprot|NX_Q9BYF1|ACE2", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome" ], "affiliations": [ "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|03ss07w66|Centre for Ocean Research and Education", "ror|0264vhs54|G\u00e9nomique Bioinformatique et Applications", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|0231an742|Jiangmen Underground Neutrino Observatory", "ror|02anj9s22|Mt. Cuba Astronomical Observatory", "ror|0231an742|Jiangmen Underground Neutrino Observatory", "ror|02anj9s22|Mt. Cuba Astronomical Observatory", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "34910734", "_score": 147.4813, "_source": { "title": "Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals.", "abstract": "The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) showed susceptibility to diverse animal species. We conducted this study to understand the spatial epidemiology, genetic diversity, and statistically significant genetic similarity along with per-gene recombination events of SARS-CoV-2 and related viruses (SC2r-CoVs) in animals globally. We collected a number of different animal species infected with SARS-CoV-2 and its related viruses. Then, we retrieved genome sequences of SARS-CoV-2 and SC2r-CoVs from GISAID and NCBI GenBank for genomic and mutational analysis. Although the evolutionary origin of SARS-CoV-2 remains elusive, the diverse SC2r-CoV have been detected in multiple Rhinolophus bat species and in Malayan pangolin. To date, human-to-animal spillover events have been reported in cat, dog, tiger, lion, gorilla, leopard, ferret, puma, cougar, otter, and mink in 25 countries. Phylogeny and genetic recombination events of SC2r-CoVs showed higher similarity to the bat coronavirus RaTG13 and BANAL-103 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the N protein from bats and pangolin showed close resemblance to SARS-CoV-2. The clustering of animal and human strains from the same geographical area has proved human-to-animal transmission of the virus. The Alpha, Delta and Mu-variant of SARS-CoV-2 was detected in dog, gorilla, lion, tiger, otter, and cat in the USA, India, Czech Republic, Belgium, and France with momentous genetic similarity with human SARS-CoV-2 sequences. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. Moreover, the dog was affected mostly by clade O (66.7%), whereas cat and American mink were affected by clade GR (31.6 and 49.7%, respectively). The \u03b1-variant was detected as 2.6% in cat, 4.8% in dog, 14.3% in tiger, 66.7% in gorilla, and 77.3% in lion. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. We recommend vaccine provision for pet and zoo animals to reduce the chance of transmission in animals. Besides, continuous epidemiological and genomic surveillance of coronaviruses in animal host is crucial to find out the immediate ancestor of SARS-CoV-2 and to prevent future CoVs threats to humans.", "coi_statement": "The authors have declared that no competing interests exist.", "journal": "PloS one", "authors": [ "Islam Ariful", "Ferdous Jinnat", "Sayeed Md Abu", "Islam Shariful", "Kaisar Rahman Md", "Abedin Josefina", "Saha Otun", "Hassan Mohammad Mahmudul", "Shirin Tahmina" ], "affiliations": [ "EcoHealth Alliance, New York, New York, United States of America.", "EcoHealth Alliance, New York, New York, United States of America.", "EcoHealth Alliance, New York, New York, United States of America.", "EcoHealth Alliance, New York, New York, United States of America.", "EcoHealth Alliance, New York, New York, United States of America.", "EcoHealth Alliance, New York, New York, United States of America.", "EcoHealth Alliance, New York, New York, United States of America.", "Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh.", "Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh." ], "pubyear": "2021", "publication_date": "2021-01-01", "entrez_date": "2021-12-15", "pmid": "34910734", "mesh_terms": [ "D000818:Animals", "D000086402:SARS-CoV-2", "D000835:Animals, Wild", "D000086382:COVID-19", "D014644:Genetic Variation", "D010802:Phylogeny", "D006801:Humans", "D000829:Animals, Domestic", "D016679:Genome, Viral", "D000086642:Pangolins", "D011995:Recombination, Genetic" ], "sup_mesh_terms": [], "chemicals": [], "publication_types": [ "Journal Article" ], "keywords": [], "pmcid": "PMC8673647", "doi": "10.1371/journal.pone.0260635", "medline_ta": "PLoS One", "docid": "34910734", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1114.json.gz", "annotations": { "title": [ "mesh|D017934|Coronavirus", "agrovoc|c_2615|epidemiology", "covocorganism|SP_6|COVID-19", "mesh|D004813|Epidemiology", "mesh|D000835|Animals, Wild", "covocbiomed|BMV_34|coronavirus", "covocbiomed|BMV_52|Genetic Diversity", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_5|Coronavirus", "agrovoc|c_24103|wild animals", "covocbiomed|BMV_46|Epidemiology", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome" ], "all": [ "mesh|D017934|Coronavirus", "agrovoc|c_2615|epidemiology", "covocorganism|SP_6|COVID-19", "mesh|D004813|Epidemiology", "mesh|D000835|Animals, Wild", "covocbiomed|BMV_34|coronavirus", "covocbiomed|BMV_52|Genetic Diversity", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_5|Coronavirus", "agrovoc|c_24103|wild animals", "covocbiomed|BMV_46|Epidemiology", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_365a18ab|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086402|SARS-CoV-2", "ncit|C85064|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_34|coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086402|SARS-CoV-2", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|10239|Viruses", "covocbiomed|BMV_119|recombination", "mesh|D000818|Animals", "covocbiomed|BMV_46|Epidemiology", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|10239|Viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017720|Molecular Epidemiology", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_2615|epidemiology", "mesh|D014780|Viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_5|Coronavirus", "covocbiomed|BMV_52|Genetic Diversity", "agrovoc|c_6475|recombination", "covocbiomed|BMV_51|Genes", "uniprot_swissprot|Q8CIQ8|Sars", "agrovoc|c_8262|viruses", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_163|viruses", "ncbitaxon_viruses|10239|Viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D014780|Viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "ncit|C189188|Infected with SARS-CoV-2", "ncbitaxon_full|10239|Viruses", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_8262|viruses", "covocbiomed|BMV_163|viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_56|Genome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_5|Coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D016678|Genome", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_134|sequence", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_4|Chiroptera", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_20|Rhinolophus macrotis", "covocorganism|SP_14|Manidae", "covocorganism|SP_6|COVID-19", "ott|756634|Rhinolophus", "mdd|1005796|Manis_javanica", "ott|644245|Manis javanica", "mesh|D000086642|Pangolins", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|49442|Rhinolophus", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D002685|Chiroptera", "mesh|D046010|Tigers", "mesh|D046011|Puma", "uniprot_swissprot|F1LP90|Mink", "mdd|1000718|Homo_sapiens", "mesh|D010041|Otters", "mdd|1006023|Panthera_tigris", "nextprot|NX_Q9BXH1|BBC3", "mdd|1006017|Puma_concolor", "ott|923119|Mustela putorius furo", "ncbitaxon_full|146712|Puma", "ncbitaxon_full|9592|Gorilla", "mesh|D046009|Panthera", "mesh|D008907|Mink", "ncbitaxon_models|taxID: 9669|Mustela putorius furo", "mdd|1005867|Mustela_furo", "cellosaurus|CVCL_0593|Mv1Lu", "ott|770315|Homo sapiens", "nextprot|NX_Q8N4C8|MINK1", "mesh|D046011|Puma", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "ott|42314|Panthera tigris", "ncbitaxon_full|9669|Mustela putorius furo", "ott|42324|Panthera pardus", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_models|452646|Mustela vison", "mdd|1006022|Panthera_pardus", "ott|86161|Puma", "uniprot_swissprot|Q80ZG6|Puma", "mdd|1006017|Puma_concolor", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "mdd|1005796|Manis_javanica", "ott|574724|Chiroptera", "ott|644245|Manis javanica", "ncbitaxon_full|2709072|Bat coronavirus RaTG13", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_6475|recombination", "covocbiomed|BMV_51|Genes", "ncbitaxon_full|2708335|Pangolin coronavirus", "pubchemmesh|439693|Pentostatin", "mesh|D013180|Sprains and Strains", "pubchemmesh|439693|Pentostatin", "covocproteinsgenomes|PG_18|Nucleoprotein", "covocorganism|SP_4|Chiroptera", "agrovoc|c_ae97fbc0|strains", "covocorganism|SP_4|Chiroptera", "covocorganism|SP_14|Manidae", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_53|Genetic Recombination", "mesh|D010802|Phylogeny", "mesh|D000086642|Pangolins", "ncbitaxon_viruses|2709072|Bat coronavirus RaTG13", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D011995|Recombination, Genetic", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "agrovoc|c_13325|phylogeny", "ncbitaxon_viruses|2708335|Pangolin coronavirus", "covocorganism|SP_5|Coronavirus", "covocbiomed|BMV_34|coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086642|Pangolins", "ncbitaxon_models|227859|Human SARS coronavirus", "mdd|1000718|Homo_sapiens", "agrovoc|c_ae97fbc0|strains", "covocbiomed|BMV_163|viruses", "covocbiomed|BMV_150|transmission", "covocorganism|SP_11|Homo sapiens", "covocorganism|SP_11|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mesh|D013180|Sprains and Strains", "mdd|1000718|Homo_sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D001530|Belgium", "covocbiomed|BMV_134|sequence", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "ott|770315|Homo sapiens", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|42314|Panthera tigris", "agrovoc|c_870|Belgium", "mesh|D005602|France", "covocorganism|SP_22|Alpha", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9592|Gorilla", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D046010|Tigers", "covocorganism|SP_25|Delta", "mdd|1006023|Panthera_tigris", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D010041|Otters", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "mdd|1000718|Homo_sapiens", "pubchemmesh|439693|Pentostatin", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "envo|ENVO_00000101|delta", "covocorganism|SP_6|COVID-19", "psimi|MI:1241|variant", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D007194|India", "mesh|D018153|Czech Republic", "cellosaurus|CVCL_0593|Mv1Lu", "psimi|MI:1115|spike", "nextprot|NX_Q8N4C8|MINK1", "mesh|D006801|Humans", "psimi|MI:0118|mutation", "ncit|C16885|Mutation", "agrovoc|c_5014|mutation", "cellosaurus|CVCL_DR98|CHO CAT-S", "psimi|MI:1241|variant", "ncbitaxon_models|452646|Mustela vison", "mesh|D008907|Mink", "mesh|D009154|Mutation", "flopo|FLOPO_0900001|inflorescence type spike", "ncbitaxon_full|9605|Homo", "ncbitaxon_full|9685|Felis catus", "covocbiomed|BMV_95|Mutation", "ott|563166|Felis catus", "agrovoc|c_1390|cats", "mesh|D002415|Cats", "ott|770309|Homo", "uniprot_swissprot|F1LP90|Mink", "ncbitaxon_models|452646|Mustela vison", "agrovoc|c_dd670e21|clade", "mesh|D008907|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "robiext|RO_e000056|affected by", "uniprot_swissprot|F1LP90|Mink", "mdd|1005879|Neogale_vison", "nextprot|NX_Q8N4C8|MINK1", "agrovoc|c_dd670e21|clade", "ott|310482|Neovison vison", "ott|42314|Panthera tigris", "mesh|D046010|Tigers", "psimi|MI:1241|variant", "ncbitaxon_full|9592|Gorilla", "mdd|1006023|Panthera_tigris", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "flopo|FLOPO_0900001|inflorescence type spike", "psimi|MI:1115|spike", "covocbiomed|BMV_95|Mutation", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "covocproteinsgenomes|PG_29|Spike glycoprotein", "ott|42314|Panthera tigris", "mdd|1006023|Panthera_tigris", "covocbiomed|BMV_95|Mutation", "ncbitaxon_full|9592|Gorilla", "mesh|D046010|Tigers", "uniprot_swissprot|P19704|hss", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "mesh|D000818|Animals", "covocbiomed|BMV_155|vaccine", "mesh|D000836|Animals, Zoo", "covocbiomed|BMV_150|transmission", "agrovoc|c_32736|zoo animals", "covocconceptualentities|CE_37|host", "mesh|D017934|Coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|9605|Homo", "ncbitaxon_models|227859|Human SARS coronavirus", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_5|Coronavirus", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|770309|Homo", "mesh|D006801|Humans", "covocconceptualentities|CE_84|surveillance", "covocorganism|SP_6|COVID-19", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|045v4z873|Chattogram Veterinary and Animal Sciences University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|03bgw1x40|\"Institute of Epidemiology", "mesh|D000818|Animals", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D000835|Animals, Wild", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "agrovoc|c_15975|genetic variation", "mesh|D014644|Genetic Variation", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "mesh|D000829|Animals, Domestic", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination", "mesh|D011995|Recombination, Genetic" ], "abstract": [ "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_365a18ab|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086402|SARS-CoV-2", "ncit|C85064|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_34|coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086402|SARS-CoV-2", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|10239|Viruses", "covocbiomed|BMV_119|recombination", "mesh|D000818|Animals", "covocbiomed|BMV_46|Epidemiology", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|10239|Viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017720|Molecular Epidemiology", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_2615|epidemiology", "mesh|D014780|Viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_5|Coronavirus", "covocbiomed|BMV_52|Genetic Diversity", "agrovoc|c_6475|recombination", "covocbiomed|BMV_51|Genes", "uniprot_swissprot|Q8CIQ8|Sars", "agrovoc|c_8262|viruses", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_163|viruses", "ncbitaxon_viruses|10239|Viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D014780|Viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "ncit|C189188|Infected with SARS-CoV-2", "ncbitaxon_full|10239|Viruses", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_8262|viruses", "covocbiomed|BMV_163|viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_56|Genome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_5|Coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D016678|Genome", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_134|sequence", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_4|Chiroptera", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_20|Rhinolophus macrotis", "covocorganism|SP_14|Manidae", "covocorganism|SP_6|COVID-19", "ott|756634|Rhinolophus", "mdd|1005796|Manis_javanica", "ott|644245|Manis javanica", "mesh|D000086642|Pangolins", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|49442|Rhinolophus", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D002685|Chiroptera", "mesh|D046010|Tigers", "mesh|D046011|Puma", "uniprot_swissprot|F1LP90|Mink", "mdd|1000718|Homo_sapiens", "mesh|D010041|Otters", "mdd|1006023|Panthera_tigris", "nextprot|NX_Q9BXH1|BBC3", "mdd|1006017|Puma_concolor", "ott|923119|Mustela putorius furo", "ncbitaxon_full|146712|Puma", "ncbitaxon_full|9592|Gorilla", "mesh|D046009|Panthera", "mesh|D008907|Mink", "ncbitaxon_models|taxID: 9669|Mustela putorius furo", "mdd|1005867|Mustela_furo", "cellosaurus|CVCL_0593|Mv1Lu", "ott|770315|Homo sapiens", "nextprot|NX_Q8N4C8|MINK1", "mesh|D046011|Puma", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "ott|42314|Panthera tigris", "ncbitaxon_full|9669|Mustela putorius furo", "ott|42324|Panthera pardus", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_models|452646|Mustela vison", "mdd|1006022|Panthera_pardus", "ott|86161|Puma", "uniprot_swissprot|Q80ZG6|Puma", "mdd|1006017|Puma_concolor", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "mdd|1005796|Manis_javanica", "ott|574724|Chiroptera", "ott|644245|Manis javanica", "ncbitaxon_full|2709072|Bat coronavirus RaTG13", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_6475|recombination", "covocbiomed|BMV_51|Genes", "ncbitaxon_full|2708335|Pangolin coronavirus", "pubchemmesh|439693|Pentostatin", "mesh|D013180|Sprains and Strains", "pubchemmesh|439693|Pentostatin", "covocproteinsgenomes|PG_18|Nucleoprotein", "covocorganism|SP_4|Chiroptera", "agrovoc|c_ae97fbc0|strains", "covocorganism|SP_4|Chiroptera", "covocorganism|SP_14|Manidae", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_53|Genetic Recombination", "mesh|D010802|Phylogeny", "mesh|D000086642|Pangolins", "ncbitaxon_viruses|2709072|Bat coronavirus RaTG13", "covocorganism|SP_6|COVID-19", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D011995|Recombination, Genetic", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "agrovoc|c_13325|phylogeny", "ncbitaxon_viruses|2708335|Pangolin coronavirus", "covocorganism|SP_5|Coronavirus", "covocbiomed|BMV_34|coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086642|Pangolins", "ncbitaxon_models|227859|Human SARS coronavirus", "mdd|1000718|Homo_sapiens", "agrovoc|c_ae97fbc0|strains", "covocbiomed|BMV_163|viruses", "covocbiomed|BMV_150|transmission", "covocorganism|SP_11|Homo sapiens", "covocorganism|SP_11|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mesh|D013180|Sprains and Strains", "mdd|1000718|Homo_sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D001530|Belgium", "covocbiomed|BMV_134|sequence", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "ott|770315|Homo sapiens", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|42314|Panthera tigris", "agrovoc|c_870|Belgium", "mesh|D005602|France", "covocorganism|SP_22|Alpha", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9592|Gorilla", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D046010|Tigers", "covocorganism|SP_25|Delta", "mdd|1006023|Panthera_tigris", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D010041|Otters", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "mdd|1000718|Homo_sapiens", "pubchemmesh|439693|Pentostatin", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "envo|ENVO_00000101|delta", "covocorganism|SP_6|COVID-19", "psimi|MI:1241|variant", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D007194|India", "mesh|D018153|Czech Republic", "cellosaurus|CVCL_0593|Mv1Lu", "psimi|MI:1115|spike", "nextprot|NX_Q8N4C8|MINK1", "mesh|D006801|Humans", "psimi|MI:0118|mutation", "ncit|C16885|Mutation", "agrovoc|c_5014|mutation", "cellosaurus|CVCL_DR98|CHO CAT-S", "psimi|MI:1241|variant", "ncbitaxon_models|452646|Mustela vison", "mesh|D008907|Mink", "mesh|D009154|Mutation", "flopo|FLOPO_0900001|inflorescence type spike", "ncbitaxon_full|9605|Homo", "ncbitaxon_full|9685|Felis catus", "covocbiomed|BMV_95|Mutation", "ott|563166|Felis catus", "agrovoc|c_1390|cats", "mesh|D002415|Cats", "ott|770309|Homo", "uniprot_swissprot|F1LP90|Mink", "ncbitaxon_models|452646|Mustela vison", "agrovoc|c_dd670e21|clade", "mesh|D008907|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "robiext|RO_e000056|affected by", "uniprot_swissprot|F1LP90|Mink", "mdd|1005879|Neogale_vison", "nextprot|NX_Q8N4C8|MINK1", "agrovoc|c_dd670e21|clade", "ott|310482|Neovison vison", "ott|42314|Panthera tigris", "mesh|D046010|Tigers", "psimi|MI:1241|variant", "ncbitaxon_full|9592|Gorilla", "mdd|1006023|Panthera_tigris", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "flopo|FLOPO_0900001|inflorescence type spike", "psimi|MI:1115|spike", "covocbiomed|BMV_95|Mutation", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "covocproteinsgenomes|PG_29|Spike glycoprotein", "ott|42314|Panthera tigris", "mdd|1006023|Panthera_tigris", "covocbiomed|BMV_95|Mutation", "ncbitaxon_full|9592|Gorilla", "mesh|D046010|Tigers", "uniprot_swissprot|P19704|hss", "mesh|D006071|Gorilla gorilla", "ott|417969|Gorilla", "mesh|D000818|Animals", "covocbiomed|BMV_155|vaccine", "mesh|D000836|Animals, Zoo", "covocbiomed|BMV_150|transmission", "agrovoc|c_32736|zoo animals", "covocconceptualentities|CE_37|host", "mesh|D017934|Coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|9605|Homo", "ncbitaxon_models|227859|Human SARS coronavirus", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_5|Coronavirus", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|770309|Homo", "mesh|D006801|Humans", "covocconceptualentities|CE_84|surveillance", "covocorganism|SP_6|COVID-19" ], "affiliations": [ "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|045v4z873|Chattogram Veterinary and Animal Sciences University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|03bgw1x40|\"Institute of Epidemiology" ], "mesh_terms": [ "mesh|D000818|Animals", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D000835|Animals, Wild", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "agrovoc|c_15975|genetic variation", "mesh|D014644|Genetic Variation", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "mesh|D000829|Animals, Domestic", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination", "mesh|D011995|Recombination, Genetic" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "33836016", "_score": 147.14172, "_source": { "title": "Mutations derived from horseshoe bat ACE2 orthologs enhance ACE2-Fc neutralization of SARS-CoV-2.", "abstract": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates infection of cells expressing angiotensin-converting enzyme 2 (ACE2). ACE2 is also the viral receptor of SARS-CoV (SARS-CoV-1), a related coronavirus that emerged in 2002-2003. Horseshoe bats (genus Rhinolophus) are presumed to be the original reservoir of both viruses, and a SARS-like coronavirus, RaTG13, closely related to SARS-CoV-2, has been identified in one horseshoe-bat species. Here we characterize the ability of the S-protein receptor-binding domains (RBDs) of SARS-CoV-1, SARS-CoV-2, pangolin coronavirus (PgCoV), RaTG13, and LyRa11, a bat virus similar to SARS-CoV-1, to bind a range of ACE2 orthologs. We observed that the PgCoV RBD bound human ACE2 at least as efficiently as the SARS-CoV-2 RBD, and that both RBDs bound pangolin ACE2 efficiently. We also observed a high level of variability in binding to closely related horseshoe-bat ACE2 orthologs consistent with the heterogeneity of their RBD-binding regions. However five consensus horseshoe-bat ACE2 residues enhanced ACE2 binding to the SARS-CoV-2 RBD and neutralization of SARS-CoV-2 pseudoviruses by an enzymatically inactive immunoadhesin form of human ACE2 (hACE2-NN-Fc). Two of these mutations impaired neutralization of SARS-CoV-1 pseudoviruses. An hACE2-NN-Fc variant bearing all five mutations neutralized both SARS-CoV-2 pseudovirus and infectious virus more efficiently than wild-type hACE2-NN-Fc. These data suggest that SARS-CoV-1 and -2 originate from distinct bat species, and identify a more potently neutralizing form of soluble ACE2.", "coi_statement": "I have read the journal\u2019s policy and the authors of this manuscript have the following competing interests: M.F., H.M. and B.D.Q had filed a patent for the application of ACE2-Fc variants as a SARS-CoV-2 treatment. M.R.G., C.C.B., M.D.A., and M.F. are all cofounders of, and have an equity interest in Emmune Inc., a biotech company that specializes in the development of antibody-like antiviral therapies.", "journal": "PLoS pathogens", "authors": [ "Mou Huihui", "Quinlan Brian D", "Peng Haiyong", "Liu Guanqun", "Guo Yan", "Peng Shoujiao", "Zhang Lizhou", "Davis-Gardner Meredith E", "Gardner Matthew R", "Crynen Gogce", "DeVaux Lindsey B", "Voo Zhi Xiang", "Bailey Charles C", "Alpert Michael D", "Rader Christoph", "Gack Michaela U", "Choe Hyeryun", "Farzan Michael" ], "affiliations": [ "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Emmune, Inc., Juno Beach, FL, United States of America.", "Emmune, Inc., Juno Beach, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America.", "Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States of America." ], "pubyear": "2021", "publication_date": "2021-04-01", "entrez_date": "2021-04-09", "pmid": "33836016", "mesh_terms": [ "D000085962:Angiotensin-Converting Enzyme 2", "D000818:Animals", "D000086382:COVID-19", "D002685:Chiroptera", "D058507:Host Specificity", "D006801:Humans", "D008958:Models, Molecular", "D009154:Mutation", "D011485:Protein Binding", "D011991:Receptors, Virus", "D000086402:SARS-CoV-2", "D064370:Spike Glycoprotein, Coronavirus" ], "sup_mesh_terms": [], "chemicals": [ "RN 0, D011991:Receptors, Virus", "RN 0, D064370:Spike Glycoprotein, Coronavirus", "RN EC 3.4.17.23, D000085962:Angiotensin-Converting Enzyme 2" ], "publication_types": [ "Journal Article", "Research Support, N.I.H., Extramural" ], "keywords": [], "pmcid": "PMC8059821", "doi": "10.1371/journal.ppat.1009501", "medline_ta": "PLoS Pathog", "docid": "33836016", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1079.json.gz", "annotations": { "title": [ "uniprot_swissprot|Q5EGZ1|Ace2", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "nextprot|NX_Q9BYF1|ACE2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_5151|neutralization", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D002685|Chiroptera", "covocproteinsgenomes|PG_2|ACE2", 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"covocbiomed|BMV_34|coronavirus", "ncbitaxon_viruses|2708335|Pangolin coronavirus", "go_mf|GO:0005488|binding", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocproteinsgenomes|PG_2|ACE2", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_14|Manidae", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "nextprot|NX_Q9BYF1|ACE2", "covocproteinsgenomes|PG_27|SARS-CoV-2 RBD", "uniprot_swissprot|Q5EGZ1|Ace2", "covocorganism|SP_6|COVID-19", "mesh|D000086642|Pangolins", "uniprot_swissprot|Q5EGZ1|Ace2", "ott|770315|Homo sapiens", "nextprot|NX_Q9BYF1|ACE2", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "mdd|1000718|Homo_sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "ott|644247|Manis", "nextprot|NX_Q9BYF1|ACE2", 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coronavirus", "uniprot_swissprot|Q5EGZ1|Ace2", "ppiptm|PPI:2|bind", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "ott|770315|Homo sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_5151|neutralization", "covocproteinsgenomes|PG_2|ACE2", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_4|Chiroptera", "nextprot|NX_Q9BYF1|ACE2", "pubchemmesh|439693|Pentostatin", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_21|SARS-CoV", "covocbiomed|BMV_95|Mutation", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "agrovoc|c_5151|neutralization", "ncbitaxon_models|227859|Human SARS coronavirus", "covocbiomed|BMV_163|viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|3092168|SARS-CoV-2 pseudovirus", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "psimi|MI:1241|variant", "covocbiomed|BMV_95|Mutation", "ncbitaxon_full|3092168|SARS-CoV-2 pseudovirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "uniprot_swissprot|Q5EGZ1|Ace2", "covocorganism|SP_21|SARS-CoV", "uniprot_swissprot|Q8CIQ8|Sars", "pubchemmesh|439693|Pentostatin", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_4|Chiroptera", "agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "nextprot|NX_Q9BYF1|ACE2", "ncbitaxon_models|227859|Human SARS coronavirus", "covocproteinsgenomes|PG_2|ACE2" ], "affiliations": [ "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|03xjacd83|Cleveland Clinic", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|03zp01h17|\"Innovation", "ror|03rvn3n08|\u0141ukasiewicz Research Network \u2013 PORT Polish Center for Technology Development", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|03ss07w66|Centre for Ocean Research and Education", "ror|02dxx6824|Scripps Research Institute", "ror|0264vhs54|G\u00e9nomique Bioinformatique et Applications", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute", "ror|0231an742|Jiangmen Underground Neutrino Observatory", "ror|02anj9s22|Mt. Cuba Astronomical Observatory", "ror|0231an742|Jiangmen Underground Neutrino Observatory", "ror|02anj9s22|Mt. Cuba Astronomical Observatory", "ror|02dxx6824|Scripps Research Institute", "ror|03xjacd83|Cleveland Clinic", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|03zp01h17|\"Innovation", "ror|03rvn3n08|\u0141ukasiewicz Research Network \u2013 PORT Polish Center for Technology Development", "ror|02dxx6824|Scripps Research Institute", "ror|02dxx6824|Scripps Research Institute" ], "mesh_terms": [ "psimi|MI:0501|enzyme", "chebi|CHEBI:48433|angiotensin", "nextprot|NX_Q9BYF1|ACE2", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "agrovoc|c_36006|angiotensin", "uniprot_swissprot|Q5EGZ1|Ace2", "mesh|D000085962|Angiotensin-Converting Enzyme 2", "mesh|D000818|Animals", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D058507|Host Specificity", "covocconceptualentities|CE_77|Specificity", "covocconceptualentities|CE_37|host", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "mesh|D008958|Models, Molecular", "agrovoc|c_5014|mutation", "covocbiomed|BMV_95|Mutation", "mesh|D009154|Mutation", "psimi|MI:0118|mutation", "ncit|C16885|Mutation", "mesh|D011485|Protein Binding", "ppiptm|PPI:2|bind", "go_mf|GO:0005515|protein binding", "mesh|D011991|Receptors, Virus", "covocbiomed|BMV_163|viruses", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "flopo|FLOPO_0900001|inflorescence type spike", "chebi|CHEBI:17089|glycoprotein", "covocorganism|SP_5|Coronavirus", "uniprot_swissprot|O39227|3", "covocbiomed|BMV_34|coronavirus", "pubchemmesh|439212|Glycoprotein", "mesh|D064370|Spike Glycoprotein, Coronavirus", "lotus|Q105157557|Glycoprotein", "covocbiomed|BMV_60|glycoprotein", "covocproteinsgenomes|PG_30|Spike glycoprotein", "psimi|MI:1115|spike" ], "chemicals": [ "mesh|D011991|Receptors, Virus", "covocbiomed|BMV_163|viruses", "covocproteinsgenomes|PG_30|Spike glycoprotein", "covocorganism|SP_5|Coronavirus", "chebi|CHEBI:17089|glycoprotein", "flopo|FLOPO_0900001|inflorescence type spike", "psimi|MI:1115|spike", "uniprot_swissprot|O39227|3", "covocbiomed|BMV_34|coronavirus", "mesh|D064370|Spike Glycoprotein, Coronavirus", "pubchemmesh|439212|Glycoprotein", "lotus|Q105157557|Glycoprotein", "covocbiomed|BMV_60|glycoprotein", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "psimi|MI:0501|enzyme", "nextprot|NX_Q9BYF1|ACE2", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "agrovoc|c_36006|angiotensin", "chebi|CHEBI:48433|angiotensin", "uniprot_swissprot|Q5EGZ1|Ace2", "mesh|D000085962|Angiotensin-Converting Enzyme 2" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "34694705", "_score": 143.83817, "_source": { "title": "Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics.", "abstract": "The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.", "coi_statement": "", "journal": "Transboundary and emerging diseases", "authors": [ "Islam Ariful", "Ferdous Jinnat", "Islam Shariful", "Sayeed Md Abu", "Rahman Md Kaisar", "Saha Otun", "Hassan Mohammad Mahmudul", "Shirin Tahmina" ], "affiliations": [ "EcoHealth Alliance, New York, United States.", "EcoHealth Alliance, New York, United States.", "EcoHealth Alliance, New York, United States.", "EcoHealth Alliance, New York, United States.", "EcoHealth Alliance, New York, United States.", "EcoHealth Alliance, New York, United States.", "Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh.", "Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh." ], "pubyear": "2022", "publication_date": "2022-09-01", "entrez_date": "2021-10-25", "pmid": "34694705", "mesh_terms": [ "D000818:Animals", "D000835:Animals, Wild", "D000086382:COVID-19", "D002417:Cattle", "D002418:Cattle Diseases", "D002685:Chiroptera", "D005289:Ferrets", "D006801:Humans", "D008907:Mink", "D000074823:One Health", "D058873:Pandemics", "D011634:Public Health", "D000086402:SARS-CoV-2", "D013552:Swine", "D013553:Swine Diseases" ], "sup_mesh_terms": [ "C000711908:SARS-CoV-2 variants" ], "chemicals": [], "publication_types": [ "Journal Article", "Review" ], "keywords": [ "COVID-19", "Rhinolophus bats", "alpha variant", "delta variant", "horseshoe bat", "mink", "pangolin" ], "pmcid": "PMC8662162", "doi": "10.1111/tbed.14356", "medline_ta": "Transbound Emerg Dis", "docid": "34694705", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1107.json.gz", "annotations": { "title": [ "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_150|transmission", "mesh|D011634|Public Health", "mesh|D000835|Animals, Wild", "covocorganism|SP_6|COVID-19", "covocconceptualentities|CE_22|epidemics", "mesh|D058873|Pandemics", "covocconceptualentities|CE_54|Pandemics", "mesh|D000074823|One Health", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D058872|Epidemics", "agrovoc|c_f17550ed|pandemics", "agrovoc|c_24103|wild animals", "covocconceptualentities|CE_84|surveillance", "agrovoc|c_b29a1475|One Health approach", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_2614|epidemics", "covocbiomed|BMV_116|Public Health", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2" ], "all": [ "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_150|transmission", "mesh|D011634|Public Health", "mesh|D000835|Animals, Wild", "covocorganism|SP_6|COVID-19", "covocconceptualentities|CE_22|epidemics", "mesh|D058873|Pandemics", "covocconceptualentities|CE_54|Pandemics", "mesh|D000074823|One Health", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D058872|Epidemics", "agrovoc|c_f17550ed|pandemics", "agrovoc|c_24103|wild animals", "covocconceptualentities|CE_84|surveillance", "agrovoc|c_b29a1475|One Health approach", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_2614|epidemics", "covocbiomed|BMV_116|Public Health", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_full|9605|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ncit|C85064|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ott|770309|Homo", "mesh|D000086402|SARS-CoV-2", "agrovoc|c_365a18ab|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D006801|Humans", "mesh|D000086402|SARS-CoV-2", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "agrovoc|c_8324|water reservoirs", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_150|transmission", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000818|Animals", "covocorganism|SP_4|Chiroptera", "ncbitaxon_full|49442|Rhinolophus", "uniprot_swissprot|Q8CIQ8|Sars", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_163|viruses", "mesh|D002685|Chiroptera", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|574724|Chiroptera", "ncbitaxon_viruses|10239|Viruses", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|10239|Viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "mesh|D014780|Viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_8262|viruses", "mesh|D006801|Humans", "covocorganism|SP_11|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "covocorganism|SP_14|Manidae", "mdd|1000718|Homo_sapiens", "ott|770309|Homo", "ncbitaxon_full|9605|Homo", "ott|644247|Manis", "mesh|D000086642|Pangolins", "ncbitaxon_full|9605|Homo", "covocbiomed|BMV_106|pathway", "mesh|D006801|Humans", "ott|770309|Homo", "covocbiomed|BMV_163|viruses", "agrovoc|c_24103|wild animals", "covocbiomed|BMV_150|transmission", "mesh|D000835|Animals, Wild", "covocorganism|SP_11|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mdd|1000718|Homo_sapiens", "mesh|D008907|Mink", "ncbitaxon_models|452646|Mustela vison", "mesh|D008907|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D000818|Animals", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "mesh|D000818|Animals", "covocconceptualentities|CE_43|infected animal", "uniprot_swissprot|F1LP90|Mink", "uniprot_swissprot|F1LP90|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "nextprot|NX_Q8N4C8|MINK1", "nextprot|NX_Q8N4C8|MINK1", "ncbitaxon_models|452646|Mustela vison", "covocbiomed|BMV_163|viruses", "covocbiomed|BMV_150|transmission", "covocorganism|SP_11|Homo sapiens", "mdd|1000718|Homo_sapiens", "ncbitaxon_models|9606|Homo sapiens", "covocorganism|SP_11|Homo sapiens", "uniprot_swissprot|F1LP90|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "ncbitaxon_models|9606|Homo sapiens", "nextprot|NX_Q8N4C8|MINK1", "covocbiomed|BMV_150|transmission", "covocbiomed|BMV_150|transmission", "ott|770315|Homo sapiens", "mdd|1000718|Homo_sapiens", "ncbitaxon_models|452646|Mustela vison", "covocbiomed|BMV_106|pathway", "ott|770315|Homo sapiens", "mesh|D008907|Mink", "mesh|D000835|Animals, Wild", "covocorganism|SP_22|Alpha", "covocorganism|SP_25|Delta", "covocorganism|SP_25|Delta", "agrovoc|c_a64e9065|captive wild animals", "psimi|MI:1241|variant", "agrovoc|c_29225|lineage", "agrovoc|c_4356|lions", "cellosaurus|CVCL_U041|VII-II-5G3-F3", "mesh|D008045|Lions", "mesh|D033062|Friends", "covocorganism|SP_22|Alpha", "envo|ENVO_00000101|delta", "psimi|MI:1241|variant", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "mdd|1000718|Homo_sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D013552|Swine", "ott|574724|Chiroptera", "ott|913935|Primates", "agrovoc|c_2859|ferrets", "drugbank|DB11008|Poultry", "ncbitaxon_full|9443|Primates", "agrovoc|c_1391|cattle", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|9823|Sus scrofa", "mesh|D011323|Primates", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D002417|Cattle", "covocorganism|SP_4|Chiroptera", "agrovoc|c_3482|hamsters", "ott|770315|Homo sapiens", "ott|730013|Sus scrofa", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|1066581|Bos", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mdd|1006267|Bos_taurus", "mesh|D006224|Cricetinae", "ott|917323|Cricetinae", "mdd|1006374|Sus_domesticus", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mesh|D005289|Ferrets", "mesh|D011200|Poultry", "agrovoc|c_6145|poultry", "ncbitaxon_models|9913|Bos taurus", "agrovoc|c_7555|swine", "agrovoc|c_6181|primates", "agrovoc|c_331043|welfare", "mesh|D000835|Animals, Wild", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ott|770309|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_8324|water reservoirs", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "mesh|D006801|Humans", "pubchemmesh|439693|Pentostatin", "agrovoc|c_8389|wildlife", "ncbitaxon_full|9605|Homo", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_163|viruses", "mesh|D057805|Pets", "agrovoc|c_5742|pet animals", "mesh|D000818|Animals", "covocorganism|SP_11|Homo sapiens", "covocconceptualentities|CE_22|epidemics", "agrovoc|c_2614|epidemics", "ncbitaxon_models|9606|Homo sapiens", "agrovoc|c_b29a1475|One Health approach", "ott|770315|Homo sapiens", "covocconceptualentities|CE_84|surveillance", "mesh|D058872|Epidemics", "mdd|1000718|Homo_sapiens", "mesh|D000074823|One Health", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "mesh|D058873|Pandemics", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|045v4z873|Chattogram Veterinary and Animal Sciences University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|03bgw1x40|\"Institute of Epidemiology", "mesh|D000818|Animals", "mesh|D000835|Animals, Wild", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "mesh|D002417|Cattle", "ncbitaxon_models|9913|Bos taurus", "mdd|1006267|Bos_taurus", "ott|1066581|Bos", "agrovoc|c_1391|cattle", "ncbitaxon_models|9913|Bos taurus", "mdd|1006267|Bos_taurus", "mesh|D002418|Cattle Diseases", "ott|1066581|Bos", "agrovoc|c_1391|cattle", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D005289|Ferrets", "agrovoc|c_2859|ferrets", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "mesh|D000074823|One Health", "agrovoc|c_b29a1475|One Health approach", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "covocbiomed|BMV_116|Public Health", "mesh|D011634|Public Health", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9823|Sus scrofa", "ott|730013|Sus scrofa", "agrovoc|c_7555|swine", "mdd|1006374|Sus_domesticus", "mesh|D013552|Swine", "ncbitaxon_full|9823|Sus scrofa", "ott|730013|Sus scrofa", "agrovoc|c_7555|swine", "mesh|D013553|Swine Diseases", "mdd|1006374|Sus_domesticus", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D002685|Chiroptera", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|49442|Rhinolophus", "psimi|MI:1241|variant", "covocorganism|SP_22|Alpha", "psimi|MI:1241|variant", "covocorganism|SP_25|Delta", "envo|ENVO_00000101|delta", "covocorganism|SP_4|Chiroptera", "mesh|D002685|Chiroptera", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins" ], "abstract": [ "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_full|9605|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ncit|C85064|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ott|770309|Homo", "mesh|D000086402|SARS-CoV-2", "agrovoc|c_365a18ab|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D006801|Humans", "mesh|D000086402|SARS-CoV-2", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "agrovoc|c_8324|water reservoirs", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_150|transmission", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000818|Animals", "covocorganism|SP_4|Chiroptera", "ncbitaxon_full|49442|Rhinolophus", "uniprot_swissprot|Q8CIQ8|Sars", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_163|viruses", "mesh|D002685|Chiroptera", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|574724|Chiroptera", "ncbitaxon_viruses|10239|Viruses", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|10239|Viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "mesh|D014780|Viruses", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_8262|viruses", "mesh|D006801|Humans", "covocorganism|SP_11|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "covocorganism|SP_14|Manidae", "mdd|1000718|Homo_sapiens", "ott|770309|Homo", "ncbitaxon_full|9605|Homo", "ott|644247|Manis", "mesh|D000086642|Pangolins", "ncbitaxon_full|9605|Homo", "covocbiomed|BMV_106|pathway", "mesh|D006801|Humans", "ott|770309|Homo", "covocbiomed|BMV_163|viruses", "agrovoc|c_24103|wild animals", "covocbiomed|BMV_150|transmission", "mesh|D000835|Animals, Wild", "covocorganism|SP_11|Homo sapiens", "ott|770315|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mdd|1000718|Homo_sapiens", "mesh|D008907|Mink", "ncbitaxon_models|452646|Mustela vison", "mesh|D008907|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D000818|Animals", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "mesh|D000818|Animals", "covocconceptualentities|CE_43|infected animal", "uniprot_swissprot|F1LP90|Mink", "uniprot_swissprot|F1LP90|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "nextprot|NX_Q8N4C8|MINK1", "nextprot|NX_Q8N4C8|MINK1", "ncbitaxon_models|452646|Mustela vison", "covocbiomed|BMV_163|viruses", "covocbiomed|BMV_150|transmission", "covocorganism|SP_11|Homo sapiens", "mdd|1000718|Homo_sapiens", "ncbitaxon_models|9606|Homo sapiens", "covocorganism|SP_11|Homo sapiens", "uniprot_swissprot|F1LP90|Mink", "cellosaurus|CVCL_0593|Mv1Lu", "ncbitaxon_models|9606|Homo sapiens", "nextprot|NX_Q8N4C8|MINK1", "covocbiomed|BMV_150|transmission", "covocbiomed|BMV_150|transmission", "ott|770315|Homo sapiens", "mdd|1000718|Homo_sapiens", "ncbitaxon_models|452646|Mustela vison", "covocbiomed|BMV_106|pathway", "ott|770315|Homo sapiens", "mesh|D008907|Mink", "mesh|D000835|Animals, Wild", "covocorganism|SP_22|Alpha", "covocorganism|SP_25|Delta", "covocorganism|SP_25|Delta", "agrovoc|c_a64e9065|captive wild animals", "psimi|MI:1241|variant", "agrovoc|c_29225|lineage", "agrovoc|c_4356|lions", "cellosaurus|CVCL_U041|VII-II-5G3-F3", "mesh|D008045|Lions", "mesh|D033062|Friends", "covocorganism|SP_22|Alpha", "envo|ENVO_00000101|delta", "psimi|MI:1241|variant", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "mdd|1000718|Homo_sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D013552|Swine", "ott|574724|Chiroptera", "ott|913935|Primates", "agrovoc|c_2859|ferrets", "drugbank|DB11008|Poultry", "ncbitaxon_full|9443|Primates", "agrovoc|c_1391|cattle", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|9823|Sus scrofa", "mesh|D011323|Primates", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D002417|Cattle", "covocorganism|SP_4|Chiroptera", "agrovoc|c_3482|hamsters", "ott|770315|Homo sapiens", "ott|730013|Sus scrofa", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|1066581|Bos", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mdd|1006267|Bos_taurus", "mesh|D006224|Cricetinae", "ott|917323|Cricetinae", "mdd|1006374|Sus_domesticus", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mesh|D005289|Ferrets", "mesh|D011200|Poultry", "agrovoc|c_6145|poultry", "ncbitaxon_models|9913|Bos taurus", "agrovoc|c_7555|swine", "agrovoc|c_6181|primates", "agrovoc|c_331043|welfare", "mesh|D000835|Animals, Wild", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ott|770309|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_8324|water reservoirs", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "mesh|D006801|Humans", "pubchemmesh|439693|Pentostatin", "agrovoc|c_8389|wildlife", "ncbitaxon_full|9605|Homo", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_163|viruses", "mesh|D057805|Pets", "agrovoc|c_5742|pet animals", "mesh|D000818|Animals", "covocorganism|SP_11|Homo sapiens", "covocconceptualentities|CE_22|epidemics", "agrovoc|c_2614|epidemics", "ncbitaxon_models|9606|Homo sapiens", "agrovoc|c_b29a1475|One Health approach", "ott|770315|Homo sapiens", "covocconceptualentities|CE_84|surveillance", "mesh|D058872|Epidemics", "mdd|1000718|Homo_sapiens", "mesh|D000074823|One Health", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "mesh|D058873|Pandemics" ], "affiliations": [ "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|02zv3m156|EcoHealth Alliance", "ror|018t0g992|\"York", "ror|045v4z873|Chattogram Veterinary and Animal Sciences University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|03bgw1x40|\"Institute of Epidemiology" ], "mesh_terms": [ "mesh|D000818|Animals", "mesh|D000835|Animals, Wild", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "mesh|D002417|Cattle", "ncbitaxon_models|9913|Bos taurus", "mdd|1006267|Bos_taurus", "ott|1066581|Bos", "agrovoc|c_1391|cattle", "ncbitaxon_models|9913|Bos taurus", "mdd|1006267|Bos_taurus", "mesh|D002418|Cattle Diseases", "ott|1066581|Bos", "agrovoc|c_1391|cattle", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D005289|Ferrets", "agrovoc|c_2859|ferrets", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "mesh|D000074823|One Health", "agrovoc|c_b29a1475|One Health approach", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "covocbiomed|BMV_116|Public Health", "mesh|D011634|Public Health", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9823|Sus scrofa", "ott|730013|Sus scrofa", "agrovoc|c_7555|swine", "mdd|1006374|Sus_domesticus", "mesh|D013552|Swine", "ncbitaxon_full|9823|Sus scrofa", "ott|730013|Sus scrofa", "agrovoc|c_7555|swine", "mesh|D013553|Swine Diseases", "mdd|1006374|Sus_domesticus" ], "sup_mesh_terms": [ "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin" ], "keywords": [ "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D002685|Chiroptera", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|49442|Rhinolophus", "psimi|MI:1241|variant", "covocorganism|SP_22|Alpha", "psimi|MI:1241|variant", "covocorganism|SP_25|Delta", "envo|ENVO_00000101|delta", "covocorganism|SP_4|Chiroptera", "mesh|D002685|Chiroptera", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "35137080", "_score": 142.63492, "_source": { "title": "Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination.", "abstract": "The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (members of the Sarbecovirus subgenus) have been identified, is fueling speculation on the natural origins of SARS-CoV-2. We performed a comprehensive phylogenetic study on SARS-CoV-2 and all the related bat and pangolin sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Distribution of the inferred recombination events is nonrandom with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift events in the ancestry of bat sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm that horseshoe bats, Rhinolophus, are the likely reservoir species for the SARS-CoV-2 progenitor. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and cocirculation of these viruses' ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100\u2009years. We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40\u2009years ago. Our analysis highlights the need for dramatically more wildlife sampling to: 1) pinpoint the exact origins of SARS-CoV-2's animal progenitor, 2) the intermediate species that facilitated transmission from bats to humans (if there is one), and 3) survey the extent of the diversity in the related sarbecoviruses' phylogeny that present high risk for future spillovers.", "coi_statement": "", "journal": "Genome biology and evolution", "authors": [ "Lytras Spyros", "Hughes Joseph", "Martin Darren", "Swanepoel Phillip", "de Klerk Arn\u00e9", "Lourens Rentia", "Kosakovsky Pond Sergei L", "Xia Wei", "Jiang Xiaowei", "Robertson David L" ], "affiliations": [ "MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.", "MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.", "Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa.", "Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa.", "Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa.", "Division of Neurosurgery, Department of Surgery, Neuroscience Institute, University of Cape Town, South Africa.", "Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, USA.", "National School of Agricultural Institution and Development, South China Agricultural University, Guangzhou, China.", "Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China.", "MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom." ], "pubyear": "2022", "publication_date": "2022-02-04", "entrez_date": "2022-02-09", "pmid": "35137080", "mesh_terms": [ "D000818:Animals", "D002685:Chiroptera", "D017934:Coronavirus", "D006801:Humans", "D000086642:Pangolins", "D010802:Phylogeny", "D058974:Phylogeography", "D011995:Recombination, Genetic" ], "sup_mesh_terms": [], "chemicals": [], "publication_types": [ "Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't" ], "keywords": [ "\n Rhinolophus\n ", "\n Sarbecoviruses\n ", "COVID-19", "SARS-CoV-2", "bats", "coronaviruses", "host range", "origin", "pangolins", "recombination" ], "pmcid": "PMC8882382", "doi": "10.1093/gbe/evac018", "medline_ta": "Genome Biol Evol", "docid": "35137080", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/updates/bib/bib_pubmed25n1442.json.gz", "annotations": { "title": [ "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocbiomed|BMV_119|recombination", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_6475|recombination" ], "all": 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"ncbitaxon_viruses|2509511|Sarbecovirus", "covocorganism|SP_6|COVID-19", "mesh|D002685|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_34|coronavirus", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D000086642|Pangolins", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", 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"covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_134|sequence", "covocconceptualentities|CE_37|host", "ncbitaxon_full|10239|Viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_6774|sampling", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "agrovoc|c_8389|wildlife", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_full|9605|Homo", "mesh|D006801|Humans", "pubchemmesh|439693|Pentostatin", "mesh|D010802|Phylogeny", "covocbiomed|BMV_150|transmission", "ott|770309|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_13325|phylogeny", "covocorganism|SP_4|Chiroptera", "ott|574724|Chiroptera", "ror|00vtgdb53|University of Glasgow", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|00vtgdb53|University of Glasgow", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|00bj04t22|\"Sciences", "ror|03p74gp79|University of Cape Town", "ror|00bj04t22|\"Sciences", "ror|03p74gp79|University of Cape Town", "ror|00bj04t22|\"Sciences", "ror|03p74gp79|University of Cape Town", "ror|03p74gp79|University of Cape Town", "ror|0240rwx68|Neuroscience Institute", "ror|00kx1jb78|Temple University", "ror|05v9jqt67|South China Agricultural University", "ror|038rjvd86|Department of Biological Sciences", "ror|03zmrmn05|Xi\u2019an Jiaotong-Liverpool University", "ror|03zmrmn05|Xi\u2019an Jiaotong-Liverpool University", "ror|00vtgdb53|University of Glasgow", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "mesh|D000818|Animals", "mesh|D002685|Chiroptera", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_34|coronavirus", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_5793|Pholidota", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "mesh|D058974|Phylogeography", "agrovoc|c_61fa2a1c|phylogeography", "covocbiomed|BMV_119|recombination", "agrovoc|c_6475|recombination", "mesh|D011995|Recombination, Genetic", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|49442|Rhinolophus", "ott|756634|Rhinolophus", "mesh|D002685|Chiroptera", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_6|COVID-19", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_5|Coronavirus", "mesh|D017934|Coronavirus", "agrovoc|c_facd9fd6|host range", "covocconceptualentities|CE_37|host", "mesh|D058507|Host Specificity", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination" ], "abstract": [ "ott|635025|Rhinolophidae", "ncbitaxon_models|227859|Human SARS coronavirus", "covocconceptualentities|CE_44|intermediate host", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocgeographicloc|LOC_16|Wu Han", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_full|2509511|Sarbecovirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|2509511|Sarbecovirus", "covocorganism|SP_6|COVID-19", "mesh|D002685|Chiroptera", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_34|coronavirus", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D000086642|Pangolins", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|644247|Manis", "covocorganism|SP_14|Manidae", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_4|Chiroptera", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocbiomed|BMV_119|recombination", "mesh|D017934|Coronavirus", "agrovoc|c_6475|recombination", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_5|Coronavirus", "agrovoc|c_6475|recombination", "agrovoc|c_394|ancestry", "agrovoc|c_11639|humoral immunity", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocconceptualentities|CE_19|distribution", "flopo|FLOPO_0900001|inflorescence type spike", "mesh|D007109|Immunity", "covocbiomed|BMV_119|recombination", "mesh|D000088603|Antigenic Drift and Shift", "covocbiomed|BMV_69|immunity", "psimi|MI:1115|spike", "covocorganism|SP_4|Chiroptera", "covocgeographicloc|LOC_3|China", "mesh|D002685|Chiroptera", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ott|756634|Rhinolophus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|635025|Rhinolophidae", "mesh|D001210|Asia, Southeastern", "covocgeographicloc|LOC_1|Asia", "ncbitaxon_full|49442|Rhinolophus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D002685|Chiroptera", "envo|ENVO_00000025|reservoir", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "agrovoc|c_3673|hosts", "covocorganism|SP_20|Rhinolophus macrotis", "agrovoc|c_6774|sampling", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|10239|Viruses", "mesh|D014780|Viruses", "covocbiomed|BMV_163|viruses", "covocgeographicloc|LOC_3|China", "mesh|D009068|Movement", "covocgeographicloc|LOC_1|Asia", "agrovoc|c_4961|movement", "mesh|D058507|Host Specificity", "agrovoc|c_8262|viruses", "mesh|D001210|Asia, Southeastern", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_134|sequence", "covocconceptualentities|CE_37|host", "ncbitaxon_full|10239|Viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_6774|sampling", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "agrovoc|c_8389|wildlife", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_full|9605|Homo", "mesh|D006801|Humans", "pubchemmesh|439693|Pentostatin", "mesh|D010802|Phylogeny", "covocbiomed|BMV_150|transmission", "ott|770309|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_13325|phylogeny", "covocorganism|SP_4|Chiroptera", "ott|574724|Chiroptera" ], "affiliations": [ "ror|00vtgdb53|University of Glasgow", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|00vtgdb53|University of Glasgow", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|00bj04t22|\"Sciences", "ror|03p74gp79|University of Cape Town", "ror|00bj04t22|\"Sciences", "ror|03p74gp79|University of Cape Town", "ror|00bj04t22|\"Sciences", "ror|03p74gp79|University of Cape Town", "ror|03p74gp79|University of Cape Town", "ror|0240rwx68|Neuroscience Institute", "ror|00kx1jb78|Temple University", "ror|05v9jqt67|South China Agricultural University", "ror|038rjvd86|Department of Biological Sciences", "ror|03zmrmn05|Xi\u2019an Jiaotong-Liverpool University", "ror|03zmrmn05|Xi\u2019an Jiaotong-Liverpool University", "ror|00vtgdb53|University of Glasgow", "ror|01w104f98|\"Conselleria d'Educaci\u00f3" ], "mesh_terms": [ "mesh|D000818|Animals", "mesh|D002685|Chiroptera", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_34|coronavirus", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_5793|Pholidota", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "mesh|D058974|Phylogeography", "agrovoc|c_61fa2a1c|phylogeography", "covocbiomed|BMV_119|recombination", "agrovoc|c_6475|recombination", "mesh|D011995|Recombination, Genetic" ], "keywords": [ "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|49442|Rhinolophus", "ott|756634|Rhinolophus", "mesh|D002685|Chiroptera", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "covocorganism|SP_6|COVID-19", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_34|coronavirus", "covocorganism|SP_5|Coronavirus", "mesh|D017934|Coronavirus", "agrovoc|c_facd9fd6|host range", "covocconceptualentities|CE_37|host", "mesh|D058507|Host Specificity", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "36036250", "_score": 120.00423, "_source": { "title": "SARS-CoV-2 origins: zoonotic Rhinolophus vs contemporary models.", "abstract": "The question of the origin of coronavirus spread like wildfire ever since it wreaked havoc among humankind, and ever since the scientific community has worked tirelessly to trace the history of the virus. In this review, we have tried to compile relevant literature pertaining to the different theories of origin of SARS-CoV-2, hopefully without any bias, and we strongly support the zoonotic origin of the infamous SARS-CoV-2 in bats and its transfer to human beings through the most probable evolutionary hosts, pangolins and minks. We also support the contemporary 'Circulation Model' that simply mirrors the concept of evolution to explain the origin of the virus which, the authors believe, is the most rational school of thought. The most recent variant of SARS-CoV-2, Omicron, has been taken as an example to clarify the concept. We recommend the community to refer to this model for further understanding and delving deep into this mystery of the origin of SARS-CoV-2.", "coi_statement": "", "journal": "Biotechnology & genetic engineering reviews", "authors": [ "Gulati Ishika", "Khan Saif", "Gulati Garima", "Verma Smita Rastogi", "Khan Mahvish", "Ahmad Saheem", "Bantun Farkad", "Mathkor Darin Mansor", "Haque Shafiul" ], "affiliations": [ "Department of Biotechnology, Delhi Technological University, Delhi, India.", "Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia.", "Department of Applied Mechanics, Motilal Nehru National Institute of Technology, Prayagraj, Allahabad, India.", "Department of Biotechnology, Delhi Technological University, Delhi, India.", "Department of Biology, College of science, University of Ha'il, Ha'il, Saudi Arabia.", "Department of clinical laboratory science, College of Applied Medical Science, University of Ha'il, Ha'il, Saudi Arabia.", "Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.", "Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia.", "Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia." ], "pubyear": "2023", "publication_date": "2023-10-01", "entrez_date": "2022-08-29", "pmid": "36036250", "mesh_terms": [ "D000086402:SARS-CoV-2", "D000818:Animals", "D006801:Humans", "D000086382:COVID-19", "D002685:Chiroptera", "D015047:Zoonoses", "D058873:Pandemics", "D000086642:Pangolins", "D000073640:Betacoronavirus", "D011024:Pneumonia, Viral", "D000086965:Viral Zoonoses", "D018352:Coronavirus Infections" ], "sup_mesh_terms": [ "C000711908:SARS-CoV-2 variants" ], "chemicals": [], "publication_types": [ "Journal Article", "Review" ], "keywords": [ "COVID-19", "Circulation model", "bioweapon", "laboratory leak", "pangolins", "zoonosis" ], "pmcid": "", "doi": "10.1080/02648725.2022.2115682", "medline_ta": "Biotechnol Genet Eng Rev", "docid": "36036250", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1151.json.gz", "annotations": { "title": [ "covocorganism|SP_6|COVID-19", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|49442|Rhinolophus", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "mesh|D002685|Chiroptera", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars" ], "all": [ "covocorganism|SP_6|COVID-19", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|49442|Rhinolophus", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "mesh|D002685|Chiroptera", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D000075923|Wildfires", "pubchemmesh|71752521|2,3-Thioepoxy Madol", "envo|ENVO_01000787|wildfire", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "covocbiomed|BMV_34|coronavirus", "covocbiomed|BMV_163|viruses", "agrovoc|c_4586|humans", "pubchemmesh|439693|Pentostatin", "ott|574724|Chiroptera", "ott|770315|Homo sapiens", "mesh|D016454|Review", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "mdd|1000718|Homo_sapiens", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_14|Manidae", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_3673|hosts", "mesh|D015982|Bias", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_5793|Pholidota", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|9606|Homo sapiens", "agrovoc|c_4859|minks", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D008907|Mink", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D000086642|Pangolins", "covocbiomed|BMV_163|viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|4537159|Omicron", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2613138|Omicron", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "psimi|MI:1241|variant", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_33|Omicron", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ror|03tjsyq23|Department of Biotechnology", "ror|01ztcvt22|Delhi Technological University", "ror|05qm21180|Beijing Advanced Sciences and Innovation Center", "ror|00bj04t22|\"Sciences", "ror|04dp7tp96|Motilal Nehru National Institute of Technology", "ror|03tjsyq23|Department of Biotechnology", "ror|01ztcvt22|Delhi Technological University", "ror|013w98a82|University of Ha'il", "ror|021ez5n36|\"College of Science", "ror|029ez4v67|\"Instituto Federal de Educa\u00e7\u00e3o", "ror|029ez4v67|\"Instituto Federal de Educa\u00e7\u00e3o", "ror|013w98a82|University of Ha'il", "ror|01xjqrm90|Umm al-Qura University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|015xjsg96|Universidade Tiradentes", "ror|00bj04t22|\"Sciences", "ror|02bjnq803|Jazan University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|015xjsg96|Universidade Tiradentes", "ror|00bj04t22|\"Sciences", "ror|02bjnq803|Jazan University", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D000818|Animals", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D015047|Zoonoses", "agrovoc|c_8530|zoonoses", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_7ec13bd4|Betacoronavirus", "ncbitaxon_full|694002|Betacoronavirus", "ncbitaxon_viruses|694002|Betacoronavirus", "mesh|D000073640|Betacoronavirus", "covocorganism|SP_1|Betacoronavirus", "covocdiseaseandsyndrom|DIS_48|pneumonia", "agrovoc|c_13471|pneumonia", "mesh|D011024|Pneumonia, Viral", "ncit|C3333|Pneumonia", "agrovoc|c_8530|zoonoses", "mesh|D000086965|Viral Zoonoses", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_18|Coronavirus Infections", "covocorganism|SP_5|Coronavirus", "mesh|D018352|Coronavirus Infections", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "covocorganism|SP_14|Manidae", "agrovoc|c_5793|Pholidota", "mesh|D000086642|Pangolins", "ncit|C35803|Zoonotic Infection" ], "abstract": [ "mesh|D000075923|Wildfires", "pubchemmesh|71752521|2,3-Thioepoxy Madol", "envo|ENVO_01000787|wildfire", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "covocbiomed|BMV_34|coronavirus", "covocbiomed|BMV_163|viruses", "agrovoc|c_4586|humans", "pubchemmesh|439693|Pentostatin", "ott|574724|Chiroptera", "ott|770315|Homo sapiens", "mesh|D016454|Review", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "mdd|1000718|Homo_sapiens", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_14|Manidae", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_3673|hosts", "mesh|D015982|Bias", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "agrovoc|c_5793|Pholidota", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|9606|Homo sapiens", "agrovoc|c_4859|minks", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D008907|Mink", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D000086642|Pangolins", "covocbiomed|BMV_163|viruses", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|4537159|Omicron", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2613138|Omicron", "uniprot_swissprot|Q8CIQ8|Sars", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "psimi|MI:1241|variant", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_33|Omicron", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus" ], "affiliations": [ "ror|03tjsyq23|Department of Biotechnology", "ror|01ztcvt22|Delhi Technological University", "ror|05qm21180|Beijing Advanced Sciences and Innovation Center", "ror|00bj04t22|\"Sciences", "ror|04dp7tp96|Motilal Nehru National Institute of Technology", "ror|03tjsyq23|Department of Biotechnology", "ror|01ztcvt22|Delhi Technological University", "ror|013w98a82|University of Ha'il", "ror|021ez5n36|\"College of Science", "ror|029ez4v67|\"Instituto Federal de Educa\u00e7\u00e3o", "ror|029ez4v67|\"Instituto Federal de Educa\u00e7\u00e3o", "ror|013w98a82|University of Ha'il", "ror|01xjqrm90|Umm al-Qura University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|015xjsg96|Universidade Tiradentes", "ror|00bj04t22|\"Sciences", "ror|02bjnq803|Jazan University", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "ror|015xjsg96|Universidade Tiradentes", "ror|00bj04t22|\"Sciences", "ror|02bjnq803|Jazan University" ], "mesh_terms": [ "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D000818|Animals", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "mesh|D015047|Zoonoses", "agrovoc|c_8530|zoonoses", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "agrovoc|c_5793|Pholidota", "covocorganism|SP_14|Manidae", "mesh|D000086642|Pangolins", "agrovoc|c_7ec13bd4|Betacoronavirus", "ncbitaxon_full|694002|Betacoronavirus", "ncbitaxon_viruses|694002|Betacoronavirus", "mesh|D000073640|Betacoronavirus", "covocorganism|SP_1|Betacoronavirus", "covocdiseaseandsyndrom|DIS_48|pneumonia", "agrovoc|c_13471|pneumonia", "mesh|D011024|Pneumonia, Viral", "ncit|C3333|Pneumonia", "agrovoc|c_8530|zoonoses", "mesh|D000086965|Viral Zoonoses", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_18|Coronavirus Infections", "covocorganism|SP_5|Coronavirus", "mesh|D018352|Coronavirus Infections" ], "sup_mesh_terms": [ "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin" ], "keywords": [ "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "covocorganism|SP_14|Manidae", "agrovoc|c_5793|Pholidota", "mesh|D000086642|Pangolins", "ncit|C35803|Zoonotic Infection" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "39427096", "_score": 117.77787, "_source": { "title": "Study on sentinel hosts for surveillance of future COVID-19-like outbreaks.", "abstract": "The spread of SARS-CoV-2 to animals has the potential to evolve independently. In this study, we distinguished several sentinel animal species and genera for monitoring the re-emergence of COVID-19 or the new outbreak of COVID-19-like disease. We analyzed SARS-CoV-2 genomic data from human and nonhuman mammals in the taxonomic hierarchies of species, genus, family and order of their host. We find that SARS-CoV-2 carried by domestic dog (Canis lupus familiaris), domestic cat (Felis catus), mink (Neovison vison), and white-tailed deer (Odocoileus virginianus) cluster closely to human-origin viruses and show no differences in the majority of amino acids, but have the most positively selected sites and should be monitored to prevent the re-emergence of COVID-19 caused by novel variants of SARS-CoV-2. Viruses from the genera Panthera (especially lion (Panthera leo)), Manis and Rhinolophus differ significantly from human-origin viruses, and long-term surveillance should be undertaken to prevent the future COVID-19-like outbreaks. Investigation of the variation dynamics of sites 142, 501, 655, 681 and 950 within the S protein may be necessary to predict the novel animal SARS-CoV-2 variants.", "coi_statement": "", "journal": "Scientific reports", "authors": [ "Li Yanjiao", "Hu Jingjing", "Hou Jingjing", "Lu Shuiping", "Xiong Jiasheng", "Wang Yuxi", "Sun Zhong", "Chen Weijie", "Pan Yue", "Thilakavathy Karuppiah", "Feng Yi", "Jiang Qingwu", "Wang Weibing", "Xiong Chenglong" ], "affiliations": [ "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Department of Pulmonary and Critical Care Medicine, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Division of Emergency Management, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, China.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, 43400, Malaysia.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, 43400, Malaysia.", "Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China. wwb@fudan.edu.cn.", "Department of Epidemiology, School of Public Health, Fudan University, Shanghai, 200433, China. xiongchenglong@fudan.edu.cn." ], "pubyear": "2024", "publication_date": "2024-10-19", "entrez_date": "2024-10-19", "pmid": "39427096", "mesh_terms": [ "D000818:Animals", "D000086382:COVID-19", "D000086402:SARS-CoV-2", "D006801:Humans", "D004196:Disease Outbreaks", "D000072739:Sentinel Species", "D010802:Phylogeny", "D004285:Dogs", "D002415:Cats", "D008907:Mink", "D016679:Genome, Viral" ], "sup_mesh_terms": [], "chemicals": [], "publication_types": [ "Journal Article" ], "keywords": [ "Amino acid polymorphism", "Phylogenetic tree", "Positively selected site", "SARS-CoV-2", "Sentinel host", "Spike protein" ], "pmcid": "PMC11490639", "doi": "10.1038/s41598-024-76506-7", "medline_ta": "Sci Rep", "docid": "39427096", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1262.json.gz", "annotations": { "title": [ "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocconceptualentities|CE_84|surveillance", "robiext|RO_0002453|host 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lupus familiaris", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|563166|Felis catus", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D002415|Cats", "agrovoc|c_6b1c31d5|Felis catus", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|10239|Viruses", "ott|247333|Canis lupus familiaris", "mdd|1000718|Homo_sapiens", "nextprot|NX_Q8N4C8|MINK1", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|452646|Neogale vison", "ott|410145|Odocoileus virginianus", "mesh|D008907|Mink", "mdd|1005940|Canis_familiaris", "ncbitaxon_full|10239|Viruses", "agrovoc|c_4ad07701|COVID-19", "covocbiomed|BMV_163|viruses", "mesh|D046009|Panthera", "mdd|1000718|Homo_sapiens", "agrovoc|c_8262|viruses", "ott|563154|Panthera", "mesh|D002685|Chiroptera", "mesh|D000086642|Pangolins", "covocbiomed|BMV_163|viruses", "ott|563151|Panthera leo", "ott|644247|Manis", "ott|756634|Rhinolophus", "covocconceptualentities|CE_84|surveillance", "ncbitaxon_full|9689|Panthera leo", "cellosaurus|CVCL_A016|Leo", "mesh|D014780|Viruses", "ncbitaxon_full|9973|Manis", "ott|770315|Homo sapiens", "mesh|D000086382|COVID-19", "mesh|D014780|Viruses", "ncbitaxon_full|49442|Rhinolophus", "ncbitaxon_full|9688|Panthera", "ncbitaxon_viruses|10239|Viruses", "covocorganism|SP_6|COVID-19", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_full|10239|Viruses", "mesh|D008045|Lions", "ncbitaxon_viruses|10239|Viruses", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|10239|Viruses", "agrovoc|c_4ad07701|COVID-19", "agrovoc|c_8262|viruses", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocproteinsgenomes|PG_29|Spike glycoprotein", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "uniprot_swissprot|P19704|hss", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|04xy45965|Tongji Hospital", "ror|03rc6as71|Tongji University", "ror|013q1eq08|Fudan University", "ror|02wvar244|EMERGENCY", "ror|04hsdam77|Center for Disease Control", "ror|013q1eq08|Fudan University", "ror|00bj04t22|\"Sciences", "ror|02e91jd64|Universiti Putra Malaysia", "ror|00bj04t22|\"Sciences", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|00bj04t22|\"Sciences", "ror|02e91jd64|Universiti Putra Malaysia", "ror|00bj04t22|\"Sciences", "ror|00bj04t22|\"Sciences", "ror|05qm21180|Beijing Advanced Sciences and Innovation Center", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "mesh|D000818|Animals", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "agrovoc|c_164ea2ee|disease outbreaks", "mesh|D004196|Disease Outbreaks", "mesh|D000072739|Sentinel Species", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "ncbitaxon_full|9615|Canis lupus familiaris", "mesh|D004285|Dogs", "ott|247333|Canis lupus familiaris", "mesh|D002415|Cats", "ncbitaxon_full|9685|Felis catus", "cellosaurus|CVCL_DR98|CHO CAT-S", "ott|563166|Felis catus", "agrovoc|c_1390|cats", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome", "mesh|D000596|Amino Acids", "chebi|CHEBI:33709|amino acid", "agrovoc|c_6088|polymorphism", "mesh|D010802|Phylogeny", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocconceptualentities|CE_37|host", "psimi|MI:1115|spike", "covocproteinsgenomes|PG_31|spike protein", "flopo|FLOPO_0900001|inflorescence type spike" ], "abstract": [ "ncbitaxon_models|227859|Human SARS coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000086382|COVID-19", "mesh|D000086382|COVID-19", "agrovoc|c_4ad07701|COVID-19", "covocorganism|SP_6|COVID-19", "agrovoc|c_4ad07701|COVID-19", "covocorganism|SP_6|COVID-19", "mesh|D000072739|Sentinel Species", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mdd|1000718|Homo_sapiens", "agrovoc|c_4560|mammals", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_11|Homo sapiens", "covocorganism|SP_6|COVID-19", "ncbitaxon_models|9606|Homo sapiens", "ott|244265|Mammalia", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocconceptualentities|CE_37|host", "mesh|D008322|Mammals", "ncbitaxon_models|227859|Human SARS coronavirus", "ott|770315|Homo sapiens", "agrovoc|c_9576|Canis lupus", "ncbitaxon_models|452646|Mustela vison", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|taxID: 9685|Felis catus", "uniprot_swissprot|Q8CIQ8|Sars", "mesh|D002415|Cats", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9685|Felis catus", "mesh|D019596|Wolves", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_8262|viruses", "ncbitaxon_full|9874|Odocoileus virginianus", "ott|770315|Homo sapiens", "covocorganism|SP_7|dog", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_342|amino acids", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|563166|Felis catus", "ott|410145|Odocoileus virginianus", "covocconceptualentities|CE_7|cluster", "uniprot_swissprot|F1LP90|Mink", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mdd|1006302|Odocoileus_virginianus", "ott|310482|Neovison vison", "covocbiomed|BMV_163|viruses", "atc|B05BA01|amino acids", "covocorganism|SP_6|COVID-19", "covocorganism|SP_11|Homo sapiens", "mdd|1005985|Felis_catus", "agrovoc|c_12896|Odocoileus virginianus", "chebi|CHEBI:33709|amino acid", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_models|452646|Mustela vison", "ncbitaxon_models|227859|Human SARS coronavirus", "mesh|D008907|Mink", "ncbitaxon_models|9615|Canis familiaris", "mesh|D000596|Amino Acids", "mesh|D000086382|COVID-19", "mesh|D014780|Viruses", "ncbitaxon_full|9615|Canis lupus familiaris", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|563166|Felis catus", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D002415|Cats", "agrovoc|c_6b1c31d5|Felis catus", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|10239|Viruses", "ott|247333|Canis lupus familiaris", "mdd|1000718|Homo_sapiens", "nextprot|NX_Q8N4C8|MINK1", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|452646|Neogale vison", "ott|410145|Odocoileus virginianus", "mesh|D008907|Mink", "mdd|1005940|Canis_familiaris", "ncbitaxon_full|10239|Viruses", "agrovoc|c_4ad07701|COVID-19", "covocbiomed|BMV_163|viruses", "mesh|D046009|Panthera", "mdd|1000718|Homo_sapiens", "agrovoc|c_8262|viruses", "ott|563154|Panthera", "mesh|D002685|Chiroptera", "mesh|D000086642|Pangolins", "covocbiomed|BMV_163|viruses", "ott|563151|Panthera leo", "ott|644247|Manis", "ott|756634|Rhinolophus", "covocconceptualentities|CE_84|surveillance", "ncbitaxon_full|9689|Panthera leo", "cellosaurus|CVCL_A016|Leo", "mesh|D014780|Viruses", "ncbitaxon_full|9973|Manis", "ott|770315|Homo sapiens", "mesh|D000086382|COVID-19", "mesh|D014780|Viruses", "ncbitaxon_full|49442|Rhinolophus", "ncbitaxon_full|9688|Panthera", "ncbitaxon_viruses|10239|Viruses", "covocorganism|SP_6|COVID-19", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_full|10239|Viruses", "mesh|D008045|Lions", "ncbitaxon_viruses|10239|Viruses", "covocorganism|SP_20|Rhinolophus macrotis", "ncbitaxon_full|10239|Viruses", "agrovoc|c_4ad07701|COVID-19", "agrovoc|c_8262|viruses", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocproteinsgenomes|PG_29|Spike glycoprotein", "pubchemmesh|439693|Pentostatin", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "uniprot_swissprot|P19704|hss", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_6|COVID-19" ], "affiliations": [ "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|04xy45965|Tongji Hospital", "ror|03rc6as71|Tongji University", "ror|013q1eq08|Fudan University", "ror|02wvar244|EMERGENCY", "ror|04hsdam77|Center for Disease Control", "ror|013q1eq08|Fudan University", "ror|00bj04t22|\"Sciences", "ror|02e91jd64|Universiti Putra Malaysia", "ror|00bj04t22|\"Sciences", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|00bj04t22|\"Sciences", "ror|02e91jd64|Universiti Putra Malaysia", "ror|00bj04t22|\"Sciences", "ror|00bj04t22|\"Sciences", "ror|05qm21180|Beijing Advanced Sciences and Innovation Center", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University", "ror|013q1eq08|Fudan University" ], "mesh_terms": [ "mesh|D000818|Animals", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "agrovoc|c_164ea2ee|disease outbreaks", "mesh|D004196|Disease Outbreaks", "mesh|D000072739|Sentinel Species", "agrovoc|c_13325|phylogeny", "mesh|D010802|Phylogeny", "ncbitaxon_full|9615|Canis lupus familiaris", "mesh|D004285|Dogs", "ott|247333|Canis lupus familiaris", "mesh|D002415|Cats", "ncbitaxon_full|9685|Felis catus", "cellosaurus|CVCL_DR98|CHO CAT-S", "ott|563166|Felis catus", "agrovoc|c_1390|cats", "ncbitaxon_models|452646|Mustela vison", "cellosaurus|CVCL_0593|Mv1Lu", "mesh|D008907|Mink", "uniprot_swissprot|F1LP90|Mink", "nextprot|NX_Q8N4C8|MINK1", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome" ], "keywords": [ "mesh|D000596|Amino Acids", "chebi|CHEBI:33709|amino acid", "agrovoc|c_6088|polymorphism", "mesh|D010802|Phylogeny", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocconceptualentities|CE_37|host", "psimi|MI:1115|spike", "covocproteinsgenomes|PG_31|spike protein", "flopo|FLOPO_0900001|inflorescence type spike" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "32893295", "_score": 117.745445, "_source": { "title": "Where Did SARS-CoV-2 Come From?", "abstract": "Identifying the origin of SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, may help us to avoid future epidemics of coronavirus and other zoonoses. Several theories about the zoonotic origin of SARS-CoV-2 have recently been proposed. Although Betacoronavirus found in Rhinolophus bats from China have been broadly implicated, their genetic dissimilarity to SARS-CoV-2 is so high that they are highly unlikely to be its direct ancestors. Thus, an intermediary host is suspected to link bat to human coronaviruses. Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastrointestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. Therefore, reduced genomic CpG alone is not a highly predictive biomarker, suggesting a need for additional biomarkers to reveal intermediate hosts or tissues. The hunt for the zoonotic origin of SARS-CoV-2 continues.", "coi_statement": "", "journal": "Molecular biology and evolution", "authors": [ "Leitner Thomas", "Kumar Sudhir" ], "affiliations": [ "Theroretical Biology and Biophysics group, Los Alamos National Laboratory, Los Alamos, NM.", "Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA." ], "pubyear": "2020", "publication_date": "2020-09-01", "entrez_date": "2020-09-07", "pmid": "32893295", "mesh_terms": [ "D000818:Animals", "D000073640:Betacoronavirus", "D000086382:COVID-19", "D002685:Chiroptera", "D018352:Coronavirus Infections", "D018899:CpG Islands", "D000073566:Eutheria", "D019143:Evolution, Molecular", "D015870:Gene Expression", "D016679:Genome, Viral", "D009154:Mutation", "D058873:Pandemics", "D011024:Pneumonia, Viral", "D016865:Reassortant Viruses", "D011995:Recombination, Genetic", "D000086402:SARS-CoV-2", "D014764:Viral Proteins", "D015047:Zoonoses" ], "sup_mesh_terms": [], "chemicals": [ "RN 0, D014764:Viral Proteins" ], "publication_types": [ "Journal Article" ], "keywords": [ "SARS-CoV-2", "evolution", "origins", "pandemic" ], "pmcid": "PMC7454771", "doi": "10.1093/molbev/msaa162", "medline_ta": "Mol Biol Evol", "docid": "32893295", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1048.json.gz", "annotations": { "title": [ "ncbitaxon_models|227859|Human SARS coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2" ], "all": [ "ncbitaxon_models|227859|Human SARS coronavirus", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", 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"covocorganism|SP_20|Rhinolophus macrotis", "covocbiomed|BMV_34|coronavirus", "ott|770315|Homo sapiens", "mdd|1000718|Homo_sapiens", "covocconceptualentities|CE_37|host", "covocorganism|SP_4|Chiroptera", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_11|Homo sapiens", "ncbitaxon_models|9606|Homo sapiens", "mesh|D006801|Humans", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "covocorganism|SP_5|Coronavirus", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_full|9605|Homo", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_3673|hosts", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D041981|Gastrointestinal Tract", "mesh|D017934|Coronavirus", "covocorganism|SP_6|COVID-19", "ott|770309|Homo", "chebi|CHEBI:47885|dinucleotide", "covocbiomed|BMV_150|transmission", 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"covocorganism|SP_6|COVID-19", "ror|01e41cf67|Los Alamos National Laboratory", "ror|00kx1jb78|Temple University", "mesh|D000818|Animals", "agrovoc|c_7ec13bd4|Betacoronavirus", "ncbitaxon_full|694002|Betacoronavirus", "ncbitaxon_viruses|694002|Betacoronavirus", "mesh|D000073640|Betacoronavirus", "covocorganism|SP_1|Betacoronavirus", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "covocbiomed|BMV_34|coronavirus", "covocdiseaseandsyndrom|DIS_18|Coronavirus Infections", "covocorganism|SP_5|Coronavirus", "mesh|D018352|Coronavirus Infections", "cellosaurus|CVCL_1G78|CPG", "mesh|D018899|CpG Islands", "agrovoc|c_3962|islands", "ott|3373561|Eutheria", "ncbitaxon_full|9347|Eutheria", "mesh|D000073566|Eutheria", "mesh|D019143|Evolution, Molecular", "mesh|D015870|Gene Expression", "agrovoc|c_27527|gene expression", "covocbiomed|BMV_49|Gene Expression", "go_bp|GO:0010467|gene expression", "mesh|D016679|Genome, Viral", "covocbiomed|BMV_56|Genome", "agrovoc|c_5014|mutation", "covocbiomed|BMV_95|Mutation", "mesh|D009154|Mutation", "psimi|MI:0118|mutation", "ncit|C16885|Mutation", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "covocdiseaseandsyndrom|DIS_48|pneumonia", "agrovoc|c_13471|pneumonia", "mesh|D011024|Pneumonia, Viral", "ncit|C3333|Pneumonia", "mesh|D016865|Reassortant Viruses", "agrovoc|c_8262|viruses", "ncbitaxon_full|10239|Viruses", "covocbiomed|BMV_163|viruses", "ncbitaxon_viruses|10239|Viruses", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination", "mesh|D011995|Recombination, Genetic", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D014764|Viral Proteins", "agrovoc|c_36663|viral proteins", "mesh|D015047|Zoonoses", "agrovoc|c_8530|zoonoses", "mesh|D014764|Viral Proteins", "agrovoc|c_36663|viral proteins", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocconceptualentities|CE_54|Pandemics" ], "abstract": [ "mesh|D000086382|COVID-19", "agrovoc|c_2614|epidemics", "agrovoc|c_8530|zoonoses", "covocconceptualentities|CE_54|Pandemics", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_34|coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory 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"covocconceptualentities|CE_44|intermediate host", "cellosaurus|CVCL_1G78|CPG", "chebi|CHEBI:59163|biomarker", "mesh|D015415|Biomarkers", "covocbiomed|BMV_17|biomarkers", "mesh|D015415|Biomarkers", "covocbiomed|BMV_17|biomarkers", "agrovoc|c_15589|intermediate hosts", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "robiext|RO_e000011|hunts", "pubchemmesh|439693|Pentostatin", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19" ], "affiliations": [ "ror|01e41cf67|Los Alamos National Laboratory", "ror|00kx1jb78|Temple University" ], "mesh_terms": [ "mesh|D000818|Animals", "agrovoc|c_7ec13bd4|Betacoronavirus", "ncbitaxon_full|694002|Betacoronavirus", "ncbitaxon_viruses|694002|Betacoronavirus", "mesh|D000073640|Betacoronavirus", 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"mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "covocconceptualentities|CE_54|Pandemics", "covocdiseaseandsyndrom|DIS_48|pneumonia", "agrovoc|c_13471|pneumonia", "mesh|D011024|Pneumonia, Viral", "ncit|C3333|Pneumonia", "mesh|D016865|Reassortant Viruses", "agrovoc|c_8262|viruses", "ncbitaxon_full|10239|Viruses", "covocbiomed|BMV_163|viruses", "ncbitaxon_viruses|10239|Viruses", "agrovoc|c_6475|recombination", "covocbiomed|BMV_119|recombination", "mesh|D011995|Recombination, Genetic", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin", "mesh|D014764|Viral Proteins", "agrovoc|c_36663|viral proteins", "mesh|D015047|Zoonoses", "agrovoc|c_8530|zoonoses" ], "chemicals": [ "mesh|D014764|Viral Proteins", "agrovoc|c_36663|viral proteins" ], "keywords": [ "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocconceptualentities|CE_54|Pandemics" ] } } }, { "_index": "sibils_med25_r1_v5.0.5.8", "_id": "36646081", "_score": 115.51269, "_source": { "title": "The Origins of Severe Acute Respiratory Syndrome-Coronavirus-2.", "abstract": "An outbreak of severe pneumonia of unknown cause was identified in Wuhan, China in December 2019: the causative agent was a novel betacoronavirus, severe acute respiratory syndrome-cotonavirus-2 (SARS-CoV-2), a virus that joins a list of coronaviruses causing severe (e.g., SARS and Middle East respiratory syndrome) or milder (e.g., 229E, OC43, NL63, and HKU1) respiratory tract infection. The World Health Organization (WHO) classified the spreading outbreak as a pandemic on March 11, 2020. Many SARS-related coronaviruses (SARSr-CoVs) have been identified in bats, particularly in Rhinolophus horseshoe bats, animals that are common in southern China and Southeast Asia. Many of the features of SARS-CoV-2 that facilitate human infection-the furin cleavage site, the receptor binding domain that binds to the human ACE2 receptor-can be identified in SARSr-CoVs. Related coronaviruses can be detected in pangolins and other animals, and human SARS-CoV-2 itself can infect various animals, some of which can transmit SARS-CoV-2 back to humans. Investigation by the WHO and others pointed to the initial outbreak being centered on the Huanan wet market in Wuhan where wild and farmed animals were sold, and where environmental testing revealed widespread SARS-CoV-2 contamination. This supports the hypothesis that bats, probably via an intermediate animal, are the origin of SARS-CoV-2. Other possible origins have been postulated, such as an accidental or deliberate laboratory leak, or virus present in frozen foods, but evidence for these ideas has not surfaced. Study of the origins of SARS-CoV-2 have been complicated by intense media and political commentary, features that may slow the studies required to understand the viral origins. Such studies are complex and may be slow: international openness and co-operation is vital. Origins explanations are needed to predict or prevent future pandemics and support the \"One Health\" approach to disease.", "coi_statement": "None declared.", "journal": "Seminars in respiratory and critical care medicine", "authors": [ "Dwyer Dominic E" ], "affiliations": [ "Public Health Pathology, New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia." ], "pubyear": "2023", "publication_date": "2023-02-01", "entrez_date": "2023-01-16", "pmid": "36646081", "mesh_terms": [ "D000818:Animals", "D006801:Humans", "D002681:China", "D002685:Chiroptera", "D000086382:COVID-19", "D000086402:SARS-CoV-2" ], "sup_mesh_terms": [], "chemicals": [], "publication_types": [ "Journal Article" ], "keywords": [], "pmcid": "", "doi": "10.1055/s-0042-1759564", "medline_ta": "Semin Respir Crit Care Med", "docid": "36646081", "ftp_archive_id": "/SIBiLS_v5.0/medline/r1/baseline/bib/bib_pubmed25n1171.json.gz", "annotations": { "title": [ "ncit|C85064|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "mesh|D045169|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "agrovoc|c_3c275990|severe acute respiratory syndrome" ], "all": [ "ncit|C85064|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "mesh|D045169|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_5|Coronavirus", "agrovoc|c_3c275990|severe acute respiratory syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_9|HKU1", "ncit|C128424|Middle East Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_42|Middle East Respiratory Syndrome", "covocgeographicloc|LOC_8|Middle East", "covocbiomed|BMV_163|viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute 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"covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocgeographicloc|LOC_16|Wu Han", "ncit|C35650|Upper Respiratory Tract Infection", "ncbitaxon_full|694002|Betacoronavirus", "mesh|D011014|Pneumonia", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_37|infection", "mesh|D000073640|Betacoronavirus", "covocconceptualentities|CE_92|World Health Organization", "covocconceptualentities|CE_54|Pandemics", "ncit|C206523|Multinucleated Neurons, Anhydramnios, Renal Dysplasia, Cerebellar Hypoplasia And Hydranencephaly", "atc|http://purl.bioontology.org/ontology/STY/T092|Organization", "mesh|D014944|World Health Organization", "covocorganism|SP_5|Coronavirus", "ott|574724|Chiroptera", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_20|Rhinolophus macrotis", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D000818|Animals", "mesh|D017934|Coronavirus", "ncbitaxon_full|49442|Rhinolophus", "uniprot_swissprot|Q8CIQ8|Sars", "covocgeographicloc|LOC_3|China", "covocbiomed|BMV_34|coronavirus", "mesh|D002685|Chiroptera", "covocgeographicloc|LOC_1|Asia", "covocorganism|SP_4|Chiroptera", "ott|635025|Rhinolophidae", "mesh|D001210|Asia, Southeastern", "mesh|D002685|Chiroptera", "nextprot|NX_P09958|FURIN", "ncbitaxon_models|227859|Human SARS coronavirus", "ppiptm|PPI:2|bind", "ott|770315|Homo sapiens", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "go_mf|GO:0005488|binding", "mdd|1000718|Homo_sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|770315|Homo sapiens", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncit|C128320|Infection", "covocorganism|SP_11|Homo sapiens", "mesh|D045683|Furin", "mdd|1000718|Homo_sapiens", "ppiptm|PPI:2|bind", "ncbitaxon_models|9606|Homo sapiens", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|P29119|furin", "covocorganism|SP_11|Homo sapiens", "covocdiseaseandsyndrom|DIS_37|infection", "covocorganism|SP_5|Coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_models|9606|Homo sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_77|infection", "ncbitaxon_full|9605|Homo", "covocorganism|SP_14|Manidae", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000818|Animals", "agrovoc|c_5793|Pholidota", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|770315|Homo sapiens", "ott|770309|Homo", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_6|COVID-19", "mdd|1000718|Homo_sapiens", "mesh|D006801|Humans", "covocbiomed|BMV_34|coronavirus", "pubchemmesh|439693|Pentostatin", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_11|Homo sapiens", "mesh|D000086642|Pangolins", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_5|Coronavirus", "agrovoc|c_28317|contamination", "covocgeographicloc|LOC_16|Wu Han", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "envo|ENVO_03501198|wet market", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_33|contamination", "robiext|RO_e000002|has contaminated", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|574724|Chiroptera", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|445354|Retinol", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "mesh|D005628|Frozen Foods", "covocbiomed|BMV_163|viruses", "agrovoc|c_16490|frozen foods", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_1855|cooperation", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "agrovoc|c_b29a1475|One Health approach", "mesh|D000074823|One Health", "covocconceptualentities|CE_54|Pandemics", "ror|04gp5yv64|Westmead Hospital", "ror|01w104f98|\"Conselleria d'Educaci\u00f3", "mesh|D000818|Animals", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "covocgeographicloc|LOC_3|China", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin" ], "abstract": [ "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_9|HKU1", "ncit|C128424|Middle East Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_42|Middle East Respiratory Syndrome", "covocgeographicloc|LOC_8|Middle East", "covocbiomed|BMV_163|viruses", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_48|pneumonia", "agrovoc|c_7ec13bd4|Betacoronavirus", "covocorganism|SP_6|COVID-19", "ncit|C3333|Pneumonia", "mesh|D017934|Coronavirus", "mesh|D018352|Coronavirus Infections", "covocorganism|SP_1|Betacoronavirus", "covocorganism|SP_17|OC43", "ncbitaxon_viruses|694002|Betacoronavirus", "ncit|C85064|Severe Acute Respiratory Syndrome", "covocbiomed|BMV_34|coronavirus", "agrovoc|c_3c275990|severe acute respiratory syndrome", "ncbitaxon_models|227859|Human SARS coronavirus", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_77|infection", "mesh|D045169|Severe Acute Respiratory Syndrome", "agrovoc|c_13471|pneumonia", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D012137|Respiratory System", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "agrovoc|c_0abecf1c|Middle East respiratory syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "covocgeographicloc|LOC_3|China", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocgeographicloc|LOC_16|Wu Han", "ncit|C35650|Upper Respiratory Tract Infection", "ncbitaxon_full|694002|Betacoronavirus", "mesh|D011014|Pneumonia", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "covocdiseaseandsyndrom|DIS_37|infection", "mesh|D000073640|Betacoronavirus", "covocconceptualentities|CE_92|World Health Organization", "covocconceptualentities|CE_54|Pandemics", "ncit|C206523|Multinucleated Neurons, Anhydramnios, Renal Dysplasia, Cerebellar Hypoplasia And Hydranencephaly", "atc|http://purl.bioontology.org/ontology/STY/T092|Organization", "mesh|D014944|World Health Organization", "covocorganism|SP_5|Coronavirus", "ott|574724|Chiroptera", "covocorganism|SP_5|Coronavirus", "covocorganism|SP_20|Rhinolophus macrotis", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|756634|Rhinolophus", "covocorganism|SP_20|Rhinolophus macrotis", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "mesh|D000818|Animals", "mesh|D017934|Coronavirus", "ncbitaxon_full|49442|Rhinolophus", "uniprot_swissprot|Q8CIQ8|Sars", "covocgeographicloc|LOC_3|China", "covocbiomed|BMV_34|coronavirus", "mesh|D002685|Chiroptera", "covocgeographicloc|LOC_1|Asia", "covocorganism|SP_4|Chiroptera", "ott|635025|Rhinolophidae", "mesh|D001210|Asia, Southeastern", "mesh|D002685|Chiroptera", "nextprot|NX_P09958|FURIN", "ncbitaxon_models|227859|Human SARS coronavirus", "ppiptm|PPI:2|bind", "ott|770315|Homo sapiens", "covocproteinsgenomes|PG_4|Angiotensin-converting enzyme 2", "uniprot_swissprot|Q5EGZ1|Ace2", "nextprot|NX_Q9BYF1|ACE2", "go_mf|GO:0005488|binding", "mdd|1000718|Homo_sapiens", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "ott|770315|Homo sapiens", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ncit|C128320|Infection", "covocorganism|SP_11|Homo sapiens", "mesh|D045683|Furin", "mdd|1000718|Homo_sapiens", "ppiptm|PPI:2|bind", "ncbitaxon_models|9606|Homo sapiens", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "uniprot_swissprot|P29119|furin", "covocorganism|SP_11|Homo sapiens", "covocdiseaseandsyndrom|DIS_37|infection", "covocorganism|SP_5|Coronavirus", "mesh|D045473|Severe acute respiratory syndrome-related coronavirus", "ncbitaxon_models|9606|Homo sapiens", "uniprot_swissprot|Q8CIQ8|Sars", "covocbiomed|BMV_77|infection", "ncbitaxon_full|9605|Homo", "covocorganism|SP_14|Manidae", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000818|Animals", "agrovoc|c_5793|Pholidota", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|770315|Homo sapiens", "ott|770309|Homo", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "mesh|D017934|Coronavirus", "covocorganism|SP_6|COVID-19", "mdd|1000718|Homo_sapiens", "mesh|D006801|Humans", "covocbiomed|BMV_34|coronavirus", "pubchemmesh|439693|Pentostatin", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_11|Homo sapiens", "mesh|D000086642|Pangolins", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|9606|Homo sapiens", "ncbitaxon_models|227859|Human SARS coronavirus", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_5|Coronavirus", "agrovoc|c_28317|contamination", "covocgeographicloc|LOC_16|Wu Han", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "envo|ENVO_03501198|wet market", "covocorganism|SP_6|COVID-19", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|439693|Pentostatin", "covocbiomed|BMV_33|contamination", "robiext|RO_e000002|has contaminated", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "mesh|D000818|Animals", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "ott|574724|Chiroptera", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "pubchemmesh|445354|Retinol", "pubchemmesh|439693|Pentostatin", "covocorganism|SP_6|COVID-19", "covocorganism|SP_4|Chiroptera", "mesh|D005628|Frozen Foods", "covocbiomed|BMV_163|viruses", "agrovoc|c_16490|frozen foods", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "uniprot_swissprot|Q8CIQ8|Sars", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocorganism|SP_6|COVID-19", "pubchemmesh|439693|Pentostatin", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "agrovoc|c_1855|cooperation", "mesh|D058873|Pandemics", "agrovoc|c_f17550ed|pandemics", "agrovoc|c_b29a1475|One Health approach", "mesh|D000074823|One Health", "covocconceptualentities|CE_54|Pandemics" ], "affiliations": [ "ror|04gp5yv64|Westmead Hospital", "ror|01w104f98|\"Conselleria d'Educaci\u00f3" ], "mesh_terms": [ "mesh|D000818|Animals", "ncbitaxon_full|9605|Homo", "ott|770309|Homo", "mesh|D006801|Humans", "covocgeographicloc|LOC_3|China", "ncbitaxon_full|9397|Chiroptera", "agrovoc|c_1560|Chiroptera", "mesh|D002685|Chiroptera", "ott|574724|Chiroptera", "covocorganism|SP_4|Chiroptera", "agrovoc|c_4ad07701|COVID-19", "mesh|D000086382|COVID-19", "covocorganism|SP_6|COVID-19", "uniprot_swissprot|Q8CIQ8|Sars", "covocorganism|SP_6|COVID-19", "ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2", "ncbitaxon_models|227859|Human SARS coronavirus", "ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2", "covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome", "pubchemmesh|439693|Pentostatin" ] } } } ] } } }