{ "sibils_version": "v4.2.5.7", "success": true, "error": "", "collection": "medline", "ndocs": 10, "original_query": "Rhinolophus and Pangolin", "transformed_query": { "query": { "bool": { "must": [ { "multi_match": { "query": "Rhinolophus", "type": "phrase", "fields": [ "title", "abstract", "text", "full_text", "chemicals", "keywords", "mesh_terms", "sup_mesh_terms", "figures_captions", "article-title", "text", "treatment_title", "_id", "pmid", "pmcid" ] } }, { "multi_match": { "query": "Pangolin", "type": "phrase", "fields": [ "title", "abstract", "text", "full_text", "chemicals", "keywords", "mesh_terms", "sup_mesh_terms", "figures_captions", "article-title", "text", "treatment_title", "_id", "pmid", "pmcid" ] } } ] } }, "concepts": [], "terms_status": [ { "term": "Rhinolophus", "status": true }, { "term": "Pangolin", "status": true } ], "annotation_status": true }, "elastic_output": { "took": 9, "timed_out": false, "_shards": { "total": 1, "successful": 1, "skipped": 0, "failed": 0 }, "hits": { "total": { "value": 18, "relation": "eq" }, "max_score": 29.197168, "hits": [ { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "32633815", "_score": 29.197168, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword", "mesh_terms.keyword" ], "_source": { "title": "An update on the origin of SARS-CoV-2: Despite closest identity, bat (RaTG13) and pangolin derived coronaviruses varied in the critical binding site and O-linked glycan residues.", "abstract": "The initial cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) occurred in Wuhan, China, in December 2019 and swept the world by 23 June 2020 with 8\u2009993\u2009659 active cases, 469\u2009587 deaths across 216 countries, areas or territories. This strongly implies global transmission occurred before the lockdown of China. However, the initial source's transmission routes of SARS-CoV-2 remain obscure and controversial. Research data suggest bat (RaTG13) and pangolin carried CoV were the proximal source of SARS-CoV-2. In this study, we used systematic phylogenetic analysis of Coronavirinae subfamily along with wild type human SARS-CoV, MERS-CoV, and SARS-CoV-2 strains. The key residues of the receptor-binding domain (RBD) and O-linked glycan were compared. SARS-CoV-2 strains were clustered with RaTG13 (97.41% identity), Pangolin-CoV (92.22% identity) and Bat-SL-CoV (80.36% identity), forms a new clade-2 in lineage B of beta-CoV. The alignments of RBD contact residues to ACE2 justified? Those SARS-CoV-2 strains sequences were 100% identical by each other, significantly varied in RaTG13 and pangolin-CoV. SARS-CoV-2 has a polybasic cleavage site with an inserted sequence of PRRA compared to RaTG13 and only PRR to pangolin. Only serine (Ser) in pangolin and both threonine (Thr) and serine (Ser) O-linked glycans were seen in RaTG13, suggesting that a detailed study needed in pangolin (Manis javanica) and bat (Rhinolophus affinis) related CoV.", "coi_statement": "", "journal": "Journal of medical virology", "authors": "Malaiyan Jeevan|Arumugam Suresh|Mohan Kamalraj|Gomathi Radhakrishnan Gokul", "affiliations": "Division of Virology, Department of Microbiology, Sri Muthukumaran Medical College Hospital and Research Institute, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Chikkarayapuram, Chennai, India.|Central Research Facility, Meenakshi Medical College Hospital and Research Institute, Meenakshi Academy of Higher Education and Research, Kancheepuram, Tamilnadu, India.|Division of Virology, Department of Microbiology, Sri Muthukumaran Medical College Hospital and Research Institute, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Chikkarayapuram, Chennai, India.|Department of General Medicine, Sri Muthukumaran Medical College Hospital and Research Institute, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Chikkarayapuram, Chennai, India.", "pubyear": "2021", "entrez_date": "2020-07-08", "pmid": "32633815", "mesh_terms": "D000818:Animals|D001665:Binding Sites|D002681:China|D002685:Chiroptera|D003140:Communicable Disease Control|D017934:Coronavirus|D000086968:Coronavirus Envelope Proteins|D015967:Gene Expression Regulation, Viral|D058507:Host Specificity|D006801:Humans|D008958:Models, Molecular|D000086642:Pangolins|D010802:Phylogeny|D011134:Polysaccharides|D011487:Protein Conformation|D000086402:SARS-CoV-2|D064370:Spike Glycoprotein, Coronavirus", "sup_mesh_terms": "", "chemicals": "RN 0, D000086968:Coronavirus Envelope Proteins|RN 0, D011134:Polysaccharides|RN 0, D064370:Spike Glycoprotein, Coronavirus", "publication_types": "Journal Article", "keywords": "COVID-19|RaTg13|SARS-CoV-2|intermediate host|pangolins", "pmcid": "PMC7361880", "doi": "10.1002/jmv.26261", "medline_ta": "J Med Virol", "archive_id": 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In this perspective, I will remark two main inconsistencies on the origins of SARS-CoV-2: polypeptide sequence alignment of the S-proteins does not return the expected identity of the receptor-binding motif among most of pangolin-CoVs and SARS-CoV-2; accurate referencing for samplings and sequencing deposition of the ancestral bat coronavirus named RaTG13 was missing since the first reports on the SARS-CoV-2 coronavirus. This contribution aims to stimulate discussion about the origins of SARS-CoV-2 and considers other intermediate hosts as a reservoir for coronavirus.", "coi_statement": "Financial & competing interests disclosure This investigation was undertaken in the course of the FORMAS Swedish Research Council project no. 2018-00891, title: \u201cKontroll av skadeinsekter p\u00e5 frukt genom att inrikta sig p\u00e5\u201d. The author has no other relevant affiliations or financial involvement with any organization or entity with a financial interest or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.", "journal": "Future virology", "authors": "Cattaneo Alberto Maria", "affiliations": "Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Chemical Ecology Group, Lomma, Box 190 234 22, Sweden.", "pubyear": "2022", "entrez_date": "2022-04-14", "pmid": "35419073", "mesh_terms": "", "sup_mesh_terms": "", "chemicals": "", "publication_types": "Journal Article|Review", "keywords": "RaTG13|S-protein|SARS-CoV-2|coronavirus|polypeptide sequence alignment|receptor-binding motif", "pmcid": "PMC8982992", "doi": "10.2217/fvl-2021-0233", "medline_ta": "Future Virol", "archive_id": "/SIBiLS_v4.2/medline/r1/baseline/bib/bib_pubmed25n1131.json.gz", "annotations_str": "gene uniprot_swissprot_Q8CIQ8|mesh mesh_D010455|biomedical_vocab covocbiomed_BMV_134|chemical chebi_CHEBI:15841|gene uniprot_swissprot_P22458|species covocorganism_SP_6|species ncbitaxon_models_227859|gene nextprot_NX_P04004|species 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host|intermediate hosts||ror|02yy8x990|Swedish University of Agricultural Sciences|swedish university of agricultural sciences" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "33610551", "_score": 27.053919, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword", "mesh_terms.keyword" ], "_source": { "title": "Evaluating angiotensin-converting enzyme 2-mediated SARS-CoV-2 entry across species.", "abstract": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents a global threat, and the interaction between the virus and angiotensin-converting enzyme 2 (ACE2), the primary entry receptor for SARS-CoV-2, is a key determinant of the range of hosts that can be infected by the virus. However, the mechanisms underpinning ACE2-mediated viral entry across species remains unclear. Using infection assay, we evaluated SARS-CoV-2 entry mediated by ACE2 of 11 different animal species. We discovered that ACE2 of Rhinolophus sinicus (Chinese rufous horseshoe bat), Felis catus (domestic cat), Canis lupus familiaris (dog), Sus scrofa (wild pig), Capra hircus (goat), and Manis javanica (Malayan pangolin) facilitated SARS-CoV-2 entry into nonsusceptible cells. Moreover, ACE2 of the pangolin also mediated SARS-CoV-2 entry, adding credence to the hypothesis that SARS-CoV-2 may have originated from pangolins. However, the ACE2 proteins of Rhinolophus ferrumequinum (greater horseshoe bat), Gallus gallus (red junglefowl), Notechis scutatus (mainland tiger snake), or Mus musculus (house mouse) did not facilitate SARS-CoV-2 entry. In addition, a natural isoform of the ACE2 protein of Macaca mulatta (rhesus monkey) with the Y217N mutation was resistant to SARS-CoV-2 infection, highlighting the possible impact of this ACE2 mutation on SARS-CoV-2 studies in rhesus monkeys. We further demonstrated that the Y217 residue of ACE2 is a critical determinant for the ability of ACE2 to mediate SARS-CoV-2 entry. Overall, these results clarify that SARS-CoV-2 can use the ACE2 receptors of multiple animal species and show that tracking the natural reservoirs and intermediate hosts of SARS-CoV-2 is complex.", "coi_statement": "Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article.", "journal": "The Journal of biological chemistry", "authors": "Zhang Hong-Liang|Li Yu-Ming|Sun Jing|Zhang Yu-Yuan|Wang Tong-Yun|Sun Ming-Xia|Wang Meng-Hang|Yang Yue-Lin|Hu Xiao-Liang|Tang Yan-Dong|Zhao Jincun|Cai Xuehui", "affiliations": "State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.|State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.|State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.|School of Life Sciences and Food Engineering, Yibin University, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin, China.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China. Electronic address: tangyandong2008@163.com.|State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China. Electronic address: zhaojincun@gird.cn.|State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China. Electronic address: caixuehui139@163.com.", "pubyear": "2021", "entrez_date": "2021-02-21", "pmid": "33610551", "mesh_terms": "D000085962:Angiotensin-Converting Enzyme 2|D000818:Animals|D000086382:COVID-19|D002415:Cats|D002645:Chickens|D002685:Chiroptera|D004285:Dogs|D017815:Elapidae|D000073566:Eutheria|D015870:Gene Expression|D006041:Goats|D057809:HEK293 Cells|D054884:Host-Pathogen Interactions|D006801:Humans|D007113:Immunity, Innate|D008253:Macaca mulatta|D051379:Mice|D008958:Models, Molecular|D009154:Mutation|D058873:Pandemics|D011485:Protein Binding|D017433:Protein Structure, Secondary|D011994:Recombinant Proteins|D000086402:SARS-CoV-2|D013045:Species Specificity|D064370:Spike Glycoprotein, Coronavirus|D013552:Swine|D053586:Virus Internalization", "sup_mesh_terms": "", "chemicals": "RN 0, D011994:Recombinant Proteins|RN 0, D064370:Spike Glycoprotein, Coronavirus|RN 0, C000657845:spike protein, SARS-CoV-2|RN EC 3.4.17.23, D000085962:Angiotensin-Converting Enzyme 2", 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infection||ncbitaxon_models|taxID: 9544|Macaca mulatta|rhesus monkeys||agrovoc|c_5014|mutation|mutation||ncit|C16885|Mutation|mutation||agrovoc|c_4912|monkeys|monkeys||mesh|D000086382|COVID-19|sars-cov-2 infection|covid-19||robiext|RO_0002453|host of|hosts of||covocconceptualentities|CE_44|intermediate host|intermediate hosts||agrovoc|c_15589|intermediate hosts|intermediate hosts||agrovoc|c_8324|water reservoirs|reservoirs||ror|00dmm3k75|State Key Laboratory of Veterinary Biotechnology|state key laboratory of veterinary biotechnology||ror|0313jb750|Chinese Academy of Agricultural Sciences|chinese academy of agricultural sciences||ror|034e92n57|Harbin Veterinary Research Institute|harbin veterinary research institute||ror|037p24858|\"The First Affiliated Hospital|the first affiliated hospital||ror|04hja5e04|State Key Laboratory of Respiratory Disease|state key laboratory of respiratory disease||ror|00z0j0d77|First Affiliated Hospital of Guangzhou Medical University|first affiliated hospital of guangzhou medical university||ror|03qb6k992|Quantum Science Center of Guangdong-Hong Kong-Macao Greater Bay Area|guangdong||ror|04d3r9p82|Becs Technology (United States)|engineering||ror|012rp6f89|Leuven Institute for Fertility and Embryology|life||ror|031sbqx87|\"Food|food||ror|03w8m2977|Yibin University|yibin university||ror|01gz25n41|\"Conservation|conservation||ror|00bj04t22|\"Sciences|sciences||mesh|D000818|Animals|animals||agrovoc|c_4ad07701|COVID-19|covid-19||cellosaurus|CVCL_DR98|CHO CAT-S|cats||agrovoc|c_1390|cats|cats||agrovoc|c_1540|chickens|chickens||agrovoc|c_1560|Chiroptera|chiroptera||ott|574724|Chiroptera|chiroptera||ncbitaxon_full|9397|Chiroptera|chiroptera||mesh|D004285|Dogs|dogs||ncbitaxon_full|8602|Elapidae|elapidae||agrovoc|c_32568|Elapidae|elapidae||ott|57862|Elapidae|elapidae||mesh|D000073566|Eutheria|eutheria||ncbitaxon_full|9347|Eutheria|eutheria||ott|3373561|Eutheria|eutheria||mesh|D015870|Gene Expression|gene expression||agrovoc|c_27527|gene expression|gene expression||covocbiomed|BMV_49|Gene Expression|gene expression||go_bp|GO:0010467|gene expression|gene expression||cellosaurus|CVCL_0045|HEK293|hek293||mesh|D057809|HEK293 Cells|hek293 cells||mesh|D054884|Host-Pathogen Interactions|host-pathogen interactions||covocbiomed|BMV_104|pathogen|pathogen||covocconceptualentities|CE_37|host|host||mesh|D006801|Humans|humans||ncbitaxon_full|9605|Homo|humans||ott|770309|Homo|humans||mesh|D007113|Immunity, Innate|immunity, innate||covocbiomed|BMV_69|immunity|immunity||ncbitaxon_full|10095|Mus sp.|mice||mesh|D008958|Models, Molecular|models, molecular||mesh|D058873|Pandemics|pandemics||agrovoc|c_f17550ed|pandemics|pandemics||mesh|D011485|Protein Binding|protein binding||ppiptm|PPI:2|bind|binding||go_mf|GO:0005515|protein binding|protein binding||mesh|D017433|Protein Structure, Secondary|protein structure, secondary||agrovoc|c_36920|recombinant proteins|recombinant proteins||mesh|D011994|Recombinant Proteins|recombinant proteins||covocconceptualentities|CE_77|Specificity|specificity||mesh|D013045|Species Specificity|species specificity||covocproteinsgenomes|PG_30|Spike glycoprotein|spike glycoprotein||covocbiomed|BMV_60|glycoprotein|glycoprotein||lotus|Q105157557|Glycoprotein|glycoprotein||mesh|D064370|Spike Glycoprotein, Coronavirus|spike glycoprotein, coronavirus||chebi|CHEBI:17089|glycoprotein|glycoprotein||psimi|MI:1115|spike|spike||pubchemmesh|439212|Glycoprotein|glycoprotein||uniprot_swissprot|O39227|3|spike glycoprotein||flopo|FLOPO_0900001|inflorescence type spike|spike||covocorganism|SP_5|Coronavirus|coronavirus||mdd|1006374|Sus_domesticus|swine||mesh|D013552|Swine|swine||agrovoc|c_7555|swine|swine||covocbiomed|BMV_161|Virus Internalization|virus internalization||covocproteinsgenomes|PG_31|spike protein|spike protein" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "35700806", "_score": 25.739498, "_ignored": [ "abstract.keyword", "annotations_str.keyword", "mesh_terms.keyword" ], "_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", "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", "archive_id": "/SIBiLS_v4.2/medline/r1/baseline/bib/bib_pubmed25n1140.json.gz", "annotations_str": "mesh mesh_D045473|mesh mesh_D016678|chemical chebi_CHEBI:36976|species covocorganism_SP_6|agriculture agrovoc_c_3224|agriculture agrovoc_c_4ad07701|mesh mesh_D000086382|species ott_644247|mesh 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agrovoc_c_3224|agriculture agrovoc_c_35087|mesh mesh_D016678|conceptual_entity covocconceptualentities_CE_37|biomedical_vocab covocbiomed_BMV_162|species ott_574724|conceptual_entity covocconceptualentities_CE_19|species covocorganism_SP_4|mesh mesh_D000086642|species covocorganism_SP_20|species ott_756634|species covocorganism_SP_4|mesh mesh_D002685|disease_syndrome covocdiseaseandsyndrom_DIS_58|species covocorganism_SP_6|species ncbitaxon_models_227859|species ncbitaxon_full_49442|mesh mesh_D045473|species covocorganism_SP_4|agriculture agrovoc_c_5793|agriculture agrovoc_c_1820|species ncbitaxon_viruses_2697049|species ncbitaxon_full_2697049|chemical pubchemmesh_439693|species ncbitaxon_viruses_3068538|species ncbitaxon_full_3068538|species covocorganism_SP_14|conceptual_entity covocconceptualentities_CE_37|species ott_574724|gene uniprot_swissprot_Q8CIQ8|mesh mesh_D002685|affiliation ror_02en5vm52|affiliation ror_02feahw73|affiliation ror_03wkt5x30|affiliation ror_04daj8721|affiliation ror_04byv8g40|affiliation ror_011abem59|affiliation ror_03wkt5x30|affiliation ror_01dadvw90|affiliation ror_046b3cj80|mesh mesh_D000818|mesh mesh_D000086382|species covocorganism_SP_6|agriculture agrovoc_c_4ad07701|geographic_location covocgeographicloc_LOC_3|species covocorganism_SP_4|agriculture agrovoc_c_1560|species ott_574724|mesh mesh_D002685|species ncbitaxon_full_9397|mesh mesh_D016679|biomedical_vocab covocbiomed_BMV_56|mesh mesh_D006801|species ncbitaxon_full_9605|species ott_770309|agriculture agrovoc_c_5259|mesh mesh_D009711|conceptual_entity covocconceptualentities_CE_54|mesh mesh_D058873|agriculture agrovoc_c_f17550ed|agriculture agrovoc_c_5793|species covocorganism_SP_14|mesh mesh_D000086642|agriculture agrovoc_c_13325|mesh mesh_D010802|disease ncit_C85064|species ncbitaxon_viruses_694009|biomedical_vocab covocbiomed_BMV_34|mesh mesh_D045473|disease_syndrome covocdiseaseandsyndrom_DIS_58|agriculture agrovoc_c_31878c8d|species ncbitaxon_full_694009|species covocorganism_SP_5|disease_syndrome covocdiseaseandsyndrom_DIS_58|chemical pubchemmesh_439693|gene uniprot_swissprot_Q8CIQ8|species ncbitaxon_viruses_2697049|species ncbitaxon_full_2697049|species covocorganism_SP_6|species ncbitaxon_models_227859|mesh mesh_D009711|agriculture agrovoc_c_5259|conceptual_entity covocconceptualentities_CE_44|mesh mesh_D000086642|species ncbitaxon_full_9974|species ott_644245|protein_genome covocproteinsgenomes_PG_26|biomedical_vocab covocbiomed_BMV_119|agriculture agrovoc_c_6475|conceptual_entity covocconceptualentities_CE_37|environment envo_ENVO_00000025|biotic_interaction robiext_RO_e000051|biomedical_vocab covocbiomed_BMV_95|mesh mesh_D000069456", "annotations_material": "mesh|D045473|Severe acute respiratory syndrome-related coronavirus|sarbecoviruses|sarbecovirus|severe acute respiratory syndrome-related coronavirus||mesh|D016678|Genome|genomes||chebi|CHEBI:36976|nucleotide|nucleotide||covocorganism|SP_6|COVID-19|covid-19|sars-cov-2||agrovoc|c_3224|genomes|genomes||agrovoc|c_4ad07701|COVID-19|covid-19||mesh|D000086382|COVID-19|covid-19|covid-19 pandemic||ott|644247|Manis|pangolin||mesh|D014780|Viruses|viruses||mdd|1000718|Homo_sapiens|human||covocbiomed|BMV_163|viruses|viruses||covocorganism|SP_14|Manidae|pangolin|pangolins||ncbitaxon_full|10239|Viruses|viruses||covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome|sars|severe acute respiratory syndrome||ncbitaxon_models|9606|Homo sapiens|human||ncbitaxon_viruses|10239|Viruses|viruses||covocorganism|SP_4|Chiroptera|bat|bats|chiroptera||pubchemmesh|439693|Pentostatin|cov||agrovoc|c_8262|viruses|viruses||ncbitaxon_models|227859|Human SARS coronavirus|sars-cov||covocconceptualentities|CE_22|epidemics|epidemic||covocorganism|SP_11|Homo sapiens|human||ncbitaxon_full|2509511|Sarbecovirus|sarbecovirus||uniprot_swissprot|Q8CIQ8|Sars|sars||covocconceptualentities|CE_54|Pandemics|pandemic|pandemics||ncbitaxon_viruses|2509511|Sarbecovirus|sarbecovirus||ott|770315|Homo sapiens|human||covocorganism|SP_21|SARS-CoV|sars-cov||ncbitaxon_viruses|2697049|Severe acute respiratory syndrome coronavirus 2|sars-cov-2||ncbitaxon_full|2697049|Severe acute respiratory syndrome coronavirus 2|sars-cov-2||mesh|D000086642|Pangolins|pangolin|pangolins|manis||mesh|D003062|Codon|codons|codon||agrovoc|c_37477|codons|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|codon||chebi|CHEBI:47885|dinucleotide|dinucleotides||covocgeographicloc|LOC_3|China|china||covocorganism|SP_5|Coronavirus|coronaviruses|coronavirus||covocbiomed|BMV_119|recombination|recombination||mesh|D002160|Cambodia|cambodia||mesh|D017934|Coronavirus|coronaviruses||mesh|D007564|Japan|japan||mesh|D002031|Bulgaria|bulgaria||ncbitaxon_full|73171|Bulgaria|bulgaria||mesh|D007630|Kenya|kenya||agrovoc|c_6475|recombination|recombination||agrovoc|c_1145|Bulgaria|bulgaria||covocbiomed|BMV_34|coronavirus|coronaviruses|coronavirus||mesh|D013785|Thailand|thailand||pubchemmesh|190|Adenine|adenines||pubchemmesh|1174|Uracil|uracils||covocbiomed|BMV_64|host cell|host cells||go_bp|GO:0019058|viral life cycle|viral replication||agrovoc|c_35087|viral replication|viral replication||covocconceptualentities|CE_37|host|host||covocbiomed|BMV_162|Virus Replication|viral replication||ott|574724|Chiroptera|bats|chiroptera||covocconceptualentities|CE_19|distribution|distribution||covocorganism|SP_20|Rhinolophus macrotis|rhinolophus||ott|756634|Rhinolophus|rhinolophus||mesh|D002685|Chiroptera|rhinolophus|horseshoe bat|chiroptera||ncbitaxon_full|49442|Rhinolophus|rhinolophus||agrovoc|c_5793|Pholidota|pangolins||agrovoc|c_1820|constraints|constraints||ncbitaxon_viruses|3068538|Horseshoe bat sarbecovirus|horseshoe bat sarbecovirus||ncbitaxon_full|3068538|Horseshoe bat sarbecovirus|horseshoe bat sarbecovirus||ror|02en5vm52|Sorbonne Universit\u00e9|sorbonne universit||ror|02feahw73|Centre National de la Recherche Scientifique|cnrs||ror|03wkt5x30|Mus\u00e9um national d'Histoire naturelle|mnhn||ror|04daj8721|\"France|france||ror|04byv8g40|\"Biodiversit\u00e9|biodiversit||ror|011abem59|\"\u00c9volution|volution||ror|01dadvw90|\"Institut de Syst\u00e9matique|institut de syst\u00e9matique||ror|046b3cj80|\u00c9cole Pratique des Hautes \u00c9tudes|ephe||mesh|D000818|Animals|animals||agrovoc|c_1560|Chiroptera|chiroptera||ncbitaxon_full|9397|Chiroptera|chiroptera||mesh|D016679|Genome, Viral|genome, viral||covocbiomed|BMV_56|Genome|genome||mesh|D006801|Humans|humans||ncbitaxon_full|9605|Homo|humans||ott|770309|Homo|humans||agrovoc|c_5259|nucleotides|nucleotides||mesh|D009711|Nucleotides|nucleotides||mesh|D058873|Pandemics|pandemics||agrovoc|c_f17550ed|pandemics|pandemics||agrovoc|c_13325|phylogeny|phylogeny||mesh|D010802|Phylogeny|phylogeny||ncit|C85064|Severe Acute Respiratory Syndrome|severe acute respiratory syndrome||ncbitaxon_viruses|694009|Severe acute respiratory syndrome-related coronavirus|severe acute respiratory syndrome-related coronavirus||agrovoc|c_31878c8d|Severe acute respiratory syndrome-related coronavirus|severe acute respiratory syndrome-related coronavirus||ncbitaxon_full|694009|Severe acute respiratory syndrome-related coronavirus|severe acute respiratory syndrome-related coronavirus||covocconceptualentities|CE_44|intermediate host|intermediate host||ncbitaxon_full|9974|Manis javanica|manis javanica||ott|644245|Manis javanica|manis javanica||covocproteinsgenomes|PG_26|RNA-dependent RNA polymerase|rdrp||envo|ENVO_00000025|reservoir|reservoir||robiext|RO_e000051|reservoir host|reservoir host||covocbiomed|BMV_95|Mutation|mutations||mesh|D000069456|Silent Mutation|synonymous mutations" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "36169743", "_score": 25.609898, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword" ], "_source": { "title": "Comparative analysis of single cell lung atlas of bat, cat, tiger, and pangolin.", "abstract": "Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as severe acute respiratory syndrome coronavirus (SARS-CoV). Bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the coronavirus disease 2019 (COVID-19) pandemic, multiple animal species were diseased by coronavirus infection, especially in the respiratory system. Herein, a comparative analysis with single nucleus transcriptomic data of the lungs across four species, including horseshoe bat, cat, tiger, and pangolin, were conducted. The distribution of entry factors for twenty-eight respiratory viruses was characterized for the four species. Our findings might increase our understanding of the immune background of horseshoe bats.", "coi_statement": "", "journal": "Cell biology and toxicology", "authors": "Wang Xiran|Ding Peiwen|Sun Chengcheng|Wang Daxi|Zhu Jiacheng|Wu Wendi|Wei Yanan|Xiang Rong|Ding Xiangning|Luo Lihua|Li Meiling|Zhang Wensheng|Jin Xin|Sun Jian|Liu Huan|Chen Dongsheng", "affiliations": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|BGI-Shenzhen, Shenzhen, 518083, China.|School of Basic Medical Sciences, Binzhou Medical University, No. 346, Guanhai Road, Laishan District, Yantai City, Shandong, China.|BGI-Shenzhen, Shenzhen, 518083, China.|National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China. jiansun@scau.edu.cn.|BGI-Shenzhen, Shenzhen, 518083, China. liuhuan@genomics.cn.|BGI-Shenzhen, Shenzhen, 518083, China. chendongsheng@genomics.cn.", "pubyear": "2023", "entrez_date": "2022-09-28", "pmid": "36169743", "mesh_terms": "D000818:Animals|D006801:Humans|D002685:Chiroptera|D000086642:Pangolins|D046010:Tigers|D000086382:COVID-19|D008168:Lung", "sup_mesh_terms": "", "chemicals": "", "publication_types": "Journal Article|Research Support, Non-U.S. Gov't", "keywords": "Bat|Comparative analysis|Cross species|Single cell", "pmcid": "PMC9516514", "doi": "10.1007/s10565-022-09771-9", "medline_ta": "Cell Biol Toxicol", "archive_id": "/SIBiLS_v4.2/medline/r1/baseline/bib/bib_pubmed25n1155.json.gz", "annotations_str": "species covocorganism_SP_14|mesh mesh_D000086642|species mdd_1006023|species ott_42314|mesh mesh_D008168|mesh mesh_D046010|agriculture agrovoc_c_ed80f2b8|mesh mesh_D020466|species ott_644247|species covocorganism_SP_4|mesh mesh_D002685|species mdd_1000718|disease_syndrome covocdiseaseandsyndrom_DIS_58|species ncbitaxon_viruses_2901879|biomedical_vocab covocbiomed_BMV_34|species ncbitaxon_full_2901879|species ncbitaxon_models_227859|species ott_635025|species covocorganism_SP_21|biomedical_vocab covocbiomed_BMV_34|species ncbitaxon_models_9606|mesh mesh_D002685|chemical pubchemmesh_439693|species ncbitaxon_full_89399|agriculture agrovoc_c_90e2dd12|mesh mesh_D045473|species covocorganism_SP_5|disease_syndrome covocdiseaseandsyndrom_DIS_58|species covocorganism_SP_11|conceptual_entity covocconceptualentities_CE_39|species covocorganism_SP_20|species ott_1047995|agriculture agrovoc_c_c722a312|mesh mesh_D045473|species covocorganism_SP_5|biotic_interaction robiext_RO_e000055|mesh mesh_D017934|species ott_770315|species ncbitaxon_models_227859|disease ncit_C85064|gene uniprot_swissprot_Q8CIQ8|species covocorganism_SP_20|biomedical_vocab covocbiomed_BMV_77|disease ncit_C3439|species ott_244265|species ott_574724|agriculture agrovoc_c_27554|disease_syndrome covocdiseaseandsyndrom_DIS_68|mesh mesh_D007107|biological_process go_bp_GO:0016032|mesh mesh_D008322|agriculture agrovoc_c_4560|species covocorganism_SP_4|disease ncit_C181757|agriculture agrovoc_c_6531|mesh mesh_D000086382|disease_syndrome covocdiseaseandsyndrom_DIS_37|biomedical_vocab covocbiomed_BMV_34|species covocorganism_SP_6|conceptual_entity covocconceptualentities_CE_54|agriculture agrovoc_c_4ad07701|mesh mesh_D018352|species covocorganism_SP_5|mesh mesh_D012137|mesh mesh_D000086382|species covocorganism_SP_5|biomedical_vocab covocbiomed_BMV_77|drug atc_R|agriculture agrovoc_c_4ad07701|biomedical_vocab covocbiomed_BMV_34|species ott_644247|species covocorganism_SP_4|biomedical_vocab covocbiomed_BMV_84|species ott_42314|mesh mesh_D002685|agriculture agrovoc_c_5260|species covocorganism_SP_14|species mdd_1006023|mesh mesh_D046010|agriculture agrovoc_c_4462|cellular_component go_cc_GO:0005634|mesh mesh_D000086642|agriculture agrovoc_c_ed80f2b8|species ncbitaxon_viruses_10239|biomedical_vocab covocbiomed_BMV_163|agriculture agrovoc_c_8262|species covocorganism_SP_19|conceptual_entity covocconceptualentities_CE_19|mesh mesh_D014780|species ncbitaxon_full_10239|mesh mesh_D002685|conceptual_entity covocconceptualentities_CE_25|species ott_635025|species covocorganism_SP_20|affiliation ror_006fhby04|affiliation ror_05v9jqt67|affiliation ror_05qm21180|affiliation ror_00bj04t22|affiliation ror_008w1vb37|affiliation ror_04489at23|affiliation ror_006fhby04|affiliation ror_05v9jqt67|affiliation ror_05v9jqt67|mesh mesh_D000818|mesh mesh_D006801|species ncbitaxon_full_9605|species ott_770309|species covocorganism_SP_4|agriculture agrovoc_c_1560|species ott_574724|mesh mesh_D002685|species ncbitaxon_full_9397|agriculture agrovoc_c_5793|species covocorganism_SP_14|mesh mesh_D000086642|mesh mesh_D046010|agriculture agrovoc_c_7766|mesh mesh_D000086382|species covocorganism_SP_6|agriculture agrovoc_c_4ad07701|mesh mesh_D008168|species covocorganism_SP_4|agriculture agrovoc_c_ed80f2b8", "annotations_material": "covocorganism|SP_14|Manidae|pangolin|pangolins||mesh|D000086642|Pangolins|pangolin|pangolins||mdd|1006023|Panthera_tigris|tiger||ott|42314|Panthera tigris|tiger||mesh|D008168|Lung|lung||mesh|D046010|Tigers|tiger|tigers||agrovoc|c_ed80f2b8|comparative analysis|comparative analysis||mesh|D020466|Atlas|atlas||ott|644247|Manis|pangolin||covocorganism|SP_4|Chiroptera|bat|bats|chiroptera||mesh|D002685|Chiroptera|rhinolophus|horseshoe bats|horseshoe bat|chiroptera||mdd|1000718|Homo_sapiens|human||covocdiseaseandsyndrom|DIS_58|Severe Acute Respiratory Syndrome|sars|severe acute respiratory syndrome||ncbitaxon_viruses|2901879|Severe acute respiratory syndrome coronavirus|severe acute respiratory syndrome coronavirus||covocbiomed|BMV_34|coronavirus|coronaviruses|coronavirus||ncbitaxon_full|2901879|Severe acute respiratory syndrome coronavirus|severe acute respiratory syndrome coronavirus||ncbitaxon_models|227859|Human SARS coronavirus|severe acute respiratory syndrome coronavirus|sars-cov||ott|635025|Rhinolophidae|horseshoe bats||covocorganism|SP_21|SARS-CoV|sars-cov||ncbitaxon_models|9606|Homo sapiens|human||pubchemmesh|439693|Pentostatin|cov||ncbitaxon_full|89399|Rhinolophus sinicus|rhinolophus sinicus||agrovoc|c_90e2dd12|Severe acute respiratory syndrome coronavirus|severe acute respiratory syndrome coronavirus||mesh|D045473|Severe acute respiratory syndrome-related coronavirus|coronavirus (sars|severe acute respiratory syndrome coronavirus||covocorganism|SP_5|Coronavirus|coronavirus|coronaviruses||covocorganism|SP_11|Homo sapiens|human||covocconceptualentities|CE_39|human health|human health||covocorganism|SP_20|Rhinolophus macrotis|horseshoe bats|rhinolophus||ott|1047995|Rhinolophus sinicus|rhinolophus sinicus||agrovoc|c_c722a312|human health|human health||robiext|RO_e000055|affecting|affecting||mesh|D017934|Coronavirus|coronaviruses||ott|770315|Homo sapiens|human||ncit|C85064|Severe Acute Respiratory Syndrome|severe acute respiratory syndrome||uniprot_swissprot|Q8CIQ8|Sars|sars||covocbiomed|BMV_77|infection|infection||ncit|C3439|Viral Infection|viral infection||ott|244265|Mammalia|mammals||ott|574724|Chiroptera|bats|chiroptera||agrovoc|c_27554|immune system|immune system||covocdiseaseandsyndrom|DIS_68|virus infection|viral infection||mesh|D007107|Immune System|immune system||go_bp|GO:0016032|viral process|viral infection||mesh|D008322|Mammals|mammals||agrovoc|c_4560|mammals|mammals||ncit|C181757|Coronavirus Infection|coronavirus infection||agrovoc|c_6531|respiratory system|respiratory system||mesh|D000086382|COVID-19|coronavirus disease 2019|covid-19) pandemic|covid-19||covocdiseaseandsyndrom|DIS_37|infection|infection||covocorganism|SP_6|COVID-19|covid-19||covocconceptualentities|CE_54|Pandemics|pandemic||agrovoc|c_4ad07701|COVID-19|coronavirus disease 2019|covid-19||mesh|D018352|Coronavirus Infections|coronavirus infection||mesh|D012137|Respiratory System|respiratory system||atc|R|RESPIRATORY SYSTEM DRUGS|respiratory system||covocbiomed|BMV_84|lungs|lungs||agrovoc|c_5260|nucleus|nucleus||agrovoc|c_4462|lungs|lungs||go_cc|GO:0005634|nucleus|nucleus||ncbitaxon_viruses|10239|Viruses|viruses||covocbiomed|BMV_163|viruses|viruses||agrovoc|c_8262|viruses|viruses||covocorganism|SP_19|respiratory viruses|respiratory viruses||covocconceptualentities|CE_19|distribution|distribution||mesh|D014780|Viruses|viruses||ncbitaxon_full|10239|Viruses|viruses||covocconceptualentities|CE_25|findings|findings||ror|006fhby04|\"Animal|animal||ror|05v9jqt67|South China Agricultural University|south china agricultural university|scau||ror|05qm21180|Beijing Advanced Sciences and Innovation Center|basic||ror|00bj04t22|\"Sciences|sciences||ror|008w1vb37|Binzhou Medical University|binzhou medical university||ror|04489at23|\"City|city||mesh|D000818|Animals|animals||mesh|D006801|Humans|humans||ncbitaxon_full|9605|Homo|humans||ott|770309|Homo|humans||agrovoc|c_1560|Chiroptera|chiroptera||ncbitaxon_full|9397|Chiroptera|chiroptera||agrovoc|c_5793|Pholidota|pangolins||agrovoc|c_7766|tigers|tigers" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "33563978", "_score": 25.4932, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword", "authors.keyword", "mesh_terms.keyword" ], "_source": { "title": "Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia.", "abstract": "Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS-CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Here we report molecular and serological evidence of SARS-CoV-2 related coronaviruses (SC2r-CoVs) actively circulating in bats in Southeast Asia. Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus in Yunnan, China. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. Antisera raised against the receptor binding domain (RBD) of RmYN02 was able to cross-neutralize SARS-CoV-2 despite the fact that the RBD of RacCS203 or RmYN02 failed to bind ACE2. Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan\u00a0and China to Thailand over a 4800-km range. Cross-border surveillance is urgently needed to find the immediate progenitor virus of SARS-CoV-2.", "coi_statement": "", "journal": "Nature communications", "authors": "Wacharapluesadee Supaporn|Tan Chee Wah|Maneeorn Patarapol|Duengkae Prateep|Zhu Feng|Joyjinda Yutthana|Kaewpom Thongchai|Chia Wan Ni|Ampoot Weenassarin|Lim Beng Lee|Worachotsueptrakun Kanthita|Chen Vivian Chih-Wei|Sirichan Nutthinee|Ruchisrisarod Chanida|Rodpan Apaporn|Noradechanon Kirana|Phaichana Thanawadee|Jantarat Niran|Thongnumchaima Boonchu|Tu Changchun|Crameri Gary|Stokes Martha M|Hemachudha Thiravat|Wang Lin-Fa", "affiliations": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.|Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand.|Forest Biology Department, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.|Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.|Forest Biology Department, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.|Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand.|Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand.|Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand.|Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand.|Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.|CSIRO Australian Animal Health Laboratory, Geelong, Australia.|Biological Threat Reduction Program, Defense Threat Reduction Agency, Virginia, USA.|Thai Red Cross Emerging Infectious Diseases Health Science Centre, WHO Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand. fmedthm@gmail.com.|Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore. linfa.wang@duke-nus.edu.sg.", "pubyear": "2021", "entrez_date": "2021-02-10", "pmid": "33563978", "mesh_terms": "D000595:Amino Acid Sequence|D000818:Animals|D057134:Antibodies, Neutralizing|D001210:Asia, Southeastern|D000086382:COVID-19|D002685:Chiroptera|D005843:Geography|D009500:Neutralization Tests|D000086642:Pangolins|D010802:Phylogeny|D000072417:Protein Domains|D011956:Receptors, Cell Surface|D000086402:SARS-CoV-2", "sup_mesh_terms": "", "chemicals": "RN 0, D057134:Antibodies, Neutralizing|RN 0, D011956:Receptors, Cell Surface", "publication_types": "Journal Article|Research Support, Non-U.S. Gov't|Research Support, U.S. Gov't, Non-P.H.S.", "keywords": "", "pmcid": "PMC7873279", "doi": "10.1038/s41467-021-21240-1", "medline_ta": "Nat Commun", "archive_id": 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25.211132, "_ignored": [ "abstract.keyword", "annotations_str.keyword" ], "_source": { "title": "Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human.", "abstract": "BACKGROUND\nThe current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome (SARS)-CoV-2, has become the most devastating public health emergency in the 21st century and one of the most influential plagues in history. Studies on the origin of SARS-CoV-2 have generally agreed that the virus probably comes from bat, closely related to a bat CoV named BCoV-RaTG13 taken from horseshoe bat (Rhinolophus affinis), with Malayan pangolin (Manis javanica) being a plausible intermediate host. However, due to the relatively low number of SARS-CoV-2-related strains available in public domain, the evolutionary history remains unclear.\n\n\nMETHODOLOGY\nNine hundred ninety-five coronavirus sequences from NCBI Genbank and GISAID were obtained and multiple sequence alignment was carried out to categorize SARS-CoV-2 related groups. Spike sequences were analyzed using similarity analysis and conservation analyses. Mutation analysis was used to identify variations within receptor-binding domain (RBD) in spike for SARS-CoV-2-related strains.\n\n\nRESULTS\nWe identified a family of SARS-CoV-2-related strains, including the closest relatives, bat CoV RaTG13 and pangolin CoV strains. Sequence similarity analysis and conservation analysis on spike sequence identified that N-terminal domain, RBD and S2 subunit display different degrees of conservation with several coronavirus strains. Mutation analysis on contact sites in SARS-CoV-2 RBD reveals that human-susceptibility probably emerges in pangolin.\n\n\nCONCLUSION AND IMPLICATION\nWe conclude that the spike sequence of SARS-CoV-2 is the result of multiple recombination events during its transmission from bat to human, and we propose a framework of evolutionary history that resolve the relationship of BCoV-RaTG13 and pangolin coronaviruses with SARS-CoV-2.\n\n\nLAY SUMMARY\nThis study analyses whole-genome and spike sequences of coronavirus from NCBI using phylogenetic and conservation analyses to reconstruct the evolutionary history of severe acute respiratory syndrome (SARS)-CoV-2 and proposes an evolutionary history of spike in the progenitors of SARS-CoV-2 from bat to human through mammal hosts before they recombine into the current form.", "coi_statement": "", "journal": "Evolution, medicine, and public health", "authors": "Lei Kuan Cheok|Zhang Xiaohua Douglas", "affiliations": "CRDA, Faculty of Health Sciences, University of Macau, Macau, China.|CRDA, Faculty of Health Sciences, University of Macau, Macau, China.", "pubyear": "2020", "entrez_date": "2020-12-29", "pmid": "33372198", "mesh_terms": "", "sup_mesh_terms": "", "chemicals": "", "publication_types": "Journal Article", "keywords": "SARS-CoV-2|bat coronavirus RaTG13|conservation analysis|pangolin coronavirus|receptor-binding domain", "pmcid": "PMC7665476", "doi": "10.1093/emph/eoaa041", "medline_ta": "Evol Med Public Health", "archive_id": "/SIBiLS_v4.2/medline/r1/baseline/bib/bib_pubmed25n1064.json.gz", "annotations_str": "gene uniprot_swissprot_Q8CIQ8|species ncbitaxon_models_227859|species ncbitaxon_viruses_2697049|species covocorganism_SP_11|species ncbitaxon_full_2697049|chemical pubchemmesh_439693|plant flopo_FLOPO_0900001|species covocorganism_SP_4|species mdd_1000718|disease_syndrome covocdiseaseandsyndrom_DIS_58|molecular_interaction psimi_MI:1115|species ott_770315|species ncbitaxon_models_9606|agriculture 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coronavirus||ncbitaxon_full|2708335|Pangolin coronavirus|pangolin coronavirus" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "32637954", "_score": 24.221146, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword" ], "_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", "entrez_date": "2020-07-09", "pmid": "32637954", "mesh_terms": "", "sup_mesh_terms": "", 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Cuba Astronomical Observatory|inc" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "34263709", "_score": 24.162058, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword" ], "_source": { "title": "Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor.", "abstract": "Severe respiratory disease coronavirus-2 (SARS-CoV-2) has been the most devastating disease COVID-19 in the century. One of the unsolved scientific questions of SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbour highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). This study identified a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities with SARS-CoV-2 in the conserved ORF1b region, it only shows less than 77.6% nucleotide identity to all known SARSr-CoVs at the genome level, thus forming a distinct lineage in the Sarbecovirus phylogenetic tree. We found that the RaTG15 receptor-binding domain (RBD) can bind to ACE2 from Rhinolophus affinis, Malayan pangolin, and use it as an entry receptor, except for ACE2 from humans. However, it contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we showed that none of the known viruses in bat SARSr-CoV-2 lineage discovered uses human ACE2 as efficiently as the pangolin-derived SARSr-CoV-2 or some viruses in the SARSr-CoV-1 lineage. Therefore, further systematic and longitudinal studies in bats are needed to prevent future spillover events caused by SARSr-CoVs or to understand the origin of SARS-CoV-2 better.", "coi_statement": "", "journal": "Emerging microbes & infections", "authors": "Guo Hua|Hu Ben|Si Hao-Rui|Zhu Yan|Zhang Wei|Li Bei|Li Ang|Geng Rong|Lin Hao-Feng|Yang Xing-Lou|Zhou Peng|Shi Zheng-Li", "affiliations": "CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.|CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan Institute of Virology, Wuhan, People's Republic of China.", "pubyear": "2021", "entrez_date": "2021-07-15", "pmid": "34263709", "mesh_terms": "D000085962:Angiotensin-Converting Enzyme 2|D000818:Animals|D019070:Cell Lineage|D002685:Chiroptera|D058507:Host Specificity|D010802:Phylogeny|D045473:Severe acute respiratory syndrome-related coronavirus|D000086402:SARS-CoV-2", "sup_mesh_terms": "", "chemicals": "RN EC 3.4.17.23, D000085962:Angiotensin-Converting Enzyme 2", "publication_types": "Journal Article", "keywords": "ACE2|SARS-related coronavirus|bat|novel lineage|reservoir host", "pmcid": "PMC8344244", "doi": "10.1080/22221751.2021.1956373", "medline_ta": "Emerg Microbes Infect", "archive_id": "/SIBiLS_v4.2/medline/r1/baseline/bib/bib_pubmed25n1093.json.gz", "annotations_str": "mesh mesh_D017934|agriculture agrovoc_c_29225|disease_syndrome covocdiseaseandsyndrom_DIS_58|protein_genome covocproteinsgenomes_PG_2|gene uniprot_swissprot_Q8CIQ8|species covocorganism_SP_4|gene uniprot_swissprot_Q5EGZ1|species covocorganism_SP_5|species covocorganism_SP_4|biomedical_vocab covocbiomed_BMV_34|gene nextprot_NX_Q9BYF1|disease_syndrome covocdiseaseandsyndrom_DIS_52|mesh mesh_D000086382|gene uniprot_swissprot_Q8CIQ8|species covocorganism_SP_6|biomedical_vocab covocbiomed_BMV_34|species covocorganism_SP_6|species ncbitaxon_models_227859|chemical pubchemmesh_439693|species covocorganism_SP_5|disease_syndrome covocdiseaseandsyndrom_DIS_58|species 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coronavirus|sars-related coronavirus" } }, { "_index": "sibils_med25_r1_v4.2.5.7", "_id": "37943512", "_score": 23.783936, "_ignored": [ "abstract.keyword", "affiliations.keyword", "annotations_str.keyword", "mesh_terms.keyword" ], "_source": { "title": "Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs.", "abstract": "Spike-receptor interaction is a critical determinant for the host range of coronaviruses. In this study, we investigated the SARS-CoV-2 WHU01 strain and five WHO-designated SARS-CoV-2 variants of concern (VOCs), including Alpha, Beta, Gamma, Delta, and the early Omicron variant, for their Spike interactions with ACE2 proteins of 18 animal species. First, the receptor-binding domains (RBDs) of Alpha, Beta, Gamma, and Omicron were found to display progressive gain of affinity to mouse ACE2. More interestingly, these RBDs were also found with progressive loss of affinities to multiple ACE2 orthologs. The Omicron RBD showed decreased or complete loss of affinity to eight tested animal ACE2 orthologs, including that of some livestock animals (horse, donkey, and pig), pet animals (dog and cat), and wild animals (pangolin, American pika, and Rhinolophus sinicus bat). These findings shed light on potential host range shift of SARS-CoV-2 VOCs, especially that of the Omicron variant.", "coi_statement": "The authors declare no conflict of interest.", "journal": "Microbiology spectrum", "authors": "Yao Weitong|Li Yujun|Ma Danting|Hou Xudong|Wang Haimin|Tang Xiaojuan|Cheng Dechun|Zhang He|Du Chengzhi|Pan Hong|Li Chao|Lin Hua|Sun Mengsi|Ding Qiang|Wang Yingjie|Gao Jiali|Zhong Guocai", "affiliations": "School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|Shenzhen Bay Laboratory , Shenzhen, China.|Shenzhen Bay Laboratory , Shenzhen, China.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|Horae Gene Therapy Center, University of Massachusetts Chan Medical School , Worcester, Massachusetts, USA.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|Shenzhen Bay Laboratory , Shenzhen, China.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|Shenzhen Bay Laboratory , Shenzhen, China.|Biomedical Research Center of South China, Fujian Normal University , Fuzhou, China.|Shenzhen Bay Laboratory , Shenzhen, China.|Center for Infectious Disease Research, School of Medicine, Tsinghua University , Beijing, China.|Shenzhen Bay Laboratory , Shenzhen, China.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, China.", "pubyear": "2023", "entrez_date": "2023-11-09", "pmid": "37943512", "mesh_terms": "D000818:Animals|D002415:Cats|D004285:Dogs|D051379:Mice|D000085962:Angiotensin-Converting Enzyme 2|D000835:Animals, Wild|D002371:Cat Diseases|D002685:Chiroptera|D000086382:COVID-19|D004283:Dog Diseases|D006736:Horses|D009154:Mutation|D011485:Protein Binding|D000086402:SARS-CoV-2|D013552:Swine|D064370:Spike Glycoprotein, Coronavirus", "sup_mesh_terms": "C000711908:SARS-CoV-2 variants", "chemicals": "RN EC 3.4.17.23, D000085962:Angiotensin-Converting Enzyme 2|RN 0, C000657845:spike protein, SARS-CoV-2|RN 0, D064370:Spike Glycoprotein, Coronavirus", "publication_types": "Journal Article|Research Support, Non-U.S. Gov't", "keywords": "ACE2|Omicron|SARS-CoV-2|host range|molecular dynamics simulations|mouse|variant of concern", "pmcid": "PMC10715038", "doi": "10.1128/spectrum.02676-23", "medline_ta": "Microbiol Spectr", "archive_id": "/SIBiLS_v4.2/medline/r1/updates/bib/bib_pubmed25n1658.json.gz", "annotations_str": "species ncbitaxon_models_227859|chemical pubchemmesh_439693|gene 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Simulation|molecular dynamics simulations" } } ] } } }