PMC:7067204 / 21663-23420 JSONTXT

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genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (Figure 6(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (Rhinolopus sinicus) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus Betacoronavirus, subgenus Sabecovirus (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from Rhinolophus bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV. Figure 6. Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T103","span":{"begin":4,"end":10},"obj":"Body_part"},{"id":"T104","span":{"begin":40,"end":50},"obj":"Body_part"},{"id":"T105","span":{"begin":242,"end":252},"obj":"Body_part"},{"id":"T106","span":{"begin":284,"end":300},"obj":"Body_part"},{"id":"T107","span":{"begin":938,"end":945},"obj":"Body_part"},{"id":"T108","span":{"begin":1623,"end":1633},"obj":"Body_part"},{"id":"T109","span":{"begin":1681,"end":1693},"obj":"Body_part"},{"id":"T110","span":{"begin":1708,"end":1715},"obj":"Body_part"},{"id":"T111","span":{"begin":1730,"end":1737},"obj":"Body_part"}],"attributes":[{"id":"A103","pred":"fma_id","subj":"T103","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A104","pred":"fma_id","subj":"T104","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A105","pred":"fma_id","subj":"T105","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A106","pred":"fma_id","subj":"T106","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A107","pred":"fma_id","subj":"T107","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A108","pred":"fma_id","subj":"T108","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A109","pred":"fma_id","subj":"T109","obj":"http://purl.org/sig/ont/fma/fma62925"},{"id":"A110","pred":"fma_id","subj":"T110","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A111","pred":"fma_id","subj":"T111","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (Figure 6(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (Rhinolopus sinicus) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus Betacoronavirus, subgenus Sabecovirus (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from Rhinolophus bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV. Figure 6. Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T107","span":{"begin":69,"end":73},"obj":"Disease"},{"id":"T108","span":{"begin":131,"end":139},"obj":"Disease"},{"id":"T109","span":{"begin":171,"end":179},"obj":"Disease"},{"id":"T110","span":{"begin":458,"end":462},"obj":"Disease"},{"id":"T111","span":{"begin":763,"end":767},"obj":"Disease"},{"id":"T112","span":{"begin":913,"end":917},"obj":"Disease"},{"id":"T113","span":{"begin":987,"end":995},"obj":"Disease"},{"id":"T114","span":{"begin":1006,"end":1010},"obj":"Disease"},{"id":"T115","span":{"begin":1035,"end":1039},"obj":"Disease"},{"id":"T116","span":{"begin":1442,"end":1450},"obj":"Disease"}],"attributes":[{"id":"A107","pred":"mondo_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A108","pred":"mondo_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A109","pred":"mondo_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A110","pred":"mondo_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A111","pred":"mondo_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A112","pred":"mondo_id","subj":"T112","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A113","pred":"mondo_id","subj":"T113","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A114","pred":"mondo_id","subj":"T114","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A115","pred":"mondo_id","subj":"T115","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A116","pred":"mondo_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (Figure 6(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (Rhinolopus sinicus) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus Betacoronavirus, subgenus Sabecovirus (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from Rhinolophus bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV. Figure 6. Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T253","span":{"begin":24,"end":27},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T254","span":{"begin":65,"end":68},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T255","span":{"begin":125,"end":130},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T256","span":{"begin":165,"end":170},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T257","span":{"begin":272,"end":273},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T258","span":{"begin":295,"end":300},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T259","span":{"begin":339,"end":342},"obj":"http://purl.obolibrary.org/obo/CLO_0051456"},{"id":"T260","span":{"begin":362,"end":372},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T261","span":{"begin":410,"end":411},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T262","span":{"begin":454,"end":457},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T263","span":{"begin":518,"end":522},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T264","span":{"begin":843,"end":846},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T265","span":{"begin":894,"end":898},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T266","span":{"begin":981,"end":986},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T267","span":{"begin":997,"end":999},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T268","span":{"begin":1031,"end":1034},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T269","span":{"begin":1086,"end":1089},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T270","span":{"begin":1121,"end":1122},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T271","span":{"begin":1161,"end":1162},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T272","span":{"begin":1245,"end":1249},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T273","span":{"begin":1321,"end":1327},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_33208"},{"id":"T274","span":{"begin":1648,"end":1649},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T275","span":{"begin":1672,"end":1673},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T276","span":{"begin":1721,"end":1729},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"}],"text":"The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (Figure 6(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (Rhinolopus sinicus) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus Betacoronavirus, subgenus Sabecovirus (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from Rhinolophus bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV. Figure 6. Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T145","span":{"begin":40,"end":50},"obj":"Chemical"},{"id":"T146","span":{"begin":86,"end":88},"obj":"Chemical"},{"id":"T147","span":{"begin":242,"end":252},"obj":"Chemical"},{"id":"T148","span":{"begin":242,"end":247},"obj":"Chemical"},{"id":"T149","span":{"begin":248,"end":252},"obj":"Chemical"},{"id":"T150","span":{"begin":1545,"end":1549},"obj":"Chemical"},{"id":"T151","span":{"begin":1623,"end":1633},"obj":"Chemical"},{"id":"T152","span":{"begin":1623,"end":1628},"obj":"Chemical"},{"id":"T153","span":{"begin":1629,"end":1633},"obj":"Chemical"},{"id":"T154","span":{"begin":1658,"end":1669},"obj":"Chemical"},{"id":"T155","span":{"begin":1681,"end":1693},"obj":"Chemical"},{"id":"T156","span":{"begin":1708,"end":1715},"obj":"Chemical"},{"id":"T157","span":{"begin":1730,"end":1737},"obj":"Chemical"}],"attributes":[{"id":"A145","pred":"chebi_id","subj":"T145","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"},{"id":"A146","pred":"chebi_id","subj":"T146","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A147","pred":"chebi_id","subj":"T147","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A148","pred":"chebi_id","subj":"T148","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A149","pred":"chebi_id","subj":"T149","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A150","pred":"chebi_id","subj":"T150","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A151","pred":"chebi_id","subj":"T151","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A152","pred":"chebi_id","subj":"T152","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A153","pred":"chebi_id","subj":"T153","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A154","pred":"chebi_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/CHEBI_15841"},{"id":"A155","pred":"chebi_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/CHEBI_17089"},{"id":"A156","pred":"chebi_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A157","pred":"chebi_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (Figure 6(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (Rhinolopus sinicus) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus Betacoronavirus, subgenus Sabecovirus (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from Rhinolophus bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV. Figure 6. Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein."}

{"project":"LitCovid-sentences","denotations":[{"id":"T214","span":{"begin":0,"end":196},"obj":"Sentence"},{"id":"T215","span":{"begin":197,"end":345},"obj":"Sentence"},{"id":"T216","span":{"begin":346,"end":418},"obj":"Sentence"},{"id":"T217","span":{"begin":419,"end":621},"obj":"Sentence"},{"id":"T218","span":{"begin":622,"end":762},"obj":"Sentence"},{"id":"T219","span":{"begin":763,"end":876},"obj":"Sentence"},{"id":"T220","span":{"begin":877,"end":1098},"obj":"Sentence"},{"id":"T221","span":{"begin":1099,"end":1169},"obj":"Sentence"},{"id":"T222","span":{"begin":1170,"end":1250},"obj":"Sentence"},{"id":"T223","span":{"begin":1251,"end":1451},"obj":"Sentence"},{"id":"T224","span":{"begin":1452,"end":1461},"obj":"Sentence"},{"id":"T225","span":{"begin":1462,"end":1757},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The genome of 2019-nCoV has overall 89% nucleotide identity with bat SARS-related-CoV SL-CoVZXC21 (MG772934.1), and 82% with human SARS-CoV BJ01 2003 (AY278488) and human SARS-CoV Tor2 (AY274119). The phylogenetic trees constructed using the amino acid sequences of orf1a/b and the 4 structural genes (S, E, M, and N) were shown (Figure 6(A–E)). For all these 5 genes, the 2019-nCoV was clustered with lineage B βCoVs. It was most closely related to the bat SARS-related CoVs ZXC21 and ZC45 found in Chinese horseshoe bats (Rhinolopus sinicus) collected from Zhoushan city, Zhejiang province, China between 2015 and 2017. Thus this novel coronavirus should belong to the genus Betacoronavirus, subgenus Sabecovirus (previously lineage 2b of Group 2 coronavirus). SARS-related coronaviruses have been found continuously especially in horseshoe bat species in the last 13 years. Between 2003 and 2018, 339 complete SARS-related coronavirus genomes have been sequenced, including 274 human SARS-CoV, 18 civet SARS coronavirus, and 47 bat SARS-related coronaviruses mainly from Rhinolophus bat species. Together, they formed a distinct subclade among other lineage B βCoVs. These results suggested that the 2019-nCoV might have also originated from bats. But we cannot ascertain whether another intermediate or amplification animal host infected by 2019-nCoV could be found in the epidemiological market, just as in the case of Paguma civets for SARS-CoV. Figure 6. Phylogenetic tree construction by the neighbour joining method was performed using MEGA X software, with bootstrap values being calculated from 1000 trees using amino acid sequences of (A) orf1ab polypeptide; (B) Spike glycoprotein; (C) Envelope protein; (D) Membrane protein; (E) Nucleoprotein."}