PMC:7067204 / 4909-7103 JSONTXT

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List of coronaviruses used in this study.\nAccession number Name displayed on the tree Name of full-length genome Year\nAY274119 Human SARS-CoV Tor2 2003 SARS-related coronavirus isolate Tor2 2003\nAY278488 Human SARS-CoV BJ01 2003 SARS coronavirus BJ01 2003\nAY278491 SARS coronavirus HKU-39849 2003 SARS coronavirus HKU-39849 2003 2003\nAY390556 Human SARS-CoV GZ02 2003 SARS coronavirus GZ02 2003\nAY391777 Human CoV OC43 2003 Human coronavirus OC43 2003\nAY515512 Paguma SARS CoV HC/SZ/61/03 2003 SARS coronavirus HC/SZ/61/03 (paguma SARS) 2018\nEF065513 Bat CoV HKU9-1 2006 Bat coronavirus HKU9-1 2006\nFJ588686 Bat SL-CoV Rs672 2006 Bat SARS CoV Rs672/2006 2006\nKC881005 Bat SL-CoV RsSHC014 2013 Bat SARS-like coronavirus RsSHC014 2013\nKC881006 Bat SL-CoV Rs3367 2013 Bat SARS-like coronavirus Rs3367 2013\nKY417146 Bat SL-CoV Rs4231 2016 Bat SARS-like coronavirus isolate Rs4231 2016\nKY417149 Bat SL-CoV Rs4255 2016 Bat SARS-like coronavirus isolate Rs4255 2016\nMG772933 Bat SL-CoV ZC45 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZC45 2018\nMG772934 Bat SL-CoV ZXC21 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21 2018\nMK211377 Bat CoV YN2018C 2018 Coronavirus BtRs-BetaCoV/YN2018C 2018\nMK211378 Bat CoV YN2018D 2018 Coronavirus BtRs-BetaCoV/YN2018Da 2018\nMN975262 HKU-SZ-005b Human 2019-nCoV HKU-SZ-005b 2020\nNC002645 Human CoV 229E 2000 Human coronavirus 229E 2000\nNC006577 Human CoV HKU1 2004 Human coronavirus HKU1 2004\nNC009019 Bat CoV HKU4-1 2006 Bat coronavirus HKU4-1 2006\nNC009020 Bat CoV HKU5-1 2006 Bat coronavirus HKU5-1 2006\nNC014470 Bat SARS-related CoV BM48-31 2009 Bat coronavirus BM48-31/BGR/2008 2008\nNC019843 Human MERS-CoV 2012 Middle East respiratory syndrome coronavirus 2012\naOne nucleotide was added within M gene to maintain the sequence in-frame."}

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MN975262) (Table 1). The representative complete genomes of other related βCoVs strains collected from human or mammals were included for comparative analysis. These included strains collected from human, bats, and Himalayan palm civet between 2003 and 2018, with one 229E coronavirus strain as the outgroup.\nTable 1. List of coronaviruses used in this study.\nAccession number Name displayed on the tree Name of full-length genome Year\nAY274119 Human SARS-CoV Tor2 2003 SARS-related coronavirus isolate Tor2 2003\nAY278488 Human SARS-CoV BJ01 2003 SARS coronavirus BJ01 2003\nAY278491 SARS coronavirus HKU-39849 2003 SARS coronavirus HKU-39849 2003 2003\nAY390556 Human SARS-CoV GZ02 2003 SARS coronavirus GZ02 2003\nAY391777 Human CoV OC43 2003 Human coronavirus OC43 2003\nAY515512 Paguma SARS CoV HC/SZ/61/03 2003 SARS coronavirus HC/SZ/61/03 (paguma SARS) 2018\nEF065513 Bat CoV HKU9-1 2006 Bat coronavirus HKU9-1 2006\nFJ588686 Bat SL-CoV Rs672 2006 Bat SARS CoV Rs672/2006 2006\nKC881005 Bat SL-CoV RsSHC014 2013 Bat SARS-like coronavirus RsSHC014 2013\nKC881006 Bat SL-CoV Rs3367 2013 Bat SARS-like coronavirus Rs3367 2013\nKY417146 Bat SL-CoV Rs4231 2016 Bat SARS-like coronavirus isolate Rs4231 2016\nKY417149 Bat SL-CoV Rs4255 2016 Bat SARS-like coronavirus isolate Rs4255 2016\nMG772933 Bat SL-CoV ZC45 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZC45 2018\nMG772934 Bat SL-CoV ZXC21 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21 2018\nMK211377 Bat CoV YN2018C 2018 Coronavirus BtRs-BetaCoV/YN2018C 2018\nMK211378 Bat CoV YN2018D 2018 Coronavirus BtRs-BetaCoV/YN2018Da 2018\nMN975262 HKU-SZ-005b Human 2019-nCoV HKU-SZ-005b 2020\nNC002645 Human CoV 229E 2000 Human coronavirus 229E 2000\nNC006577 Human CoV HKU1 2004 Human coronavirus HKU1 2004\nNC009019 Bat CoV HKU4-1 2006 Bat coronavirus HKU4-1 2006\nNC009020 Bat CoV HKU5-1 2006 Bat coronavirus HKU5-1 2006\nNC014470 Bat SARS-related CoV BM48-31 2009 Bat coronavirus BM48-31/BGR/2008 2008\nNC019843 Human MERS-CoV 2012 Middle East respiratory syndrome coronavirus 2012\naOne nucleotide was added within M gene to maintain the sequence in-frame."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T61","span":{"begin":197,"end":205},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T62","span":{"begin":292,"end":297},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T63","span":{"begin":299,"end":303},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T64","span":{"begin":347,"end":351},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T65","span":{"begin":539,"end":544},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T66","span":{"begin":616,"end":621},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T67","span":{"begin":755,"end":760},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T68","span":{"begin":816,"end":821},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T69","span":{"begin":836,"end":841},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T70","span":{"begin":949,"end":953},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T71","span":{"begin":1396,"end":1400},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T72","span":{"begin":1435,"end":1438},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T73","span":{"begin":1450,"end":1454},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T74","span":{"begin":1481,"end":1485},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T75","span":{"begin":1520,"end":1523},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T76","span":{"begin":1536,"end":1540},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T77","span":{"begin":1566,"end":1570},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T78","span":{"begin":1604,"end":1608},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T79","span":{"begin":1634,"end":1638},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T80","span":{"begin":1673,"end":1677},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T81","span":{"begin":1699,"end":1704},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T82","span":{"begin":1741,"end":1746},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T83","span":{"begin":1761,"end":1766},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T84","span":{"begin":1798,"end":1803},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T85","span":{"begin":1818,"end":1823},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T86","span":{"begin":2027,"end":2030},"obj":"http://purl.obolibrary.org/obo/PR_000001807"},{"id":"T87","span":{"begin":2050,"end":2055},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T88","span":{"begin":2155,"end":2159},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"text":"The complete genome sequence of 2019-nCoV HKU-SZ-005b was available at GenBank (accession no. MN975262) (Table 1). The representative complete genomes of other related βCoVs strains collected from human or mammals were included for comparative analysis. These included strains collected from human, bats, and Himalayan palm civet between 2003 and 2018, with one 229E coronavirus strain as the outgroup.\nTable 1. List of coronaviruses used in this study.\nAccession number Name displayed on the tree Name of full-length genome Year\nAY274119 Human SARS-CoV Tor2 2003 SARS-related coronavirus isolate Tor2 2003\nAY278488 Human SARS-CoV BJ01 2003 SARS coronavirus BJ01 2003\nAY278491 SARS coronavirus HKU-39849 2003 SARS coronavirus HKU-39849 2003 2003\nAY390556 Human SARS-CoV GZ02 2003 SARS coronavirus GZ02 2003\nAY391777 Human CoV OC43 2003 Human coronavirus OC43 2003\nAY515512 Paguma SARS CoV HC/SZ/61/03 2003 SARS coronavirus HC/SZ/61/03 (paguma SARS) 2018\nEF065513 Bat CoV HKU9-1 2006 Bat coronavirus HKU9-1 2006\nFJ588686 Bat SL-CoV Rs672 2006 Bat SARS CoV Rs672/2006 2006\nKC881005 Bat SL-CoV RsSHC014 2013 Bat SARS-like coronavirus RsSHC014 2013\nKC881006 Bat SL-CoV Rs3367 2013 Bat SARS-like coronavirus Rs3367 2013\nKY417146 Bat SL-CoV Rs4231 2016 Bat SARS-like coronavirus isolate Rs4231 2016\nKY417149 Bat SL-CoV Rs4255 2016 Bat SARS-like coronavirus isolate Rs4255 2016\nMG772933 Bat SL-CoV ZC45 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZC45 2018\nMG772934 Bat SL-CoV ZXC21 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21 2018\nMK211377 Bat CoV YN2018C 2018 Coronavirus BtRs-BetaCoV/YN2018C 2018\nMK211378 Bat CoV YN2018D 2018 Coronavirus BtRs-BetaCoV/YN2018Da 2018\nMN975262 HKU-SZ-005b Human 2019-nCoV HKU-SZ-005b 2020\nNC002645 Human CoV 229E 2000 Human coronavirus 229E 2000\nNC006577 Human CoV HKU1 2004 Human coronavirus HKU1 2004\nNC009019 Bat CoV HKU4-1 2006 Bat coronavirus HKU4-1 2006\nNC009020 Bat CoV HKU5-1 2006 Bat coronavirus HKU5-1 2006\nNC014470 Bat SARS-related CoV BM48-31 2009 Bat coronavirus BM48-31/BGR/2008 2008\nNC019843 Human MERS-CoV 2012 Middle East respiratory syndrome coronavirus 2012\naOne nucleotide was added within M gene to maintain the sequence in-frame."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T12","span":{"begin":1024,"end":1026},"obj":"Chemical"},{"id":"T13","span":{"begin":1084,"end":1086},"obj":"Chemical"},{"id":"T14","span":{"begin":1158,"end":1160},"obj":"Chemical"},{"id":"T15","span":{"begin":1228,"end":1230},"obj":"Chemical"},{"id":"T16","span":{"begin":1306,"end":1308},"obj":"Chemical"},{"id":"T17","span":{"begin":1384,"end":1386},"obj":"Chemical"},{"id":"T18","span":{"begin":1439,"end":1441},"obj":"Chemical"},{"id":"T19","span":{"begin":1468,"end":1470},"obj":"Chemical"},{"id":"T20","span":{"begin":1524,"end":1526},"obj":"Chemical"},{"id":"T21","span":{"begin":2125,"end":2135},"obj":"Chemical"}],"attributes":[{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A14","pred":"chebi_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A15","pred":"chebi_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A16","pred":"chebi_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A17","pred":"chebi_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A18","pred":"chebi_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A19","pred":"chebi_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A21","pred":"chebi_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"}],"text":"The complete genome sequence of 2019-nCoV HKU-SZ-005b was available at GenBank (accession no. MN975262) (Table 1). The representative complete genomes of other related βCoVs strains collected from human or mammals were included for comparative analysis. These included strains collected from human, bats, and Himalayan palm civet between 2003 and 2018, with one 229E coronavirus strain as the outgroup.\nTable 1. List of coronaviruses used in this study.\nAccession number Name displayed on the tree Name of full-length genome Year\nAY274119 Human SARS-CoV Tor2 2003 SARS-related coronavirus isolate Tor2 2003\nAY278488 Human SARS-CoV BJ01 2003 SARS coronavirus BJ01 2003\nAY278491 SARS coronavirus HKU-39849 2003 SARS coronavirus HKU-39849 2003 2003\nAY390556 Human SARS-CoV GZ02 2003 SARS coronavirus GZ02 2003\nAY391777 Human CoV OC43 2003 Human coronavirus OC43 2003\nAY515512 Paguma SARS CoV HC/SZ/61/03 2003 SARS coronavirus HC/SZ/61/03 (paguma SARS) 2018\nEF065513 Bat CoV HKU9-1 2006 Bat coronavirus HKU9-1 2006\nFJ588686 Bat SL-CoV Rs672 2006 Bat SARS CoV Rs672/2006 2006\nKC881005 Bat SL-CoV RsSHC014 2013 Bat SARS-like coronavirus RsSHC014 2013\nKC881006 Bat SL-CoV Rs3367 2013 Bat SARS-like coronavirus Rs3367 2013\nKY417146 Bat SL-CoV Rs4231 2016 Bat SARS-like coronavirus isolate Rs4231 2016\nKY417149 Bat SL-CoV Rs4255 2016 Bat SARS-like coronavirus isolate Rs4255 2016\nMG772933 Bat SL-CoV ZC45 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZC45 2018\nMG772934 Bat SL-CoV ZXC21 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21 2018\nMK211377 Bat CoV YN2018C 2018 Coronavirus BtRs-BetaCoV/YN2018C 2018\nMK211378 Bat CoV YN2018D 2018 Coronavirus BtRs-BetaCoV/YN2018Da 2018\nMN975262 HKU-SZ-005b Human 2019-nCoV HKU-SZ-005b 2020\nNC002645 Human CoV 229E 2000 Human coronavirus 229E 2000\nNC006577 Human CoV HKU1 2004 Human coronavirus HKU1 2004\nNC009019 Bat CoV HKU4-1 2006 Bat coronavirus HKU4-1 2006\nNC009020 Bat CoV HKU5-1 2006 Bat coronavirus HKU5-1 2006\nNC014470 Bat SARS-related CoV BM48-31 2009 Bat coronavirus BM48-31/BGR/2008 2008\nNC019843 Human MERS-CoV 2012 Middle East respiratory syndrome coronavirus 2012\naOne nucleotide was added within M gene to maintain the sequence in-frame."}

{"project":"LitCovid-sentences","denotations":[{"id":"T39","span":{"begin":0,"end":93},"obj":"Sentence"},{"id":"T40","span":{"begin":94,"end":114},"obj":"Sentence"},{"id":"T41","span":{"begin":115,"end":253},"obj":"Sentence"},{"id":"T42","span":{"begin":254,"end":402},"obj":"Sentence"},{"id":"T43","span":{"begin":403,"end":411},"obj":"Sentence"},{"id":"T44","span":{"begin":412,"end":453},"obj":"Sentence"},{"id":"T45","span":{"begin":454,"end":529},"obj":"Sentence"},{"id":"T46","span":{"begin":530,"end":606},"obj":"Sentence"},{"id":"T47","span":{"begin":607,"end":667},"obj":"Sentence"},{"id":"T48","span":{"begin":668,"end":745},"obj":"Sentence"},{"id":"T49","span":{"begin":746,"end":806},"obj":"Sentence"},{"id":"T50","span":{"begin":807,"end":863},"obj":"Sentence"},{"id":"T51","span":{"begin":864,"end":953},"obj":"Sentence"},{"id":"T52","span":{"begin":954,"end":1010},"obj":"Sentence"},{"id":"T53","span":{"begin":1011,"end":1070},"obj":"Sentence"},{"id":"T54","span":{"begin":1071,"end":1144},"obj":"Sentence"},{"id":"T55","span":{"begin":1145,"end":1214},"obj":"Sentence"},{"id":"T56","span":{"begin":1215,"end":1292},"obj":"Sentence"},{"id":"T57","span":{"begin":1293,"end":1370},"obj":"Sentence"},{"id":"T58","span":{"begin":1371,"end":1454},"obj":"Sentence"},{"id":"T59","span":{"begin":1455,"end":1540},"obj":"Sentence"},{"id":"T60","span":{"begin":1541,"end":1608},"obj":"Sentence"},{"id":"T61","span":{"begin":1609,"end":1677},"obj":"Sentence"},{"id":"T62","span":{"begin":1678,"end":1731},"obj":"Sentence"},{"id":"T63","span":{"begin":1732,"end":1788},"obj":"Sentence"},{"id":"T64","span":{"begin":1789,"end":1845},"obj":"Sentence"},{"id":"T65","span":{"begin":1846,"end":1902},"obj":"Sentence"},{"id":"T66","span":{"begin":1903,"end":1959},"obj":"Sentence"},{"id":"T67","span":{"begin":1960,"end":2040},"obj":"Sentence"},{"id":"T68","span":{"begin":2041,"end":2119},"obj":"Sentence"},{"id":"T69","span":{"begin":2120,"end":2194},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The complete genome sequence of 2019-nCoV HKU-SZ-005b was available at GenBank (accession no. MN975262) (Table 1). The representative complete genomes of other related βCoVs strains collected from human or mammals were included for comparative analysis. These included strains collected from human, bats, and Himalayan palm civet between 2003 and 2018, with one 229E coronavirus strain as the outgroup.\nTable 1. List of coronaviruses used in this study.\nAccession number Name displayed on the tree Name of full-length genome Year\nAY274119 Human SARS-CoV Tor2 2003 SARS-related coronavirus isolate Tor2 2003\nAY278488 Human SARS-CoV BJ01 2003 SARS coronavirus BJ01 2003\nAY278491 SARS coronavirus HKU-39849 2003 SARS coronavirus HKU-39849 2003 2003\nAY390556 Human SARS-CoV GZ02 2003 SARS coronavirus GZ02 2003\nAY391777 Human CoV OC43 2003 Human coronavirus OC43 2003\nAY515512 Paguma SARS CoV HC/SZ/61/03 2003 SARS coronavirus HC/SZ/61/03 (paguma SARS) 2018\nEF065513 Bat CoV HKU9-1 2006 Bat coronavirus HKU9-1 2006\nFJ588686 Bat SL-CoV Rs672 2006 Bat SARS CoV Rs672/2006 2006\nKC881005 Bat SL-CoV RsSHC014 2013 Bat SARS-like coronavirus RsSHC014 2013\nKC881006 Bat SL-CoV Rs3367 2013 Bat SARS-like coronavirus Rs3367 2013\nKY417146 Bat SL-CoV Rs4231 2016 Bat SARS-like coronavirus isolate Rs4231 2016\nKY417149 Bat SL-CoV Rs4255 2016 Bat SARS-like coronavirus isolate Rs4255 2016\nMG772933 Bat SL-CoV ZC45 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZC45 2018\nMG772934 Bat SL-CoV ZXC21 2018 Bat SARS-like coronavirus isolate bat-SL-CoVZXC21 2018\nMK211377 Bat CoV YN2018C 2018 Coronavirus BtRs-BetaCoV/YN2018C 2018\nMK211378 Bat CoV YN2018D 2018 Coronavirus BtRs-BetaCoV/YN2018Da 2018\nMN975262 HKU-SZ-005b Human 2019-nCoV HKU-SZ-005b 2020\nNC002645 Human CoV 229E 2000 Human coronavirus 229E 2000\nNC006577 Human CoV HKU1 2004 Human coronavirus HKU1 2004\nNC009019 Bat CoV HKU4-1 2006 Bat coronavirus HKU4-1 2006\nNC009020 Bat CoV HKU5-1 2006 Bat coronavirus HKU5-1 2006\nNC014470 Bat SARS-related CoV BM48-31 2009 Bat coronavirus BM48-31/BGR/2008 2008\nNC019843 Human MERS-CoV 2012 Middle East respiratory syndrome coronavirus 2012\naOne nucleotide was added within M gene to maintain the sequence in-frame."}