PMC:7033720 / 17580-18444 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"287","span":{"begin":173,"end":178},"obj":"Gene"},{"id":"288","span":{"begin":62,"end":66},"obj":"Species"},{"id":"289","span":{"begin":87,"end":96},"obj":"Species"},{"id":"290","span":{"begin":129,"end":133},"obj":"Species"},{"id":"291","span":{"begin":237,"end":242},"obj":"Species"},{"id":"292","span":{"begin":344,"end":348},"obj":"Species"},{"id":"293","span":{"begin":466,"end":474},"obj":"Species"},{"id":"294","span":{"begin":650,"end":654},"obj":"Species"},{"id":"295","span":{"begin":828,"end":837},"obj":"Species"}],"attributes":[{"id":"A287","pred":"tao:has_database_id","subj":"287","obj":"Gene:43740578"},{"id":"A288","pred":"tao:has_database_id","subj":"288","obj":"Tax:11118"},{"id":"A289","pred":"tao:has_database_id","subj":"289","obj":"Tax:2697049"},{"id":"A290","pred":"tao:has_database_id","subj":"290","obj":"Tax:11118"},{"id":"A291","pred":"tao:has_database_id","subj":"291","obj":"Tax:9606"},{"id":"A292","pred":"tao:has_database_id","subj":"292","obj":"Tax:11118"},{"id":"A293","pred":"tao:has_database_id","subj":"293","obj":"Tax:694009"},{"id":"A294","pred":"tao:has_database_id","subj":"294","obj":"Tax:11118"},{"id":"A295","pred":"tao:has_database_id","subj":"295","obj":"Tax:694009"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Figure 3. Origin and evolutionary history of newly identified CoVs. A. the position of 2019-nCoV in the context of all reference CoVs. The phylogeny is constructed based on ORF1b protein alignment. For clarity, names were only shown for human-associated viruses. Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively. B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome. Recombination breakpoints are shown as dashed vertical lines. C. the relationship of WHU viruses with the other SARS-like CoVs. Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N. Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T79","span":{"begin":179,"end":186},"obj":"Body_part"},{"id":"T80","span":{"begin":366,"end":372},"obj":"Body_part"},{"id":"T81","span":{"begin":520,"end":526},"obj":"Body_part"},{"id":"T82","span":{"begin":696,"end":706},"obj":"Body_part"},{"id":"T83","span":{"begin":784,"end":788},"obj":"Body_part"},{"id":"T84","span":{"begin":843,"end":847},"obj":"Body_part"}],"attributes":[{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma82740"},{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma74402"},{"id":"A84","pred":"fma_id","subj":"T84","obj":"http://purl.org/sig/ont/fma/fma74402"}],"text":"Figure 3. Origin and evolutionary history of newly identified CoVs. A. the position of 2019-nCoV in the context of all reference CoVs. The phylogeny is constructed based on ORF1b protein alignment. For clarity, names were only shown for human-associated viruses. Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively. B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome. Recombination breakpoints are shown as dashed vertical lines. C. the relationship of WHU viruses with the other SARS-like CoVs. Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N. Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T31","span":{"begin":466,"end":474},"obj":"Disease"},{"id":"T32","span":{"begin":640,"end":644},"obj":"Disease"},{"id":"T33","span":{"begin":828,"end":832},"obj":"Disease"}],"attributes":[{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Figure 3. Origin and evolutionary history of newly identified CoVs. A. the position of 2019-nCoV in the context of all reference CoVs. The phylogeny is constructed based on ORF1b protein alignment. For clarity, names were only shown for human-associated viruses. Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively. B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome. Recombination breakpoints are shown as dashed vertical lines. C. the relationship of WHU viruses with the other SARS-like CoVs. Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N. Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T179","span":{"begin":68,"end":69},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T180","span":{"begin":237,"end":242},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T181","span":{"begin":254,"end":261},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T182","span":{"begin":363,"end":364},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T183","span":{"begin":403,"end":410},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T184","span":{"begin":447,"end":450},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T185","span":{"begin":478,"end":479},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T186","span":{"begin":617,"end":624},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T187","span":{"begin":724,"end":729},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T188","span":{"begin":784,"end":788},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T189","span":{"begin":843,"end":847},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"}],"text":"Figure 3. Origin and evolutionary history of newly identified CoVs. A. the position of 2019-nCoV in the context of all reference CoVs. The phylogeny is constructed based on ORF1b protein alignment. For clarity, names were only shown for human-associated viruses. Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively. B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome. Recombination breakpoints are shown as dashed vertical lines. C. the relationship of WHU viruses with the other SARS-like CoVs. Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N. Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T49","span":{"begin":179,"end":186},"obj":"Chemical"},{"id":"T50","span":{"begin":328,"end":333},"obj":"Chemical"},{"id":"T51","span":{"begin":339,"end":343},"obj":"Chemical"},{"id":"T52","span":{"begin":451,"end":453},"obj":"Chemical"},{"id":"T53","span":{"begin":696,"end":706},"obj":"Chemical"}],"attributes":[{"id":"A49","pred":"chebi_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A50","pred":"chebi_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/CHEBI_30216"},{"id":"A51","pred":"chebi_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/CHEBI_10545"},{"id":"A52","pred":"chebi_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A53","pred":"chebi_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/CHEBI_36976"}],"text":"Figure 3. Origin and evolutionary history of newly identified CoVs. A. the position of 2019-nCoV in the context of all reference CoVs. The phylogeny is constructed based on ORF1b protein alignment. For clarity, names were only shown for human-associated viruses. Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively. B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome. Recombination breakpoints are shown as dashed vertical lines. C. the relationship of WHU viruses with the other SARS-like CoVs. Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N. Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue."}

{"project":"LitCovid-sentences","denotations":[{"id":"T168","span":{"begin":0,"end":9},"obj":"Sentence"},{"id":"T169","span":{"begin":10,"end":67},"obj":"Sentence"},{"id":"T170","span":{"begin":68,"end":134},"obj":"Sentence"},{"id":"T171","span":{"begin":135,"end":197},"obj":"Sentence"},{"id":"T172","span":{"begin":198,"end":262},"obj":"Sentence"},{"id":"T173","span":{"begin":263,"end":362},"obj":"Sentence"},{"id":"T174","span":{"begin":363,"end":527},"obj":"Sentence"},{"id":"T175","span":{"begin":528,"end":589},"obj":"Sentence"},{"id":"T176","span":{"begin":590,"end":655},"obj":"Sentence"},{"id":"T177","span":{"begin":656,"end":755},"obj":"Sentence"},{"id":"T178","span":{"begin":756,"end":864},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Figure 3. Origin and evolutionary history of newly identified CoVs. A. the position of 2019-nCoV in the context of all reference CoVs. The phylogeny is constructed based on ORF1b protein alignment. For clarity, names were only shown for human-associated viruses. Bat associated diversity is shaded with blue and green boxes for alpha- and beta-CoVs respectively. B. genome structure of newly identified viruses and its sequence similarity against bat-SL-CoVZC45 and SARS-CoV in a 1000bp sliding window across the entire genome. Recombination breakpoints are shown as dashed vertical lines. C. the relationship of WHU viruses with the other SARS-like CoVs. Phylogeny is reconstructed based on the nucleotide sequence of four genes: namely 1a, 1b, S, and N. Those grouped with WHU at S gene are marked red, and those grouped with SARS CoVs at S gene are marked blue."}