PMC:7126544 / 46482-47767 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T140","span":{"begin":37,"end":44},"obj":"Body_part"},{"id":"T141","span":{"begin":1074,"end":1082},"obj":"Body_part"}],"attributes":[{"id":"A140","pred":"fma_id","subj":"T140","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A141","pred":"fma_id","subj":"T141","obj":"http://purl.org/sig/ont/fma/fma82763"}],"text":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T401","span":{"begin":57,"end":65},"obj":"Disease"},{"id":"T402","span":{"begin":57,"end":61},"obj":"Disease"},{"id":"T403","span":{"begin":99,"end":103},"obj":"Disease"},{"id":"T404","span":{"begin":395,"end":403},"obj":"Disease"},{"id":"T405","span":{"begin":395,"end":399},"obj":"Disease"},{"id":"T406","span":{"begin":668,"end":676},"obj":"Disease"},{"id":"T407","span":{"begin":668,"end":672},"obj":"Disease"},{"id":"T408","span":{"begin":719,"end":723},"obj":"Disease"},{"id":"T409","span":{"begin":865,"end":873},"obj":"Disease"},{"id":"T410","span":{"begin":865,"end":869},"obj":"Disease"},{"id":"T411","span":{"begin":1039,"end":1047},"obj":"Disease"},{"id":"T412","span":{"begin":1039,"end":1043},"obj":"Disease"},{"id":"T413","span":{"begin":1086,"end":1094},"obj":"Disease"},{"id":"T414","span":{"begin":1086,"end":1090},"obj":"Disease"},{"id":"T415","span":{"begin":1197,"end":1205},"obj":"Disease"},{"id":"T416","span":{"begin":1197,"end":1201},"obj":"Disease"}],"attributes":[{"id":"A401","pred":"mondo_id","subj":"T401","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A402","pred":"mondo_id","subj":"T402","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A403","pred":"mondo_id","subj":"T403","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A404","pred":"mondo_id","subj":"T404","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A405","pred":"mondo_id","subj":"T405","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A406","pred":"mondo_id","subj":"T406","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A407","pred":"mondo_id","subj":"T407","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A408","pred":"mondo_id","subj":"T408","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A409","pred":"mondo_id","subj":"T409","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A410","pred":"mondo_id","subj":"T410","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A411","pred":"mondo_id","subj":"T411","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A412","pred":"mondo_id","subj":"T412","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A413","pred":"mondo_id","subj":"T413","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A414","pred":"mondo_id","subj":"T414","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A415","pred":"mondo_id","subj":"T415","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A416","pred":"mondo_id","subj":"T416","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T384","span":{"begin":95,"end":98},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T385","span":{"begin":121,"end":124},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T386","span":{"begin":173,"end":176},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T387","span":{"begin":291,"end":303},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T388","span":{"begin":318,"end":319},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T389","span":{"begin":328,"end":329},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T390","span":{"begin":378,"end":381},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T391","span":{"begin":409,"end":410},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T392","span":{"begin":463,"end":466},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T393","span":{"begin":486,"end":487},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T394","span":{"begin":502,"end":505},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T395","span":{"begin":530,"end":531},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T396","span":{"begin":532,"end":535},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T397","span":{"begin":604,"end":609},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T398","span":{"begin":689,"end":690},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T399","span":{"begin":774,"end":775},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T400","span":{"begin":786,"end":787},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T401","span":{"begin":1007,"end":1009},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"},{"id":"T402","span":{"begin":1010,"end":1012},"obj":"http://purl.obolibrary.org/obo/CLO_0008922"},{"id":"T403","span":{"begin":1010,"end":1012},"obj":"http://purl.obolibrary.org/obo/CLO_0050052"}],"text":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T128","span":{"begin":125,"end":127},"obj":"Chemical"},{"id":"T129","span":{"begin":177,"end":179},"obj":"Chemical"},{"id":"T130","span":{"begin":330,"end":334},"obj":"Chemical"},{"id":"T131","span":{"begin":1010,"end":1012},"obj":"Chemical"},{"id":"T132","span":{"begin":1074,"end":1082},"obj":"Chemical"}],"attributes":[{"id":"A128","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A129","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_74815"},{"id":"A130","pred":"chebi_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/CHEBI_10545"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_29387"},{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_29016"}],"text":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T390","span":{"begin":0,"end":276},"obj":"Sentence"},{"id":"T391","span":{"begin":277,"end":347},"obj":"Sentence"},{"id":"T392","span":{"begin":348,"end":729},"obj":"Sentence"},{"id":"T393","span":{"begin":730,"end":816},"obj":"Sentence"},{"id":"T394","span":{"begin":817,"end":1285},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1269","span":{"begin":57,"end":67},"obj":"Species"},{"id":"1270","span":{"begin":95,"end":120},"obj":"Species"},{"id":"1271","span":{"begin":330,"end":346},"obj":"Species"},{"id":"1272","span":{"begin":395,"end":405},"obj":"Species"},{"id":"1273","span":{"begin":467,"end":480},"obj":"Species"},{"id":"1274","span":{"begin":536,"end":540},"obj":"Species"},{"id":"1275","span":{"begin":668,"end":678},"obj":"Species"},{"id":"1276","span":{"begin":719,"end":728},"obj":"Species"},{"id":"1277","span":{"begin":865,"end":875},"obj":"Species"},{"id":"1278","span":{"begin":1039,"end":1049},"obj":"Species"},{"id":"1279","span":{"begin":1086,"end":1094},"obj":"Species"},{"id":"1280","span":{"begin":1197,"end":1207},"obj":"Species"},{"id":"1281","span":{"begin":1074,"end":1082},"obj":"Chemical"},{"id":"1282","span":{"begin":882,"end":890},"obj":"CellLine"},{"id":"1283","span":{"begin":1214,"end":1222},"obj":"CellLine"}],"attributes":[{"id":"A1269","pred":"tao:has_database_id","subj":"1269","obj":"Tax:2697049"},{"id":"A1270","pred":"tao:has_database_id","subj":"1270","obj":"Tax:1508227"},{"id":"A1271","pred":"tao:has_database_id","subj":"1271","obj":"Tax:694002"},{"id":"A1272","pred":"tao:has_database_id","subj":"1272","obj":"Tax:2697049"},{"id":"A1273","pred":"tao:has_database_id","subj":"1273","obj":"Tax:11118"},{"id":"A1274","pred":"tao:has_database_id","subj":"1274","obj":"Tax:11118"},{"id":"A1275","pred":"tao:has_database_id","subj":"1275","obj":"Tax:2697049"},{"id":"A1276","pred":"tao:has_database_id","subj":"1276","obj":"Tax:694009"},{"id":"A1277","pred":"tao:has_database_id","subj":"1277","obj":"Tax:2697049"},{"id":"A1278","pred":"tao:has_database_id","subj":"1278","obj":"Tax:2697049"},{"id":"A1279","pred":"tao:has_database_id","subj":"1279","obj":"Tax:694009"},{"id":"A1280","pred":"tao:has_database_id","subj":"1280","obj":"Tax:2697049"},{"id":"A1281","pred":"tao:has_database_id","subj":"1281","obj":"MESH:D001120"},{"id":"A1282","pred":"tao:has_database_id","subj":"1282","obj":"CVCL:AR51"},{"id":"A1283","pred":"tao:has_database_id","subj":"1283","obj":"CVCL:AR51"}],"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":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}

{"project":"2_test","denotations":[{"id":"32143990-32007145-55637418","span":{"begin":265,"end":267},"obj":"32007145"},{"id":"32143990-32004758-55637419","span":{"begin":812,"end":814},"obj":"32004758"},{"id":"32143990-14647384-55637420","span":{"begin":1103,"end":1105},"obj":"14647384"},{"id":"32143990-18562523-55637421","span":{"begin":1109,"end":1111},"obj":"18562523"},{"id":"32143990-19321428-55637422","span":{"begin":1115,"end":1118},"obj":"19321428"},{"id":"32143990-21325420-55637423","span":{"begin":1122,"end":1125},"obj":"21325420"}],"text":"The phylogenetic tree based on whole genomes showed that SARS-CoV-2 is most closely related to bat SARS-like coronavirus bat-SL-CoVZC21 (NCBI accession number MG772934) and bat-SL-CoVZC45 (NCBI accession number MG772933), which share ~89% sequence homology [[91], [92], [93]]. Their genomic organization is typical of a lineage B beta coronavirus. Further phylogenetic analysis has posited that SARS-CoV-2 is a product of recombination with previously identified bat coronaviruses, but a recent report has subsequently identified a bat CoVs sequence, RaTG13, with 92–96% sequence identity with the novel virus, demonstrating that RaTG13 is the closest relative of the SARS-CoV-2 and forms a distinct lineage from other SARS-CoVs. This rejects the hypothesis of emergence as a result of a recombination event [94,96]. Even though there are high similarities between SARS-CoV-2 S and RaTG13 S, there are two distinct differences: one is an “RRAR” furin recognition site formed by an insertion residues in the S1/S2 protease cleavage site in SARS-CoV-2, rather than the single Arginine in SARS-CoV [[97], [98], [99], [100], [101]]; the other difference is the presence of 29 variant residues between SARS-CoV-2 S and RaTG13 S, 17 of which mapped to the receptor binding domain (RBD) [97]."}