PMC:7081066 / 11189-12901 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"331","span":{"begin":935,"end":939},"obj":"Gene"},{"id":"332","span":{"begin":1085,"end":1089},"obj":"Gene"},{"id":"333","span":{"begin":1171,"end":1176},"obj":"Gene"},{"id":"334","span":{"begin":1355,"end":1360},"obj":"Gene"},{"id":"335","span":{"begin":1439,"end":1444},"obj":"Gene"},{"id":"336","span":{"begin":497,"end":502},"obj":"Gene"},{"id":"337","span":{"begin":18,"end":28},"obj":"Species"},{"id":"338","span":{"begin":196,"end":209},"obj":"Species"},{"id":"339","span":{"begin":245,"end":255},"obj":"Species"},{"id":"340","span":{"begin":291,"end":310},"obj":"Species"},{"id":"341","span":{"begin":422,"end":427},"obj":"Species"},{"id":"342","span":{"begin":486,"end":491},"obj":"Species"},{"id":"343","span":{"begin":558,"end":566},"obj":"Species"},{"id":"344","span":{"begin":571,"end":581},"obj":"Species"},{"id":"345","span":{"begin":754,"end":764},"obj":"Species"},{"id":"346","span":{"begin":815,"end":834},"obj":"Species"},{"id":"347","span":{"begin":1106,"end":1116},"obj":"Species"},{"id":"348","span":{"begin":1188,"end":1198},"obj":"Species"},{"id":"349","span":{"begin":1617,"end":1625},"obj":"Species"},{"id":"350","span":{"begin":1630,"end":1640},"obj":"Species"},{"id":"351","span":{"begin":351,"end":359},"obj":"Chemical"},{"id":"352","span":{"begin":1488,"end":1497},"obj":"Disease"},{"id":"353","span":{"begin":1683,"end":1691},"obj":"Disease"}],"attributes":[{"id":"A331","pred":"tao:has_database_id","subj":"331","obj":"Gene:59272"},{"id":"A332","pred":"tao:has_database_id","subj":"332","obj":"Gene:59272"},{"id":"A333","pred":"tao:has_database_id","subj":"333","obj":"Gene:43740568"},{"id":"A334","pred":"tao:has_database_id","subj":"334","obj":"Gene:43740568"},{"id":"A335","pred":"tao:has_database_id","subj":"335","obj":"Gene:43740568"},{"id":"A336","pred":"tao:has_database_id","subj":"336","obj":"Gene:43740568"},{"id":"A337","pred":"tao:has_database_id","subj":"337","obj":"Tax:2697049"},{"id":"A338","pred":"tao:has_database_id","subj":"338","obj":"Tax:11118"},{"id":"A339","pred":"tao:has_database_id","subj":"339","obj":"Tax:2697049"},{"id":"A340","pred":"tao:has_database_id","subj":"340","obj":"Tax:59477"},{"id":"A341","pred":"tao:has_database_id","subj":"341","obj":"Tax:9606"},{"id":"A342","pred":"tao:has_database_id","subj":"342","obj":"Tax:9606"},{"id":"A343","pred":"tao:has_database_id","subj":"343","obj":"Tax:694009"},{"id":"A344","pred":"tao:has_database_id","subj":"344","obj":"Tax:2697049"},{"id":"A345","pred":"tao:has_database_id","subj":"345","obj":"Tax:2697049"},{"id":"A346","pred":"tao:has_database_id","subj":"346","obj":"Tax:59477"},{"id":"A347","pred":"tao:has_database_id","subj":"347","obj":"Tax:2697049"},{"id":"A348","pred":"tao:has_database_id","subj":"348","obj":"Tax:2697049"},{"id":"A349","pred":"tao:has_database_id","subj":"349","obj":"Tax:694009"},{"id":"A350","pred":"tao:has_database_id","subj":"350","obj":"Tax:2697049"},{"id":"A352","pred":"tao:has_database_id","subj":"352","obj":"MESH:D007239"},{"id":"A353","pred":"tao:has_database_id","subj":"353","obj":"MESH:D015047"}],"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 origin of the SARS-CoV-2 has been not fully elucidated. While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13). The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human. The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown). The protein sequence of the receptor binding motif, has 5 important amino acids. When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]). These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study. Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein. Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading. Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T50","span":{"begin":161,"end":168},"obj":"Body_part"},{"id":"T51","span":{"begin":646,"end":653},"obj":"Body_part"},{"id":"T52","span":{"begin":710,"end":721},"obj":"Body_part"},{"id":"T53","span":{"begin":889,"end":900},"obj":"Body_part"},{"id":"T54","span":{"begin":1177,"end":1184},"obj":"Body_part"},{"id":"T55","span":{"begin":1246,"end":1256},"obj":"Body_part"},{"id":"T56","span":{"begin":1361,"end":1368},"obj":"Body_part"},{"id":"T57","span":{"begin":1445,"end":1452},"obj":"Body_part"}],"attributes":[{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A52","pred":"fma_id","subj":"T52","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A53","pred":"fma_id","subj":"T53","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A54","pred":"fma_id","subj":"T54","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A55","pred":"fma_id","subj":"T55","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A56","pred":"fma_id","subj":"T56","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A57","pred":"fma_id","subj":"T57","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"The origin of the SARS-CoV-2 has been not fully elucidated. While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13). The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human. The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown). The protein sequence of the receptor binding motif, has 5 important amino acids. When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]). These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study. Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein. Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading. Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T58","span":{"begin":18,"end":26},"obj":"Disease"},{"id":"T59","span":{"begin":245,"end":253},"obj":"Disease"},{"id":"T60","span":{"begin":558,"end":566},"obj":"Disease"},{"id":"T61","span":{"begin":571,"end":579},"obj":"Disease"},{"id":"T62","span":{"begin":754,"end":762},"obj":"Disease"},{"id":"T63","span":{"begin":1106,"end":1114},"obj":"Disease"},{"id":"T64","span":{"begin":1188,"end":1196},"obj":"Disease"},{"id":"T65","span":{"begin":1488,"end":1497},"obj":"Disease"},{"id":"T66","span":{"begin":1617,"end":1625},"obj":"Disease"},{"id":"T67","span":{"begin":1630,"end":1638},"obj":"Disease"}],"attributes":[{"id":"A58","pred":"mondo_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A59","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A60","pred":"mondo_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A61","pred":"mondo_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A62","pred":"mondo_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A63","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A64","pred":"mondo_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A65","pred":"mondo_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A66","pred":"mondo_id","subj":"T66","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A67","pred":"mondo_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The origin of the SARS-CoV-2 has been not fully elucidated. While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13). The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human. The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown). The protein sequence of the receptor binding motif, has 5 important amino acids. When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]). These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study. Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein. Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading. Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T62","span":{"begin":29,"end":32},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T63","span":{"begin":127,"end":129},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T64","span":{"begin":140,"end":141},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":397,"end":398},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T66","span":{"begin":422,"end":427},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T67","span":{"begin":428,"end":433},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T68","span":{"begin":478,"end":481},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T69","span":{"begin":486,"end":491},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T70","span":{"begin":694,"end":697},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T71","span":{"begin":791,"end":798},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T72","span":{"begin":981,"end":983},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T73","span":{"begin":1072,"end":1079},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"text":"The origin of the SARS-CoV-2 has been not fully elucidated. While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13). The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human. The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown). The protein sequence of the receptor binding motif, has 5 important amino acids. When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]). These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study. Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein. Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading. Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T68","span":{"begin":161,"end":168},"obj":"Chemical"},{"id":"T69","span":{"begin":646,"end":653},"obj":"Chemical"},{"id":"T70","span":{"begin":710,"end":721},"obj":"Chemical"},{"id":"T71","span":{"begin":710,"end":715},"obj":"Chemical"},{"id":"T72","span":{"begin":716,"end":721},"obj":"Chemical"},{"id":"T73","span":{"begin":889,"end":900},"obj":"Chemical"},{"id":"T74","span":{"begin":889,"end":894},"obj":"Chemical"},{"id":"T75","span":{"begin":895,"end":900},"obj":"Chemical"},{"id":"T76","span":{"begin":1177,"end":1184},"obj":"Chemical"},{"id":"T77","span":{"begin":1246,"end":1256},"obj":"Chemical"},{"id":"T78","span":{"begin":1246,"end":1251},"obj":"Chemical"},{"id":"T79","span":{"begin":1252,"end":1256},"obj":"Chemical"},{"id":"T80","span":{"begin":1361,"end":1368},"obj":"Chemical"},{"id":"T81","span":{"begin":1445,"end":1452},"obj":"Chemical"}],"attributes":[{"id":"A68","pred":"chebi_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A69","pred":"chebi_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A70","pred":"chebi_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A71","pred":"chebi_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A72","pred":"chebi_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A73","pred":"chebi_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A74","pred":"chebi_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A75","pred":"chebi_id","subj":"T75","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A76","pred":"chebi_id","subj":"T76","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A77","pred":"chebi_id","subj":"T77","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A78","pred":"chebi_id","subj":"T78","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A79","pred":"chebi_id","subj":"T79","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A81","pred":"chebi_id","subj":"T81","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"The origin of the SARS-CoV-2 has been not fully elucidated. While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13). The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human. The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown). The protein sequence of the receptor binding motif, has 5 important amino acids. When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]). These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study. Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein. Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading. Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future."}

{"project":"LitCovid-sentences","denotations":[{"id":"T95","span":{"begin":0,"end":59},"obj":"Sentence"},{"id":"T96","span":{"begin":60,"end":320},"obj":"Sentence"},{"id":"T97","span":{"begin":321,"end":492},"obj":"Sentence"},{"id":"T98","span":{"begin":493,"end":641},"obj":"Sentence"},{"id":"T99","span":{"begin":642,"end":722},"obj":"Sentence"},{"id":"T100","span":{"begin":723,"end":986},"obj":"Sentence"},{"id":"T101","span":{"begin":987,"end":1138},"obj":"Sentence"},{"id":"T102","span":{"begin":1139,"end":1369},"obj":"Sentence"},{"id":"T103","span":{"begin":1370,"end":1527},"obj":"Sentence"},{"id":"T104","span":{"begin":1528,"end":1712},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The origin of the SARS-CoV-2 has been not fully elucidated. While this study was in course, another study of Wong et al. (2020[18]), showed a high similarity at protein level in the RBD among the coronaviruses isolated from the recent outbreak (SARS-CoV-2), those isolated from pangolin and Rhinolophus affinis (RaTG13). The authors also suggest that Pangolin might be the intermediate host, with a 98 % identity with the human virus, at the receptor binding motif, between the bat and human. The spike model of RaTG13 is quite similar to that obtained from SARS-CoV and SARS-CoV-2 and the loops in the RBD are also present (data not shown). The protein sequence of the receptor binding motif, has 5 important amino acids. When comparing the sequence of SARS-CoV-2 with that of the isolated viruses of pangolin and Rhinolophus affinis, 1 and 4 differences are observed respectively in the amino acids considered key for the union with ACE2 (Yan et al., 2020[20]; Wong et al., 2020[18]). These differences should mean slightly less favorable binding energies between these viruses with ACE2 compared to the SARS-CoV-2, shown in this study. Thus, the loops observed in the spike protein of SARS-CoV-2 could play an important role together with the amino acid substitutions, being an interesting clue to determine the host receptor specificity for the viral spike protein. Altogether, structural changes and residues composition in the viral spike protein could be associated with increased infection kinetics and viral spreading. Comparative studies to determine the impact in vitro of the mutation and loops in RBD of SARS-CoV and SARS-CoV-2 are required in order to predict possible zoonotic event in the future."}