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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid_AGAC

{"project":"LitCovid_AGAC","denotations":[{"id":"p24456s3","span":{"begin":395,"end":410},"obj":"MPA"},{"id":"p24456s14","span":{"begin":442,"end":460},"obj":"MPA"},{"id":"p24458s16","span":{"begin":723,"end":732},"obj":"PosReg"},{"id":"p24458s18","span":{"begin":737,"end":748},"obj":"MPA"},{"id":"p24458s24","span":{"begin":773,"end":782},"obj":"PosReg"},{"id":"p24458s26","span":{"begin":787,"end":794},"obj":"MPA"},{"id":"p24459s14","span":{"begin":977,"end":995},"obj":"MPA"}],"text":"Discussion\nSeveral amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV. Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]). HIV infection is a good model of change in viral tropism by mutations in the envelope proteins. These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]). Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition. The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab. 1) and 2(Tab. 2)). The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab. 1)). Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.\nThe 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."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T57","span":{"begin":188,"end":189},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T58","span":{"begin":190,"end":195},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T59","span":{"begin":293,"end":294},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T60","span":{"begin":589,"end":594},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T61","span":{"begin":1157,"end":1162},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T62","span":{"begin":1193,"end":1196},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T63","span":{"begin":1291,"end":1293},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T64","span":{"begin":1304,"end":1305},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":1561,"end":1562},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T66","span":{"begin":1586,"end":1591},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T67","span":{"begin":1592,"end":1597},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T68","span":{"begin":1642,"end":1645},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9397"},{"id":"T69","span":{"begin":1650,"end":1655},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T70","span":{"begin":1858,"end":1861},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T71","span":{"begin":1955,"end":1962},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T72","span":{"begin":2145,"end":2147},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T73","span":{"begin":2236,"end":2243},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"}],"text":"Discussion\nSeveral amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV. Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]). HIV infection is a good model of change in viral tropism by mutations in the envelope proteins. These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]). Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition. The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab. 1) and 2(Tab. 2)). The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab. 1)). Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.\nThe 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."}

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":177,"end":184},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T3","span":{"begin":237,"end":249},"obj":"http://purl.obolibrary.org/obo/GO_0009405"},{"id":"T4","span":{"begin":325,"end":332},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T5","span":{"begin":420,"end":425},"obj":"http://purl.obolibrary.org/obo/GO_0038147"},{"id":"T6","span":{"begin":448,"end":460},"obj":"http://purl.obolibrary.org/obo/GO_0009405"}],"text":"Discussion\nSeveral amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV. Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]). HIV infection is a good model of change in viral tropism by mutations in the envelope proteins. These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]). Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition. The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab. 1) and 2(Tab. 2)). The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab. 1)). Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.\nThe 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."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T83","span":{"begin":0,"end":10},"obj":"Sentence"},{"id":"T84","span":{"begin":11,"end":128},"obj":"Sentence"},{"id":"T85","span":{"begin":129,"end":275},"obj":"Sentence"},{"id":"T86","span":{"begin":276,"end":371},"obj":"Sentence"},{"id":"T87","span":{"begin":372,"end":478},"obj":"Sentence"},{"id":"T88","span":{"begin":479,"end":658},"obj":"Sentence"},{"id":"T89","span":{"begin":659,"end":869},"obj":"Sentence"},{"id":"T90","span":{"begin":870,"end":883},"obj":"Sentence"},{"id":"T91","span":{"begin":884,"end":888},"obj":"Sentence"},{"id":"T92","span":{"begin":889,"end":1044},"obj":"Sentence"},{"id":"T93","span":{"begin":1045,"end":1049},"obj":"Sentence"},{"id":"T94","span":{"begin":1050,"end":1163},"obj":"Sentence"},{"id":"T95","span":{"begin":1164,"end":1223},"obj":"Sentence"},{"id":"T96","span":{"begin":1224,"end":1484},"obj":"Sentence"},{"id":"T97","span":{"begin":1485,"end":1656},"obj":"Sentence"},{"id":"T98","span":{"begin":1657,"end":1805},"obj":"Sentence"},{"id":"T99","span":{"begin":1806,"end":1886},"obj":"Sentence"},{"id":"T100","span":{"begin":1887,"end":2150},"obj":"Sentence"},{"id":"T101","span":{"begin":2151,"end":2302},"obj":"Sentence"},{"id":"T102","span":{"begin":2303,"end":2533},"obj":"Sentence"},{"id":"T103","span":{"begin":2534,"end":2691},"obj":"Sentence"},{"id":"T104","span":{"begin":2692,"end":2876},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Discussion\nSeveral amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV. Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]). HIV infection is a good model of change in viral tropism by mutations in the envelope proteins. These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]). Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition. The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab. 1) and 2(Tab. 2)). The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab. 1)). Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.\nThe 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."}

MyTest

{"project":"MyTest","denotations":[{"id":"32210742-32150576-29811238","span":{"begin":270,"end":272},"obj":"32150576"},{"id":"32210742-19339951-29811239","span":{"begin":474,"end":475},"obj":"19339951"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Discussion\nSeveral amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV. Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]). HIV infection is a good model of change in viral tropism by mutations in the envelope proteins. These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]). Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition. The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab. 1) and 2(Tab. 2)). The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab. 1)). Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.\nThe 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."}

2_test

{"project":"2_test","denotations":[{"id":"32210742-32150576-29811238","span":{"begin":270,"end":272},"obj":"32150576"},{"id":"32210742-19339951-29811239","span":{"begin":474,"end":475},"obj":"19339951"}],"text":"Discussion\nSeveral amino acid substitutions in RBD were identified in the SARS-CoV-2 RBD compared to Bat-SARS-CoVs and SARS-CoV. Mutations in the spike protein could change the tropism of a virus, including new hosts or increasing viral pathogenesis (Shang et al., 2020[13]). HIV infection is a good model of change in viral tropism by mutations in the envelope proteins. These mutations switch co-receptor use (CCR5 to CXCR4) increasing the viral pathogenesis (Mosier 2009[7]). Interestingly, our data showed that these changes are not only related to the ability of interaction with the human ACE2 receptor but also for improving this receptor recognition. The presence of two loops around the RBD of SARS-CoV-2 might be promoting the interaction with the ACE2 receptor, improving the binding to this receptor by increasing the number of atoms involved (Tables 1(Tab. 1) and 2(Tab. 2)). The amino acid substitutions and the longer capping loops could explain the increase in binding affinities in SARS-CoV-2 compared to SARS-CoV (Table 1(Tab. 1)). Higher affinity values might be related to the dynamic of infection and the rapid spread observed for this virus.\nThe 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."}

PMC:7081066 / 10025-12901 JSONTXT

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PMC:7081066 / 10025-12901 JSON TXT