PMC:7307149 / 759-2240 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T9","span":{"begin":37,"end":69},"obj":"Body_part"},{"id":"T10","span":{"begin":71,"end":74},"obj":"Body_part"},{"id":"T11","span":{"begin":97,"end":106},"obj":"Body_part"},{"id":"T12","span":{"begin":118,"end":121},"obj":"Body_part"},{"id":"T13","span":{"begin":401,"end":404},"obj":"Body_part"},{"id":"T14","span":{"begin":441,"end":444},"obj":"Body_part"},{"id":"T15","span":{"begin":713,"end":716},"obj":"Body_part"},{"id":"T16","span":{"begin":749,"end":752},"obj":"Body_part"},{"id":"T17","span":{"begin":1131,"end":1134},"obj":"Body_part"},{"id":"T18","span":{"begin":1321,"end":1325},"obj":"Body_part"},{"id":"T19","span":{"begin":1387,"end":1390},"obj":"Body_part"}],"attributes":[{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma62852"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma84079"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma84795"}],"text":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T8","span":{"begin":211,"end":258},"obj":"Disease"},{"id":"T9","span":{"begin":211,"end":244},"obj":"Disease"},{"id":"T10","span":{"begin":260,"end":268},"obj":"Disease"},{"id":"T11","span":{"begin":299,"end":323},"obj":"Disease"},{"id":"T12","span":{"begin":325,"end":333},"obj":"Disease"},{"id":"T13","span":{"begin":477,"end":485},"obj":"Disease"},{"id":"T14","span":{"begin":630,"end":638},"obj":"Disease"},{"id":"T15","span":{"begin":807,"end":815},"obj":"Disease"},{"id":"T16","span":{"begin":898,"end":906},"obj":"Disease"},{"id":"T17","span":{"begin":948,"end":952},"obj":"Disease"},{"id":"T18","span":{"begin":1200,"end":1208},"obj":"Disease"}],"attributes":[{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A14","pred":"mondo_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T8","span":{"begin":84,"end":89},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T9","span":{"begin":91,"end":96},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T10","span":{"begin":115,"end":116},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T11","span":{"begin":122,"end":123},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T12","span":{"begin":127,"end":128},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T13","span":{"begin":137,"end":142},"obj":"http://purl.obolibrary.org/obo/OGG_0000000002"},{"id":"T14","span":{"begin":277,"end":282},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T15","span":{"begin":349,"end":350},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T16","span":{"begin":393,"end":400},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T17","span":{"begin":445,"end":446},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T18","span":{"begin":449,"end":450},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T19","span":{"begin":488,"end":496},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T20","span":{"begin":605,"end":610},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T21","span":{"begin":698,"end":699},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T22","span":{"begin":753,"end":754},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T23","span":{"begin":794,"end":802},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T24","span":{"begin":962,"end":966},"obj":"http://purl.obolibrary.org/obo/CLO_0004265"},{"id":"T25","span":{"begin":978,"end":979},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T26","span":{"begin":1135,"end":1136},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T27","span":{"begin":1211,"end":1219},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T28","span":{"begin":1249,"end":1254},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T29","span":{"begin":1319,"end":1325},"obj":"http://purl.obolibrary.org/obo/CL_0000084"}],"text":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":107,"end":114},"obj":"Chemical"},{"id":"T2","span":{"begin":393,"end":400},"obj":"Chemical"},{"id":"T3","span":{"begin":488,"end":496},"obj":"Chemical"},{"id":"T4","span":{"begin":794,"end":802},"obj":"Chemical"},{"id":"T5","span":{"begin":957,"end":960},"obj":"Chemical"},{"id":"T6","span":{"begin":1009,"end":1012},"obj":"Chemical"},{"id":"T7","span":{"begin":1211,"end":1219},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_59132"},{"id":"A2","pred":"chebi_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_32386"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_3392"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"}],"text":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}

{"project":"LitCovid-PubTator","denotations":[{"id":"33","span":{"begin":118,"end":136},"obj":"Gene"},{"id":"34","span":{"begin":749,"end":754},"obj":"Gene"},{"id":"35","span":{"begin":1131,"end":1136},"obj":"Gene"},{"id":"36","span":{"begin":954,"end":955},"obj":"Gene"},{"id":"37","span":{"begin":211,"end":258},"obj":"Species"},{"id":"38","span":{"begin":260,"end":270},"obj":"Species"},{"id":"39","span":{"begin":477,"end":487},"obj":"Species"},{"id":"40","span":{"begin":605,"end":610},"obj":"Species"},{"id":"41","span":{"begin":611,"end":624},"obj":"Species"},{"id":"42","span":{"begin":630,"end":640},"obj":"Species"},{"id":"43","span":{"begin":807,"end":817},"obj":"Species"},{"id":"44","span":{"begin":1200,"end":1210},"obj":"Species"},{"id":"45","span":{"begin":1249,"end":1254},"obj":"Species"},{"id":"46","span":{"begin":1255,"end":1268},"obj":"Species"},{"id":"47","span":{"begin":91,"end":96},"obj":"Species"},{"id":"48","span":{"begin":441,"end":458},"obj":"Gene"},{"id":"49","span":{"begin":299,"end":323},"obj":"Disease"},{"id":"50","span":{"begin":325,"end":333},"obj":"Disease"},{"id":"51","span":{"begin":898,"end":906},"obj":"Disease"}],"attributes":[{"id":"A33","pred":"tao:has_database_id","subj":"33","obj":"Gene:3105"},{"id":"A34","pred":"tao:has_database_id","subj":"34","obj":"Gene:3106"},{"id":"A35","pred":"tao:has_database_id","subj":"35","obj":"Gene:3106"},{"id":"A36","pred":"tao:has_database_id","subj":"36","obj":"Gene:43740571"},{"id":"A37","pred":"tao:has_database_id","subj":"37","obj":"Tax:2697049"},{"id":"A38","pred":"tao:has_database_id","subj":"38","obj":"Tax:2697049"},{"id":"A39","pred":"tao:has_database_id","subj":"39","obj":"Tax:2697049"},{"id":"A40","pred":"tao:has_database_id","subj":"40","obj":"Tax:9606"},{"id":"A41","pred":"tao:has_database_id","subj":"41","obj":"Tax:11118"},{"id":"A42","pred":"tao:has_database_id","subj":"42","obj":"Tax:2697049"},{"id":"A43","pred":"tao:has_database_id","subj":"43","obj":"Tax:2697049"},{"id":"A44","pred":"tao:has_database_id","subj":"44","obj":"Tax:2697049"},{"id":"A45","pred":"tao:has_database_id","subj":"45","obj":"Tax:9606"},{"id":"A46","pred":"tao:has_database_id","subj":"46","obj":"Tax:11118"},{"id":"A47","pred":"tao:has_database_id","subj":"47","obj":"Tax:9606"},{"id":"A48","pred":"tao:has_database_id","subj":"48","obj":"Gene:3106"},{"id":"A49","pred":"tao:has_database_id","subj":"49","obj":"MESH:C000657245"},{"id":"A50","pred":"tao:has_database_id","subj":"50","obj":"MESH:C000657245"},{"id":"A51","pred":"tao:has_database_id","subj":"51","obj":"MESH:C000657245"}],"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":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T2","span":{"begin":37,"end":69},"obj":"http://purl.obolibrary.org/obo/GO_0046776"},{"id":"T3","span":{"begin":71,"end":74},"obj":"http://purl.obolibrary.org/obo/GO_0046776"},{"id":"T4","span":{"begin":401,"end":404},"obj":"http://purl.obolibrary.org/obo/GO_0046776"}],"text":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}

{"project":"LitCovid-sentences","denotations":[{"id":"T11","span":{"begin":0,"end":335},"obj":"Sentence"},{"id":"T12","span":{"begin":336,"end":497},"obj":"Sentence"},{"id":"T13","span":{"begin":498,"end":625},"obj":"Sentence"},{"id":"T14","span":{"begin":626,"end":725},"obj":"Sentence"},{"id":"T15","span":{"begin":726,"end":956},"obj":"Sentence"},{"id":"T16","span":{"begin":957,"end":967},"obj":"Sentence"},{"id":"T17","span":{"begin":968,"end":977},"obj":"Sentence"},{"id":"T18","span":{"begin":978,"end":980},"obj":"Sentence"},{"id":"T19","span":{"begin":981,"end":995},"obj":"Sentence"},{"id":"T20","span":{"begin":996,"end":1104},"obj":"Sentence"},{"id":"T21","span":{"begin":1105,"end":1341},"obj":"Sentence"},{"id":"T22","span":{"begin":1342,"end":1481},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen A [HLA-A], -B, and -C genes) may affect susceptibility to and severity of the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19). We performed a comprehensive in silico analysis of viral peptide-MHC class I binding affinity across 145 HLA-A, -B, and -C genotypes for all SARS-CoV-2 peptides. We further explored the potential for cross-protective immunity conferred by prior exposure to four common human coronaviruses. The SARS-CoV-2 proteome was successfully sampled and was represented by a diversity of HLA alleles. However, we found that HLA-B*46:01 had the fewest predicted binding peptides for SARS-CoV-2, suggesting that individuals with this allele may be particularly vulnerable to COVID-19, as they were previously shown to be for SARS (M. Lin, H.-T. Tseng, J. A. Trejaut, H.-L. Lee, et al., BMC Med Genet 4:9, 2003, https://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2350-4-9). Conversely, we found that HLA-B*15:03 showed the greatest capacity to present highly conserved SARS-CoV-2 peptides that are shared among common human coronaviruses, suggesting that it could enable cross-protective T-cell-based immunity. Finally, we reported global distributions of HLA types with potential epidemiological ramifications in the setting of the current pandemic."}