PMC:7253482 / 36122-37851 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"1026","span":{"begin":1337,"end":1350},"obj":"Chemical"},{"id":"1027","span":{"begin":1400,"end":1416},"obj":"Chemical"},{"id":"1033","span":{"begin":1611,"end":1616},"obj":"Gene"},{"id":"1034","span":{"begin":1670,"end":1671},"obj":"Gene"},{"id":"1035","span":{"begin":1645,"end":1646},"obj":"Gene"},{"id":"1036","span":{"begin":1599,"end":1610},"obj":"Species"},{"id":"1037","span":{"begin":1709,"end":1718},"obj":"Species"}],"attributes":[{"id":"A1026","pred":"tao:has_database_id","subj":"1026","obj":"MESH:D006020"},{"id":"A1033","pred":"tao:has_database_id","subj":"1033","obj":"Gene:43740568"},{"id":"A1034","pred":"tao:has_database_id","subj":"1034","obj":"Gene:43740568"},{"id":"A1035","pred":"tao:has_database_id","subj":"1035","obj":"Gene:43740568"},{"id":"A1036","pred":"tao:has_database_id","subj":"1036","obj":"Tax:11118"},{"id":"A1037","pred":"tao:has_database_id","subj":"1037","obj":"Tax:2697049"}],"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":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T179","span":{"begin":960,"end":963},"obj":"Body_part"},{"id":"T180","span":{"begin":1337,"end":1350},"obj":"Body_part"},{"id":"T181","span":{"begin":1617,"end":1625},"obj":"Body_part"}],"attributes":[{"id":"A179","pred":"fma_id","subj":"T179","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A180","pred":"fma_id","subj":"T180","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A181","pred":"fma_id","subj":"T181","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T105","span":{"begin":762,"end":766},"obj":"Disease"},{"id":"T106","span":{"begin":851,"end":855},"obj":"Disease"}],"attributes":[{"id":"A105","pred":"mondo_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/MONDO_0012268"},{"id":"A106","pred":"mondo_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/MONDO_0012268"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

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{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T381","span":{"begin":542,"end":544},"obj":"Chemical"},{"id":"T382","span":{"begin":1337,"end":1350},"obj":"Chemical"},{"id":"T383","span":{"begin":1409,"end":1416},"obj":"Chemical"},{"id":"T384","span":{"begin":1560,"end":1571},"obj":"Chemical"},{"id":"T385","span":{"begin":1680,"end":1691},"obj":"Chemical"}],"attributes":[{"id":"A381","pred":"chebi_id","subj":"T381","obj":"http://purl.obolibrary.org/obo/CHEBI_74698"},{"id":"A382","pred":"chebi_id","subj":"T382","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A383","pred":"chebi_id","subj":"T383","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A384","pred":"chebi_id","subj":"T384","obj":"http://purl.obolibrary.org/obo/CHEBI_33232"},{"id":"A385","pred":"chebi_id","subj":"T385","obj":"http://purl.obolibrary.org/obo/CHEBI_33232"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

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review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). 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{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T179","span":{"begin":1617,"end":1625},"obj":"Body_part"},{"id":"T177","span":{"begin":960,"end":963},"obj":"Body_part"},{"id":"T178","span":{"begin":1337,"end":1350},"obj":"Body_part"}],"attributes":[{"id":"A177","pred":"fma_id","subj":"T177","obj":"http://purl.org/sig/ont/fma/fma278683"},{"id":"A178","pred":"fma_id","subj":"T178","obj":"http://purl.org/sig/ont/fma/fma82784"},{"id":"A179","pred":"fma_id","subj":"T179","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T261","span":{"begin":1337,"end":1350},"obj":"Chemical"},{"id":"T262","span":{"begin":1409,"end":1416},"obj":"Chemical"}],"attributes":[{"id":"A261","pred":"chebi_id","subj":"T261","obj":"http://purl.obolibrary.org/obo/CHEBI_24396"},{"id":"A262","pred":"chebi_id","subj":"T262","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T218","span":{"begin":451,"end":456},"obj":"Species"},{"id":"T219","span":{"begin":960,"end":963},"obj":"Species"},{"id":"T224","span":{"begin":1709,"end":1718},"obj":"Species"}],"attributes":[{"id":"A218","pred":"ncbi_taxonomy_id","subj":"T218","obj":"NCBItxid:9606"},{"id":"A219","pred":"ncbi_taxonomy_id","subj":"T219","obj":"NCBItxid:57667"},{"id":"A220","pred":"ncbi_taxonomy_id","subj":"T219","obj":"NCBItxid:35274"},{"id":"A221","pred":"ncbi_taxonomy_id","subj":"T219","obj":"NCBItxid:12721"},{"id":"A222","pred":"ncbi_taxonomy_id","subj":"T219","obj":"NCBItxid:11709"},{"id":"A223","pred":"ncbi_taxonomy_id","subj":"T219","obj":"NCBItxid:11676"},{"id":"A224","pred":"ncbi_taxonomy_id","subj":"T224","obj":"NCBItxid:2697049"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T223","span":{"begin":0,"end":63},"obj":"Sentence"},{"id":"T224","span":{"begin":64,"end":160},"obj":"Sentence"},{"id":"T225","span":{"begin":161,"end":296},"obj":"Sentence"},{"id":"T226","span":{"begin":298,"end":323},"obj":"Sentence"},{"id":"T227","span":{"begin":324,"end":408},"obj":"Sentence"},{"id":"T228","span":{"begin":410,"end":426},"obj":"Sentence"},{"id":"T229","span":{"begin":427,"end":502},"obj":"Sentence"},{"id":"T230","span":{"begin":503,"end":590},"obj":"Sentence"},{"id":"T231","span":{"begin":591,"end":1034},"obj":"Sentence"},{"id":"T232","span":{"begin":1036,"end":1053},"obj":"Sentence"},{"id":"T233","span":{"begin":1054,"end":1436},"obj":"Sentence"},{"id":"T234","span":{"begin":1438,"end":1455},"obj":"Sentence"},{"id":"T235","span":{"begin":1456,"end":1491},"obj":"Sentence"},{"id":"T236","span":{"begin":1493,"end":1512},"obj":"Sentence"},{"id":"T237","span":{"begin":1513,"end":1575},"obj":"Sentence"},{"id":"T238","span":{"begin":1576,"end":1642},"obj":"Sentence"},{"id":"T239","span":{"begin":1643,"end":1695},"obj":"Sentence"},{"id":"T240","span":{"begin":1696,"end":1729},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T100","span":{"begin":762,"end":766},"obj":"Disease"},{"id":"T101","span":{"begin":851,"end":855},"obj":"Disease"}],"attributes":[{"id":"A100","pred":"mondo_id","subj":"T100","obj":"http://purl.obolibrary.org/obo/MONDO_0012268"},{"id":"A101","pred":"mondo_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/MONDO_0012268"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-Pubtator","denotations":[{"id":"1026","span":{"begin":1337,"end":1350},"obj":"Chemical"},{"id":"1027","span":{"begin":1400,"end":1416},"obj":"Chemical"},{"id":"1036","span":{"begin":1599,"end":1610},"obj":"Species"},{"id":"1033","span":{"begin":1611,"end":1616},"obj":"Gene"},{"id":"1035","span":{"begin":1645,"end":1646},"obj":"Gene"},{"id":"1034","span":{"begin":1670,"end":1671},"obj":"Gene"},{"id":"1037","span":{"begin":1709,"end":1718},"obj":"Species"}],"attributes":[{"id":"A1036","pred":"pubann:denotes","subj":"1036","obj":"Tax:11118"},{"id":"A1033","pred":"pubann:denotes","subj":"1033","obj":"Gene:43740568"},{"id":"A1034","pred":"pubann:denotes","subj":"1034","obj":"Gene:43740568"},{"id":"A1035","pred":"pubann:denotes","subj":"1035","obj":"Gene:43740568"},{"id":"A1037","pred":"pubann:denotes","subj":"1037","obj":"Tax:2697049"},{"id":"A1026","pred":"pubann:denotes","subj":"1026","obj":"MESH:D006020"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T6529","span":{"begin":1611,"end":1625},"obj":"Protein"}],"attributes":[{"id":"A6529","pred":"uniprot_id","subj":"T6529","obj":"https://www.uniprot.org/uniprot/P31340"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T223","span":{"begin":0,"end":63},"obj":"Sentence"},{"id":"T224","span":{"begin":64,"end":160},"obj":"Sentence"},{"id":"T225","span":{"begin":161,"end":296},"obj":"Sentence"},{"id":"T226","span":{"begin":298,"end":323},"obj":"Sentence"},{"id":"T227","span":{"begin":324,"end":408},"obj":"Sentence"},{"id":"T228","span":{"begin":410,"end":426},"obj":"Sentence"},{"id":"T229","span":{"begin":427,"end":502},"obj":"Sentence"},{"id":"T230","span":{"begin":503,"end":590},"obj":"Sentence"},{"id":"T231","span":{"begin":591,"end":1034},"obj":"Sentence"},{"id":"T232","span":{"begin":1036,"end":1053},"obj":"Sentence"},{"id":"T233","span":{"begin":1054,"end":1436},"obj":"Sentence"},{"id":"T234","span":{"begin":1438,"end":1455},"obj":"Sentence"},{"id":"T235","span":{"begin":1456,"end":1491},"obj":"Sentence"},{"id":"T236","span":{"begin":1493,"end":1512},"obj":"Sentence"},{"id":"T237","span":{"begin":1513,"end":1575},"obj":"Sentence"},{"id":"T238","span":{"begin":1576,"end":1642},"obj":"Sentence"},{"id":"T239","span":{"begin":1643,"end":1695},"obj":"Sentence"},{"id":"T240","span":{"begin":1696,"end":1729},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}

{"project":"LitCovid-sample-Glycan","denotations":[{"id":"T51","span":{"begin":1456,"end":1459},"obj":"https://glytoucan.org/Structures/Glycans/G05518TD"}],"text":"Peer review information Nature Communications thanks Matthew B. Renfrow and other, anonymous, reviewers for their contributions to the peer review of this work.\nPublisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\n\nSupplementary information\nSupplementary information is available for this paper at 10.1038/s41467-020-16567-0.\n\nAcknowledgements\nThe Wellcome Centre for Human Genetics is supported by grant 203141/Z/16/Z. We thank the Medical Research Council (MR/S007555/1 to T.A.B.), NIH (R56 AI127371 to I. A.W., R01 AI127521 to J.S.M. and A.B.W.), Bill and Melinda Gates Foundation (grants OPP1115782 to A.B.W. and M.C., and OPP1170236 to I.A.W. and A.B.W.), the International AIDS Vaccine Initiative, Bill and Melinda Gates Foundation through the Collaboration for AIDS Discovery (grants OPP1084519 and OPP1196345 to I.A.W., A.B.W. and M.C.), and the Scripps Consortium for HIV Vaccine Development (CHAVD) (UM1 AI144462 to M.C., A.B.W. and I.A.W.).\n\nData availability\nIn addition to the data reported in this paper and accompanying supplementary materials, the raw mass spectrometric data that support the findings of this study presented have been deposited on the MassIVE server (https://massive.ucsd.edu) with the accession codes (MSV000084993 for glycopeptides analysis [10.25345/C58T21]; and MSV000085152 for N-linked glycans [10.25345/C54705]).\n\nCode availability\nAll code is available upon request.\n\nCompeting interests\nJ.S.M. and A.B.W. are inventors on U.S. patent application no. 62/412,703 (“Prefusion Coronavirus Spike Proteins and Their Use”). J.S.M. is an inventor on U.S. patent application no. 62/972,886 (“2019-nCoV Vaccine”)."}