{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T06:34:40Z","timestamp":1788244480572,"version":"build-2803163510"},"reference-count":19,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T00:00:00Z","timestamp":1740355200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000877","name":"Rockefeller Foundation","doi-asserted-by":"publisher","award":["NA"],"award-info":[{"award-number":["NA"]}],"id":[{"id":"10.13039\/100000877","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U01CA260584"],"award-info":[{"award-number":["U01CA260584"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Permanente Medical Group Delivery Science and Applied Research Program","award":["NA"],"award-info":[{"award-number":["NA"]}]},{"DOI":"10.13039\/100000008","name":"Packard Foundation","doi-asserted-by":"crossref","award":["42937"],"award-info":[{"award-number":["42937"]}],"id":[{"id":"10.13039\/100000008","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Sergey Brin Family Foundation","award":["47769"],"award-info":[{"award-number":["47769"]}]},{"name":"Centers for Disease Control and Prevention, Epidemiology and Laboratory Capacity for Infectious Diseases","award":["NU50CK000539"],"award-info":[{"award-number":["NU50CK000539"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec040\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The possibility of association between SARS-CoV-2 genomic variation and immune evasion is not known among persons with Omicron variant SARS-CoV-2 infection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec041\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In a retrospective cohort, using Poisson regression adjusting for sociodemographic variables and month of infection, we examined associations between individual non-lineage defining mutations and SARS-CoV-2 immunity status, defined as a) no prior recorded infection, b) not vaccinated but with at least one prior recorded infection, c) complete primary series vaccination, and\/or d) primary series vaccination and \u22651 booster. We identified all non-synonymous single nucleotide polymorphisms (SNPs), insertions and deletions in SARS-CoV-2 genomes with \u22655% allelic frequency and population frequency of \u22655% and \u226495%. We also examined correlations between the presence of SNPs with each other, with subvariants, and over time.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec042\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Seventy-nine mutations met inclusion criteria. Among 15,566 persons infected with Omicron SARS-CoV-2, 1,825 (12%) were unvaccinated with no prior recorded infection, 360 (2%) were unvaccinated with a recorded prior infection, 13,381 (86%) had a complete primary series vaccination, and 9,172 (58%) had at least one booster. After examining correlation between SNPs, 79 individual non-lineage defining mutations were organized into 38 groups. After correction for multiple testing, no individual SNPs or SNP groups were significantly associated with immunity status levels.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec043\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Genomic variation identified within SARS-CoV-2 Omicron specimens was not significantly associated with immunity status, suggesting that contribution of non-lineage defining SNPs to immune evasion is minimal. Larger-scale surveillance of SARS-CoV-2 genomes linked with clinical data can help provide information to inform future vaccine development.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0319218","type":"journal-article","created":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T13:41:53Z","timestamp":1740404513000},"page":"e0319218","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["SARS-CoV-2 Omicron subvariant genomic variation associations with immune evasion in Northern California: A retrospective cohort study"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4479-9673","authenticated-orcid":true,"given":"Joshua R.","family":"Nugent","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariah S.","family":"Wood","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liyan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9043-6155","authenticated-orcid":true,"given":"Teal","family":"Bullick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey M.","family":"Schapiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2446-4227","authenticated-orcid":true,"given":"Phacharee","family":"Arunleung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6858-5346","authenticated-orcid":true,"given":"Gautham","family":"Gautham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiffen","family":"Getabecha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Morales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1178-2792","authenticated-orcid":true,"given":"Laura B.","family":"Amsden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0806-2671","authenticated-orcid":true,"given":"Crystal A.","family":"Hsiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8630-427X","authenticated-orcid":true,"given":"Debra A.","family":"Wadford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8937-8397","authenticated-orcid":true,"given":"Stacia K.","family":"Wyman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1630-5733","authenticated-orcid":true,"given":"Jacek","family":"Skarbinski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,2,24]]},"reference":[{"key":"pone.0319218.ref001","doi-asserted-by":"crossref","first-page":"744242","DOI":"10.3389\/fimmu.2021.744242","article-title":"Understanding the secret of SARS-CoV-2 variants of concern\/interest and immune escape","volume":"12","author":"F Lou","year":"2021","journal-title":"Front Immunol"},{"issue":"7","key":"pone.0319218.ref002","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"COVID-19 Genomics UK (COG-UK) Consortium","year":"2021","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"pone.0319218.ref003","doi-asserted-by":"crossref","first-page":"87","DOI":"10.7812\/TPP\/22.172","article-title":"Comparing kaiser permanente members to the general population: implications for generalizability of research","volume":"27","author":"AC Davis","year":"2023","journal-title":"Perm J"},{"issue":"1","key":"pone.0319218.ref004","first-page":"1049","article-title":"The HMO research network virtual data warehouse: a public data model to support collaboration.","volume":"2","author":"TR Ross","year":"2014","journal-title":"EGEMS (Washington, DC)"},{"issue":"1","key":"pone.0319218.ref005","first-page":"4","article-title":"Learning to share health care data: a brief timeline of influential common data models and distributed health data networks in U.S. Health care research","volume":"7","author":"J Weeks","year":"2019","journal-title":"EGEMS (Washington, DC)"},{"key":"pone.0319218.ref006","doi-asserted-by":"crossref","first-page":"1249614","DOI":"10.3389\/fpubh.2023.1249614","article-title":"Implementation of California COVIDNet\u2014a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance","volume":"11","author":"DA Wadford","year":"2023","journal-title":"Front Public Health"},{"issue":"18","key":"pone.0319218.ref007","first-page":"3094","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"H Li","year":"2018","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"pone.0319218.ref008","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"ND Grubaugh","year":"2019","journal-title":"Genome Biol"},{"issue":"2","key":"pone.0319218.ref009","doi-asserted-by":"crossref","first-page":"veab064","DOI":"10.1093\/ve\/veab064","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"A O\u2019Toole","year":"2021","journal-title":"Virus Evol"},{"issue":"1","key":"pone.0319218.ref010","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Series B Stat Methodol"},{"issue":"5","key":"pone.0319218.ref011","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/0021-9681(87)90171-8","article-title":"A new method of classifying prognostic comorbidity in longitudinal studies: development and validation","volume":"40","author":"ME Charlson","year":"1987","journal-title":"J Chronic Dis"},{"issue":"10","key":"pone.0319218.ref012","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1038\/s41576-023-00610-z","article-title":"Fitness, growth and transmissibility of SARS-CoV-2 genetic variants","volume":"24","author":"E Volz","year":"2023","journal-title":"Nat Rev Genet"},{"issue":"4","key":"pone.0319218.ref013","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41588-022-01033-y","article-title":"Global landscape of SARS-CoV-2 genomic surveillance and data sharing","volume":"54","author":"Z Chen","year":"2022","journal-title":"Nat Genet"},{"key":"pone.0319218.ref014","article-title":"Guidance for surveillance of SARS-CoV-2 variants: interim guidance, 9 august 2021","author":"World Health Organization","year":"2021"},{"issue":"6","key":"pone.0319218.ref015","doi-asserted-by":"crossref","first-page":"206","DOI":"10.15585\/mmwr.mm7106a4","article-title":"Genomic surveillance for SARS-CoV-2 variants: predominance of the delta (B.1.617.2) and omicron (B.1.1.529) variants\u2014United States, June 2021\u2013January 2022","volume":"71","author":"Strain Surveillance and Emerging Variants Bioinformatic Working Group","year":"2022","journal-title":"MMWR Morb Mortal Wkly Rep"},{"issue":"9","key":"pone.0319218.ref016","doi-asserted-by":"crossref","first-page":"e481","DOI":"10.1016\/S2666-5247(21)00121-X","article-title":"Genomic surveillance to combat COVID-19: challenges and opportunities","volume":"2","author":"JD Robishaw","year":"2021","journal-title":"Lancet Microbe"},{"key":"pone.0319218.ref017","doi-asserted-by":"crossref","first-page":"e66857","DOI":"10.7554\/eLife.66857","article-title":"Patterns of within-host genetic diversity in SARS-CoV-2","volume":"10","author":"COVID-19 Genomics UK (COG-UK) Consortium","year":"2021","journal-title":"eLife"},{"issue":"1","key":"pone.0319218.ref018","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1080\/21505594.2021.1911477","article-title":"Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis","volume":"12","author":"R Gao","year":"2021","journal-title":"Virulence"},{"issue":"1","key":"pone.0319218.ref019","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1186\/s13059-021-02395-y","article-title":"CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance","volume":"22","author":"COVID-19 Genomics UK (COG-UK) Consortium","year":"2021","journal-title":"Genome Biol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0319218","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,24]],"date-time":"2025-02-24T13:42:09Z","timestamp":1740404529000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0319218"}},"subtitle":[],"editor":[{"given":"Victor C","family":"Huber","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,2,24]]},"references-count":19,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0319218","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.08.21.24312253","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,24]]}}}