tetano
Editor, Senior Moderator
PLoS One
. 2025 Feb 24;20(2):e0319218.
doi: 10.1371/journal.pone.0319218. eCollection 2025. SARS-CoV-2 Omicron subvariant genomic variation associations with immune evasion in Northern California: A retrospective cohort study
Joshua R Nugent[SUP] 1 [/SUP], Mariah S Wood[SUP] 1 [/SUP], Liyan Liu[SUP] 1 [/SUP], Teal Bullick[SUP] 2 [/SUP], Jeffrey M Schapiro[SUP] 3 [/SUP], Phacharee Arunleung[SUP] 2 [/SUP], Gautham Gautham[SUP] 2 [/SUP], Shiffen Getabecha[SUP] 2 [/SUP], Christina Morales[SUP] 2 [/SUP], Laura B Amsden[SUP] 1 [/SUP], Crystal A Hsiao[SUP] 1 [/SUP], Debra A Wadford[SUP] 2 [/SUP], Stacia K Wyman[SUP] 4 [/SUP], Jacek Skarbinski[SUP] 1 3 5 6 [/SUP]
Affiliations
Background: 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.
Methods: 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 ≥1 booster. We identified all non-synonymous single nucleotide polymorphisms (SNPs), insertions and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. We also examined correlations between the presence of SNPs with each other, with subvariants, and over time.
Results: 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.
Conclusions: 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.
. 2025 Feb 24;20(2):e0319218.
doi: 10.1371/journal.pone.0319218. eCollection 2025. SARS-CoV-2 Omicron subvariant genomic variation associations with immune evasion in Northern California: A retrospective cohort study
Joshua R Nugent[SUP] 1 [/SUP], Mariah S Wood[SUP] 1 [/SUP], Liyan Liu[SUP] 1 [/SUP], Teal Bullick[SUP] 2 [/SUP], Jeffrey M Schapiro[SUP] 3 [/SUP], Phacharee Arunleung[SUP] 2 [/SUP], Gautham Gautham[SUP] 2 [/SUP], Shiffen Getabecha[SUP] 2 [/SUP], Christina Morales[SUP] 2 [/SUP], Laura B Amsden[SUP] 1 [/SUP], Crystal A Hsiao[SUP] 1 [/SUP], Debra A Wadford[SUP] 2 [/SUP], Stacia K Wyman[SUP] 4 [/SUP], Jacek Skarbinski[SUP] 1 3 5 6 [/SUP]
Affiliations
- PMID: 39992939
- DOI: 10.1371/journal.pone.0319218
Background: 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.
Methods: 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 ≥1 booster. We identified all non-synonymous single nucleotide polymorphisms (SNPs), insertions and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. We also examined correlations between the presence of SNPs with each other, with subvariants, and over time.
Results: 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.
Conclusions: 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.