We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Genomic Variation Associated With Breakthrough Infection in Northern California: A Retrospective Cohort Study.
- Authors
Skarbinski, Jacek; Nugent, Joshua R; Wood, Mariah S; Liu, Liyan; Bullick, Teal; Schapiro, Jeffrey M; Arunleung, Phacharee; Morales, Christina; Amsden, Laura B; Hsiao, Crystal A; Wadford, Debra A; Chai, Shua J; Reingold, Arthur; Wyman, Stacia K
- Abstract
Background The association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic variation and breakthrough infection is not well defined among persons with Delta variant SARS-CoV-2 infection. Methods In a retrospective cohort, we assessed whether individual nonlineage defining mutations and overall genomic variation (including low-frequency alleles) were associated with breakthrough infection, defined as SARS-CoV-2 infection after coronavirus disease 2019 primary vaccine series. We identified all nonsynonymous single-nucleotide polymorphisms, insertions, and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. Using Poisson regression, we assessed the association with breakthrough infection for each individual mutation and a viral genomic risk score. Results Thirty-six mutations met our inclusion criteria. Among 12 744 persons infected with Delta variant SARS-CoV-2, 5949 (47%) were vaccinated and 6795 (53%) were unvaccinated. Viruses with a viral genomic risk score in the highest quintile were 9% more likely to be associated with breakthrough infection than viruses in the lowest quintile, but including the risk score improved overall predictive model performance (measured by C statistic) by only +0.0006. Conclusions Genomic variation within SARS-CoV-2 Delta variant was weakly associated with breakthrough infection, but several potential nonlineage defining mutations were identified that might contribute to immune evasion by SARS-CoV-2.
- Subjects
CALIFORNIA; SARS-CoV-2; SARS-CoV-2 Delta variant; BREAKTHROUGH infections; CORONAVIRUS diseases; COVID-19; DISEASE risk factors
- Publication
Journal of Infectious Diseases, 2023, Vol 228, Issue 7, p878
- ISSN
0022-1899
- Publication type
Article
- DOI
10.1093/infdis/jiad164