SARS-CoV-2 Delta variant genomic variation associated with breakthrough infection in Northern California: A retrospective cohort study.
J Infect Dis
; 2023 May 17.
Article
in English
| MEDLINE | ID: covidwho-2326360
ABSTRACT
BACKGROUND:
The association between 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 non-lineage defining mutations and overall genomic variation (including low frequency alleles) were associated with breakthrough infection defined as SARS-CoV-2 infection after COVID-19 primary vaccine series. We identified all non-synonymous 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, 5,949 (47%) were vaccinated and 6,795 (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, however several potential non-lineage defining mutations were identified that might contribute to immune evasion by SARS-CoV-2.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Type of study:
Cohort study
/
Observational study
/
Prognostic study
Topics:
Vaccines
/
Variants
Language:
English
Year:
2023
Document Type:
Article
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