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- Title
Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals.
- Authors
Gu, Haogao; Quadeer, Ahmed Abdul; Krishnan, Pavithra; Ng, Daisy Y. M.; Chang, Lydia D. J.; Liu, Gigi Y. Z.; Cheng, Samuel M. S.; Lam, Tommy T. Y.; Peiris, Malik; McKay, Matthew R.; Poon, Leo L. M.
- Abstract
Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants. There is limited data on within-host SARS-CoV-2 genetic diversity and how it is affected by vaccination. The authors analysed intra-host sequence diversity and found that VOCs may have more sequence variations than non-VOCs and that breakthrough infections in vaccinated individuals do not seem to increase non-silent mutations.
- Subjects
GENETIC variation; SARS-CoV-2; VACCINATION status; VACCINATION; IMMUNOGLOBULINS; BREAKTHROUGH infections
- Publication
Nature Communications, 2023, Vol 14, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-023-37468-y