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Emergence of S gene-based quasispecies explains an optimal adaptation of Omicron BA.5 subvariant in the immunocompetent vaccinated human host.

In this study, we collected two subsequent swabs from 7 immunocompetent up to date vaccinated healthcare workers undergoing mild symptomatic SARS-CoV-2 infection, and applied a next generation sequencing approach to establish the intra-host dynamics of SARS-CoV-2 quasispecies. Data obtained show that complex dynamics of viral quasispecies occur over a short period of time in patients infected with BA.1 and BA.2. as compared to patients infected with BA.2.3 and BA.5. The low frequency of quasispecies in BA.2.3- and BA.5-infected patients supports the hypothesis that these omicron sub-lineages are adapted to vaccine-elicited immune responses. This article is protected by copyright. All rights reserved.