Whole genome sequencing and analysis of the clinical implications of SARS-CoV-2 strains.

Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that emerged shortly after the coronavirus disease 2019 (COVID-19) pandemic began have altered epidemiological and clinical findings; and these variants changed the course of this health crisis.

Methodology: Whole-genome sequencing was performed on SARS-CoV-2 strains isolated from 21 patients with COVID-19. The frequency of structural changes in the virus and their effects on clinical findings of the disease were analyzed.

Results: The spike Q493R mutation was detected more frequently in patients who had received four or more doses of a COVID-19 vaccine (p = 0.043). The clinical effect of the spike R346K and A263T mutations (reported in Türkiye for the first time) detected in a patient who had received four doses of the vaccine in the 3 months prior to being infected with COVID-19 could be related to escape from the antibody response. The spike R21T mutation may increase the virus's entry into intestinal cells; and, as a result it may be responsible for severe clinical course and gastrointestinal symptoms. The patient infected with the Omicron BA.2 subvariant with the spike L452M mutation exhibited a significant increase in inflammatory parameters; suggesting that this mutation may trigger an excessive immune response and hyperinflammation.

Conclusions: This is the first study based in Türkiye that evaluated the clinical impact of variations in the sequences of SARS-CoV-2 variants. There is a need for further investigation into the clinical impact of these results in a larger population spread over more centers, and more sequencing studies.