SARS-CoV-2 intra-host evolution during acute infection in COVID-19 patients

Introduction: The intra-host evolution represents the mechanism causing the continued emergence of new, highly divergent SARS-CoV-2 variants. The aim of this work was to investigate the intra-host evolution to ass the conditions associated with the acquisition of new viral mutations. Methods: Whole genome sequences of 58 cases of COVID-19 with 2 or more consecutive positive swabs were analyzed. Variant calling and minority mutations analysis were performed using Nextclade and Stanford Coronavirus Antiviral & Resistance Database. Results: Fifty-seven subjects were hospitalized for a median of 23 days, and 12 died (20.7%) after a median of 25 days. 78.9% (45/58) were vaccinated and 22.4% (13/58) received more than one treatment for SARS-CoV-2 infection. None reported previous SARS-CoV-2 infection. Negativization period showed longer intervals in BQ.1 infections (38.5 days) and shorter in BA.1 infections (16.5 days). Comparing the first positive swab to the second swab (T1 and T2), 36.7 and 38.8% decreased/increased number of mutations while 24.5% maintained the same number. Subjects with constant numbers of mutations maintained the same pattern while 57% of the acquisitions and losses were confirmed compared to the previous timepoint. Comparing the second to the third swab (T2 and T3), 66.7 and 33.3% of strains increased or maintained the same number of mutations, respectively. 75% of subjects with constant number of mutations maintained the same pattern. 63% of the acquisitions were confirmed. In T1 vs. T2 the acquisitions were prevalent in the S gene and the losses in ORF1a, in T2 vs. T3 the opposite was observed. Subjects with cardiovascular disease showed a significantly higher acquisition of mutations over time. Discussion: Our data suggested a mechanism with different steps of fitness selection of SARS-CoV-2 mutations and highlighted the presence of highly divergent intra-patient variants within 3 weeks of infection, regardless of treatment, confirming data from other studies showing that new viral variants can also emerge during acute infections.