Background
Intra-host evolution reflects a general mechanism for the continued emergence of novel highly divergent SARS-CoV-2 variants. The intra-host evolution of SARS-CoV-2 was investigated with the aim of assessing conditions associated with the acquisition of new viral mutations through the sequencing of viral genomes.
Methods
58 cases of COVID-19 with 2 or more longitudinally positive SARS-CoV-2 swabs collected at intervals of at least 7 days from the first positive swab in the period 2021-2023 were analysed. All samples were subjected to whole genome sequencing with next-generation procedures.
Results
The median age was 83 years (IQR:73-88) and 55% were males.57 were hospitalized for a median of 23 days (IQR:16-32), and 12 died (21%) after a median of 25 days (IQR:19-34). No one reported previous SARS-CoV-2 infection; 79% were vaccinated.23% received more than one treatment for SARS-CoV-2 infection.
Negativization period showed longer intervals in BQ.1 (39 days) and shorter in BA.1 infections (17 days,p=.04). No drug resistance mutations were observed over time.In T1 vs. T2 38% decreased/increased number of mutations and 24% maintained the same number. Subjects with constant numbers of mutations maintained the same pattern while 50% of the acquisitions and losses were confirmed. Acquired mutations at T2 were not present as minority mutations at T1, 50% of the lost mutations did not persist at T2.In T2 vs. T3, 67% and 33% increased or maintained the same number of mutations, respectively. 75% of subjects with constant number of mutations maintained the same pattern, 50% of the acquisitions were confirmed. New mutations at T3 were not present as minority mutations at T2.Globally total number of acquired mutations were higher than lost ones in all comparisons. 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.Significant mutations disappearing was observed in all genes in BA.1 (p<.0001), while in XBB variant a significant mutation emerging was detected in ORF1a, ORF1b and S genes (p=.016). Subjects with cardiovascular disease showed a significant acquisition of mutations over time (p=.048).
Conclusions
Our data suggested a mechanism of 2-step fitness selection of SARS-CoV-2 mutations. The first step indicated that genetic diversity increases during the first week of viral infection. In the second week a purifying selection process was observed. A further increase in new mutations was observed at week 3.