Complete genome sequencing of SARS-CoV-2 strains that were circulating in Uzbekistan over the course of four pandemic waves

Since the rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a global COVID-19 pandemic affecting millions of people globally, it has become one of the most urgent research topics worldwide to better understand the pathogenesis of COVID-19 and the impact of the harmful variants. In the present study, we conducted whole genome sequencing (WGS) analysis of 110 SARS-CoV-2 genomes, to give more data about the circulation of SARS-CoV-2 variants during the four waves of pandemic in Uzbekistan. The whole genome sequencing of SARS-CoV-2 samples isolated from PCR-positive patients from Tashkent, Uzbekistan, in the period of 2021 and 2022 were generated using next-generation sequencing approaches and subjected to further genomic analysis. According to our previous studies and the current genome-wide annotations of clinical samples, we have identified four waves of SARS-CoV-2 in Uzbekistan between 2020 and 2022. The dominant variants observed in each wave were Wuhan, Alpha, Delta, and Omicron, respectively. A total of 347 amino acid level variants were identified and of these changes, the most frequent mutations were identified in the ORF1ab region (n = 159), followed by the S gene (n = 115). There were several mutations in all parts of the SAR-CoV-2 genomes but S: D614G, E: T9I, M: A63T, N: G204 R and R203K, NSP12: P323L, and ORF3a(NS3): T223I were the most frequent mutations in these studied viruses. In our previous study, no mutation was found in the envelope (E) protein. In contrast, in our present study, we identified 3 (T9I, T11A and V58F) mutations that made changes to the structure and function of the E protein of SARS-CoV-2. In conclusion, our findings showed that with the emergence of each new variant in our country, the COVID-19 pandemic has also progressed. This may be due to the considerable increase in the number of mutations (Alpha-46, Delta- 146, and Omicron-200 mutations were observed in our samples) in each emerged variant that shows the SARS-CoV-2 evolution.