Laboratory of Biotechnology, Center for Advanced Technologies under the Ministry of Higher Education, Science and Innovations, Tashkent, Uzbekistan.
Laboratory of Genomics, Institute of Biophysics and Biochemistry under National University of Uzbekistan, Tashkent, Uzbekistan.
PLoS One. 2024 Nov 19;19(11):e0298940. doi: 10.1371/journal.pone.0298940. eCollection 2024.
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.
自严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 作为一种影响全球数百万人的全球 COVID-19 大流行迅速出现以来，更好地了解 COVID-19 的发病机制和有害变异的影响已成为全球最紧迫的研究课题之一。在本研究中，我们对 110 个 SARS-CoV-2 基因组进行了全基因组测序 (WGS) 分析，以提供更多关于 SARS-CoV-2 变异在乌兹别克斯坦四次大流行期间传播的数据。从 2021 年和 2022 年期间从乌兹别克斯坦塔什干 PCR 阳性患者中分离的 SARS-CoV-2 样本的全基因组测序是使用下一代测序方法生成的，并进行了进一步的基因组分析。根据我们之前的研究和当前对临床样本的全基因组注释，我们在 2020 年至 2022 年间确定了乌兹别克斯坦的四次 SARS-CoV-2 波。在每一波中观察到的主要变异分别是武汉、阿尔法、德尔塔和奥密克戎。总共鉴定了 347 个氨基酸水平的变异，其中最常见的变化发生在 ORF1ab 区 (n = 159)，其次是 S 基因 (n = 115)。SARS-CoV-2 基因组的所有部分都有几个突变，但 S：D614G、E：T9I、M：A63T、N：G204R 和 R203K、NSP12：P323L 和 ORF3a(NS3)：T223I 是这些研究病毒中最常见的突变。在我们之前的研究中，包膜 (E) 蛋白中没有发现突变。相比之下，在我们目前的研究中，我们鉴定了 3 个 (T9I、T11A 和 V58F) 突变，这些突变改变了 SARS-CoV-2 的 E 蛋白的结构和功能。总之，我们的研究结果表明，随着我国新变异的出现，COVID-19 大流行也在不断发展。这可能是由于每个新出现的变异中发生的突变数量相当大（在我们的样本中观察到阿尔法-46、德尔塔-146 和奥密克戎-200 个突变），表明 SARS-CoV-2 的进化。
