Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram 4331, Bangladesh; Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Chattogram 4202, Bangladesh.
Virus Res. 2021 May;297:198390. doi: 10.1016/j.virusres.2021.198390. Epub 2021 Mar 15.
Coronavirus Disease 2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations, and pathogenesis. Nearly 0.4 million mutations have been identified so far among the ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared a total of 371 SARS-CoV-2 published whole genomes reported from different parts of Bangladesh with 467 sequences reported globally to understand the origin of viruses, possible patterns of mutations, and availability of unique mutations. Phylogenetic analyses indicated that SARS-CoV-2 viruses might have transmitted through infected travelers from European countries, and the GR clade was found as predominant in Bangladesh. Our analyses revealed 4604 mutations at the RNA level including 2862 missense mutations, 1192 synonymous mutations, 25 insertions and deletions and 525 other types of mutation. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (98 %) in Bangladeshi isolates. Interestingly, we found the average number of mutations in ORF1ab, S, ORF3a, M, and N were significantly higher (p < 0.001) for sequences containing the G614 variant compared to those having D614. Previously reported frequent mutations, such as R203K, D614G, G204R, P4715L and I300F at protein levels were also prevalent in Bangladeshi isolates. Additionally, 34 unique amino acid changes were revealed and categorized as originating from different cities. These analyses may increase our understanding of variations in SARS-CoV-2 virus genomes, circulating in Bangladesh and elsewhere.
新型冠状病毒病（COVID-19）需要对可公开获取的严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）基因组进行全面调查，以深入了解其流行病学、突变和发病机制。到目前为止，在约 60000 个 SARS-CoV-2 基因组序列中已经鉴定出近 0.4 百万个突变。在这项研究中，我们比较了来自孟加拉国不同地区的总共 371 个已发表的 SARS-CoV-2 全基因组序列和全球报告的 467 个序列，以了解病毒的起源、可能的突变模式和独特突变的出现。系统进化分析表明，SARS-CoV-2 病毒可能通过来自欧洲国家的受感染旅行者传播，GR 分支在孟加拉国占主导地位。我们的分析显示在 RNA 水平上有 4604 个突变，包括 2862 个错义突变、1192 个同义突变、25 个插入和缺失以及 525 个其他类型的突变。与全球趋势一致，在孟加拉国分离株中，刺突糖蛋白中的 D614G 突变占主导地位（98%）。有趣的是，我们发现与具有 D614 的序列相比，含有 G614 变异的 ORF1ab、S、ORF3a、M 和 N 中的突变数量平均更高（p<0.001）。在蛋白质水平上，以前报道的频繁突变，如 R203K、D614G、G204R、P4715L 和 I300F，在孟加拉国分离株中也很普遍。此外，还揭示了 34 个独特的氨基酸变化，并分类为源自不同城市。这些分析可能会增加我们对在孟加拉国和其他地方流行的 SARS-CoV-2 病毒基因组变异的理解。
