严重急性呼吸系统综合症冠状病毒2(SARS-CoV-2)是一种积极意义,含有单链RNA基因组的病毒,已经感染了全世界数百万人。病毒变异得足够快,导致新的变体和子变体的出现,据报道这些变体是从中国武汉市传播的,病毒的中心,到中国和世界各地。病毒基因组中突变的发生,特别是在病毒刺突蛋白区域,已经导致了多种变体和亚变体的进化,这给病毒带来了宿主免疫逃避的好处,从而使现代疫苗和疗法无效。因此,持续需要研究SARS-CoV-2变种的遗传特征和进化动态.因此,在这项研究中,来自中国太原和武汉的SARS-CoV-2变体的832个完整基因组进行了遗传表征,并使用系统发育学研究了它们的系统发育和进化动力学,遗传相似性,和系统发育网络分析。这项研究表明,太原和武汉最普遍的四个谱系如下:Omicron谱系EG.5.1.1,其次是HK.3,FY.3和XBB.1.16(穿山甲分类),和进化枝23F(EG.5.1),其次是23H(HK.3),22F(XBB),和23D(XBB.1.9)(Nextclade分类),谱系B,其次是OmicronFY.3,谱系A,和OmicronFL.3(穿山甲分类),和进化枝19A,其次是22F(XBB),23F(EG.5.1),和23H(HK.3)(下分类),分别。此外,我们的遗传相似性分析表明,来自武汉的SARS-CoV-2进化枝19A-B.4(名称以412981开头)与来自太原的OmicronXBB.2.3.2(名称以18495234开头)的查询序列相比,在基因组的尖峰区域具有约95.5%的遗传相似性。其次是太原的OmicronFR.1.4(名称以18495199开头),相似度为97.2%,OmicronDY.3(名称以17485740开头)相似度为97.9%。其余变体与来自太原的OmicronXBB.2.3.2的查询序列(名称以18495234开头)显示≥98%的相似性。此外,我们的重组分析结果表明,SARS-CoV-2变体具有三个统计学意义的重组事件,这可能导致OmicronXBB.1.16的出现(重组事件3),FY.3(重组事件5),和FL.2.4(重组事件7),暗示了一些关于病毒进化的非常重要的信息。此外,我们的系统发育树和网络分析显示,总共有14个簇和超过10,000个突变,这些突变可能导致了簇I的出现,其次是47个突变,导致II簇的出现等等。这两个城市的病毒变体的聚类揭示了有关其中病毒的系统动力学的重要信息。我们的时间系统发育分析结果表明,太原的变异很可能是独立于武汉变异的独立变异。这项研究,据我们所知,是中国太原和武汉城市之间的首次遗传比较研究。这项研究将帮助我们更好地了解病毒,并应对新变种在本地和国际层面的出现和传播,并随时通知公共卫生当局,以便他们在设计新的病毒疫苗和疗法时做出更好的决定。它还将帮助疫情调查人员更好地检查未来的任何疫情。
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA genome-containing virus which has infected millions of people all over the world. The virus has been mutating rapidly enough, resulting in the emergence of new variants and sub-variants which have reportedly been spread from Wuhan city in China, the epicenter of the virus, to the rest of China and all over the world. The occurrence of mutations in the viral genome, especially in the viral spike protein region, has resulted in the evolution of multiple variants and sub-variants which gives the virus the benefit of host immune evasion and thus renders modern-day vaccines and therapeutics ineffective. Therefore, there is a continuous need to study the genetic characteristics and evolutionary dynamics of the SARS-CoV-2 variants. Hence, in this study, a total of 832 complete genomes of SARS-CoV-2 variants from the cities of Taiyuan and Wuhan in China was genetically characterized and their phylogenetic and evolutionary dynamics studied using phylogenetics, genetic similarity, and phylogenetic network analyses. This study shows that the four most prevalent lineages in Taiyuan and Wuhan are as follows: the Omicron lineages EG.5.1.1, followed by HK.3, FY.3, and XBB.1.16 (Pangolin classification), and clades 23F (EG.5.1), followed by 23H (HK.3), 22F (XBB), and 23D (XBB.1.9) (Nextclade classification), and lineage B followed by the Omicron FY.3, lineage A, and Omicron FL.2.3 (Pangolin classification), and the clades 19A, followed by 22F (XBB), 23F (EG.5.1), and 23H (HK.3) (Nextclade classification), respectively. Furthermore, our genetic similarity analysis show that the SARS-CoV-2 clade 19A-B.4 from Wuhan (name starting with 412981) has the least genetic similarity of about 95.5% in the spike region of the genome as compared to the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234), followed by the Omicron FR.1.4 from Taiyuan (name starting with 18495199) with ~97.2% similarity and Omicron DY.3 (name starting with 17485740) with ~97.9% similarity. The rest of the variants showed ≥98% similarity with the query sequence of Omicron XBB.2.3.2 from Taiyuan (name starting with 18495234). In addition, our recombination analysis results show that the SARS-CoV-2 variants have three statistically significant recombinant events which could have possibly resulted in the emergence of Omicron XBB.1.16 (recombination event 3), FY.3 (recombination event 5), and FL.2.4 (recombination event 7), suggesting some very important information regarding viral evolution. Also, our phylogenetic tree and network analyses show that there are a total of 14 clusters and more than 10,000 mutations which may have probably resulted in the emergence of cluster-I, followed by 47 mutations resulting in the emergence of cluster-II and so on. The clustering of the viral variants of both cities reveals significant information regarding the phylodynamics of the virus among them. The results of our temporal phylogenetic analysis suggest that the variants of Taiyuan have likely emerged as independent variants separate from the variants of Wuhan. This study, to the best of our knowledge, is the first ever genetic comparative study between Taiyuan and Wuhan cities in China. This study will help us better understand the virus and cope with the emergence and spread of new variants at a local as well as an international level, and keep the public health authorities informed for them to make better decisions in designing new viral vaccines and therapeutics. It will also help the outbreak investigators to better examine any future outbreak.