Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China.
Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
Front Cell Infect Microbiol. 2024 Oct 22;14:1484637. doi: 10.3389/fcimb.2024.1484637. eCollection 2024.
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed extraordinary challenges to global health systems and economies. The virus's rapid evolution has resulted in several variants of concern (VOCs), including the highly transmissible Omicron variant, characterized by extensive mutations. In this study, we investigated the genetic diversity, population differentiation, and evolutionary dynamics of the Omicron VOC during the fifth wave of COVID-19 in Pakistan.
A total of 954 Omicron genomes sequenced during the fifth wave of COVID-19 in Pakistan were analyzed. A Bayesian framework was employed for phylogenetic reconstructions, molecular dating, and population dynamics analysis.
Using a population genomics approach, we analyzed Pakistani Omicron samples, revealing low within-population genetic diversity and significant structural variation in the spike (S) protein. Phylogenetic analysis showed that the Omicron variant in Pakistan originated from two distinct lineages, BA.1 and BA.2, which were introduced from South Africa, Thailand, Spain, and Belgium. Omicron-specific mutations, including those in the receptor-binding domain, were identified. The estimated molecular evolutionary rate was 2.562E-3 mutations per site per year (95% HPD interval: 8.8067E-4 to 4.1462E-3). Bayesian skyline plot analysis indicated a significant population expansion at the end of 2021, coinciding with the global Omicron outbreak. Comparative analysis with other VOCs showed Omicron as a highly divergent, monophyletic group, suggesting a unique evolutionary pathway.
This study provides a comprehensive overview of Omicron's genetic diversity, genomic epidemiology, and evolutionary dynamics in Pakistan, emphasizing the need for global collaboration in monitoring variants and enhancing pandemic preparedness.
由严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）引起的 2019 年冠状病毒病（COVID-19）大流行对全球卫生系统和经济造成了巨大挑战。该病毒的快速进化导致了几种关注的变体（VOC），包括高度传染性的奥密克戎变体，其特征是广泛的突变。在这项研究中，我们研究了 COVID-19 第五波在巴基斯坦的奥密克戎 VOC 的遗传多样性、种群分化和进化动态。
分析了在 COVID-19 第五波期间在巴基斯坦测序的 954 个奥密克戎基因组。采用贝叶斯框架进行系统发育重建、分子年代测定和种群动态分析。
使用群体基因组学方法，我们分析了巴基斯坦的奥密克戎样本，发现其 S 蛋白的种群内遗传多样性较低，结构变异显著。系统发育分析表明，巴基斯坦的奥密克戎变体源自两个不同的谱系，BA.1 和 BA.2，它们是从南非、泰国、西班牙和比利时传入的。鉴定了奥密克戎特异性突变，包括受体结合域中的突变。估计的分子进化率为每年每位点 2.562E-3 突变（95%HPD 区间：8.8067E-4 至 4.1462E-3）。贝叶斯天空线图分析表明，2021 年底种群出现显著扩张，与全球奥密克戎爆发时间一致。与其他 VOC 的比较分析表明，奥密克戎是一个高度分化的单系群体，表明其具有独特的进化途径。
本研究提供了奥密克戎在巴基斯坦的遗传多样性、基因组流行病学和进化动态的全面概述，强调了全球合作监测变体和加强大流行防范的必要性。
