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ORIGINAL RESEARCH article

Front. Cell. Infect. Microbiol.
Sec. Molecular Viral Pathogenesis
Volume 14 - 2024 | doi: 10.3389/fcimb.2024.1484637

Genomic Epidemiology and Evolutionary Dynamics of the Omicron Variant of SARS-CoV-2 during the fifth wave of COVID-19 in Pakistan

Provisionally accepted
Aroona Razzaq Aroona Razzaq 1Cyrollah Disoma Cyrollah Disoma 1Sonia Iqbal Sonia Iqbal 2Ayesha Nisar Ayesha Nisar 3Muddassar Hameed Muddassar Hameed 4Abdul Qadeer Abdul Qadeer 1Muhammad Waqar Muhammad Waqar 2Sardar A. Mehmood Sardar A. Mehmood 5Lidong Gao Lidong Gao 6Sawar Khan Sawar Khan 1*Zanxian Xia Zanxian Xia 1*
  • 1 School of Life Science, Central South University, Changsha, China
  • 2 Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Punjab, Pakistan
  • 3 Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, China
  • 4 Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
  • 5 Department of Zoology, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan
  • 6 Hunan Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Hunan Provincial Center for Disease Control and Prevention, Changsha, China, Changsha, Anhui Province, China

The final, formatted version of the article will be published soon.

    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 withinpopulation 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.

    Keywords: COVID-19, omicron, Genomic epidemiology, SARS-CoV-2, VOCs

    Received: 22 Aug 2024; Accepted: 04 Oct 2024.

    Copyright: © 2024 Razzaq, Disoma, Iqbal, Nisar, Hameed, Qadeer, Waqar, Mehmood, Gao, Khan and Xia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Sawar Khan, School of Life Science, Central South University, Changsha, China
    Zanxian Xia, School of Life Science, Central South University, Changsha, China

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