Citation: Zaira Rehman, Massab Umair, Aamer Ikram, Ammad Fahim, Muhammad Salman. Footprints of SARS-CoV-2 genome diversity in Pakistan, 2020–2021 .VIROLOGICA SINICA, 2022, 37(1) : 153-155.  http://dx.doi.org/10.1016/j.virs.2022.01.009

Footprints of SARS-CoV-2 genome diversity in Pakistan, 2020–2021

  • The rapid spread of SARS-CoV-2 has significantly impacted the worldwide health system. The SARS-CoV-2 currently bears a remarkably low genetic diversity even though it carries one of the largest RNA genomes among viruses (Rausch et al., 2020). However, the coronaviruses harbor the capability of undergoing recombination at a high rate which can lead to the emergence of novel viral derivatives (Rausch et al., 2020; Gribble et al., 2021). This in turn requires not only global surveillance of SARS-CoV-2 genome in various countries but also careful scrutiny in animal genomic reservoirs. Conventionally, RNA viruses evolve with a high mutation rate, however, the presence of ExoN ribonuclease in SARS-CoV-2 genome has made its case different from other viral species (Gribble et al., 2021). The variables of natural selection which potentially drift the SARS-CoV-2 evolutionary dynamics can be recorded by analyzing deposited sequence genomes for its fitness, transmissibility potential, and pathogenicity (Rouchka et al., 2020). This can potentially provide a way to draw a holistic picture at a national level, while simultaneously providing a comparative overview with worldwide sequences.

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    1. Ali, A. 2020. Second Wave Of Covid-19 In Pakistan; Are More Episodes Down The Road? https://www.bmj.com/content/371/bmj.m4113/rr-0. Accessed 21st April 2021.

    2. Daily Sabah. 2021. Around 1,000 Indian Sikh Pilgrims Arrive In Pakistan, https://www.dailysabah.com/world/asia-pacific/around-1000-indian-sikh-pilgrims-arrive-in-pakistan. Accessed 21st April 2021.

    3. Government of Pakistan. 2021. Covid-19 Dashboard, Government of Pakistan. https://covid.gov.pk/stats/pakistan. Accessed 17 April 2021.

    4. Gribble, J., Stevens, L. J., Agostini, M. L., Anderson-Daniels, J., Chappell, J. D., Lu, X., Pruijssers, A. J., Routh, A. L., Denison, M. R., 2021. The coronavirus proofreading exoribonuclease mediates extensive viral recombination. Plos Pathog, 17, E1009226.

    5. Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., Neher, R. A., 2018. Nextstrain: Real-time tracking of pathogen evolution. bioinformatics, 34, 4121-4123.

    6. Rambaut, A., Holmes, E. C., O'toole, A., Hill, V., Mccrone, J. T., Ruis, C., Du Plessis, L., Pybus, O. G., 2020. A dynamic nomenclature proposal for sars-cov-2 lineages to assist genomic epidemiology. Nat Microbiol, 5, 1403-1407.

    7. Rausch, J. W., Capoferri, A. A., Katusiime, M. G., Patro, S. C., Kearney, M. F., 2020. Low Genetic Diversity May Be An Achilles Heel Of Sars-Cov-2. Proc Natl Acad Sci U S A, 117, 24614-24616.

    8. Rouchka, E. C., Chariker, J. H., Chung, D. 2020. Variant analysis of 1,040 SARS-Cov-2 genomes. Plos One, 15, E0241535.

    9. Science Media Center. 2021. Expert Reaction To Cases Of Variant B.1.617 (The ‘Indian Variant’) Being Investigated In The Uk, https://www.Sciencemediacentre.Org/Expert-Reaction-To-Cases-Of-Variant-B-1-617-The-Indian-Variant-Being-Investigated-In-The-Uk/?Cli_Action=1618957124.823 Accessed 21st April 2021

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    Footprints of SARS-CoV-2 genome diversity in Pakistan, 2020–2021

      Corresponding author: Zaira Rehman, rehman.zaira@yahoo.com
      Corresponding author: Massab Umair, m.umair@nih.org.pk
    • a National Institute of Health (NIH), Islamabad, 44000, Pakistan
    • b Maroof International Hospital, Islamabad, 44000, Pakistan

    Abstract: The rapid spread of SARS-CoV-2 has significantly impacted the worldwide health system. The SARS-CoV-2 currently bears a remarkably low genetic diversity even though it carries one of the largest RNA genomes among viruses (Rausch et al., 2020). However, the coronaviruses harbor the capability of undergoing recombination at a high rate which can lead to the emergence of novel viral derivatives (Rausch et al., 2020; Gribble et al., 2021). This in turn requires not only global surveillance of SARS-CoV-2 genome in various countries but also careful scrutiny in animal genomic reservoirs. Conventionally, RNA viruses evolve with a high mutation rate, however, the presence of ExoN ribonuclease in SARS-CoV-2 genome has made its case different from other viral species (Gribble et al., 2021). The variables of natural selection which potentially drift the SARS-CoV-2 evolutionary dynamics can be recorded by analyzing deposited sequence genomes for its fitness, transmissibility potential, and pathogenicity (Rouchka et al., 2020). This can potentially provide a way to draw a holistic picture at a national level, while simultaneously providing a comparative overview with worldwide sequences.

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