SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021

  1. Muhammad Bilal Sarwar
  2. Muhammad Yasir
  3. Nabil-Fareed Alikhan
  4. Nadeem Afzal
  5. Leonardo de Oliveira Martins
  6. Thanh Le Viet
  7. Alexander J. Trotter
  8. Sophie J. Prosolek
  9. Gemma L. Kay
  10. Ebenezer Foster-Nyarko
  11. Steven Rudder
  12. David J. Baker
  13. Sidra Tul Muntaha
  14. Muhammad Roman
  15. Mark A. Webber
  16. Almina Shafiq
  17. Bilquis Shabbir
  18. Javed Akram
  19. Andrew J. Page
  20. Shah Jahan

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Abstract

The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the world’s largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 that began in March 2021. In Pakistan, during the third wave until now only 12 SARS-CoV-2 genomes have been collected and among these nine are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact, more genomes are available among travellers with a travel history from Pakistan, than from within the country itself. We thus aimed to provide a snapshot assessment of circulating lineages in Lahore and surrounding areas with a combined population of 11.1 million. Within a week of April 2021, 102 samples were sequenced. The samples were randomly collected from two hospitals with a diagnostic PCR cutoff value of less than 25 cycles. Analysis of the lineages shows that the Alpha variant of concern (first identified in the UK) dominates, accounting for 97.9 % (97/99) of cases, with the Beta variant of concern (first identified in South Africa) accounting for 2.0 % (2/99) of cases. No other lineages were observed. In depth analysis of the Alpha lineages indicated multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (seven UK, one Switzerland), indicating recent transmission. Genomes of other samples show evidence that these have evolved, indicating sustained transmission over a period of time either within Pakistan or other countries with low-density genome sequencing. Vaccines remain effective against Alpha, however, the low level of Beta against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.

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  1. Version published to 10.1099/mgen.0.000693 on Access Microbiology
  2. Version published to 10.1101/2021.06.04.21258352v2 on medRxiv
  3. ScreenIT

    SciScore for 10.1101/2021.06.04.21258352: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    RandomizationPositive samples with a CT < 25 were randomly selected for genome sequencing.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: Clusters distant and unrelated to Pakistan sequences were reduced or removed by visual inspection of maximum likelihood trees.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The raw reads were demultiplexed using bcl2fastq (v2.20).
    bcl2fastq
    suggested: (bcl2fastq , RRID:SCR_015058)
    Briefly, the reads had adapters trimmed with TrimGalore (Krueger, 2020) and were aligned to the WuhanHu-1 reference genome (accession MN908947.3) using BWA-MEM (v0.7.17) (Li, 2013); the ARTIC amplicons were trimmed and a consensus built using iVAR (v.1.2.3) (Grubaugh et al., 2019).
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    PANGO lineages assigned using Pangolin v2.4.2 and PangoLEARN model dated 2021-05-12 (Rambaut et al., 2020).
    Pangolin
    suggested: None

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  4. Version published to 10.1101/2021.06.04.21258352v1 on medRxiv