Genomic diversity of SARS‐CoV‐2 in Pakistan during the fourth wave of pandemic

  1. Massab Umair
  2. Aamer Ikram
  3. Zaira Rehman
  4. Syed A. Haider
  5. Muhammad Ammar
  6. Nazish Badar
  7. Qasim Ali
  8. Muhammad S. Rana
  9. Muhammad Salman

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Abstract

The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has resulted in upsurges of coronavirus disease 2019 (COVID‐19) cases around the globe. Pakistan faced the fourth wave of COVID‐19 from July to August 2021 with 314,786 cases. To understand the genomic diversity of circulating SARS‐CoV‐2 strains during the fourth wave of the pandemic in Pakistan, this study was conducted. The samples from 140 COVID‐19‐positive patients were subjected to whole‐genome sequencing using the iSeq Sequencer by Illumina. The results showed that 97% ( n  = 136) of isolates belonged to the delta variant while three isolates belonged to alpha and only one isolate belonged to the beta variant. Among delta variant cases, 20.5% ( n  = 28) isolates were showing B.1.617.2 while 23.5% ( n  = 25), 17.59% ( n  = 19), 14.81% ( n  = 16), and 13.89% ( n  = 15) of isolates were showing AY.108, AY.43 AY.127, and AY.125 lineages, respectively. Islamabad was found to be the most affected city with 65% ( n  = 89) of delta variant cases, followed by Karachi (17%, n  = 23), and Rawalpindi (10%, n  = 14). Apart from the characteristic spike mutations (T19R, L452R, T478K, P681R, and D950N) of the delta variant, the sublineages exhibited other spike mutations as E156del, G142D, T95I, A222V, G446V, K529N, N532S, Q613H, and V483A. The phylogenetic analysis revealed the introductions from Singapore, the United Kingdom, and Germany. This study highlights the circulation of delta variants (B.1.617.2 and sublineages) during the fourth wave of pandemic in Pakistan.

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  1. Version published to 10.1002/jmv.27957
  2. ScreenIT

    SciScore for 10.1101/2021.09.30.21264343: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study was approved by ethical review committee of National Institute of Health, Islamabad. RNA Extraction and real-time PCR: Total RNA was extracted from the specimens using KingFisher™ Flex Purification System (ThermoFisher Scientific, US).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data Analysis: The Fastq files were exported using File Exporter plugin from Torrent Suite 5.14.0 and then processed for quality assessment using the FastQC tool (v0.11.9) [8].
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    Trimmomatic (v0.39) [9] was employed to eliminate artifacts and technical biases by removing adapter sequences and low-quality base calls (< 20).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The filtered reads were aligned using the Burrows-Wheeler Aligner’s (BWA, v0.7.17) [10] and available reference genome (Wuhan-Hu-1, Accession number: MN908947.3).
    BWA
    suggested: (BWA, RRID:SCR_010910)

    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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.09.30.21264343v1 on medRxiv