Genomic surveillance reveals the emergence of SARS-CoV-2 Lineage A from Islamabad Pakistan

  1. Massab Umair
  2. Aamer Ikram
  3. Zaira Rehman
  4. Syed Adnan Haider
  5. Nazish Badar
  6. Muhammad Ammar
  7. Qasim Ali
  8. Abdul Ahad
  9. Rana Suleman
  10. Muhammad Salman

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Abstract

The lineage A of SARS-CoV-2 has been around the world since the start of the pandemic. In Pakistan the last case of lineage A was reported in April, 2021 since then no case has been reported. In November, 2021 during routine genomic surveillance at National Institute of Health we have found 07 cases of lineage A from Islamabad, Pakistan. The study reports two novel deletions in the spike glycoprotein. One 09 amino acid deletion (68-76 a.a) is found in the S1 subunit while another 10 amino acid deletion (679-688 a.a) observed at the junction of S1/S2 referred as furin cleavage site. The removal of furin cleavage site may result in impaired virus replication thus decreasing its pathogenesis. The actual impact of these two deletions on the virus replication and disease dynamics needs to be studied in detail. Moreover, the enhanced genomic surveillance will be required to track the spread of this lineage in other parts of the country.

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  1. ScreenIT

    SciScore for 10.1101/2021.12.24.21268367: (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.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data Analysis: The quality of sequencing reads were assessed through FastQC tool (v0.11.9) [18].
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    The low quality low-quality base calls (< 30) and adapter sequences were removed using Trimmomatic (v0.39).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The alignment of filtered reads were performed through Burrows-Wheeler Aligner’s (BWA, v0.7.17) using Wuhan-WHU-01
    BWA
    suggested: (BWA, RRID:SCR_010910)
    The homology model of spike glycoprotein was built through Modeller V9.2 using pdb ID:6VSB as template and 100 models were generated.
    Modeller
    suggested: (MODELLER, RRID:SCR_008395)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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.

  2. Version published to 10.1101/2021.12.24.21268367v1 on medRxiv