Detection and upsurge of SARS-CoV-2 Omicron variant in 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. Ayesha Khalid
  11. Amna Tariq
  12. Zunera Jamal
  13. Muhammad Salman

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Abstract

The SARS-CoV-2 omicron variant was first detected in South Africa in November, 2021 and has rapidly spread to more than 90 countries. The emergence of Omicron variant demands for enhanced genomic surveillance to track the mutation profile and spread of virus. In the current study, we have sequenced 15 whole-genome sequences of SARS-CoV-2 Omicron variant from Islamabad region of Pakistan. Among the 15 isolates, 66% were from Islamabad whereas 33% of cases had international travel history of United Kingdom, Maldives, South Africa, and Oman. The detection of Omicron in local community and in travelers highlights the need for rigorous screening at national level and at entry points in order to contain the spread of variant.

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  1. ScreenIT

    SciScore for 10.1101/2022.01.13.22268997: (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 Fastq files were processed for quality assessment using the FastQC tool (v0.11.9) [5].
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    Trimmomatic (v0.39) [6] was employed to eliminate artifacts and technical biases by removing adapter sequences and low-quality base calls (< 30).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The filtered reads were aligned using the Burrows-Wheeler Aligner’s (BWA, v0.7.17) [7] and available reference genome (Wuhan-Hu-1, GISAID ID: EPI_ISL_402125).
    BWA
    suggested: (BWA, RRID:SCR_010910)

    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 10.1101/2022.01.13.22268997v1 on medRxiv