Genomic surveillance of SARS-CoV-2 reveals emergence of Omicron BA.2 in Islamabad, Pakistan

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

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Abstract

The Omicron variant of SARS-CoV-2 has rapidly replace previous variants of SARS CoV2 around the globe and is now a major variant of concern. The genomic surveillance of Omicron variant also reveals spread of its subvariant BA.2 which has differing transmissibility in comparison to its other subvariant BA.1. BA.1 and BA.2 harbors different mutational profile. One of the important change in both the subvariants is the presence of 69-70 deletion in BA.1 and absence of this deletion in BA.2. This deletion can be used as tool for the detection of omicron sub variants using real time PCR. In the current study we have used the TaqPath COVID-19 PCR kit for the detection of 69-70 deletion followed by genotyping using SNPsig® SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK) that target K417N, E484K, and P681R mutations. The samples with the amplification of spike gene and K417N were termed as probable BA.2 cases. A subset of samples (n=13) were further subjected to whole genome sequencing. The results showed all the 13 samples were of BA.2. Hence, this assay can be used as a cost effective method for the detection of omicron BA.2 variant using real time PCR in resource limiting settings. Moreover, the detection of BA.2 with highly transmissible mutations in Islamabad, Pakistan may potentially increase the number of positive cases. In that scenario, there has to be stringent genomic surveillance to understand the circulating lineages in the country.

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    SciScore for 10.1101/2022.02.23.22271372: (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
    The prepared libraries were pooled and sequenced on the Illumina iSeq platform with the iSeq 100 i1 Reagent v2 (300-cycle) (Illumina, Inc, USA) at the Department of Virology, National Institute of Health, Islamabad, Pakistan. Data Analysis: FastQC (v0.11.9) was used to process the Fastq files for quality assessment [2].
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    Trimmomatic (v0.39) [3] was used to remove adapter sequences and low-quality base calls (< 30).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Alignment of the filtered reads was performed with the available reference genome (Wuhan-Hu-1, GISAID ID: EPI_ISL_402125) using the Burrows-Wheeler Aligner (BWA, v0.7.17) [4].
    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

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  2. Version published to 10.1101/2022.02.23.22271372v1 on medRxiv