Genomic characterization of SARS-CoV-2 from Islamabad, Pakistan by Rapid Nanopore sequencing

  1. Nazish Badar
  2. Aamer Ikram
  3. Muhammad Salman
  4. Massab Umair
  5. Zaira Rehman
  6. Abdul Ahad
  7. Hamza Ahmed Mirza
  8. Masroor Alam
  9. Nayab mehmood
  10. Uzma Bashir

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Abstract

Since the start of COVID-19 pandemic, Pakistan has experienced four waves of pandemic. The fourth wave ended in October, 2021 while the fifth wave of pandemic starts in January, 2022. The data regarding the circulating strains after the fourth wave of pandemic from Pakistan is not available. The current study explore the genomic diversity of SARS-CoV-2 after fourth wave and before fifth wave of pandemic through whole genome sequencing. The results showed the circulation of different strains of SARS-CoV-2 during November-December, 2021. We have Omicron BA.1 (n=4), Lineage A (n=2) and delta AY.27 (n=1) variants of SARS-CoV-2 in the population of Islamabad. All the isolates harbors characteristics mutations of omicron and delta variant in the genome. The lineage A isolate harbors a nine amino acid (68-76) and a ten amino acid (679-688) deletion in the genome. The circulation of omicron in the population before the fifth wave of pandemic and subsequent upsurges of COVID-19 positive cases in Pakistan highlights the importance of genomic surveillance.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.17.480826: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The National Institute of Health’s Internal Review Board accepted the study design, and the datasets were anonymised and free of personally identifiable information.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Samples were sequenced for 72 hours using FLO-MIN106 flowcells on MinION MK1b sequencing equipment with high sequence basecalling enabled using MinKNOW (Version 4.2.8, Oxford Nanopore Technologies).
    MinION
    suggested: (MinION, RRID:SCR_017985)
    Read length filtering and reference alignment to the Wuhan-Hu-1 genome were used to test variant polishing in Nanopolish v0.13.2, Medaka v0.11.5, and samtools 1.9.
    Nanopolish
    suggested: (Nanopolish, RRID:SCR_016157)
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Genomic dataset and Phylogenetic classification: For phylogenetic tree NCBI BLAST search of the study isolates were performed in order to get closely related sequence of SARS-CoV-2.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    For multiple sequence alignment MAFFT software was used.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    For substitution model prediction jModelTest was used, Maximum Likelihood (ML) phylogenetic tree was build using IQtree (http://www.iqtree.org/).
    IQtree
    suggested: None
    http://www.iqtree.org/
    suggested: (IQ-TREE, RRID:SCR_017254)
    The tree was edited and visualized using Figtree software (http://tree.bio.ed.ac.uk/software/figtree/).
    Figtree
    suggested: (FigTree, RRID:SCR_008515)

    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.
    • No funding statement was detected.
    • 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 10.1101/2022.02.17.480826v1 on bioRxiv