Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic

  1. Muhammad Shakeel
  2. Muhammad Irfan
  3. Zaibunnisa
  4. Muhammad Rashid
  5. Sabeeta Kanwal Ansari
  6. Ishtiaq Ahmad Khan

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Abstract

Surveillance of genetic diversity in the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we monitored mutational events in the SARS-CoV-2 genome through whole genome sequencing. The samples (n=48) were collected from the hot spot regions of the metropolitan city Karachi, Pakistan during the four months (May 2020 to August 2020) of first wave of the COVID-19 pandemic. The data analysis highlighted 122 mutations, including 120 single nucleotide variations (SNV), and 2 deletions. Among the 122 mutations, there were 71 singletons, and 51 recurrent mutations. A total of 16 mutations, including 5 nonsynonymous mutations, were detected in spike protein. Notably, the spike protein missense mutation D614G was observed in 31 genomes. The phylogenetic analysis revealed majority of the genomes (36) classified as B lineage, where 2 genomes were from B.6 lineage, 5 genomes from B.1 ancestral lineage and remaining from B.1 sub-lineages. It was noteworthy that three clusters of B.1 sub-lineages were observed, including B.1.36 lineage (10 genomes), B.1.160 lineage (11 genomes), and B.1.255 lineage (5 genomes), which represent independent events of SARS-CoV-2 transmission within the city. The sub-lineage B.1.36 had higher representation from the Asian countries and the UK, B.1.160 correspond to the European countries with highest representation from the UK, Denmark, and lesser representation from India, Saudi Arabia, France and Switzerland, and the third sub-lineage (B.1.255) correspond to the USA. Collectively, our study provides meaningful insight into the evolution of SARS-CoV-2 lineages in spatio-temporal local transmission during the first wave of the pandemic.

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    SciScore for 10.1101/2021.01.13.426548: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: 2.1 Ethical Consideration, recruitment of patients, and samples collection: The study was approved by the Research Ethics Committee of the International Center for Chemical and Biological Sciences, University of Karachi, and the study design adhered to the ethical considerations according to the Declaration of Helsinki (Helsinki, 2013).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variable2.3 DNA library preparation, and whole genome sequencing: A total of 48 samples (male n=29, female n=19) were selected for SARS-CoV-2 whole genome sequencing.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Paired-end sequencing (2×75 bases) using MiSeq reaget v2 kit was carried out on Illumina MiSeq (Illumina Inc., San Diego, CA, USA). 2.4 Analysis of the sequencing data: The raw data in the binary base call format (.
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    Quality of the DNA short reads was assessed using FastQC tool (Andrews, 2010).
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    The post alignment processing and variants calling was carried out by using the Samtools package (Dhandapany et al., 2009).
    Samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The functional annotation of the variants was carried out by using ANNOVAR (Yang et al., 2015).
    ANNOVAR
    suggested: (ANNOVAR, RRID:SCR_012821)
    The phylogeny was constructed using the RAxML 8.2.12 tool (Stamatakis, 2014) using maximum likelihood algorithm and 100 bootstrap replicates.
    RAxML
    suggested: (RAxML, RRID:SCR_006086)

    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.

    About SciScore

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  2. Version published to 10.1101/2021.01.13.426548v1 on bioRxiv