High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020–2021

  1. Nihad A. M. Al-Rashedi
  2. Hussein Alburkat
  3. Abas O. Hadi
  4. Murad G. Munahi
  5. Ali Jasim
  6. Alaa Hameed
  7. Basel Saber Oda
  8. Kareem Moamin Lilo
  9. Laith A. H. AlObaidi
  10. Olli Vapalahti
  11. Tarja Sironen
  12. Teemu Smura

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Abstract

Since the first reported case of coronavirus disease 2019 (COVID-19) in China, SARS-CoV-2 has been spreading worldwide. Genomic surveillance of SARS-CoV-2 has had a critical role in tracking the emergence, introduction, and spread of new variants, which may affect transmissibility, pathogenicity, and escape from infection or vaccine-induced immunity. As anticipated, the rapid increase in COVID-19 infections in Iraq in February 2021 is due to the introduction of variants of concern during the second wave of the COVID-19 pandemic. To understand the molecular epidemiology of SARS-CoV-2 during the second wave in Iraq (2021), we sequenced 76 complete SARS-CoV-2 genomes using NGS technology and identified genomic mutations and proportions of circulating variants among these. Also, we performed an in silico study to predict the effect of the truncation of NS7a protein (ORF7a) on its function. We detected nine different lineages of SARS-CoV-2. The B.1.1.7 lineage was predominant (80.20%) from February to May 2021, while only one B.1.351 strain was detected. Interestingly, the phylogenetic analysis showed that multiple strains of the B.1.1.7 lineage clustered closely with those from European countries. A notable frequency (43.33%) of stop codon mutation (NS7a Q62stop) was detected among the B.1.1.7 lineage sequences. In silico analysis of NS7a with Q62stop found that this stop codon had no considerable effect on the function of NS7a. This work provides molecular epidemiological insights into the spread variants of SARS-CoV-2 in Iraq, which are most likely imported from Europe.

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  1. Version published to 10.1371/journal.pone.0267295
  2. ScreenIT

    SciScore for 10.1101/2021.10.20.21265042: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variableSampling: Combined naso- and oropharyngeal swabs were collected from 76 patients (46 males and 30 females, age ranging between 13 and 85 years) in Samawa, Iraq (31.3188° N, 45.2806° E) during the second epidemic wave of COVID-19 in Iraq (between December 27, 2020 and February 28, 2021).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Additionally, sequencing reads with low-quality (quality score <30) and short sequence (<50 nt) were removed using Trimmomatic [15], assembly using BWA-MEM [16], variant calling using LoFreq [17], and consensus calling using SAMtools [18] implemented in the HaVoC pipeline [19].
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    LoFreq
    suggested: (LoFreq, RRID:SCR_013054)
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    HaVoC
    suggested: None
    Structural comparison was performed between the selected template and the built model to assign their similarity and dissimilarity using TM-align [24] and FATCAT web tools [25].
    FATCAT
    suggested: (FATCAT, RRID:SCR_014631)
    Finally, the refined model structure was prepared for docking by adding polar hydrogen atoms and Gasteiger charges using the Autodock tool 1.5.6 [29].
    Autodock
    suggested: (AutoDock, RRID:SCR_012746)
    Phylogenetic Tree: Genome sequence alignment was performed using alignment of multiple complete SARS-CoV-2 genomes (MAFFT online version April 11, 2020) [31].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The phylogenetic tree was mapped by a maximum likelihood estimation using a fit substitution model (ModelFinder) and replicate number with 1000 bootstrap on IQ-TREE (version: 1.6.10) [32] with ultrafast bootstrap support.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.10.20.21265042v1 on medRxiv