The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

  1. Safia Zeghbib
  2. Balázs A. Somogyi
  3. Brigitta Zana
  4. Gábor Kemenesi
  5. Róbert Herczeg
  6. Fawzi Derrar
  7. Ferenc Jakab

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Abstract

To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.

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  1. Version published to 10.3390/v13081525
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    SciScore for 10.1101/2020.11.19.20235135: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Therefore, sequences were aligned by MAFFT using default parameters [33].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Temporal signal assessment, time-calibrated phylogeny reconstruction, and Phylogeographic analysis in discrete space: To effectively assess the clock-likeliness regarding the data, the aforementioned maximum likelihood resultant tree was used as an input file in TempEst [36].
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Subsequently, the effective sampling sizes /ESS>200 were examined using TRACER v1.6.0 [41].
    TRACER
    suggested: (Tracer, RRID:SCR_019121)
    Furthermore, the Maximum clade credibility tree/MCC was annotated by means of TreeAnnotator v1.10.4 and visualized in FigTree v1.4.4 [21].
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    The samples’ spatial data/location of isolation was used to infer the geographical spreading patterns of the virus by combining the Bayesian stochastic search variable selection/BSSVS with a standard symmetric substitution implemented using Beast v1.10.4. [42].
    Beast
    suggested: (BEAST, RRID:SCR_010228)
    Thereafter, the MCC tree was loaded in SpreaD3 v0.9.7 to visualize and analyze the transmission routes, and the log file to calculate the Bayes Factor/BF [43].
    SpreaD3
    suggested: None
    Genome investigations: MEGA X was first used to calculate the pairwise genetic distances employing the p distance parameter [44].
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    Subsequently, the DnaSP v6.12.03 package was applied in reference to further genome exploration, beginning with polymorphic region assessment.
    DnaSP
    suggested: (DnaSP, RRID:SCR_003067)
    Additionally, the population density data regarding all Algerian cities was retrieved from the Wikipedia website [56].
    Wikipedia
    suggested: (Wikipedia, RRID:SCR_004897)

    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.

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  3. Version published to 10.1101/2020.11.19.20235135v1 on medRxiv