Genetic Diversity and Genomic Epidemiology of SARS-COV-2 in Morocco

  1. Bouabid Badaoui
  2. Khalid Sadki
  3. Chouhra Talbi
  4. Salah Driss
  5. Lina Tazi

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Abstract

COVID-A9 is an infection disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), declared as a pandemic due to its rapid expansion worldwide. In this study we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 using 22 virus genome sequences reported by three different laboratories in Morocco till the date 07/06/2020 as well as (40366) virus genomes from all around the world.

The SARS-CoV-2 genomes from Moroccan patients revealed 62 mutations of which 30 were missense mutations. The mutations Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by N_G204R and N_R203K which occurred in 9 among the 22 sequences. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F occurred one time in our sequences with no record in other sequence worldwide. These mutations should be investigated to figure out their potential effects on all around the world virulence. Phylogenetic analyses revealed that Moroccan SARS-CoV-2 genomes included 9 viruses pertaining to clade 20A, 9 to clade 20B and 2 to clade 20C. This finding suggest that the epidemic spread in Morocco did not show a predominant SARS-CoV-2 route. For multiple and unrelated introductions of SARS-CoV-2 into Morocco via different routes have occurred, giving rise to the diversity of virus genomes in the country. Furthermore, very likely, the SARS-CoV-2 virus circulated in cryptic way in Morocco starting from the fifteen January before the discovering of the first case the second of March.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.23.165902: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    For comparative analyze of SARS-Cov-2 genome sequences we have used the following protocol: i) Collection of SARS-CoV-2 Sequences and the corresponding metadata from the GISAID database. ii) Filtering the SARS-CoV-2 Sequences to exclude inaccurate sequences based on missing bases and sequence length and to set a fixed number of samples per group according to their similarities.
    GISAID
    suggested: (GISAID, RRID:SCR_018279)
    In this stage, 20 sequences from the 22 corresponding to the Moroccan patients remained for the subsequent analyses. iii) Performing a multi sequence alignment via MAFFT. vi) Inferring a phylogenetic tree from the multi-sequence alignment, getting a time-resolved tree via TreeTime and inferring ancestral traits sequences v) Identifying the mutations.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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: We detected the following sentences addressing limitations in the study:
    This genomic survey of SARS-CoV-2 in Morocco has at least two limitations. First, the sampling size is relatively weak which might hinder a compelling interpretation of the epidemiological situation in the country. Second, all the samples analyzed, except one, were obtained from public health laboratories and thus may not be representative of the general population.

    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.

    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 10.1101/2020.06.23.165902 on bioRxiv