Do the Moroccan SARS-CoV-2 genetic diversity hamper the use of the developed universal vaccines in Morocco?

  1. Meriem Laamarti
  2. Abdelomunim Essabbar
  3. Tarek Alouane
  4. Souad Kartti
  5. Nasma Boumajdi
  6. Houda Bendani
  7. Rokia Laamarti
  8. Loubna Allam
  9. Mouna Ouadghiri
  10. M.W. Chemao-Elfihri
  11. Fatima Ghrifi
  12. Imane Smyej
  13. Jalila Rahoui
  14. Houda Benrahma
  15. Idrissa Diawara
  16. Tarik Aanniz
  17. Naima El Hafidi
  18. Rachid El Jaoudi
  19. Chakib Nejjari
  20. Saaid Amzazi
  21. Rachid Mentag
  22. Lahcen Belyamani
  23. Azeddine Ibrahimi

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Abstract

The SARS-CoV-2 identified as coronavirus species associated with severe acute respiratory syndrome. At the time of writing, the genetic diversity of Moroccan strains of SARS-CoV-2 is poorly documented. The present study aims to analyze and identify the genetic variants of fortyeight Moroccan strains of SARS-CoV-2 collected from mid-March to the end of May and the prediction of their possible sources. Our results revealed 108 mutations in Moroccan SARS-CoV-2, 50% were non-synonymous were present in seven genes (S, M, N, E, ORF1ab, ORF3a, and ORF8) with variable frequencies. Remarkably, eight non-synonymous mutations were predicted to have a deleterious effect for (ORF1ab, ORF3a, and the N protein. The analysis of the haplotype network of Moroccan strains suggests different sources of SARS-CoV-2 infection in Morocco. Likewise, the phylogenetic analysis revealed that these Moroccan strains were closely related to those belonging to the five continents, indicating no specific strain dominating in Morocco. These findings have the potential to lead to new comprehensive investigations combining genomic data, epidemiological information, and clinical characteristics of SARS-CoV-2 patients in Morocco and could indicate that the developed vaccines are likely to be effective against Moroccan strains.

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  1. Version published to 10.1101/2020.06.30.181123v2 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2020.06.30.181123: (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
    Following the ligation sequencing kit (SQK-LSK109) protocol, the sequencing was performed using the MinION Mk1B device.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    The reads generated by MinION Nanopore-Oxford of the nine isolates were mapped to the reference sequence genome Wuhan-Hu-1/2019 using BWA-MEM v0.7.17-r1188 (11) with default parameters, while the data downloaded from the GISAID database were mapped using Minimap v2.12-r847 (12) The BAM files were sorted using SAMtools (13)and were subsequently used to call the genetic variants in variant call format (VCF) by BCFtools (13).
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    First, the SnpEff databases were built locally using annotations of the reference genome NC_045512.2 obtained in the GFF format from the NCBI database.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    Then, the SnpEff database was used to annotate SNPs and with putative functional effects according to the categories defined in the SnpEff manual (http://snpeff.sourceforge.net/SnpEff_manual.html).
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)
    The variants were also evaluated for functional consequences using the SIFT algorithm (34).
    SIFT
    suggested: (SIFT, RRID:SCR_012813)
    Phylogenetic and haplotype network analysis: In order to determine the source(s) of strains circulating in morocco, we performed a multiple sequence alignment using Muscle v 3.8 (15) for the 48 Moroccan strains with 225 genomes of SARS-CoV-2 from Africa, Asia, Europe, North, South America, and Oceania (Supplementary Material; Table S2).
    Muscle
    suggested: (MUSCLE, RRID:SCR_011812)
    Maximum-likelihood trees were inferred with IQ-TREE v1.5.5 under the GTR model (16).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Generated trees were visualized using FigTree 1.4.3 To generate haplotypes for the 48 Moroccan genomes, we aligned the viruses’ complete genomes using Muscle v 3.8 (15).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    In order to estimate genealogical relationships of haplotype groups, the phylogenetic networks were inferred by PopART package v1.7.2 (18)using the TCS method and MSN, respectively.
    PopART
    suggested: None

    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 10.1101/2020.06.30.181123v1 on bioRxiv