Do the Moroccan SARS-CoV-2 genetic diversity hamper the use of the developed universal vaccines in Morocco?
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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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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 Sentences Resources Following the ligation sequencing kit (SQK-LSK109) protocol, the sequencing was performed using the MinION Mk1B device. MinIONsuggested: (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-MEMsu…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 Sentences Resources Following the ligation sequencing kit (SQK-LSK109) protocol, the sequencing was performed using the MinION Mk1B device. MinIONsuggested: (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-MEMsuggested: (Sniffles, RRID:SCR_017619)SAMtoolssuggested: (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. NCBIsuggested: (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). SnpEffsuggested: (SnpEff, RRID:SCR_005191)The variants were also evaluated for functional consequences using the SIFT algorithm (34). SIFTsuggested: (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). Musclesuggested: (MUSCLE, RRID:SCR_011812)Maximum-likelihood trees were inferred with IQ-TREE v1.5.5 under the GTR model (16). IQ-TREEsuggested: (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). FigTreesuggested: (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. PopARTsuggested: NoneResults 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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