Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?
Metadata
Show full item recordEditorial
MDPI
Materia
North Africa SARS-CoV-2 Algeria Genomics Clade Omicron Mutation annotation
Date
2022-02-18Referencia bibliográfica
Menasria, T.; Aguilera, M. Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: WhatWe Know So Far and What We Expect?. Microorganisms 2022, 10, 467. [https://doi.org/10.3390/microorganisms10020467]
Abstract
Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating
in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with
respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 highcoverage
whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer
clades and mutation annotation compared with the wild-type variantWuhan-Hu-1. Phylogenetic
analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of
the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding
protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and
19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). Lower prevalence
was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the
ORF3a coding protein NS3-G251V) (2.0%). Interestingly, 1.5% of total genomes were assigned as
GRA (Omicron), the newly emerged clade. Across the North African countries, 108 SARS-CoV-2
lineages using the Pangolin assignment were identified, whereby most genomes fell within six major
lineages and variants of concern (VOC) including B.1, the Delta variants (AY.X, B.1.617.2), C.36,
B.1.1.7 and B.1.1. The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with
D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total
sequences, respectively. In addition, mutations affecting other viral proteins appeared frequently
including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. These
findings highlight the importance of genomic surveillance for understanding the SARS-CoV-2 genetic
diversity and its spread patterns, leading to a better guiding of public health intervention measures.
The know-how analysis of the present work could be implemented worldwide in order to overcome
this health crisis through harmonized approaches.