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 high-coverage whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-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.
Highlights
In late December 2019, the World Health Organization (WHO) was notified by the Chinese Health Authorities of pneumonia cases of unknown etiology detected inWuhan City, Hubei Province [1], which could mark the emergence of a novel and serious threat to public health
By 20 December 2021, over 2,500,000 SARS-CoV-2 cumulative cases had been reported in North African countries (Figure 1A) of which 214,592 cases were confirmed in Algeria with more than 6190 deaths attributed to the virus and a case fatality ratio (CFR) of
This paper presents the first insight into a comprehensive analysis of genome sequences of SARS-CoV-2 circulating in Algeria and North African countries
Summary
In late December 2019, the World Health Organization (WHO) was notified by the Chinese Health Authorities of pneumonia cases of unknown etiology detected inWuhan City, Hubei Province [1], which could mark the emergence of a novel and serious threat to public health. Clinical left and School of Public Health reported the isolation of a new type of coronavirus (novel coronavirus, nCoV) [2] and a preliminary analysis of the Wuhan virus sequence (WH-Human_1.fasta.gz), [Genbank/NCBI release (MN908947.1)] suggesting a possible zoonotic origin [3]. Microorganisms 2022, 10, 467 outside China have reported cases among travelers returning from different countries and the epidemiologic picture is changing on a daily basis. As of 30 January 2020, the WHO officially declared that the new coronavirus outbreak [coronavirus disease (COVID-19)] is a public health emergency of international concern and later on March 11 declared it as a pandemic, acknowledging what has seemed clear—that the virus will likely spread to all countries on the globe, possibly intensified by high population density, socio-demographic profiles, host immune responses, and viral genetics [5]. The current estimates of the case fatality rate of SARS-CoV-2 at any time point of analysis should be interpreted with caution since the outcome of the emerging COVID-19 is as yet unknown
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