PT  - JOURNAL ARTICLE
AU  - Meriem Laamarti
AU  - Souad Kartti
AU  - Tarek Alouane
AU  - Rokia Laamarti
AU  - Loubna Allam
AU  - Mouna Ouadghiri
AU  - M.W. Chemao-Elfihri
AU  - Imane Smyej
AU  - Jalila Rahoui
AU  - Houda Benrahma
AU  - Idrissa Diawara
AU  - Abdelomunim Essabbar
AU  - Nasma Boumajdi
AU  - Houda Bendani
AU  - El Mehdi Bouricha
AU  - Tarik Aanniz
AU  - Jalil Elattar
AU  - Naima EL Hafidi
AU  - Rachid EL Jaoudi
AU  - Laila Sbabou
AU  - Chakib Nejjari
AU  - Saaid Amzazi
AU  - Rachid Mentag
AU  - Lahcen Belyamani
AU  - Azeddine Ibrahimi
TI  - Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum
AID  - 10.1101/2020.06.30.181123
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.30.181123
4099  - http://biorxiv.org/content/early/2020/07/01/2020.06.30.181123.short
4100  - http://biorxiv.org/content/early/2020/07/01/2020.06.30.181123.full
AB  - In Morocco two waves of SARS-CoV-2 infections have been recorded. The first one occurred from March 02, 2020 with infections mostly imported from Europe and the second one dominated by local infections.At the time of writing, the genetic diversity of Moroccan isolates of SARS-CoV-2 has not yet been reported. The present study aimed to analyze first the genomic variation of the twenty-eight Moroccan strains of SARS-CoV-2 isolated from March 03, 2020 to May 15, 2020, to compare their distributions with twelve other viral genomes from North Africa as well as to identify their possible sources.Our finding revealed 61 mutations in the Moroccan genomes of SARS-CoV-2 compared to the reference sequence Wuhan-Hu-1/2019, of them 23 (37.7%) were present in two or more genomes. Focusing on non-synonymous mutations, 29 (47.54%) were distributed in five genes (ORF1ab, spike, membrane, nucleocapsid and ORF3a) with variable frequencies. The non-structural protein coding regions nsp3-Multi domain and nsp12-RdRp of the ORF1ab gene harbored more mutations, with six for each. The comparison of genetic variants of fourty North African strains revealed that two non-synonymous mutations D614G (in spike) and Q57H (in ORF3a) were common in four countries (Morocco, Tunisia, Algeria and Egypt), with a prevalence of 92.5% (n = 37) and 42.5% (n = 17), respectively, of the total genomes.Phylogenetic analysis showed that the Moroccan and Tunisian SARS-CoV-2 strains were closely related to those from different origins (Asia, Europe, North and South America) and distributed in different distinct subclades. This could indicate different sources of infection with no specific strain dominating yet in in these countries. These results have the potential to lead to new comprehensive investigations combining genomic data, epidemiological information and the clinical characteristics of patients with SARS-CoV-2.Competing Interest StatementThe authors have declared no competing interest.