Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum

Laamarti, M.; Kartti, S.; Alouane, T.; Laamarti, R.; Allam, L.; Ouadghiri, M.; Chemao-Elfihri, M. W.; Smyej, I.; Rahoui, J.; Benrahma, H.; Diawara, I.; Essabbar, A.; Boumajdi, N.; Bendani, H.; Bouricha, E. M.; Aanniz, T.; El Attar, J.; El Hafidi, N.; El Jaoudi, R.; Sbabou, L.; Nejjari, C.; Amzazi, S.; Mentag, R.; Belyamani, L.; Ibrahimi, A.

doi:10.1101/2020.06.30.181123

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bioRxiv · 10.1101/2020.06.30.181123

Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum

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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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Laamarti, M., Kartti, S., Alouane, T., Laamarti, R., Allam, L., Ouadghiri, M., Chemao-Elfihri, M. W., Smyej, I., Rahoui, J., Benrahma, H., Diawara, I., Essabbar, A., Boumajdi, N., Bendani, H., Bouricha, E. M., Aanniz, T., El Attar, J., El Hafidi, N., El Jaoudi, R., Sbabou, L., Nejjari, C., Amzazi, S., Mentag, R., Belyamani, L., Ibrahimi, A.. 2020-07-01. Genetic analysis of SARS-CoV-2 strains collected from North Africa: viral origins and mutational spectrum. https://doi.org/10.1101/2020.06.30.181123

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