Genomic evidence of multiple SARS-CoV-2 introductions into Morocco

Abstract

Background: The recent emergence of a novel coronavirus (SARS-CoV-2) has caused serious public health concerns due to its rapid dissemination worldwide. A total of 8,931 positive cases had been reported in Morocco by the 16th of June 2020. Methods: To better understand the SARS-CoV-2 pandemic in this North African country, we analyzed the complete genome sequences of the virus related to Morocco by constructing a phylogenetic tree and creating a variant network using the available Moroccan and other sequences in dedicated databases. Results: Phylogenetic and variant network analyses of SARS-CoV-2 strains from early patients with COVID-19 in Morocco showed multiple spatiotemporal introductions from Italy (ten), France (seven), Spain (one) and Portugal (one). This is consistent with the assumption that the early infections in Morocco were imported, mainly from Europe. The 17 virus strains form two independent phylogenetic clusters and provide evidence for early community-based transmission following the initial introductions of the virus. We then catalogued 13 novel mutations in the SARS-CoV-2 isolates from Moroccan patients. Interestingly, the recurrent missense variant A>G at position 23,403 in the spike gene, known to be associated with virus severity, has been identified in all Moroccan isolates. Conclusions: These primary findings testify of the importance of the genomic surveillance strategies as a means of understanding the virus spread dynamics, counteracting the pandemic outbreak, and drawing useful lessons for dealing with any future emerging infectious pathogens.