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

Bouchra Chaouni,Youssef Bakri,Saaïd Amzazi,Najib Al Idrissi,Mustapha Mahmoud,Wajih Rhalem,Sofia Sehli,Hassan Ghazal,Abderrahmane Bakkali,Imane Allali,Lahcen Wakrim,Abdellah Idrissi Azami,Nihal Habib,Laila Bouguenouch,Salsabil Hamdi,Said Barrijal

doi:10.12688/f1000research.24810.1

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.

Highlights

Following its onset in December 2019, several cases of a new respiratory illness were reported in the city of Wuhan, Hubei province, China[1]
On the 12th of March 2020, the ongoing SARS-CoV-2 outbreak was declared as a pandemic by the World Health Organization (WHO)[3]
To gain further understanding of the molecular epidemiology of the outbreak in Morocco, we conducted a phylogenetic and a Variant Network Analyses of the full-genome sequences of 21 SARS-CoV-2 strains, 19 were isolated from Covid-19 patients in Morocco, one sequence was isolated from a patient in Melilla and another one was isolated from a Moroccan patient in Cadiz, Andalusia

Summary

Introduction

Following its onset in December 2019, several cases of a new respiratory illness were reported in the city of Wuhan, Hubei province, China[1]. Morocco has reported 8931 confirmed cases and 212 deaths associated with COVID-19 (JHC update of June 16th 2020). To gain further understanding of the molecular epidemiology of the outbreak in Morocco, we conducted a phylogenetic and a Variant Network Analyses of the full-genome sequences of 21 SARS-CoV-2 strains, 19 were isolated from Covid-19 patients in Morocco, one sequence was isolated from a patient in Melilla and another one was isolated from a Moroccan patient in Cadiz, Andalusia. 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 recurrent missense variant A>G at position 23,403 in the spike gene, known to be associated with virus severity, has been version 2 (revision)

Methods

Results

Conclusion