Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa

Wasfi Fares,Guillain Mikaty,Véronique Hourdel ,Mariem Gdoura ,Walid Hammami,Jean Claude Manuguerra ,Kaïs Ghedira ,Valérie Caro ,Anissa Chouikha,Dorra Rezig,Zina Meddeb,Imen Abouda,Sondès Haddad-Boubaker ,Nissaf Ben Alaya,Imen Ben Dhifallah,Henda Touzi,Amel Sadraoui ,Nahed Hogga,Aurélia Kwasiborski ,Henda Triki

doi:10.1186/s12864-021-07870-1

Abstract

BackgroundIn Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. Since then, an increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide.MethodsWhole genome sequencing was performed using NGS approach on six SARS.CoV-2 highly positive samples detected during the early phase of the outbreak.ResultsFull genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These SNP mutations are critical for diagnosis and vaccine development.ConclusionsThese results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.

Highlights

In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020
The totality of complete genome sequences available at writing time, of SARS-CoV-2 were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) and the NCBI databases
Three out of six Tunisian sequences clustered with sequences from France: one case came from France (COV0425, Fig. 1g) and two were locally infected (COV1482 and COV1663, Fig. 1d and e)

Summary

Introduction

In Tunisia a first SARS-CoV-2 confirmed case was reported in March 03, 2020. An increase of cases number was observed from either imported or local cases. The aim of this preliminary study was to better understand the molecular epidemiology and genetic variability of SARS-CoV-2 viruses circulating in Tunisia and worldwide. Human Coronaviruses (HCoV’s) are members of the subfamily Coronavirinae in the family of Coronaviridae in the order of Nidovirales. The outbreak of the coronavirus disease (COVID-19) spread further worldwide and the World Health Organization. The WHO report dated on June 21st, 2020 confirmed 8,708, 008 cases of SARS-CoV-2 with 461715deaths from 215 countries and territories [5]

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