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

Wasfi Fares (1, 2) , Anissa Chouikha (1, 2) , Kais Ghedira (3) , Meriam Gdoura (1, 2) , Dorra Rezig (1, 2) , Sondes Haddad Boubaker (1, 2) , Imen Ben Dhifallah (1, 2) , Henda Touzi (1, 2) , Walid Hammami (1, 2) , Zina Meddeb (1, 2) , Amel Sadraoui (1, 2) , Nahed Hogga (1, 2) , Imen Abouda (1, 2) , Aurélia Kwasiborski (4) , Véronique Hourdel (4) , Guillain Mikaty (4) , Valérie Caro (4) , Jean-Claude Manuguerra (4) , Nissaf Ben Alaya (5, 2) , Henda Triki (1, 2)

1 Laboratoire de Virologie Clinique, Référence Régional OMS pour la Poliomyélite et la Rougeole - Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles
2 UTM - Université de Tunis El Manar
3 LR11IPT09 - Laboratoire de Bioinformatique, biomathématiques, biostatistiques (BIMS)
4 CIBU - Cellule d'Intervention Biologique d'Urgence (Centre National de Référence) - Laboratory for Urgent Response to Biological Threats (National Reference Center)
5 Ministère de la santé Publique [Tunisie]

Background: In 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. Methods: Whole genome sequencing was performed using NGS approach on six SARS. CoV-2 highly positive samples detected during the early phase of the outbreak. Results: Full 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. Conclusions: These results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level.

Keywords: Whole genome sequencing; SARS-CoV-2; SNPs; Genotype; Tunisia

Domains: Life Sciences [q-bio]

Wasfi Fares, Anissa Chouikha, Kais Ghedira, Meriam Gdoura, Dorra Rezig, et al.. Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa. BMC Genomics, 2021, 22 (1), pp.540. ⟨10.1186/s12864-021-07870-1⟩. ⟨pasteur-03574784⟩