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

BMC Genomics

Aurélia Kwasiborski¹  Véronique Hourdel¹  Valérie Caro¹  Jean-Claude Manuguerra¹  Guillain Mikaty¹  Kais Ghedira²  Wasfi Fares³  Anissa Chouikha³  Zina Meddeb³  Nahed Hogga³  Amel Sadraoui³  Imen Ben Dhifallah³  Dorra Rezig³  Imen Abouda³  Sondes Haddad Boubaker³  Henda Touzi³  Meriam Gdoura³  Walid Hammami³  Henda Triki⁴  Nissaf Ben Alaya⁵ 

[1] Laboratory for Urgent Response to Biological Threats (CIBU), Environment and Infectious Risks (ERI) research and expertise unit, Institut Pasteur, Paris, France;Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institut Pasteur Tunis, Tunis, Tunisia;Laboratory of Clinical Virology, Institut Pasteur, University Tunis-El Manar, Tunis, Tunisia;Laboratory of Clinical Virology, Institut Pasteur, University Tunis-El Manar, Tunis, Tunisia;Faculty of Medicine, University Tunis-El Manar, Tunis, Tunisia;National Observatory for New and Emerging Diseases, Ministry of Health, Tunis, Tunisia;Faculty of Medicine, University Tunis-El Manar, Tunis, Tunisia;

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

DOI  :  10.1186/s12864-021-07870-1

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY