Journal Article

Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19

Ben Dhifallah, Imen, Belaiba, Zeineb, Krichen, Henda, Touzi, Henda, Ben Halima, Samar, Chouikha, Anissa, Azouz, Saifeddine, Fares, Wasfi, Ayouni, Kaouther, Ardhaoui, Monia, Safer, Mouna, Khamessi, Oussema, Laamari, Asma, Khedhiri, Marwa, Ghedira, Kais, Guizani, Ikram, Kammoun Rebai, Wafa, Kefi, Rym, Ben Alaya, Nissaf, Gdoura, Mariem, Guerfali, Fatma Z., Atri, Chiraz, Triki, Henda, Haddad-Boubaker, Sondes

2022

Overview

Documenting the circulation dynamics of SARS-CoV-2 variants in different regions of the world is crucial for monitoring virus transmission worldwide and contributing to global efforts towards combating the pandemic. Tunisia has experienced several waves of COVID-19 with a significant number of infections and deaths. The present study provides genetic information on the different lineages of SARS-CoV-2 that circulated in Tunisia over 17 months. Lineages were assigned for 1359 samples using whole-genome sequencing, partial S gene sequencing and variant-specific real-time RT-PCR tests. Forty-eight different lineages of SARS-CoV-2 were identified, including variants of concern (VOCs), variants of interest (VOIs) and variants under monitoring (VUMs), particularly Alpha, Beta, Delta, A.27, Zeta and Eta. The first wave, limited to imported and import-related cases, was characterized by a small number of positive samples and lineages. During the second wave, a large number of lineages were detected; the third wave was marked by the predominance of the Alpha VOC, and the fourth wave was characterized by the predominance of the Delta VOC. This study adds new genomic data to the global context of COVID-19, particularly from the North African region, and highlights the importance of the timely molecular characterization of circulating strains.

• Publisher: MDPI AG,MDPI
• Subject: Bioinformatics / Coronaviruses / COVID-19 / COVID-19 - epidemiology / COVID-19 infection / COVID-19 vaccines / Disease transmission / Epidemiology / Gene amplification / genes / Genome, Viral / Genomes / genomics / Humans / Molecular Epidemiology / Mutation / next-generation sequencing / pandemic / Pipelines / Polymerase chain reaction / Proteins / S gene / SARS-CoV-2 / SARS-CoV-2 - genetics / Severe acute respiratory syndrome coronavirus 2 / Tunisia / Tunisia - epidemiology / variant of concern / variant of interest / variants / virus transmission / Whole genome sequencing