Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

Wasfi Fares (1, 2) , Kais Ghedira (3) , Mariem Gdoura (1, 2, 4) , Anissa Chouikha (1, 2) , Sondes Haddad-Boubaker (1, 2) , Marwa Khedhiri (1, 2) , Kaouthar Ayouni (1, 2) , Asma Lamari (1, 2) , Henda Touzi (1, 2) , Walid Hammemi (1, 2) , Zina Medeb (1, 2) , Amel Sadraoui (1, 2) , Nahed Hogga (1, 2) , Nissaf Ben Alaya (5, 2) , Henda Triki (1, 2)

1 Virus, Vecteurs et Hôtes [Tunis]
2 UTM - Université de Tunis El Manar
3 LR11IPT09 - Laboratoire de Bioinformatique, biomathématiques, biostatistiques (BIMS)
4 UM - Université de Monastir - University of Monastir
5 Ministère de la santé Publique [Tunisie]

Recent efforts have reported numerous variants that influence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral characteristics, including pathogenicity, transmission rate, and detectability by molecular tests. Whole-genome sequencing based on next-generation sequencing technologies is the method of choice to identify all viral variants; however, the resources needed to use these techniques for a representative number of specimens remain limited in many low- and middle-income countries. To decrease sequencing costs, we developed a primer set allowing partial sequences to be generated in the viral S gene, enabling rapid detection of numerous variants of concern (VOCs) and variants of interest (VOIs); whole-genome sequencing is then performed on a selection of viruses based on partial sequencing results. Two hundred one nasopharyngeal specimens collected during the decreasing phase of a high-transmission COVID-19 wave in Tunisia were analyzed. The results reveal high genetic variability within the sequenced fragment and allow the detection of first introductions in the country of already-known VOCs and VOIs, as well as other variants that have interesting genomic mutations and need to be kept under surveillance.

Keywords: VOIs; spike protein; whole-genome sequencing; COVID-19; SARS-CoV-2; Tunisia; VOCs

Domains: Life Sciences [q-bio]

Wasfi Fares, Kais Ghedira, Mariem Gdoura, Anissa Chouikha, Sondes Haddad-Boubaker, et al.. Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia. Microbiology Spectrum, 2021, 9 (3), pp.e0063921. ⟨10.1128/Spectrum.00639-21⟩. ⟨pasteur-03554629⟩