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; Kais Ghedira; Mariem Gdoura; Anissa Chouikha; Sondes Haddad-Boubaker; Marwa Khedhiri; Kaouthar Ayouni; Asma Lamari; Henda Touzi; Walid Hammemi; Zina Medeb; Amel Sadraoui; Nahed Hogga; Nissaf Ben Alaya; Henda Triki

doi:10.1128/Spectrum.00639-21

Journal articles

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}

* Corresponding author

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]

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

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Journal articles

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Life Sciences [q-bio]

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Submitted on : Thursday, February 3, 2022 - 12:08:52 PM
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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

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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

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