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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

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.
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https://hal-riip.archives-ouvertes.fr/pasteur-03554629
Contributor : Abdelhakim Ben Hassine Connect in order to contact the contributor
Submitted on : Thursday, February 3, 2022 - 12:08:52 PM
Last modification on : Friday, February 4, 2022 - 3:06:54 AM
Long-term archiving on: : Wednesday, May 4, 2022 - 7:56:43 PM

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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, American Society for Microbiology, 2021, 9 (3), pp.e0063921. ⟨10.1128/Spectrum.00639-21⟩. ⟨pasteur-03554629⟩

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