RT Journal Article SR Electronic T1 Sequencing using a two-steps strategy reveals high genetic diversity in the S gene of SARS-CoV-2 after a high transmission period in Tunis, Tunisia JF bioRxiv FD Cold Spring Harbor Laboratory SP 2021.06.18.449083 DO 10.1101/2021.06.18.449083 A1 Wasfi Fares A1 Kais Ghedira A1 Mariem Gdoura A1 Anissa Chouikha A1 Sondes Haddad-Boubaker A1 Marwa Khedhiri A1 Kaouthar Ayouni A1 Asma Lamari A1 Henda Touzi A1 Walid Hammemi A1 Zina Medeb A1 Amel Sadraoui A1 Nahed Hogga A1 Nissaf ben Alaya A1 Henda Triki YR 2021 UL http://biorxiv.org/content/early/2021/06/19/2021.06.18.449083.abstract AB Recent efforts have reported numerous variants that influence SARS-CoV-2 viral characteristics including pathogenicity, transmission rate and ability of detection by molecular tests. Whole genome sequencing based on NGS 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 cost, we developed a couple of primers allowing to generate partial sequences in the viral S gene allowing 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 and one nasopharyngeal specimens collected during the decreasing phase of a high transmission COVID-19 wave in T unisia were analyzed. The results reveal high genetic variability within the sequenced fragment and allowed the detection of first introduction in the country of already known VOCs and VOIs as well as others variants that have interesting genomic mutations and need to be kept under surveillance.Importance The method of choice for SARS-CoV-2 variants detection is whole genome sequencing using NGS technologies. Resources for this technology remain limited in many low and middle income countries where it is not possible to perform whole genome sequencing for representative number of SARS-CoV-2 positive cases. In the present work, we developed a novel strategy based on a first partial sanger screening in the S gene including key mutations of the already known VOCs and VOIs for rapid identification of these VOCs and VOIs and helps to better select specimens that need to be sequenced by NGS technologies. The second step consisting in whole genome sequencing allowed to have a holistic view of all variants within the selected viral strains and confirmed the initial classification of the strains based on partial S gene sequencing.