The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage

Abstract

IntroductionThe Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated.MethodsViral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs.ResultsThe age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country.DiscussionThis study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.

Dynamic of SARS-CoV-2 variants circulation in Tunisian pediatric population, during successive waves, from March 2020 to September 2022

“…Twenty-three different variants were detected including three VOCs (Alpha, Delta, Omicron), VOIs (P.2, A.27, B.1.525) and other minor variants ( n = 17). Previous published data from Tunisia during the period of March 2020 to December 2021, reported the circulation of the same VOCs and VOIs ( Chouikha et al, 2022 ; Haddad-Boubaker et al, 2023 ). However, different SARS-CoV-2 variants were identified as part of the present study.…”

“…The 369 sequenced samples presented a cycle threshold (CT) cutoff value of less than 33. Both sequencing sites used nearly equivalent sequencing protocols to those previously described ( Chouikha et al, 2022 ; Fares et al, 2021 b; Haddad-Boubaker et al, 2023 ; Molini et al, 2022 ).…”

“…In Tunisia, reported data focused on the general population and described various SARS-CoV-2 lineages circulating from March 2020 to December 2021 ( Fares et al, 2021a ; Chouikha et al, 2022 ; Fares et al, 2021b ; Haddad-Boubaker et al, 2023 ). The first and second waves occurred from March to June 2020 and from July 2020 to January 2021, respectively, characterized by the circulation of different imported lineages.…”

“…The first and second waves occurred from March to June 2020 and from July 2020 to January 2021, respectively, characterized by the circulation of different imported lineages. The third and fourth waves, from February to May 2021 and May to December 2021, were caused by the Alpha and delta variants, respectively ( Chouikha et al, 2022 ; Haddad-Boubaker et al, 2023 ). Since December 2021, the Omicron variant has been detected, causing the fifth wave, which has been poorly documented.…”

Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing

“…These findings are consistent with the broader global trend of the continuous evolution and diversification of SARS-CoV-2 lineages and emphasize the importance of ongoing genomic surveillance to monitor the spread and impact of the virus. This study's results contribute to the growing body of knowledge on the genetic diversity and lineage dynamics of SARS-CoV-2 in North Africa, providing a foundation for further research and public health efforts in the region [ 11 , [21] , [22] , [23] , [24] , [25] ]. The distribution of lineages in Mauritania and Libya is seriously lacking in information, which highlights the need for improved data collection and reporting practices to ensure a more comprehensive understanding of the virus's impact on different demographic groups.…”