Frontiers in Public Health (Jan 2023)

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

  • Sondes Haddad-Boubaker,
  • Sondes Haddad-Boubaker,
  • Sondes Haddad-Boubaker,
  • Marwa Arbi,
  • Marwa Arbi,
  • Oussema Souiai,
  • Anissa Chouikha,
  • Anissa Chouikha,
  • Anissa Chouikha,
  • Wasfi Fares,
  • Wasfi Fares,
  • Wasfi Fares,
  • Kate Edington,
  • Sam Sims,
  • Cesare Camma,
  • Alessio Lorusso,
  • Moussa Moïse Diagne,
  • Amadou Diallo,
  • Ilhem Boutiba Ben Boubaker,
  • Ilhem Boutiba Ben Boubaker,
  • Sana Ferjani,
  • Sana Ferjani,
  • Maha Mastouri,
  • Maha Mastouri,
  • Salma Mhalla,
  • Salma Mhalla,
  • Hela Karray,
  • Saba Gargouri,
  • Olfa Bahri,
  • Abdelhalim Trabelsi,
  • Ouafa Kallala,
  • Naila Hannachi,
  • Yassine Chaabouni,
  • Yassine Chaabouni,
  • Hanen Smaoui,
  • Hanen Smaoui,
  • Hanen Smaoui,
  • Khaoula Meftah,
  • Khaoula Meftah,
  • Khaoula Meftah,
  • Sophia Besbes Bouhalila,
  • Soumaya Foughali,
  • Mariem Zribi,
  • Asma Lamari,
  • Asma Lamari,
  • Henda Touzi,
  • Henda Touzi,
  • Henda Touzi,
  • Mouna Safer,
  • Nissaf Ben Alaya,
  • Nissaf Ben Alaya,
  • Alia Ben Kahla,
  • Mariem Gdoura,
  • Mariem Gdoura,
  • Mariem Gdoura,
  • Mariem Gdoura,
  • Henda Triki,
  • Henda Triki,
  • Henda Triki,
  • Henda Triki

DOI
https://doi.org/10.3389/fpubh.2022.990832
Journal volume & issue
Vol. 10

Abstract

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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.

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