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. 2023 Jan 4:10:990832.
doi: 10.3389/fpubh.2022.990832. eCollection 2022.

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  1   2   3 , Marwa Arbi  1   4 , Oussema Souiai  4 , Anissa Chouikha  1   2   3 , Wasfi Fares  1   2   3 , Kate Edington  5 , Sam Sims  5 , Cesare Camma  6 , Alessio Lorusso  6 , Moussa Moïse Diagne  7 , Amadou Diallo  7 , Ilhem Boutiba Ben Boubaker  8   9 , Sana Ferjani  8   9 , Maha Mastouri  10   11 , Salma Mhalla  10   11 , Hela Karray  12 , Saba Gargouri  12 , Olfa Bahri  13 , Abdelhalim Trabelsi  14 , Ouafa Kallala  14 , Naila Hannachi  15 , Yassine Chaabouni  16   17 , Hanen Smaoui  17   18   19 , Khaoula Meftah  17   18   19 , Sophia Besbes Bouhalila  20 , Soumaya Foughali  21 , Mariem Zribi  22 , Asma Lamari  1   2 , Henda Touzi  1   2   3 , Mouna Safer  23 , Nissaf Ben Alaya  17   23 , Alia Ben Kahla  4 , Mariem Gdoura  1   2   3   24 , Henda Triki  1   2   3   17
Affiliations

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 et al. Front Public Health. .

Abstract

Introduction: The 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.

Methods: Viral 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.

Results: The 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.

Discussion: This 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.

Keywords: AY.122; Delta variant; SARS-CoV2; next-generation sequencing; phylogeny; spatio-temporal dynamic.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
COVID-19 confirmed case counts in Tunisia starting from March 2020 (https://covid19.who.int/region/emro/country/tn, accessed by 18/03/2022) and sample collection period.
Figure 2
Figure 2
Distribution of Delta SARS-CoV2 sequences according to the age.
Figure 3
Figure 3
Distribution of Delta sub-lineages, during the study period. (A) Global distribution. (B) Temporal distribution. (C) Geographic distribution of Delta sub-lineages, during the study period. Delta sub-lineages are indicated by colored circles, as indicated in the legend.
Figure 4
Figure 4
Mutational cascade of AY.122 variant emerged in Tunisia with respect to first reported AY.122 strain. The panels (A–D) show the most mutated samples, mutations per sample, most frequent events per class of mutation, most frequent mutational events per type, respectively.
Figure 5
Figure 5
Phylogenetic analysis of AY.122 sub-lineage's Delta strains obtained in Tunisia between May and December. The Maximum Likelihood tree was obtained by comparison of 391 High quality AY.122 genomes obtained from Tunisia and other regions of the word. Tunisian sequences are indicated in Green (Cluster1), Blue (Cluster 2) and Pink (Cluster3) and other sequences different the world in Black. The tree was generated by IqTree software with 1000 boostrap cycles and visualized by FigTree software.
Figure 6
Figure 6
Mutational profile of Tunisian sequences from Cluster 1, 2 and 3 in comparison with the AY.122 sub-lineage.
Figure 7
Figure 7
Spatial dynamics of AY.122 Delta variant of SARS-CoV-2 among different Tunisian governorates. The snapshots (A–F) show the different stages of AY.122 variant spread in Tunisian governorates. Transition lines linking different locations represent the branches in the MCC. Diameters of the circles are proportional to square root of the number of MCC branches maintaining a particular location state at each time point.
Figure 8
Figure 8
Chord diagram of theAY.122 SARS-CoV-2 variant representing Bayes Factor (BF) of transitions between different locations in Tunisia. (A) BF of transitions between Tunisian governorates. (B) BF of transitions between Tunisian regions. Tunisian governorates and regions are presented by different colors. Chord width is proportional to BF support levels: BF <3 no support, BF > 3 substantial support, BF > 10 strong support, BF > 30 very strong support, BF > 100 decisive support.
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