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Haddad-Boubaker S, Arbi M, Souiai O, Chouikha A, Fares W, Edington K, Sims S, Camma C, Lorusso A, Diagne MM, Diallo A, Boubaker IBB, Ferjani S, Mastouri M, Mhalla S, Karray H, Gargouri S, Bahri O, Trabelsi A, Kallala O, Hannachi N, Chaabouni Y, Smaoui H, Meftah K, Bouhalila SB, Foughali S, Zribi M, Lamari A, Touzi H, Safer M, Alaya NB, Kahla AB, Gdoura M, Triki H. The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage. Front Public Health 2023; 10:990832. [PMID: 36684874 PMCID: PMC9846204 DOI: 10.3389/fpubh.2022.990832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
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.
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Affiliation(s)
- Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Marwa Arbi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Wasfi Fares
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kate Edington
- New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom
| | - Sam Sims
- New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom
| | - Cesare Camma
- Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy
| | - Alessio Lorusso
- Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy
| | | | - Amadou Diallo
- Department of Virology, Pasteur Institute of Dakar, Dakar, Senegal
| | - Ilhem Boutiba Ben Boubaker
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
- Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Sana Ferjani
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
- Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Maha Mastouri
- Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir, Tunisia
- Laboratory Research Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Salma Mhalla
- Laboratory of Microbiology, Fattouma Bourguiba Hospital, Monastir, Tunisia
- Laboratory Research Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Hela Karray
- Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Saba Gargouri
- Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Olfa Bahri
- Laboratory of Microbiology and Biochemistry, Aziza Othmana Hospital, Tunis, Tunisia
| | | | - Ouafa Kallala
- Laboratory of Virology, Sahloul Hospital of Sousse, Sousse, Tunisia
| | - Naila Hannachi
- Laboratory of Microbiology, Farhat Hached Hospital of Sousse, Sousse, Tunisia
| | - Yassine Chaabouni
- Laboratory of Medical Biology, Ibn El Jazzar Hospital, Kairouan, Tunisia
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanen Smaoui
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Khaoula Meftah
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Bechir Hamza Children's Hospital, Tunis, Tunisia
| | - Sophia Besbes Bouhalila
- Laboratory of Medical Biology and Blood Bank, Institute Mohamed Kassab d'orthopédie, Manouba, Tunisia
| | - Soumaya Foughali
- Laboratory of Medical Biology, Menzel Bourguiba Hospital, Bizerte, Tunisia
| | - Mariem Zribi
- Laboratory of Microbiology, La Rabta Hospital, Tunis, Tunisia
| | - Asma Lamari
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mouna Safer
- National Observatory of New and Emergent Diseases, Tunis, Tunisia
| | - Nissaf Ben Alaya
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- National Observatory of New and Emergent Diseases, Tunis, Tunisia
| | - Alia Ben Kahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Virology, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia
- Laboratory of Viruses, Hosts and Vectors, Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
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