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

Autor:	Haddad-Boubaker S; 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., Arbi M; 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., Souiai O; Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia., Chouikha A; 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., Fares W; 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., Edington K; New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom., Sims S; New Variant Assessment Platform (NVAP), UK Health Security Agency, London, United Kingdom., Camma C; Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy., Lorusso A; Department of Virology, Instituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale (IZSAM), Teramo, Italy., Diagne MM; Department of Virology, Pasteur Institute of Dakar, Dakar, Senegal., Diallo A; Department of Virology, Pasteur Institute of Dakar, Dakar, Senegal., Boubaker IBB; Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia.; Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia., Ferjani S; Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia.; Laboratory Research Antimicrobial Resistance, Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia., Mastouri M; 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., Mhalla S; 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., Karray H; Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia., Gargouri S; Laboratory of Microbiology, Habib Bourguiba Hospital, Sfax, Tunisia., Bahri O; Laboratory of Microbiology and Biochemistry, Aziza Othmana Hospital, Tunis, Tunisia., Trabelsi A; Laboratory of Virology, Sahloul Hospital of Sousse, Sousse, Tunisia., Kallala O; Laboratory of Virology, Sahloul Hospital of Sousse, Sousse, Tunisia., Hannachi N; Laboratory of Microbiology, Farhat Hached Hospital of Sousse, Sousse, Tunisia., Chaabouni Y; 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., Smaoui H; 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., Meftah K; 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., Bouhalila SB; Laboratory of Medical Biology and Blood Bank, Institute Mohamed Kassab d'orthopédie, Manouba, Tunisia., Foughali S; Laboratory of Medical Biology, Menzel Bourguiba Hospital, Bizerte, Tunisia., Zribi M; Laboratory of Microbiology, La Rabta Hospital, Tunis, Tunisia., Lamari A; 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., Touzi H; 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., Safer M; National Observatory of New and Emergent Diseases, Tunis, Tunisia., Alaya NB; Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia.; National Observatory of New and Emergent Diseases, Tunis, Tunisia., Kahla AB; Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur de Tunis, University of Tunis El-Manar, Tunis, Tunisia., Gdoura M; 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., Triki H; 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.
Jazyk:	angličtina
Zdroj:	Frontiers in public health [Front Public Health] 2023 Jan 04; Vol. 10, pp. 990832. Date of Electronic Publication: 2023 Jan 04 (Print Publication: 2022).
DOI:	10.3389/fpubh.2022.990832
Abstrakt:	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. Competing Interests: 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. (Copyright © 2023 Haddad-Boubaker, Arbi, Souiai, Chouikha, Fares, Edington, Sims, Camma, Lorusso, Diagne, Diallo, Boubaker, Ferjani, Mastouri, Mhalla, Karray, Gargouri, Bahri, Trabelsi, Kallala, Hannachi, Chaabouni, Smaoui, Meftah, Bouhalila, Foughali, Zribi, Lamari, Touzi, Safer, Alaya, Kahla, Gdoura and Triki.)
Databáze:	MEDLINE
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