{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T10:56:04Z","timestamp":1786964164669,"version":"build-2736575974"},"reference-count":40,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T00:00:00Z","timestamp":1758067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tunisian Ministry of Health","award":["LR20IPT02"],"award-info":[{"award-number":["LR20IPT02"]}]},{"name":"World Health Organization Tunisia office","award":["LR20IPT02"],"award-info":[{"award-number":["LR20IPT02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The SARS-CoV-2 Omicron variant has exhibited a rapid progression around the world, but its molecular insights in North Africa remain understudied. This study characterizes the genetic diversity, dynamics, and evolutionary trends of the Omicron variant in Tunisia over a 33-month period (December 2021\u2013August 2024). In total, 928 high-quality whole-genome sequences were considered in this study, of which 559 were retrieved from the GISAID database and 369 were generated in our laboratory. Phylogenetic analysis of the dominant subvariants (BA.1, BA.2, and BA.5) was performed using IQ-TREE. BA.2 was the predominant subvariant (38%), followed by BA.1 (24.0%), Omicron recombinants (19%), and BA.5 (18%). BA.2 diversified into JN, KP, and BN sub-lineages. Recombinants were dominated by XBB (98.8%), primarily including EG.4, XBB.1.5, and XBB.2.3.11, with rare detection of XDK and XDQ. Phylogenetic analysis revealed local clusters in BA.1, BA.2, and BA.5 alongside imported strains. Tunisia\u2019s Omicron wave was mainly driven by BA.2 and its recombinants, with evidence of localized viral evolution and sporadic introductions. The detection of rare recombinants underlines the importance of integrating regional genomic surveillance with epidemiological data in order to help guide future public health strategies.<\/jats:p>","DOI":"10.3390\/microorganisms13092162","type":"journal-article","created":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T05:59:51Z","timestamp":1758088791000},"page":"2162","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The Omicron Wave in Tunisia: Dynamic, Diversity, and Phylogenetic Analyses"],"prefix":"10.3390","volume":"13","author":[{"given":"Yasmine","family":"Chaari","sequence":"first","affiliation":[{"name":"Faculty of Pharmacy of Monastir, University of Monastir, Monastir 5000, Tunisia"},{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9705-4387","authenticated-orcid":false,"given":"Sondes","family":"Haddad-Boubaker","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haifa","family":"Khemiri","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wasfi","family":"Fares","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5616-0204","authenticated-orcid":false,"given":"Anissa","family":"Chouikha","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7547-1195","authenticated-orcid":false,"given":"Cesare","family":"Camma","sequence":"additional","affiliation":[{"name":"Department of Virology, Istituto Zooprofilattico Sperimentale dell\u2019Abruzzo e del Molise, 64100 Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6156-8212","authenticated-orcid":false,"given":"Alessio","family":"Lorusso","sequence":"additional","affiliation":[{"name":"Department of Virology, Istituto Zooprofilattico Sperimentale dell\u2019Abruzzo e del Molise, 64100 Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4026-0259","authenticated-orcid":false,"given":"Hanen","family":"Smaoui","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia"},{"name":"Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia"},{"name":"Laboratory of Microbiology, Bechir Hamza Children\u2019s Hospital, Tunis 1006, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3312-8265","authenticated-orcid":false,"given":"Khaoula","family":"Meftah","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia"},{"name":"Laboratory of Microbiology, Microbiology of Children and Immunocompromised, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia"},{"name":"Laboratory of Microbiology, Bechir Hamza Children\u2019s Hospital, Tunis 1006, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3240-3045","authenticated-orcid":false,"given":"Ouafa","family":"Kallala","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Sahloul Hospital of Sousse, Sousse 4054, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdelhalim","family":"Trabelsi","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Sahloul Hospital of Sousse, Sousse 4054, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amel","family":"Chtourou","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Habib Bourguiba University Hospital, Rue El Ferdaous, Sfax 3003, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Awatef","family":"Taktak","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Habib Bourguiba University Hospital, Rue El Ferdaous, Sfax 3003, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0610-2708","authenticated-orcid":false,"given":"Olfa","family":"Bahri","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia"},{"name":"Laboratory of Microbiology and Biochemistry, Aziza Othmana Hospital, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8175-1743","authenticated-orcid":false,"given":"Manel","family":"Hamdoun","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia"},{"name":"Laboratory of Microbiology and Biochemistry, Aziza Othmana Hospital, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yassine","family":"Chaabouni","sequence":"additional","affiliation":[{"name":"Laboratory of Medical Biology, Ibn El Jazzar Hospital, Kairouan 3100, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henda","family":"Touzi","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amel","family":"Sadraoui","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zina","family":"Meddeb","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3326-9861","authenticated-orcid":false,"given":"Nissaf","family":"Ben Alaya","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia"},{"name":"National Observatory of New and Emergent Diseases, Ministry of Health, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2031-6534","authenticated-orcid":false,"given":"Mariem","family":"Gdoura","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Department of Virology, Faculty of Pharmacy of Monastir, University of Monastir, Monastir 5000, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henda","family":"Triki","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belv\u00e9d\u00e8re, Tunis 1002, Tunisia"},{"name":"Research Laboratory \u201cViruses, Vectors, and Hosts\u201d (LR20IPT02), Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Clinical Investigation Center (CIC), Institute Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Department of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,17]]},"reference":[{"key":"ref_1","first-page":"157","article-title":"WHO Declares COVID-19 a Pandemic","volume":"91","author":"Cucinotta","year":"2020","journal-title":"Acta Biomed."},{"key":"ref_2","unstructured":"World Health Organization (2024, June 02). COVID-19 Cases|WHO COVID-19 Dashboard. Available online: https:\/\/data.who.int\/dashboards\/covid19\/cases."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1016\/S0140-6736(20)30185-9","article-title":"A Novel Coronavirus Outbreak of Global Health Concern","volume":"395","author":"Wang","year":"2020","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Rouzine, I.M. (2025). Evolutionary mechanisms of the emergence of the variants of concern of SARS-CoV-2. Viruses, 17.","DOI":"10.3390\/v17020197"},{"key":"ref_5","unstructured":"World Health Organization (2024, November 13). Tracking SARS-CoV-2 Variants. Available online: https:\/\/www.who.int\/activities\/tracking-SARS-CoV-2-variants."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1038\/s41564-020-0770-5","article-title":"A Dynamic Nomenclature Proposal for SARS-CoV-2 Lineages to Assist Genomic Epidemiology","volume":"5","author":"Rambaut","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Chatterjee, S., Bhattacharya, M., Nag, S., Dhama, K., and Chakraborty, C. (2023). A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies. Viruses, 15.","DOI":"10.3390\/v15010167"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"102332","DOI":"10.1016\/j.tmaid.2022.102332","article-title":"Is Omicron the End of Pandemic or Start of a New Innings?","volume":"48","author":"Das","year":"2022","journal-title":"Travel Med. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1002\/mco2.110","article-title":"SARS-CoV-2 Omicron Variant: Characteristics and Prevention","volume":"2","author":"He","year":"2021","journal-title":"MedComm"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Shah, M., and Woo, H.G. (2022). Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.830527"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.cytogfr.2023.03.001","article-title":"Immune Evasion of Neutralizing Antibodies by SARS-CoV-2 Omicron","volume":"70","author":"Wang","year":"2023","journal-title":"Cytokine Growth Factor Rev."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"106727","DOI":"10.1016\/j.ijsu.2022.106727","article-title":"Emergence of Novel Omicron Hybrid Variants: BA(x), XE, XD, XF More Than Just Alphabets","volume":"104","author":"Thakur","year":"2022","journal-title":"Int. J. Surg."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Chouikha, A., Fares, W., Laamari, A., Haddad-Boubaker, S., Belaiba, Z., Ghedira, K., Kammoun Rebai, W., Ayouni, K., Khedhiri, M., and Ben Halima, S. (2022). Molecular epidemiology of SARS-CoV-2 in Tunisia (North Africa) through several successive waves of COVID-19. Viruses, 14.","DOI":"10.3390\/v14030624"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Haddad-Boubaker, S., Arbi, M., Souiai, O., Chouikha, A., Fares, W., Edington, K., Sims, S., Camma, C., Lorusso, A., and Diagne, M.M. (2023). 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, 10.","DOI":"10.3389\/fpubh.2022.990832"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"199353","DOI":"10.1016\/j.virusres.2024.199353","article-title":"Dynamic of SARS-CoV-2 Variants Circulation in Tunisian Pediatric Population, During Successive Waves, from March 2020 to September 2022","volume":"344","author":"Khemiri","year":"2024","journal-title":"Virus Res."},{"key":"ref_16","unstructured":"(2025, April 09). GISAID Initiative. Available online: https:\/\/www.epicov.org\/epi3\/frontend#d95e5."},{"key":"ref_17","unstructured":"(2025, June 16). NCBI VirusBethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information, Available online: https:\/\/www.ncbi.nlm.nih.gov\/labs\/virus\/vssi\/#\/."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_20","unstructured":"Rambaut, A. (2025, April 09). FigTree v1.3.1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh. Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"104869","DOI":"10.1016\/j.meegid.2021.104869","article-title":"One Year into the Pandemic: Short-Term Evolution of SARS-CoV-2 and Emergence of New Lineages","volume":"92","author":"Shaw","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1556\/030.2024.02247","article-title":"Unveiling the Emergence of SARS-CoV-2 JN.1 Sub-Variant: Insights from the First Cases at Charles Nicolle Hospital, Tunisia","volume":"71","author":"Hamzaoui","year":"2024","journal-title":"Acta Microbiol. Immunol. Hung."},{"key":"ref_23","first-page":"664","article-title":"Exploratory Analysis of SARS-CoV-2 Omicron Variant and Its Subvariant Propagation: Global Predominance of BA.1, BA.2, BA.5, BE.1, and BQ.1","volume":"89","author":"Muthusami","year":"2023","journal-title":"Proc. Indian Natl. Sci. Acad. Part A Phys. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e70215","DOI":"10.1002\/jmv.70215","article-title":"Genomic Epidemiology of the Main SARS-CoV-2 Variants Circulating in Italy During the Omicron Era","volume":"97","author":"Bergna","year":"2025","journal-title":"J. Med. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1002\/jmv.27526","article-title":"Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike Protein","volume":"94","author":"Kumar","year":"2022","journal-title":"J. Med. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Menasria, T., and Aguilera, M. (2022). Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020467"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Abroug, H., Ouanes-Besbes, L., Dachraoui, F., Ouanes, I., Addad, F., Hdiji, A., and Ben Romdhane, H. (2024). Impact of Pharmaceutical and Non-Pharmaceutical Interventions on COVID-19 in Tunisia. BMC Public Health, 24.","DOI":"10.1186\/s12889-024-19236-9"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"100503","DOI":"10.1016\/j.ijregi.2024.100503","article-title":"SARS-CoV-2 Omicron XBB Infections Boost Cross-Variant Neutralizing Antibodies, Potentially Explaining the Observed Delay of the JN.1 Wave in Some Brazilian Regions","volume":"14","author":"Tort","year":"2024","journal-title":"IJID Reg."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7033","DOI":"10.1038\/s41467-024-51141-y","article-title":"Molecular Epidemiology and Population Immunity of SARS-CoV-2 in Guangdong (2022\u20132023) Following a Pivotal Shift in the Pandemic","volume":"15","author":"Li","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e03220","DOI":"10.1128\/mbio.03220-23","article-title":"Molecular and Structural Insights into SARS-CoV-2 Evolution: From BA.2 to XBB Subvariants","volume":"15","author":"Yajima","year":"2024","journal-title":"mBio"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/s41586-022-04980-y","article-title":"BA.2.12.1, BA.4 and BA.5 Escape Antibodies Elicited by Omicron Infection","volume":"608","author":"Cao","year":"2022","journal-title":"Nature"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1016\/S1473-3099(23)00271-2","article-title":"Associations of COVID-19 Symptoms with Omicron Subvariants BA.2 and BA.5, Host Status, and Clinical Outcomes: A registry-based observational study in Sapporo, Japan","volume":"23","author":"Nakakubo","year":"2023","journal-title":"Lancet Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Focosi, D., and Maggi, F. (2022). Recombination in Coronaviruses, with a Focus on SARS-CoV-2. Viruses, 14.","DOI":"10.3390\/v14061239"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.cell.2022.12.018","article-title":"Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants","volume":"186","author":"Wang","year":"2023","journal-title":"Cell"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"2800","DOI":"10.1038\/s41467-023-38435-3","article-title":"Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants","volume":"14","author":"Tamura","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_36","unstructured":"Chia, T.R.T., Young, B.E., and Chia, P.Y. (2025, April 01). The Omicron-Transformer: Rise of the Subvariants in the Age of Vaccines. Annals Singapore. Available online: https:\/\/annals.edu.sg\/the-omicron-transformer-rise-of-the-subvariants-in-the-age-of-vaccines\/."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Focosi, D., Quiroga, R., McConnell, S., Johnson, M.C., and Casadevall, A. (2023). Convergent evolution in SARS-CoV-2 spike creates a variant soup from which new COVID-19 waves emerge. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24032264"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Sil, D., Gautam, S., Saxena, S., Joshi, S., Kumar, D., Mehta, A., Jindal, P., Sharma, S., Pandey, P. (2025, March 25). Comprehensive Analysis of Omicron Subvariants: EG.5 Rise, Vaccination Strategies, and Global Impact. EurekaSelect. Available online: https:\/\/www.eurekaselect.com\/article\/140269.","DOI":"10.2174\/0113894501296586240430061915"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"165","DOI":"10.36519\/idcm.2023.251","article-title":"COVID-19: An Update on Epidemiology, Prevention and Treatment, September-2023","volume":"5","year":"2023","journal-title":"Infect. Dis. Clin. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Chakraborty, A.K. (2024). Rapid Worldwide Spread of 17MPLF Spike Insertion Mutants (JN.1-JN.1.25, KP.1, KP.2, KQ.1, KR.1, XDD, XDP, XDK, XDQ Subvariants) of Omicron Coronaviruses and Spike Gene 5\u2032-End Sequencing Problem. SciTe.ai. ResearchSquare, 1\u201321.","DOI":"10.21203\/rs.3.rs-4741070\/v1"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/9\/2162\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:46:47Z","timestamp":1760035607000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/9\/2162"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,17]]},"references-count":40,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["microorganisms13092162"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms13092162","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,17]]}}}