{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T18:07:44Z","timestamp":1777486064761,"version":"3.51.4"},"reference-count":44,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tunisian Ministry of Health"},{"name":"Tunisian Ministry of Higher Education and Research","award":["LR20IPT02"],"award-info":[{"award-number":["LR20IPT02"]}]},{"name":"World Health Organization, Tunisia office"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Enteroviruses (EVs) are small, non-enveloped RNA viruses that can cause diverse clinical outcomes, particularly severe in patients with primary immunodeficiency (PID) due to their impaired ability to clear infections. This study aimed to characterize EV excretion among 138 Tunisian PID patients over a five-year period, to identify circulating EV serotypes and assess their genetic diversity. A total of 558 stool samples were collected and analyzed by virus isolation and intratypic differentiation using RT-qPCR. Molecular typing was performed through Sanger sequencing of the VP1 region and whole genome sequencing using Next-Generation Sequencing (NGS) technologies. Phylogenetic analysis was conducted using the Maximum Likelihood (ML) method. EVs were detected in 55 stool samples from 23 patients. The excretion kinetics of EVs ranged between 30 and 946 days. Thirteen serotypes were identified, including one Poliovirus (PV) and twelve Non-Polio Enteroviruses (NPEVs), predominantly belonging to species B. Two previously unreported serotypes in Tunisia were detected: Coxsackievirus A5 (CVA5) and Echovirus type 19 (E19). In addition, five patients presented enhanced susceptibility to the excretion of successive EV serotypes, and one patient exhibited a co-infection. A possible recombination event was identified in one patient involving Coxsackievirus B5 (CVB5), Coxsackievirus A9 (CVA9) and Coxsackievirus B1 (CVB1) sequences. Phylogenetic analysis showed close genetic relationships with European, American and Asian strains. These findings underscore the dynamic nature of EV circulation and the importance of ongoing molecular surveillance to detect emerging serotypes and guide public health strategies.<\/jats:p>","DOI":"10.3390\/microorganisms14020329","type":"journal-article","created":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T11:09:22Z","timestamp":1769771362000},"page":"329","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genetic Diversity and Excretion Kinetics of Enteroviruses Excreted by Patients with Primary Immunodeficiency in Tunisia over a Five-Year Period (2020\u20132024)"],"prefix":"10.3390","volume":"14","author":[{"given":"Imene","family":"Ben Salem","sequence":"first","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur of Tunis, 13 Place Pasteur, le Belvedere, Tunis 1002, Tunisia"},{"name":"Laboratory of Virus, Host and Vectors (LR 20 IPT 02), Institute Pasteur of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haifa","family":"Khemiri","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur of Tunis, 13 Place Pasteur, le Belvedere, Tunis 1002, Tunisia"},{"name":"Laboratory of Virus, Host and Vectors (LR 20 IPT 02), Institute Pasteur of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5722-1646","authenticated-orcid":false,"given":"Marwa","family":"Khedhiri","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur of Tunis, 13 Place Pasteur, le Belvedere, Tunis 1002, Tunisia"},{"name":"Laboratory of Virus, Host and Vectors (LR 20 IPT 02), Institute Pasteur of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Najla","family":"Mekki","sequence":"additional","affiliation":[{"name":"Laboratory of Transmission, Control and Immunology of Infections (LR 16 IPT 02), Department of Immunobiology of Infections, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"Faculty of Medicine, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Line","family":"Joffret","sequence":"additional","affiliation":[{"name":"Virus Sensing and Signaling Unit, CNRS UMR 3569, Institut Pasteur, Universit\u00e9 de Paris Cit\u00e9, 75006 Paris, France"},{"name":"Laboratoire Associ\u00e9 Au Centre National de R\u00e9f\u00e9rence Ent\u00e9rovirus\/Par\u00e9chovirus, 75015 Paris, 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Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institute Pasteur of Tunis, 13 Place Pasteur, le Belvedere, Tunis 1002, Tunisia"},{"name":"Laboratory of Virus, Host and Vectors (LR 20 IPT 02), Institute Pasteur of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monia","family":"Ouederni","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, University of Tunis El Manar, Tunis 1002, Tunisia"},{"name":"National Bone Marrow Transplant Center, Tunis 1002, Tunisia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6758-9591","authenticated-orcid":false,"given":"Ma\u00ebl","family":"Bessaud","sequence":"additional","affiliation":[{"name":"Virus Sensing and Signaling Unit, CNRS UMR 3569, Institut Pasteur, Universit\u00e9 de Paris Cit\u00e9, 75006 Paris, France"},{"name":"Laboratoire Associ\u00e9 Au Centre National de 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