{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:10:16Z","timestamp":1787163016600,"version":"build-2736575974"},"reference-count":86,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T00:00:00Z","timestamp":1716854400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2024,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Severe acute respiratory syndrome coronavirus\u20102 (SARS\u2010CoV\u20102) persistence in COVID\u201019 patients could play a key role in the emergence of variants of concern. The rapid\n                    <jats:italic>intra<\/jats:italic>\n                    \u2010host evolution of SARS\u2010CoV\u20102 may result in an increased transmissibility, immune and therapeutic escape which could be a direct consequence of COVID\u201019 epidemic currents. In this context, a longitudinal retrospective study on eight consecutive COVID\u201019 patients with persistent SARS\u2010CoV\u20102 infection, from January 2022 to March 2023, was conducted. To characterize the\n                    <jats:italic>intra<\/jats:italic>\n                    \u2010 and\n                    <jats:italic>inter<\/jats:italic>\n                    \u2010host viral evolution, whole genome sequencing and phylogenetic analysis were performed on nasopharyngeal samples collected at different time points. Phylogenetic reconstruction revealed an accelerated SARS\u2010CoV\u20102\n                    <jats:italic>intra<\/jats:italic>\n                    \u2010host evolution and emergence of antigenically divergent variants. The Bayesian inference and principal coordinate analysis analysis showed a host\u2010based genomic structuring among antigenically divergent variants, that might reflect the positive effect of containment practices, within the critical hospital area. All longitudinal antigenically divergent isolates shared a wide range of amino acidic (aa) changes, particularly in the Spike (S) glycoprotein, that increased viral transmissibility (K417N, S477N, N501Y and Q498R), enhanced infectivity (R346T, S373P, R408S, T478K, Q498R, Y505H, D614G, H655Y, N679K and P681H), caused host immune escape (S371L, S375F, T376A, K417N, and K444T\/R) and displayed partial or complete resistance to treatments (G339D, R346K\/T, S371F\/L, S375F, T376A, D405N, N440K, G446S, N460K, E484A, F486V, Q493R, G496S and Q498R). These results suggest that multiple novel variants which emerge in the patient during persistent infection, might spread to another individual and continue to evolve. A pro\u2010active genomic surveillance of persistent SARS\u2010CoV\u20102 infected patients is recommended to identify genetically divergent lineages before their diffusion.\n                  <\/jats:p>","DOI":"10.1002\/jmv.29708","type":"journal-article","created":{"date-parts":[[2024,5,28]],"date-time":"2024-05-28T05:39:45Z","timestamp":1716874785000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Persistence of SARS\u2010CoV\u20102 infection and viral\n                    <i>intra<\/i>\n                    \u2010 and\n                    <i>inter<\/i>\n                    \u2010host evolution in COVID\u201019 hospitalized patients"],"prefix":"10.1002","volume":"96","author":[{"given":"Grazia","family":"Pavia","sequence":"first","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela","family":"Quirino","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadia","family":"Marascio","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia","family":"Veneziano","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine \u201cMagna Graecia\u201d University of Catanzaro Catanzaro Italy"},{"name":"Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology \u201cMagna Gr\u00e6cia\u201d University of Catanzaro Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Federico","family":"Longhini","sequence":"additional","affiliation":[{"name":"Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences \u201cMagna Graecia\u201d University Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Bruni","sequence":"additional","affiliation":[{"name":"Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences \u201cMagna Graecia\u201d University Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugenio","family":"Garofalo","sequence":"additional","affiliation":[{"name":"Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences \u201cMagna Graecia\u201d University Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Pantanella","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"Manno","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simona","family":"Gigliotti","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aida","family":"Giancotti","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgio Settimo","family":"Barreca","sequence":"additional","affiliation":[{"name":"Unit of Clinical Microbiology, Department of Health Sciences \u201cMagna Gr\u00e6cia\u201d University Hospital Catanzaro Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Branda","sequence":"additional","affiliation":[{"name":"Unit of Medical Statistics and Molecular Epidemiology Universit\u00e0 Campus Bio\u2010Medico di Roma Rome Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7631-5453","authenticated-orcid":false,"given":"Carlo","family":"Torti","sequence":"additional","affiliation":[{"name":"Dipartimento di Scienze di Laboratorio e Infettivologiche Fondazione Policlinico Universitario \u201cA. 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