{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:14:25Z","timestamp":1792790065843,"version":"4.5.0"},"reference-count":47,"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":"Direccion General de Politicas de Investigacion en Salud","award":["FPIS2024-INER-4886"],"award-info":[{"award-number":["FPIS2024-INER-4886"]}]},{"name":"Direccion General de Politicas de Investigacion en Salud","award":["F003-2022-321366"],"award-info":[{"award-number":["F003-2022-321366"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Immunocompromised patients, including those with advanced HIV infection, hematologic malignancies treated with anti-CD20 monoclonal antibodies, or combined immunodeficiencies, are at increased risk of persistent SARS-CoV-2 infection. While long-term viral shedding has been described in these patients, the extent and nature of intra-host viral evolution during long-term infection remain insufficiently documented. In this study, we report longitudinal genomic analyses of SARS-CoV-2 from three immunocompromised individuals with persistent COVID-19: (i) a female patient with follicular lymphoma receiving bendamustine-rituximab therapy with 9 months of persistence, (ii) a male patient with advanced HIV infection following prolonged antiretroviral therapy interruption with 10 months of persistence, and (iii) a female patient with Good\u2019s Syndrome characterized by combined humoral and cellular immune deficiency with apparently four years of persistence. Replication-competent virus was detected over extended periods. Sequential whole-genome sequencing revealed the gradual accumulation of non-synonymous mutations across multiple viral genes, consistent with ongoing viral replication and intra-host diversification in the absence of effective immune control. Although based on a limited number of cases, these findings provide descriptive evidence that persistent SARS-CoV-2 infection in immunocompromised hosts can be associated with sustained viral evolution. This work highlights the importance of continued virological monitoring in selected patients with prolonged infection and contributes to the understanding of SARS-CoV-2 dynamics in settings of impaired immunity.<\/jats:p>","DOI":"10.3390\/v18020189","type":"journal-article","created":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T11:09:22Z","timestamp":1769771362000},"page":"189","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Molecular Characterization of Persistent SARS-CoV-2 Infections in Immunocompromised Patients"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1991-0923","authenticated-orcid":false,"given":"Patricia","family":"Volkow-Fern\u00e1ndez","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-2941","authenticated-orcid":false,"given":"Marco","family":"Villanueva-Reza","sequence":"additional","affiliation":[{"name":"Hospital Epidemiology and Infectology Department, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago","family":"\u00c1vila-R\u00edos","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Enfermedades Infecciosas, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-4900-5965","authenticated-orcid":false,"given":"Enrique","family":"Mendoza-Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology of Emergent Infectious Disease, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Am\u00e9rica Citlali","family":"Vera-Jimenez","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology of Emergent Infectious Disease, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8627-404X","authenticated-orcid":false,"given":"Alexandra","family":"Martin-Onraet","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8720-617X","authenticated-orcid":false,"given":"Beda","family":"Islas-Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8873-8573","authenticated-orcid":false,"given":"Pamela","family":"Alatorre-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rogelio","family":"P\u00e9rez-Padilla","sequence":"additional","affiliation":[{"name":"Department of Research in Tobacco and COPD, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7252-7666","authenticated-orcid":false,"given":"Daniel","family":"Carpio-Guadarrama","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-1827-3283","authenticated-orcid":false,"given":"Andrea","family":"C\u00e1rdenas-Ortega","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Enfermedades Infecciosas, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V\u00edctor Hugo","family":"Ahumada-Topete","sequence":"additional","affiliation":[{"name":"Hospital Epidemiology and Infectology Department, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clara","family":"Espitia","sequence":"additional","affiliation":[{"name":"Department of Immunology, Institute of Biomedical Research, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Mexico City 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3251-4236","authenticated-orcid":false,"given":"Karen Lizbeth","family":"Reyes-Barrera","sequence":"additional","affiliation":[{"name":"Department of Immunology, Institute of Biomedical Research, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Mexico City 04510, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7047-0222","authenticated-orcid":false,"given":"Edgar","family":"Sevilla-Reyes","sequence":"additional","affiliation":[{"name":"Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8508-3698","authenticated-orcid":false,"given":"Joel 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