{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T22:01:07Z","timestamp":1763071267773,"version":"build-2065373602"},"reference-count":30,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T00:00:00Z","timestamp":1674864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible \u00df-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection. Case presentation. We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin\u2019s lymphoma and COVID-19. We used RT-qPCR to quantify SARS-CoV-2 viral load over time and whole-virus genome sequencing to identify viral lineage and mutation profile. The patient presented with a persistent infection through 102 days while being treated with cytotoxic chemotherapy for non-Hodgkin\u2019s lymphoma and received targeted therapy for COVID-19 with remdesivir and hyperimmune plasma. All sequenced samples belonged to the BA.1.1 lineage. We detected nine amino acid substitutions in five viral genes (Nucleocapsid, ORF1a, ORF1b, ORF13a, and ORF9b), grouped in two clusters: the first cluster with amino acid substitutions only detected on days 39 and 87 of sample collection, and the second cluster with amino acid substitutions only detected on day 95 of sample collection. The Spike gene remained unchanged in all samples. Viral load was dynamic but consistent with the disease flares. Conclusions. This report shows that the multiple mutations that occur in an immunocompromised patient with persistent COVID-19 could provide information regarding viral evolution and emergence of new SARS-CoV-2 variants.<\/jats:p>","DOI":"10.3390\/v15020377","type":"journal-article","created":{"date-parts":[[2023,1,30]],"date-time":"2023-01-30T07:34:41Z","timestamp":1675064081000},"page":"377","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin\u2019s Lymphoma"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5750-884X","authenticated-orcid":false,"given":"Rodrigo","family":"Villase\u00f1or-Echavarri","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"},{"name":"School of Medicine, Universidad Panamericana, Mexico City 03920, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9685-6492","authenticated-orcid":false,"given":"Laura","family":"Gomez-Romero","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8627-404X","authenticated-orcid":false,"given":"Alexandra","family":"Martin-Onraet","sequence":"additional","affiliation":[{"name":"School of Medicine, Universidad Panamericana, Mexico City 03920, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3998-9306","authenticated-orcid":false,"given":"Luis A.","family":"Herrera","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"},{"name":"Unidad de Investigaci\u00f3n Biom\u00e9dica en C\u00e1ncer, Instituto Nacional de Cancerolog\u00eda-Instituto de Investigaciones Biom\u00e9dicas, UNAM, Mexico City 14080, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3834-4709","authenticated-orcid":false,"given":"Marco A.","family":"Escobar-Arrazola","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"},{"name":"Unidad de Investigaci\u00f3n Biom\u00e9dica en C\u00e1ncer, Instituto Nacional de Cancerolog\u00eda-Instituto de Investigaciones Biom\u00e9dicas, UNAM, Mexico City 14080, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2246-4485","authenticated-orcid":false,"given":"Oscar A.","family":"Ramirez-Vega","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"},{"name":"Unidad de Investigaci\u00f3n Biom\u00e9dica en C\u00e1ncer, Instituto Nacional de Cancerolog\u00eda-Instituto de Investigaciones Biom\u00e9dicas, UNAM, Mexico City 14080, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7449-5961","authenticated-orcid":false,"given":"Coraz\u00f3n","family":"Barrientos-Flores","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfredo","family":"Mendoza-Vargas","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2315-3977","authenticated-orcid":false,"given":"Alfredo","family":"Hidalgo-Miranda","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8564-8735","authenticated-orcid":false,"given":"Diana","family":"Vilar-Compte","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Instituto Nacional de Cancerolog\u00eda, Mexico City 14080, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8708-462X","authenticated-orcid":false,"given":"Alberto","family":"Cedro-Tanda","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Medicina Gen\u00f3mica, Mexico City 14610, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2020.08.011","article-title":"The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic 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