Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-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’s 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’s 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.

Objectives: Vaccination is the best preventive measure for SARS-CoV-2 infection; however, efficacy is lower in cancer patients. During the pandemic period, Mexico was characterized by the use of seven different COVID-19 vaccine platforms, and oncologic patients were not prioritized for vaccination. We report the outcomes of COVID-19 in cancer patients after the beginning of the national vaccine campaign in Mexico. Methods: All patients with cancer and COVID-19 diagnosed at Instituto Nacional de Cancerología from 14 February 2021 to 28 February 2022 were included. Primary outcomes were the proportion of individuals who required hospital admission and/or invasive mechanical ventilation, according to the vaccination status; 30-day mortality; the period of infection; and other cancer-related variables. Results: A total of 691 patients were included; 524 (76%) had solid tumors (STs), and 167 (24%) had hematologic malignancies (HMs). Patients infected in the first two periods, had lower rates of vaccination and higher rates of mortality and hospitalization compared to those infected in the Omicron period. In the multivariate analysis, vaccination status was independently associated with hospitalization in patients with STs (aOR 0.38, 95%CI 0.19–0.75, p = 0.005), but it was not associated with invasive mechanical ventilation and 30-day mortality. In those with HMs, vaccination status was not associated with any outcome; in this group, only recent chemotherapy and time of infection were associated with invasive ventilation. Conclusions: Vaccination significantly reduced hospital admissions in patients with STs. Infections occurring during the Omicron period were associated with improved outcomes in both ST and HM patients. Despite having a lesser impact in immunosuppressed patients, vaccination is an essential strategy, and access to vaccination campaigns in patients with cancer needs to be prioritized.