SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin's Lymphoma.

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.

Impact of COVID-19 pandemic in the care of people living with HIV and cancer at an oncologic center in Mexico.

BACKGROUND: People living with HIV(PLWH) and cancer are among the most vulnerable patients and require constant access to medical services. We compared the characteristics of PLWH and cancer in Mexico, before and during the COVID-19 pandemic. METHODS: Patients admitted 1 year before (pre-pandemic) and 1 year after the start of the pandemic (pandemic) were included. Clinical characteristics, HIV-related variables, and 90-day mortality were compared. Data are described a proportions (N,%) and central tendency measures. A multiple regression model for variables associated with 90-day mortality was performed. RESULTS: Seventy-nine patients were seen in the pre-pandemic period; 92 during the pandemic. Main diagnoses were Kaposi Sarcoma and lymphoma. CD4+ cell count at diagnosis was lower during the pandemic: 81 cells/mm3 vs. 128 cells/mm3, p = .035. CD4+<100 cells/mm3 at first consultation increased from 41% to 58% during the pandemic (p = .041). Only BMI <20 kg/m2 was associated to death (aOR 8.27, 95%CI 1.74-39.25) (p = .008). The pandemic period was not associated with a higher 90-day mortality. CONCLUSIONS: PLWH and cancer presented to care with advanced disease overall. This was more pronounced during the pandemic period. Mortality was associated with AIDS-related variables regardless of study period. This underscores the need for strategies to maintain in-person access to health-care services for PLWH.

Use of remdesivir for COVID-19 in patients with hematologic cancer.

PURPOSES: Patients with hematologic malignancies (HM) are among the individuals with highest risk of COVID-19 complications. We report the impact of remdesivir in patients with hematologic malignancies (HM) during Omicron in Mexico City. METHODS: All patients with HM and COVID-19 during December 2021-March 2022 were included. Socio-demographic and clinical data were collected. The primary outcome was COVID-19 progression. Variables associated with progression were analyzed. RESULTS: 115 patients were included. Median age was 50 years (IQR 35-63); 36% (N = 41) had at least one comorbidity. Fifty-two percent had non-Hodgkin lymphoma. Fifty patients (44%) had at least two doses of SARS-CoV-2 vaccine. COVID-19 was classified as mild (52.6%), moderate (9.7%), and severe/critical (28%). Twenty-eight patients (24%) received remdesivir. Nine patients received remdesivir at the ambulatory clinic (33%), the rest during hospital admission. Overall, 22(19%) patients progressed to severe/critical COVID-19; nine died due to COVID-19(8%). Hospital admission for non-COVID-19 causes was associated with higher odds of progression. Remdesivir did not reduce the risk of progression in hospitalized patients; none of the patients who received remdesivir in the ambulatory clinic progressed to severe COVID-19 or died. CONCLUSIONS: Patients with HM and COVID-19 continue to present with high risk of complications. More prospective studies are needed to define the impact of antivirals in this high-risk group, including the best duration of treatment. Also, better vaccine coverage and access to treatment are mandatory.

Clinical characteristics and outcomes in a cohort of oncologic patients with COVID-19 during the first year of the pandemic in Mexico.

BACKGROUND: Literature on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in cancer patients is scarce in Latin America. This population seems to have a higher risk for adverse outcomes. This study aims to correlate clinical characteristics with outcomes in patients with cancer. METHODS: We included all patients with cancer and confirmed SARS-CoV-2 infection from April 19 to December 31, 2020, at the Instituto Nacional de Cancerologia, Mexico. Clinical information was obtained from medical and epidemiological records. For the association between variables and hospitalization, invasive mechanical ventilation (IMV), and mortality, univariate and multivariate logistic regression were performed; odds ratios and 95% confidence intervals were calculated. RESULTS: Four hundred thirty-three patients were included; 268 (62%) were female, the median age was 55 years. One hundred thirty-five (31%), 131 (30%), and 93 (21%) patients had obesity, hypertension, and diabetes mellitus (DM), respectively. Three hundred forty-one (79%) had solid cancer. One hundred seventy (39%) had advanced cancer. Two hundred (46%) patients were hospitalized. Age (p < 0.01), male gender (p = 0.03), hematological malignancies (HM) (p = 0.04) and advanced cancer (p = 0.03) increased the risk for hospital admission. Forty-five (10%) patients required IMV. Age (p = 0.02); DM (p = 0.04); high C-reactive protein (p < 0.01), and lactate dehydrogenase (p = 0.03) were associated with IMV. Mortality within 30 days after diagnosis was 18% (76 cases). Associated characteristics were age (p = 0.04) and low albumin (p < 0.01). CONCLUSIONS: In this study, patients with cancer showed higher mortality, need for hospitalization, and IMV compared with other non-cancer cohorts. We did not find an increased risk in mortality for HM. Although our cohort was younger than others previously reported, age was a strong predictor of adverse outcomes. Variables associated with IMV and death were similar to those previously described in cancer patients with COVID-19.