Genomic Surveillance of SARS-CoV-2 Variants at a Reference Cancer Hospital in Rio de Janeiro, Brazil

Abstract

Introduction: The fast SARS-CoV-2 spread and high mutation rates during viral replication led to virus diversification and the emergence of new variants. Genomic surveillance has been key to monitoring SARS-CoV-2 variants across the globe. Immune suppression, as observed in cancer patients, is a risk factor for SARS-CoV-2 infection and severe COVID-19. Objective: To report a two-year genomic surveillance of SARS-CoV-2 in cancer patients followed up at the Brazilian National Cancer Institute, Rio de Janeiro, Brazil. Method: Prospective observational study with 384 SARS-CoV-2+ swabs specimens collected and evaluated between October 2020 and September 2022. SARS-CoV-2 spike was analyzed by PCR and Sanger sequencing to determine the infecting variant. Results: Most of the patients had solid organ malignancies (298/384; 77.6%) and 16.1% (62/384) had metastatic disease. Severe COVID-19 cases accounted for 29.4% (113/384) and 27.1% (104/384) of deaths registered. The most common SARS-CoV-2 infecting variants were Gamma (n=137) and Omicron (BA.1) (n=73). The variant distribution overtime was similar to what has been reported for the general population of Brazil in the same period. When patients’ cancer topographies were analyzed, it was found that Gamma infected patients with breast (47/137; 34.3%) and cervical (11/137; 8%) cancer were more frequent than other variants, while Omicron predominated among rectum (10/122; 8.2%) and prostate (8/122; 6.6%) cancer compared to other variants. Conclusion: Genomic surveillance is an important tool for identifying and evaluating the impact of SARS-CoV-2 variants, and should continue especially in immunosuppressed populations.