ROLE OF SARS-COV-2 LINEAGE IN COVID-19 IN CANCER PATIENTS

SARS-CoV-2 infection and resulting COVID-19 remains a significant concern for oncology patients, making it important to understand COVID-19 treatment and outcomes within this patient population. More specifically, understanding how the variety of SARS-CoV-2 lineages observed to date during the pandemic have differentially impacted clinical outcomes may help guide care as novel lineages continue to emerge. Here, we analyzed a cohort of one hundred patients with a clinical history of cancer, taken as a subgroup of a large university hospital SARS-CoV-2 surveillance study. Following a positive viral PCR test, SARS-CoV-2 genomes were sequenced by amplicon sequencing, classified by Pango lineage, and further analyzed. Extensive clinical metadata was used for additional analysis, including general and oncology-related patient medical history, COVID-19 vaccination status and vaccine type, and detailed records of COVID-19 severity and treatment. The COVID-19 cases observed in this cohort cover a broad range of the COVID-19 pandemic, from April 2020 to January 2022; however, the majority of cases in this cohort were observed towards the beginning and middle of this range. The most frequently observed SARS-CoV-2 Pango lineages in this cohort were B.1.1 and P.1 (WHO variant of concern Gamma), followed by B.1.1.33 and P.2 (WHO variant of concern Zeta). B.1.1 and B.1.1.33, a Brazilian lineage, were observed largely in 2020, while P.2 and P.1 were observed at the end of 2020 and through the first half of 2021. As vaccination increased throughout 2021, we observed a reduction in both COVID-19 cases as well as hospitalization and intensive treatment, suggesting vaccination had a strong protective effect for this cohort. The differential effects of each lineage on hospitalization for COVID-19 and resulting treatment, such as use of ventilation or specific therapeutics, were examined for the cohort as a whole. The cohort was then divided based on oncology-specific factors, including by cancer type and treatment, as well as by general medical history, including both COVID-19 vaccination status as well as other medical risk factors, to understand lineage effect in these areas. These results improve the understanding of how the variety of SARS-CoV-2 lineages observed to date have affected COVID-19 severity and treatment of oncology patients and may help the management of cancer patients during the emergence of new SARS-CoV-2 lineages.