Hospital onset SARS CoV-2 infections before and after the emergence of the highly transmissible variant B.1.1.529 in a comprehensive cancer center

ABSTRACT

SARS-CoV-2 B.1.1.529 (Omicron) variant was first identified in November 2021 and was notable for its transmissibility and rapid spread worldwide. Here, we compared the incidence and characteristics of hospital-onset COVID-19 (HO-COVID-19) in our cancer patients prior to and during the surge of the Omicron variant. Following CDC definitions, we identified HO-COVID-19 from our infection control surveillance database. Whole-genome sequencing studies were conducted randomly on positive nasopharyngeal swabs during the study period. Twenty-six HO-COVID-19 infections were identified from February 2020 through February 2022. Only 17 cases occurred over 22 months from the beginning of the pandemic through early December 2021. These HO-COVID-19 occurred during the 3 COVID-19 surges that were epidemiologically attributed to the variants seen prior to Omicron. Among these 17 patients, 12 (70%) were symptomatic, 9 (53%) had a link to an infected employee, 7 (41%) died during their hospitalization (3 deaths were attributable to COVID-19), and 10 (59%) recovered and were discharged. From December 22nd, 2021, through February 1st, 2022, 9 HO-COVID-19 were discovered during the Omicron variant surge. Six (67%) of these patients were symptomatic, 8 (89%) had a link to an infected employee, 2 (22%) died (1 death was attributed to COVID-19), and 7 (78%) recovered and were discharged. The Omicron variant surge led to marked increases in HO-COVID- 19 despite the continuous adoption of enhanced infection control practices, testing on admission, and daily symptoms screening of patients and employees.