Longitudinal Surveillance for SARS-CoV-2 RNA Among Asymptomatic Staff in Five Colorado Skilled Nursing Facilities: Epidemiologic, Virologic and Sequence Analysis

Abstract

SARS-CoV-2 emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 also has been notable due to its impacts on individuals residing within skilled nursing facilities (SNFs) such as rehabilitation centers and nursing homes. SNF residents tend to possess several risk factors for the most severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of multiple comorbidities. Indeed, residents of long-term care facilities represent approximately 40 percent of US SARS-CoV-2 deaths. To assess the prevalence and incidence of SARS-CoV-2 among SNF workers, determine the extent of asymptomatic infection by SARS-CoV-2, and provide information on the genomic epidemiology of the virus within these unique care settings, we sampled workers weekly at five SNFs in Colorado using nasopharyngeal swabs, determined the presence of viral RNA and infectious virus among these workers, and sequenced 48 nearly complete genomes. This manuscript reports results from the first five to six weeks of observation. Our data reveal a strikingly high degree of asymptomatic infection, a strong correlation between RNA detection and the presence of infectious virus in NP swabs, persistent RNA in a subset of individuals, and declining incidence over time. Our data suggests that asymptomatic individuals infected by SARS-CoV-2 may contribute to virus transmission within the workplace.