Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.

Abstract

BackgroundThroughout the SARS-CoV-2 pandemic, healthcare workers (HCWs) have faced risk of infection from within the workplace via patients and staff as well as from the outside community, complicating our ability to resolve transmission chains in order to inform hospital infection control policy. Here we show how the incorporation of sequences from public genomic databases aided genomic surveillance early in the pandemic when circulating viral diversity was limited.MethodsWe sequenced a subset of discarded, diagnostic SARS-CoV-2 isolates between March and May 2020 from Boston Medical Center HCW and combined this dataset with publicly available sequences from the surrounding community deposited in GISAID with the goal of inferring specific transmission routes.ResultsContextualizing our data with publicly available sequences reveals that 73%, 95% CI [.63, .84] of HCW COVID-19 cases are likely novel introductions rather than nosocomial spread.ConclusionsWe argue that introductions of SARS-CoV-2 into the hospital environment are frequent, and that expanding public genomic surveillance can better aid infection control when determining routes of transmission.