Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital

Abstract

Background Identifying the source of healthcare personnel (HCP) COVID-19 is important to guide safety efforts. We used a combined whole genome sequencing (WGS) and epidemiologic approach to investigate the source of HCP COVID-19 at a tertiary-care center early in the COVID-19 pandemic. Methods Remnant nasopharyngeal swab samples from HCP and patients with PCR-proven COVID-19 from a period with complete sample retention (March 14, 2020 to April 10, 2020) at Rush University Medical Center in Chicago, IL underwent viral RNA extraction and WGS. Genomes with >90% coverage underwent cluster detection using a 2 single nucleotide variant genetic distance cutoff. Genomic clusters were evaluated for epidemiologic linkages, with strong linkages defined by evidence of time/location overlap. Results We analyzed 1031 sequences, identifying 49 clusters that included ≥1 HCP (265 patients, 115 HCP). Most HCP infections were not healthcare-associated (88/115, 76.5%). We did not identify any strong epidemiologic linkages for patient-to-HCP transmission. Thirteen HCP cases (11.3%) were attributed to a potential patient source (weak evidence involving non-clinical staff that lacked location data to prove or disprove contact with patients in same cluster). Fourteen HCP cases (12.2%) were attributed to HCP source (11 with strong evidence). Conclusion Using genomic and epidemiologic data, we found that most HCP SARS-CoV-2 infections were not healthcare associated. We did not find strong evidence of patient-to-HCP transmission of SARS-CoV-2.

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 in a County Jail

“…Within-jail transmission was detected in specific buildings, which may be targeted for enhanced infection prevention. Numerous infection prevention practices at intake and during incarceration were implemented in the jail to limit the spread of SARS-CoV-2 [ 7 , 11 ] ( Supplementary Table 1 ). However, compliance with these measures was variable among detainees and staff, making containment of SARS-CoV-2 more challenging [ 7 ].…”

“…Deep sequencing of libraries was performed on an Illumina NovaSeq6000 instrument with a 300-cycle SP flow cell at the DNA Services Facility at the University of Illinois at Urbana-Champaign. The SARS-CoV-2 isolates yielded full genomes (95% coverage) using a custom analysis pipeline described previously [ 11 ]. Pango lineages were determined using pangolin v3.0 [ 12 ].…”

“…Pango lineages were determined using pangolin v3.0 [ 12 ]. A previously published set of isolates processed at Rush University Medical Center (RUMC, Chicago, Illinois) [ 11 ] was used to place jail isolates in the context of strains circulating in local communities. Globally distributed publicly available SARS-CoV-2 genomes from the early pandemic were downloaded from the Global Initiative on Sharing All Influenza Data (GISAID) and used for time-scaled phylogenetic analysis.…”