tetano
Editor, Senior Moderator
Open Forum Infect Dis
. 2022 Oct 31;9(11)
fac581.
doi: 10.1093/ofid/ofac581. eCollection 2022 Nov.
Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital
Sarah E Sansom[SUP] 1 [/SUP], Hannah Barbian[SUP] 1 [/SUP], Mary K Hayden[SUP] 1 [/SUP], Christine Fukuda[SUP] 1 [/SUP], Nicholas M Moore[SUP] 1 [/SUP], Lahari Thotapalli[SUP] 1 [/SUP], Elias J Baied[SUP] 1 [/SUP], Do Young Kim[SUP] 1 [/SUP], Evan Snitkin[SUP] 2 [/SUP], Michael Y Lin[SUP] 1 [/SUP], CDC Prevention Epicenter Program
Affiliations
Abstract
Background: Identifying the source of healthcare personnel (HCP) coronavirus disease 2019 (COVID-19) is important to guide occupational 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 polymerase chain reaction-proven COVID-19 from a period with complete sample retention (14 March 2020 to 10 April 2020) at Rush University Medical Center in Chicago, Illinois, 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 nonclinical 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).
Conclusions: Using genomic and epidemiologic data, we found that most HCP severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were not healthcare associated. We did not find strong evidence of patient-to-HCP transmission of SARS-CoV-2.
Keywords: COVID-19; SARS-CoV-2; acute care hospital; healthcare personnel; whole genome sequencing.
. 2022 Oct 31;9(11)
fac581.doi: 10.1093/ofid/ofac581. eCollection 2022 Nov.
Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital
Sarah E Sansom[SUP] 1 [/SUP], Hannah Barbian[SUP] 1 [/SUP], Mary K Hayden[SUP] 1 [/SUP], Christine Fukuda[SUP] 1 [/SUP], Nicholas M Moore[SUP] 1 [/SUP], Lahari Thotapalli[SUP] 1 [/SUP], Elias J Baied[SUP] 1 [/SUP], Do Young Kim[SUP] 1 [/SUP], Evan Snitkin[SUP] 2 [/SUP], Michael Y Lin[SUP] 1 [/SUP], CDC Prevention Epicenter Program
Affiliations
- PMID: 36467294
- PMCID: PMC9709631
- DOI: 10.1093/ofid/ofac581
Abstract
Background: Identifying the source of healthcare personnel (HCP) coronavirus disease 2019 (COVID-19) is important to guide occupational 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 polymerase chain reaction-proven COVID-19 from a period with complete sample retention (14 March 2020 to 10 April 2020) at Rush University Medical Center in Chicago, Illinois, 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 nonclinical 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).
Conclusions: Using genomic and epidemiologic data, we found that most HCP severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were not healthcare associated. We did not find strong evidence of patient-to-HCP transmission of SARS-CoV-2.
Keywords: COVID-19; SARS-CoV-2; acute care hospital; healthcare personnel; whole genome sequencing.