TY - JOUR
T1 - Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission
AU - COVID-19 Genomics UK (COG-UK) Consortium
AU - Snell, Luke B
AU - Fisher, Chloe L
AU - Taj, Usman
AU - Stirrup, Oliver
AU - Merrick, Blair
AU - Alcolea-Medina, Adela
AU - Charalampous, Themoula
AU - Signell, Adrian W
AU - Wilson, Harry D
AU - Betancor, Gilberto
AU - Kia Ik, Mark Tan
AU - Cunningham, Emma
AU - Cliff, Penelope R
AU - Pickering, Suzanne
AU - Galao, Rui Pedro
AU - Batra, Rahul
AU - Neil, Stuart J D
AU - Malim, Michael H
AU - Doores, Katie J
AU - Douthwaite, Sam T
AU - Nebbia, Gaia
AU - Edgeworth, Jonathan D
AU - Awan, Ali R
AU - Beggs, Andrew
N1 - Copyright © 2021. Published by Elsevier Ltd.
PY - 2021/8/13
Y1 - 2021/8/13
N2 - OBJECTIVES: To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions.METHODS: Viral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic.RESULTS: Forty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90%). Only 75/168 (45%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77%). Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50%), (b) four clusters (29%) had additional evidence of cryptic transmission, and (c) in three clusters (21%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0-2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40-50 per day) and before the impact of introducing universal face masks and banning hospital visitors.CONCLUSION: Genomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases-such as healthcare workers or asymptomatic patients-as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.
AB - OBJECTIVES: To analyse nosocomial transmission in the early stages of the coronavirus 2019 (COVID-19) pandemic at a large multisite healthcare institution. Nosocomial incidence is linked with infection control interventions.METHODS: Viral genome sequence and epidemiological data were analysed for 574 consecutive patients, including 86 nosocomial cases, with a positive PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the first 19 days of the pandemic.RESULTS: Forty-four putative transmission clusters were found through epidemiological analysis; these included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequences were obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 nosocomial cases (90%). Only 75/168 (45%) of epidemiologically linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 sequenced nosocomial cases (77%). Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: (a) community-onset or indeterminate cases were absent in 7/14 clusters (50%), (b) four clusters (29%) had additional evidence of cryptic transmission, and (c) in three clusters (21%) diagnosis of the earliest case was delayed, which may have facilitated transmission. Nosocomial cases decreased to low levels (0-2 per day) despite continuing high numbers of admissions of community-onset SARS-CoV-2 cases (40-50 per day) and before the impact of introducing universal face masks and banning hospital visitors.CONCLUSION: Genomics was necessary to accurately resolve transmission clusters. Our data support unidentified cases-such as healthcare workers or asymptomatic patients-as important vectors of transmission. Evidence is needed to ascertain whether routine screening increases case ascertainment and limits nosocomial transmission.
KW - Healthcare-associated infection
KW - Molecular epidemiology
KW - Nosocomial transmission
KW - SARS-CoV-2
KW - Whole-genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85114931471&partnerID=8YFLogxK
U2 - 10.1016/j.cmi.2021.07.040
DO - 10.1016/j.cmi.2021.07.040
M3 - Article
C2 - 34400345
SN - 1198-743X
VL - 28
SP - 93
EP - 100
JO - Clinical Microbiology and Infection
JF - Clinical Microbiology and Infection
IS - 1
ER -