UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission

Snell, LB; Fisher, CL; Taj, U; Stirrup, O; Merrick, B; Alcolea-Medina, A; Charalampous, T; ... Awan, AR; + view all (2022) Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission. Clinical Microbiology and Infection , 28 (1) pp. 93-100. 10.1016/j.cmi.2021.07.040. Green open access

[thumbnail of Snell_CMI_2021.pdf]
Preview
Text
Snell_CMI_2021.pdf - Accepted Version

Download (4MB) | Preview

Abstract

OBJECTIVES: Analysis of nosocomial transmission in the early stages of the pandemic at a large multi-site healthcare institution. Nosocomial incidence is linked with infection control interventions. METHODS: Viral genome sequence and epidemiological data were analysed for 574 consecutive SARS-CoV-2 PCR-positive patients including 86 nosocomial cases during the first 19 days of the pandemic. RESULTS: 44 putative transmission clusters were found through epidemiological analysis, which included 234 cases and all 86 nosocomial cases. SARS-CoV-2 genome sequence was obtained from 168/234 (72%) of these cases in epidemiological clusters, including 77/86 (90%) nosocomial cases. Only 75/168 (45%) linked, sequenced cases were not refuted by applying genomic data, creating 14 final clusters accounting for 59/77 (77%) sequenced nosocomial cases. Viral haplotypes from these clusters were enriched 1-14x (median 4x) compared to the community. Three factors implicated unidentified cases in transmission: i) community-onset or indeterminate cases were absent in 7/14 (50%) of clusters ii) 4 (29%) clusters had additional evidence of cryptic transmission. iii) In 3 (21%) clusters, 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 or banning hospital visitors. CONCLUSION: Genomics was necessary to accurately resolve transmission clusters Our data supports 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.

Type: Article
Title: Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.cmi.2021.07.040
Publisher version: https://doi.org/10.1016/j.cmi.2021.07.040
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher's terms and conditions.
Keywords: SARS-CoV-2, nosocomial transmission, healthcare-associated infection, molecular epidemiology, whole genome sequencing
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute for Global Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Institute for Global Health > Infection and Population Health
URI: https://discovery.ucl.ac.uk/id/eprint/10132978
Downloads since deposit
72Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item