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.
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 |
Archive Staff Only
 |
View Item |
