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The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19)

Published online by Cambridge University Press:  09 September 2022

Tina M. Marinelli Open the ORCID record for Tina M. Marinelli [Opens in a new window] ,
Leanne Dolan ,
Frances Jenkins ,
Andie Lee ,
Rebecca J. Davis ,
Simeon Crawford Open the ORCID record for Simeon Crawford [Opens in a new window] ,
Blake Nield ,
Amrita Ronnachit  and
Sebastiaan J. Van Hal Open the ORCID record for Sebastiaan J. Van Hal [Opens in a new window]
Tina M. Marinelli*
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
Leanne Dolan
Affiliation:
Infection Prevention and Control Unit, Royal Prince Alfred Hospital, Sydney, Australia
Frances Jenkins
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
Andie Lee
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia Department of Medicine, The University of Sydney, Sydney, Australia
Rebecca J. Davis
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia Department of Medicine, The University of Sydney, Sydney, Australia
Simeon Crawford
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
Blake Nield
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia
Amrita Ronnachit
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia Department of Medicine, The University of Sydney, Sydney, Australia
Sebastiaan J. Van Hal
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney, Australia Department of Medicine, The University of Sydney, Sydney, Australia
*
Author for correspondence: Dr Tina M. Marinelli, E-mail: Tina.marinelli@health.nsw.gov.au
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Abstract

Objective:

We aimed to demonstrate the role of real-time, on-site, whole-genome sequencing (WGS) of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in the management of hospital outbreaks of coronavirus disease 2019 (COVID-19).

Design:

This retrospective study was undertaken at our institutions in Sydney, New South Wales, Australia, between July 2021 and April 2022. We included SARS-CoV-2 outbreaks due to SARS-CoV-2 δ (delta) and ο (omicron) variants. All unexpected SARS-CoV-2–positive cases identified within the hospital were managed by the infection control team. An outbreak was defined as 2 or more cases acquired on a single ward. We included only outbreaks with 2 or more suspected transmission events in which WGS was utilized to assist with outbreak assessment and management.

Results:

We studied 8 outbreaks involving 266 patients and 486 staff, of whom 73 (27.4%) and 39 (8.0%), respectively, tested positive for SARS-CoV-2 during the outbreak management. WGS was used to evaluate the source of the outbreak, to establish transmission chains, to highlight deficiencies in infection control practices, and to delineate between community and healthcare acquired infection.

Conclusions:

Real-time, on-site WGS combined with epidemiologic assessment is a useful tool to guide management of hospital SARS-CoV-2 outbreaks. WGS allowed us (1) to establish likely transmission events due to personal protective equipment (PPE) breaches; (2) to detect inadequacies in infection control infrastructure including ventilation; and (3) to confirm multiple viral introductions during periods of high community SARS-CoV-2 transmission. Insights gained from WGS-guides outbreak management directly influenced policy including modifying PPE requirements, instituting routine inpatient SARS-CoV-2 surveillance, and confirmatory SARS-CoV-2 testing prior to placing patients in a cohort setting.

Type
Original Article
Information
Infection Control & Hospital Epidemiology , Volume 44 , Issue 7 , July 2023 , pp. 1116 - 1120
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Copyright
© Royal Prince Alfred Hospital, 2022. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America

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References

Meredith, LW, Hamilton, WL, Warne, B, et al. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of healthcare-associated COVID-19: a prospective genomic surveillance study. Lancet 2020;20:1263–1272.10.1016/S1473-3099(20)30562-4CrossRefGoogle Scholar
Wang, X, Zhou, Q, He, Y, Liu, L, Ma, X, Wei, X. Nosocomial outbreak of COVID-19 pneumonia in Wuhan, China. Eur Respir J 2020;55:2000544.10.1183/13993003.00544-2020CrossRefGoogle ScholarPubMed
Rickman, H, Rampling, T, Shaw, K, Martinez-Garcia, G, Hail, L. Nosocomial transmission of coronavirus disease 2019: a retrospective study of 66 hospital-acquired cases in a London teaching hospital. Clin Infect Dis 2021;72:690–693.10.1093/cid/ciaa816CrossRefGoogle Scholar
Buchtele, N, Rabitsch, W, Knaus, H, Wohlfarth, P. Containment of a traceable COVID-19 outbreak among healthcare workers at a hematopoietic stem-cell transplantation unit. Bone Marrow Transp 2020;55:1491–1492.10.1038/s41409-020-0958-6CrossRefGoogle Scholar
Transmission of SARS-CoV-2: implications for infection prevention precautions. WHO Scientific Brief. World Health Organization website. https://www.who.int/news-room/commentaries/detail/transmission-of-sars-cov-2-implications-for-infection-prevention-precautions. Published 2020. Accessed April 29, 2022.Google Scholar
Zou, L, Ruan, F, Huang, M, et al. SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med 2020;382:1177–1179.10.1056/NEJMc2001737CrossRefGoogle ScholarPubMed
Johansson, M, Quandelacy, T, Kada, S, Prasad, P, Steele, M, Brooks, J. SARS-CoV-2 transmission from people without COVID-19 symptoms. JAMA Netw Open 2021;4:e2035057.10.1001/jamanetworkopen.2020.35057CrossRefGoogle ScholarPubMed
Carrara, E, Ong, DSY, Hussein, K, et al. ESCMID guidelines on testing for SARS-CoV-2 transmission in asymptomatic individuals to prevent transmission in the healthcare setting. Clin Microbiol Infect 2022;28:672–680.10.1016/j.cmi.2022.01.007CrossRefGoogle Scholar
IDSA guidelines on the diagnosis of COVID-19: molecular diagnostic testing available. Infectious Diseases Society of America website. https://www.idsociety.org/practice-guideline/covid-19-guideline-diagnostics/. Published 2020. Accessed April 29, 2022.Google Scholar
CDC infection control guidance. Centers for Disease Control website. https://www.cdc.gov/coronavirus/2019-ncov/hcp/infection-control-recommendations.html. Published 2022. Accessed April 29, 2022.Google Scholar
COVID-19 infection prevention and control manual, 2022. NSW Government Clinical Excellence Commission website. https://www.cec.health.nsw.gov.au/keep-patients-safe/COVID-19/COVID-19-IPAC-manual. Published 2022. Accessed August 30, 2022.Google Scholar
Putri, N, Johor, E, Dewi, Y, Indrasari, N, Wilandari, D. Whole-genome sequencing of SARS-CoV-2 infection in a cluster of immunocompromised children in Indonesia. Front Med 2022;9:835998.10.3389/fmed.2022.835998CrossRefGoogle Scholar
Ishikawa, F, Udaka, Y, Oyamada, H, et al. Genetic epidemiology using whole-genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak. Infect Prev Pract 2021;3:100190.10.1016/j.infpip.2021.100190CrossRefGoogle ScholarPubMed
Aggarwal, D, Myer, R, Hamilton, W, Bachrucha, T, Tumelty, N, Brown, C. The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. Lancet Microbe 2022;3:E151–E158.10.1016/S2666-5247(21)00208-1CrossRefGoogle ScholarPubMed
Stirrup, O, Blackstone, J, Mapp, F, et al. Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study. medRxiv 2022. doi: 10.1101/2022.02.10.22270799v1.Google Scholar
Bull, RA, Adikari, TN, Ferguson, JM, et al. Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nat Commun 2020;11:6272.10.1038/s41467-020-20075-6CrossRefGoogle ScholarPubMed
PANGOLIN COVID lineages. https://github.com/cov-lineages/pangolin. Accessed May 12, 2022.Google Scholar
Minh, B, Schmidt, H, Chernomor, O, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020;37:1530–1534.10.1093/molbev/msaa015CrossRefGoogle ScholarPubMed
Stimson, J, Gardy, J, Mathema, B, Crudu, V, Cohen, T, Colijn, C. Beyond the SNP threshold: identifying outbreak clusters using inferred transmissions. Mol Biol Evol 2019;36:587–603.10.1093/molbev/msy242CrossRefGoogle ScholarPubMed
Bouzid, D, Visseaux, B, Kassasseya, C, Beaune, S, Javaud, N. Comparison of patients infected with delta versus omicron COVID-19 variants presenting to Paris emergency departments. Ann Intern Med 2022;175:831–837.10.7326/M22-0308CrossRefGoogle ScholarPubMed
Fall, A, Eldesouki, RE, Sachithanandham, J, et al. The displacement of the SARS-CoV-2 variant delta with omicron: an investigation of hospital admissions and upper-respiratory viral loads. Lancet 2022;79:104008.Google ScholarPubMed
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