{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T14:59:10Z","timestamp":1787065150151,"version":"build-2736575974"},"reference-count":21,"publisher":"Cambridge University Press (CUP)","issue":"7","license":[{"start":{"date-parts":[[2022,9,9]],"date-time":"2022-09-09T00:00:00Z","timestamp":1662681600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/www.cambridge.org\/core\/terms"}],"content-domain":{"domain":["cambridge.org"],"crossmark-restriction":true},"short-container-title":["Infect. Control Hosp. Epidemiol."],"published-print":{"date-parts":[[2023,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec id=\"S0899823X22002203_as1\">\n                    <jats:title>Objective:<\/jats:title>\n                    <jats:p>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).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S0899823X22002203_as2\">\n                    <jats:title>Design:<\/jats:title>\n                    <jats:p>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 \u03b4 (delta) and \u03bf (omicron) variants. All unexpected SARS-CoV-2\u2013positive 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S0899823X22002203_as3\">\n                    <jats:title>Results:<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"S0899823X22002203_as4\">\n                    <jats:title>Conclusions:<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1017\/ice.2022.220","type":"journal-article","created":{"date-parts":[[2022,9,9]],"date-time":"2022-09-09T13:21:01Z","timestamp":1662729661000},"page":"1116-1120","update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":3,"title":["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)"],"prefix":"10.1017","volume":"44","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0404-787X","authenticated-orcid":false,"given":"Tina M.","family":"Marinelli","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leanne","family":"Dolan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frances","family":"Jenkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andie","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca J.","family":"Davis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3104-1289","authenticated-orcid":false,"given":"Simeon","family":"Crawford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blake","family":"Nield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amrita","family":"Ronnachit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5852-4155","authenticated-orcid":false,"given":"Sebastiaan J.","family":"Van Hal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2022,9,9]]},"reference":[{"key":"S0899823X22002203_ref6","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMc2001737"},{"key":"S0899823X22002203_ref12","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2022.835998"},{"key":"S0899823X22002203_ref3","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa816"},{"key":"S0899823X22002203_ref7","doi-asserted-by":"publisher","DOI":"10.1001\/jamanetworkopen.2020.35057"},{"key":"S0899823X22002203_ref10","unstructured":"10. 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."},{"key":"S0899823X22002203_ref15","article-title":"Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study","author":"Stirrup","year":"2022","journal-title":"medRxiv"},{"key":"S0899823X22002203_ref4","doi-asserted-by":"publisher","DOI":"10.1038\/s41409-020-0958-6"},{"key":"S0899823X22002203_ref5","unstructured":"5. 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."},{"key":"S0899823X22002203_ref9","unstructured":"9. 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."},{"key":"S0899823X22002203_ref2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00544-2020"},{"key":"S0899823X22002203_ref1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(20)30562-4"},{"key":"S0899823X22002203_ref11","unstructured":"11. 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."},{"key":"S0899823X22002203_ref14","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(21)00208-1"},{"key":"S0899823X22002203_ref17","unstructured":"17. PANGOLIN COVID lineages. https:\/\/github.com\/cov-lineages\/pangolin. Accessed May 12, 2022."},{"key":"S0899823X22002203_ref21","first-page":"104008","article-title":"The displacement of the SARS-CoV-2 variant delta with omicron: an investigation of hospital admissions and upper-respiratory viral loads","volume":"79","author":"Fall","year":"2022","journal-title":"Lancet"},{"key":"S0899823X22002203_ref19","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy242"},{"key":"S0899823X22002203_ref13","doi-asserted-by":"publisher","DOI":"10.1016\/j.infpip.2021.100190"},{"key":"S0899823X22002203_ref8","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2022.01.007"},{"key":"S0899823X22002203_ref16","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20075-6"},{"key":"S0899823X22002203_ref20","doi-asserted-by":"publisher","DOI":"10.7326\/M22-0308"},{"key":"S0899823X22002203_ref18","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"}],"container-title":["Infection Control &amp; Hospital Epidemiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.cambridge.org\/core\/services\/aop-cambridge-core\/content\/view\/S0899823X22002203","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,26]],"date-time":"2023-07-26T04:09:19Z","timestamp":1690344559000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.cambridge.org\/core\/product\/identifier\/S0899823X22002203\/type\/journal_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,9]]},"references-count":21,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2023,7]]}},"alternative-id":["S0899823X22002203"],"URL":"https:\/\/doi.org\/10.1017\/ice.2022.220","relation":{},"ISSN":["0899-823X","1559-6834"],"issn-type":[{"value":"0899-823X","type":"print"},{"value":"1559-6834","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,9]]},"assertion":[{"value":"\u00a9 Royal Prince Alfred Hospital, 2022. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America","name":"copyright","label":"Copyright","group":{"name":"copyright_and_licensing","label":"Copyright and Licensing"}}]}}