{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T19:45:00Z","timestamp":1790624700835,"version":"4.1.0"},"reference-count":24,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T00:00:00Z","timestamp":1617235200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia and Ag\u00eancia de Investiga\u00e7\u00e3o Cl\u00ednica e Inova\u00e7\u00e3o Biom\u00e9dica","award":["234_596874175 - Research 4 COVID-19"],"award-info":[{"award-number":["234_596874175 - Research 4 COVID-19"]}]},{"name":"COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI)","award":["POCI-01-0145-FEDER-022184 (GenomePT project)"],"award-info":[{"award-number":["POCI-01-0145-FEDER-022184 (GenomePT project)"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a \u201cnon-COVID-19\u201d hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12\/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.<\/jats:p>","DOI":"10.3390\/v13040604","type":"journal-article","created":{"date-parts":[[2021,4,1]],"date-time":"2021-04-01T10:44:01Z","timestamp":1617273841000},"page":"604","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":54,"title":["Nosocomial Outbreak of SARS-CoV-2 in a \u201cNon-COVID-19\u201d Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3767-2209","authenticated-orcid":false,"given":"V\u00edtor","family":"Borges","sequence":"first","affiliation":[{"name":"Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8529-9878","authenticated-orcid":false,"given":"Joana","family":"Isidro","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4557-1216","authenticated-orcid":false,"given":"Filipe","family":"Macedo","sequence":"additional","affiliation":[{"name":"Local Coordination Group for the Prevention and Control of Infections and Antimicrobial Resistance Program, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Neves","sequence":"additional","affiliation":[{"name":"Local Coordination Group for the Prevention and Control of Infections and Antimicrobial Resistance Program, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu\u00eds","family":"Silva","sequence":"additional","affiliation":[{"name":"Clinical Pathology Department, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e1rio","family":"Paiva","sequence":"additional","affiliation":[{"name":"Clinical Department, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Barata","sequence":"additional","affiliation":[{"name":"Internal Medicine Department, Vila Franca de Xira Hospital, 2600-009 Vila Franca de Xira, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judite","family":"Catarino","sequence":"additional","affiliation":[{"name":"Public Health Authority, Regional Health Administration of Lisbon and Tagus Valley, Health Centers Groups of Tagus Valley, 2615-042 Alverca do Ribatejo, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liliana","family":"Ciobanu","sequence":"additional","affiliation":[{"name":"Public Health Authority, Regional Health Administration of Lisbon and Tagus Valley, Health Centers Groups of Tagus Valley, 2615-042 Alverca do Ribatejo, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00edlvia","family":"Duarte","sequence":"additional","affiliation":[{"name":"Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu\u00eds","family":"Vieira","sequence":"additional","affiliation":[{"name":"Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"},{"name":"Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School|Faculdade de Ci\u00eancias M\u00e9dicas, Universidade Nova de Lisboa, 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4563-6315","authenticated-orcid":false,"given":"Raquel","family":"Guiomar","sequence":"additional","affiliation":[{"name":"National Reference Laboratory for Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo\u00e3o Paulo","family":"Gomes","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, 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