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The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.
Aggarwal, Dinesh; Myers, Richard; Hamilton, William L; Bharucha, Tehmina; Tumelty, Niamh M; Brown, Colin S; Meader, Emma J; Connor, Tom; Smith, Darren L; Bradley, Declan T; Robson, Samuel; Bashton, Matthew; Shallcross, Laura; Zambon, Maria; Goodfellow, Ian; Chand, Meera; O'Grady, Justin; Török, M Estée; Peacock, Sharon J; Page, Andrew J.
  • Aggarwal D; Department of Medicine, University of Cambridge, Cambridge, UK.
  • Myers R; Public Health England, London, UK.
  • Hamilton WL; Cambridge University Hospital NHS Foundation Trust, Cambridge, UK.
  • Bharucha T; Wellcome Sanger Institute, Hinxton, Cambridge, UK.
  • Tumelty NM; Public Health England, London, UK.
  • Brown CS; Department of Medicine, University of Cambridge, Cambridge, UK.
  • Meader EJ; Cambridge University Hospital NHS Foundation Trust, Cambridge, UK.
  • Connor T; Public Health England, London, UK.
  • Smith DL; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK.
  • Bradley DT; Lao-Oxford-Mahosot Hospital, Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
  • Robson S; Cambridge University Libraries, University of Cambridge, Cambridge, UK.
  • Bashton M; Public Health England, London, UK.
  • Shallcross L; Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK.
  • Zambon M; Lao-Oxford-Mahosot Hospital, Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos.
  • Goodfellow I; Norfolk and Norwich University Hospital, Norwich, UK.
  • Chand M; Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, UK.
  • O'Grady J; Public Health Wales, University Hospital of Wales, Cardiff, UK.
  • Török ME; Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
  • Peacock SJ; Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK.
  • Page AJ; Public Health Agency, Belfast, UK.
Lancet Microbe ; 3(2): e151-e158, 2022 02.
Article in English | MEDLINE | ID: covidwho-1440435
ABSTRACT
We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Observational study Topics: Long Covid Limits: Humans Language: English Journal: Lancet Microbe Year: 2022 Document Type: Article Affiliation country: S2666-5247(21)00208-1

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Observational study Topics: Long Covid Limits: Humans Language: English Journal: Lancet Microbe Year: 2022 Document Type: Article Affiliation country: S2666-5247(21)00208-1