The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

Dinesh Aggarwal, Richard Myers, William L Hamilton, Tehmina Bharucha, Niamh M Tumelty, Colin S. Brown, Emma J. Meader, Tom Connor, Darren L Smith, Declan T Bradley, Samuel Robson, Matthew Bashton, Laura Shallcross, Maria Zambon, Ian Goodfellow, Meera Chand, Justin O'Grady, M Estée Török, Sharon J. Peacock, Andrew J. Page*The COVID-19 Genomics UK (COG-UK) Consortium, John Allan, Joshua Loh, Andrew Nelson, Wen C. Yew, Gregory R. Young

*Corresponding author for this work

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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.
Original languageEnglish
Pages (from-to)1-9
Number of pages9
JournalThe Lancet Microbe
Early online date29 Sep 2021
DOIs
Publication statusE-pub ahead of print - 29 Sep 2021

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