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

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.

SUBMITTER: Aggarwal D

PROVIDER: S-EPMC8480962 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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

Aggarwal Dinesh D Myers Richard R Hamilton William L WL Bharucha Tehmina T Tumelty Niamh M NM Brown Colin S CS Meader Emma J EJ Connor Tom T Smith Darren L DL Bradley Declan T DT Robson Samuel S Bashton Matthew M Shallcross Laura L Zambon Maria M Goodfellow Ian I Chand Meera M O'Grady Justin J Török M Estée ME Peacock Sharon J SJ Page Andrew J AJ

The Lancet. Microbe 20210929 2

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 ...[more]

PMID: 34608459

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Project description:BackgroundThe COVID-19 pandemic has devastatingly affected Long-Term Care Facilities (LTCF), exposing aging people, staff members, and visitors. The world has learned through the pandemic and lessons can be taken to adopt effective measures to deal with COVID-19 outbreaks in LTCF. We aimed to systematically review the available evidence on the effect of measures to minimize the risk of transmission of COVID-19 in LTCs during outbreaks since 2021.MethodsThe search method was guided by the preferred reporting items for systematic reviews (PRISMA) and the reporting guideline synthesis without meta-analysis (SWiM) in systematic reviews. The search was performed in April 2023. Observational and interventional studies from the databases of PubMed, Web of Science, Scopus, Cochrane Systematic Reviews, CINAHL, and Academic Search were systematically reviewed. We included studies conducted in the LTCF with outbreaks that quantitatively assess the effect of non-pharmacological measures on cases of COVID-19. Two review authors independently reviewed titles for inclusion, extracted data, and undertook the risk of bias according to pre-specified criteria. The quality of studies was analyzed using the Joanna Briggs Institute Critical Appraisal.ResultsThirteen studies were included, with 8442 LTCF experiencing COVID-19 outbreaks and 598 thousand participants (residents and staff members). Prevention and control of COVID-19 infection interventions were grouped into three themes: strategic, tactical, and operational measures. The strategic measures reveal the importance of COVID-19 prevention and control as LTCF structural characteristics, namely the LTCF size, new admissions, infection control surveillance, and architectural structure. At the tactical level, the lack of personal and long staff shifts is related to COVID-19's spread. Operational measures with a favorable effect on preventing COVID-19 transmission are sufficient. Personal protective equipment stock, correct mask use, signaling, social distancing, and resident cohorting.ConclusionsOperational, tactical, and strategic approaches may have a favorable effect on preventing the spread of COVID-19 in LTCFs experiencing outbreaks. Given the heterogeneous nature of the measures, performing a meta-analysis was not possible. Future research should use more robust study designs to explore similar infection control measures in LTCFs during endemic situations with comparable outbreaks.Trial registrationThe protocol of this systematic review was registered in PROSPERO (CRD42020214566).

Dataset Information

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

Publications

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

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