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

Dinesh Aggarwal,Samuel Robson,Meera Chand,Tom Connor,Laura Shallcross,Richard Myers,Ian Goodfellow,Tehmina Bharucha,Matthew Bashton,Maria Zambon,M Estée Török ,Sharon J Peacock ,Emma Meader ,Declan Bradley ,Darren Smith ,William L Hamilton ,Colin Brown ,Niamh Tumelty ,Justin O’grady ,Andrew J Page

doi:10.1016/s2666-5247(21)00208-1

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.

Highlights

Many studies of COVID-19 in long-term care facilities (LTCFs) have reported high mortality.[1,2,3] Possible explanations for this finding include recognised risk factors such as increased age and comorbidities.[2,4] In England and Wales, it has been estimated that nearly 30% (15 819 of 54 325 total in the week ending Oct 16, 2020) of all deaths due to COVID-19 occurred in LTCFs5 with outbreaks reported in 45% of all LTCFs.[6]
Samples that are sequenced as part of surveillance studies can provide early insight into outbreaks in LTCFs.18,19,23,24 5·8% of COVID-19 infections in residents of LTCFs were suspected to be acquired in hospital.[18]
We have presented findings from multiple genomic epidemiology studies of transmission in LTCFs in an evolving pandemic

Summary

Introduction

Many studies of COVID-19 in long-term care facilities (LTCFs) have reported high mortality.[1,2,3] Possible explanations for this finding include recognised risk factors such as increased age and comorbidities.[2,4] In England and Wales, it has been estimated that nearly 30% (15 819 of 54 325 total in the week ending Oct 16, 2020) of all deaths due to COVID-19 occurred in LTCFs5 with outbreaks reported in 45% of all LTCFs.[6]. After a full text review, 11 genomic epidemiology studies in LTCFs were identified for inclusion in this analysis. The serial sampling of residents and health-care workers provided information about the duration of infection in individuals, the duration of outbreaks in LTCFs, and the reproducibility of genome sequencing and lineage identification.[28]. Nine studies sequenced both staff and patients to better understand the transmission dynamics within a LTCF. Three studies were found to display deficiencies relating to the bioinformatics methods used or the results presented These deficiencies included assembling amplicons,[20] using poor-quality sequencing data in phylogenetic analysis,[21] and imputing reference bases to replace missing bases;[25] the effect of these methods on down stream analysis is unknown.

Data availability*

Summary of findings

Findings

Conclusions