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

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 ITCFs 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 ITCFs 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.

Automated summary

This study reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) and found that staff and residents usually had identical or very similar SARS-CoV-2 genomes. Outbreaks typically involved one main cluster, and the same lineages persisted despite infection control measures. It was also observed that the sequencing technique was reliable over time, and when combined with local epidemiology, genomics could help identify probable transmission sources. Multiple studies detected transmission between LTCFs, and the mortality rate among residents was high regardless of the lineage.