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

(From an article published in the Lancet) Many studies of COVID-19 in long-term care facilities (LTCFs) have reported high mortality. Possible explanations for this finding include recognised risk factors such as increased age and comorbidities. The drivers for the introduction and transmission of SARS-CoV-2 in the care sector are under investigation and are incompletely understood. 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.

Read the full article in The Lancet