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.

Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study

“…The current evidence does not support the use of real-time genomics for control of SARS-CoV-2 nosocomial outbreaks ( Stirrup et al, 2021 ; Stirrup et al, 2022 ). Nevertheless, in this investigation, as in many others, we performed WGS to investigate transmission patterns ( Aggarwal et al, 2022 ). Although we were able to gain considerable insight from the powerful combination of genetic sequencing data and rich epidemiological data, we controlled the outbreaks without using WGS, as was the case in many published reports ( Arons et al, 2020 ; Taylor et al, 2020 ).…”

“…The role of healthcare workers (HCWs) in nosocomial Covid-19 transmission dynamics is complex, as they can be victims and/or vectors of SARS-CoV-2 infection, and can acquire from or transmit to their peers and patients and the community ( Abbas et al, 2021b ; Ellingford et al, 2021 ). There is ongoing controversy and uncertainty surrounding the role of HCWs in infecting patients during nosocomial outbreaks, and findings from acute-care hospitals cannot be applied directly to LTCFs and geriatric hospitals ( Abbas et al, 2021a ; Klompas et al, 2021 ; Lucey et al, 2021 ; Aggarwal et al, 2022 ).…”

Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol

“…Genomic sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been instrumental in understanding the biology, emergence and spread of the virus globally ( 1 – 3 ). SARS-CoV-2 genomes help explain virus evolution and transmission ( 4 , 5 ), identify sites on the genome that may aid vaccine/antibody evasion and inform vaccine design ( 6 ), improve design of molecular and serological assays ( 7 ) and influence public health policy ( 8 ).…”

Temporal distribution and clinical characteristics of the Alpha, Delta and Omicron SARS-CoV-2 variants of concern in Laikipia, Kenya: institutional and community-based genomic surveillance

“…Genomic surveillance of the SARS-CoV-2 VOCs in hospital settings has been instrumental in understanding the clinical characteristics and outcomes associated with emerging variants 10,13,14 , with evidence mostly originating from highincome countries. In Africa, limited data from Malawi, a lowincome setting, showed higher mortality among Delta VOC cases, OR 4.99 (95% CI: 1.0 -25.0), especially among those older than 70 years (OR 9.55; 95% CI: 1.31 -69.77, p= 0.026), and with an oxygen saturation (Sp0 2 ) less than 87% (OR 11.22; 95% CI: 2.59 -48.65, p= 0.001) on admission 15 .…”