How genomic surveillance helps understand outbreaks of COVID-19 in care homes

30th September 2021

If we are to learn to live with COVID, it’s vital we also learn the lessons of how to protect the most vulnerable in society

In England and Wales, an estimated 30% of deaths due to COVID-19 occurred in care homes, with long term residents being susceptible because of a combination of risk factors, such as increased age and other underlying health conditions.

One tool that has shown its value during the pandemic is genomic epidemiology. This involves reading the genetic sequence of SARS-CoV-2 virus samples and seeing how related different samples are. Combining this with epidemiological data, such as when and where the sample was taken, builds a picture of the dynamics of an outbreak showing routes of infection and transmission.

Genomic epidemiology has helped public health authorities trace and control outbreaks, and can also be used to show how control measures work, or where things need tightening.

A number of studies have focused on the genomic epidemiology of care homes.

Now in a review published in the journal Lancet Microbe, Dr Andrew Page from the Quadram Institute and colleagues from the COVID-19 Genomics UK (COG-UK) Consortium have sought to bring those studies together in a meta-analysis of COVID-19 outbreaks in long term care facilities.

COG-UK has been at the forefront of genomic surveillance for COVID-19, recently sequencing its millionth genome, from samples collected from across the UK, including care homes.

One study from the Quadram Institute used genomics to show how the virus spread between care homes in the East of England. This helped public health authorities pinpoint staff moving between homes, particularly agency staff, as a source of transmission, whilst also showing how effective measures to prevent transmission within homes were.

The meta-analysis combines this study with others to get a global overview of COVID-19 in care homes. In total, 11 studies from the UK, USA and Netherlands were included. Some were small, focused on one care home, others looked at multiple homes in an area. Some tracked outbreaks, others were part of surveillance for the virus.

So, what did this analysis show?

Most infections in care homes came from the community, not hospitals, and usually associated with a small number of introductions, rather than repeated “seeding” of the virus. Sometimes shared “clusters” across different care homes were seen. When COVID-19 are high in the community, there are also higher numbers of care home outbreaks.

Commonly, a high percentage of cases were asymptomatic. By the time two symptomatic cases were identified in a care home, the outbreak was likely to be widespread. The virus can spread rapidly once in a care home, usually through one dominant lineage in both residents and staff. Whatever the lineage, mortality rates are high.

Based on their findings, a number of recommendations have been made to control COVID-19 in care homes:

  • To take steps to limit the spread of SARS-CoV-2 to care homes from the community, staff, healthcare workers and hospitals
  • To treat all care home staff (not just staff with direct contact with residents) as one group subject to the same infection control measures
  • Residents whose rooms are located near the bedroom of a resident who is positive should be considered at very high risk
  • To continue to use genomics in a targeted way in care homes to help identify, track and control the virus

The data behind this meta-analysis was collected in 2020, and since then the deployment of vaccinations provides an additional level of protection. In the UK, over 90% of care home residents and 80% of staff have now been fully vaccinated. The rollout of vaccinations has allowed society to start to lift lockdown restrictions, but this has seen rise in the number of cases in the community. The link shown in this study between community cases and care home outbreaks, and the fact that their residents remain the most vulnerable to serious harm from the virus, means we should maintain viral genomic surveillance so we can protect everyone.

Reference:

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities, Dinesh Aggarwal et al, Lancet Microbe DOI: 10.1016/S2666-5247(21)00208-1