Genomics helps understand COVID-19 in care homes
23rd November 2020
The SARS-CoV-2 pandemic has hit the residents of care homes harder than any other part of the population. We know the oldest people in our society have borne the brunt of deaths from COVID-19 but what can genome sequencing usefully do to help safeguard our most vulnerable?
Genome sequencing (or genomics) of positive SARS-CoV-2 viral samples allows us to understand what is happening. You can think of it as viral detective work. As the virus makes copies of itself, occasionally a random change happens that propagates, and it is through tracking these changes that we can build up a picture of how the virus spreads.
Using genomics, we can tell when two people have an identical, or very similar copy of the virus which we group into ‘lineages’, and we can see when people have different lineages. We looked at all the studies worldwide which have used genome sequencing to better understand outbreaks in care homes. Only a small amount of work has been done on this area, with 11 studies in total from the UK, USA and The Netherlands.
In the UK, through the COVID-19 Genomics UK Consortium (COG-UK), we are sequencing more SARS-CoV-2 samples than the rest of the world combined. This gives us a very powerful base to work from. With genomics we can look at an outbreak in a single care home and get an idea of where the first infected person potentially came from. Knowing the source helps us to understand what we need to do better to prevent it happening again.
So, what have we learned from genome sequencing in care homes?
- The majority of infections in care homes have not come from hospitals but from the local community
- As a result, when infections are high in a community you will find there are more care home outbreaks
- A high percentage of cases without symptoms (asymptomatic) is common
- Once the virus is established in care homes it tends to be of one dominant lineage (identical or nearly identical virus) found in both residents and staff
- Once the virus has entered a care home it spreads rapidly despite infection control measures
- To date there is no difference in the mortality rate between different lineages and in care homes which have outbreaks. The mortality rates are high.
At the Quadram Institute, one of the 17 sequencing centres in COG-UK, we were able to use genomics to show where the virus has spread between care homes. In the East of England, six care homes had the same distinct lineage of the virus, suggesting staff moving between the care homes may have led to the outbreaks. These linked outbreaks were found by looking for unusual patterns in the genome sequencing data for the region and could not realistically have been linked together by other means.
We don’t believe every sample needs to be genome sequenced in a care home outbreak, once you do a few, it is enough to get a reasonable picture about what is circulating. What is more important is to take a wide selection of samples from those who tests positive, and randomly choose a few, on an ongoing basis and genome sequence those, so you can get a picture of the pandemic in real-time.
Interestingly, one US study in Washington state took all residents’ genomes in an outbreak, and if they were 100 per cent identical, gave them the same letter, then took a map of the care home residents’ bedrooms and overlaid the corresponding letters. This clearly showed that residents whose bedrooms were beside each other were more likely to be infected with a 100 per cent identical virus.
Given we now have a much more developed knowledge through genomics of the virus in relation to care homes, what do we need to change to better protect society’s most vulnerable? The COG-UK recommendations to the UK Scientific Advisory Group for Emergencies (SAGE) are:
- 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
- For the science community, genomic and epidemiological data with sufficient metadata should be released to public archives
Finally, a vital aspect of undertaking genome sequencing is rapidly and openly sharing the results and underlying data with others. This virus is on track to be the most widely sequenced organism in history. We need to follow a common set of other details (metadata) about samples so that people from all over the world can understand what they are looking at. We still have work to do on this front, with many studies not making their data openly available, or public archives not allowing data to be openly available.
The role of genomics in understanding COVID-19 outbreaks in long term care facilities is published as a preprint at https://osf.io/7y9rk/ DOI: 10.31219/osf.io/7y9rk