Genomic surveillance can help recognize how SARS-CoV-2 spreads in care homes

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• Source: University of Cambridge


• Date: 04 Mar,2021

Care homes are at high risk of experiencing outbreaks of COVID-19, the disease brought on by SARS-CoV-2. Older people and people affected by heart disease, respiratory disease and type 2 diabetes – all of which increase with age – are at greatest risk of severe disease and even death, which makes the care home population especially vulnerable.

Care homes are known to be high-risk configurations for infectious diseases, because of a combination of the underlying vulnerability of residents who are often frail and elderly, the common living environment with numerous communal spaces, and the high number of contacts between residents, visitors and staff in an enclosed space.

In research published in eLife, a team led by scientists at the University of Cambridge and Wellcome Sanger Institute used a combination of genome sequencing and detailed epidemiological information to examine the impact of COVID-19 on care homes and to look at how the virus spreads in these configurations.

SARS-CoV-2 is an RNA virus and as such its genetic code is more prone to mistakes each time it replicates. It’s presently estimated that the virus mutates at a rate of 2.5 nucleotides (the A, C, G and U of its genetic code) a month. Reading – or’sequencing’ – the genetic code of the virus can offer valuable information on its biology and transmission. It enables researchers to create’family trees’ – called phylogenetic trees – that reveal how samples relate to each other.

Researchers and clinicians in Cambridge have pioneered the use of genome sequencing and epidemiological information to trace outbreaks and transmission networks in hospitals and community-based health care settings, helping inform infection control steps and break the chains of transmission. Since March 2020, they have been applying this method to SARS-CoV-2 as part of the COVID-19 Genomics UK (COG-UK) Consortium.

In this new study, researchers analyzed samples collected from 6,600 patients between 26 February and 10 May 2020 and analyzed at the Public Health England (PHE) Laboratory in Cambridge. Out of all of the circumstances, 1,167 (18%) were care home residents from 337 care homes, 193 of which were residential homes and 144 nursing homes, most in the East of England.

While the median number of instances per care home was two, the ten care homes with the greatest number of cases accounted for 164 cases. There was a slight tendency for nursing homes to have more instances per house than residential homes, with a median of three cases.

Compared with non-care home residents admitted to hospital with COVID-19, hospitalized care home residents were less likely to be admitted to intensive care units (less than 7% versus 21%) and more likely to die (47% versus 20%).

The researchers also explored links between care homes and hospitals. 68% of care home residents were admitted to hospital during the study period. 57% were admitted with COVID-19, 6% of cases had guessed hospital-acquired infection, and 33% were discharged from hospital within seven days of a positive test. These findings highlight the ample opportunities for SARS-CoV-2 transmission between hospital and care home settings.

When the researchers examined the viral sequences, they found that for several of the care homes with the highest number of cases, each of the cases bunched closely together on a phylogenetic tree with either identical genomes or just a single base pair difference. This was consistent with one outbreak spreading within the care home.

By contrast, for several other care homes, instances were distributed across the phylogenetic tree, with more widespread genetic differences, suggesting that all these cases was separate and not connected to a shared transmission resource.

“Older people, particularly those in care homes who may be frail, are at particular risk from COVID-19, so it’s essential we do all that we can to protect them,” explained Dr Estée Török, an Honorary Consultant at Addenbrooke’s Hospital, Cambridge University Hospitals (CUH), and an Honorary Senior Visiting Fellow at the University of Cambridge.

“preventing the introduction of new infections into care homes ought to be a key priority to limit outbreaks, together with infection control efforts to limit transmission in care homes, including once an outbreak has been identified.”

The group found two clusters which were linked to healthcare workers. One of these involved care home residents, a carer from that home and another from an unknown maintenance home, paramedics and individuals living with them. The second involved several care home residents and acute medical staff at Cambridge University Hospitals NHS Foundation Trust who cared for at least one of the residents. It wasn’t possible to state where these clusters originated from and how the virus spread.

Using this technique of ‘genomic surveillance’ can help institutions such as care homes and hospitals better understand the transmission networks that allow the spread of COVID-19. This can then inform infection control measures, helping ensure that these places are as safe as possible for residents, patients, staff and visitors.”

Dr William Hamilton, University of Cambridge and CUH

The absolute number of diagnosed COVID-19 instances from care home residents declined more slowly in April than for non-care home residents, raising the percentage of cases from care homes and contributing to the slow rate of decrease in total case numbers during April and early May 2020.

“Our data suggest that care home transmission was more resistant to lockdown steps than non-care home settings. This may reflect the inherent vulnerability of the care home population, and the infection control challenges of nursing multiple residents who may also share communal living spaces,” said Gerry Tonkin-Hill in the Wellcome Sanger Institute.

The team found no new viral lineages from outside the united kingdom, which may reflect the success of travel restrictions in limiting new viral chatter to the general population during the first epidemic wave and lockdown period.