How SARS-CoV-2 spreads in care home settings?

Genomics study identifies routes of transmission of coronavirus in care homes.


COVID-19 poses a significant challenge to care homes. Older people and other patients affected by heart disease, respiratory disease, and type 2 diabetes- are at the most significant risk of severe disease and even death.

This makes the care home population especially vulnerable.

A recent study led by scientists at the University of Cambridge and Wellcome Sanger Institute has shed light on how SARS-CoV-2 spreads in care home settings. For the study, scientists used a combination of genome sequencing and detailed epidemiological information to study the impact of COVID-19 on care homes.

Scientists read and sequence the genetic code of the virus. This provides significant information on its biology and transmission. Also, it allowed scientists to create ‘family trees’ – known as phylogenetic trees – that show how samples relate to each other.

Using genome sequencing and epidemiological information, scientists traced the outbreaks and transmission networks in hospitals and community-based healthcare settings.

The study involved 6,600 patients. Scientists analyzed the samples taken between 26 February and 10 May 2020 and tested them at the Public Health England (PHE) Laboratory in Cambridge. Out of all the cases, 1,167 (18%) cared for home residents from 337 care homes, 193 of which were residential homes and 144 nursing homes, most in the East of England. The median age of care home residents was 86 years.

While the median number of cases per care home was two, the ten care homes with the most significant number of cases accounted for 164 cases. There was a slight trend for nursing homes to have more cases per home 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 study also determined the links between care homes and hospitals.68% of care home residents were admitted to the hospital during the study period. 57% were admitted with COVID-19, 6% of cases had suspected hospital-acquired infection, and 33% were discharged from the 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.

After studying the viral sequences, scientists found that several care homes with the highest number of cases clustered closely together on a phylogenetic tree with either identical genomes or just one base pair difference. This was consistent with a single outbreak spreading within the care home.

In contrast, for a few other care homes, cases were circulated across the phylogenetic tree, with more broad genetic differences. This recommends that every one of these cases was free and not identified with a common transmission source.

Dr. Estée Török, an Honorary Consultant at Addenbrooke’s Hospital, Cambridge University Hospitals (CUH), said, “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.”

“Preventing the introduction of new infections into care homes should be a key priority to limit outbreaks, alongside infection control efforts to limit transmission within care homes, including once an outbreak has been identified.”

The team discovered two groups that were connected to healthcare workers. One of these involved care home residents, and another from an unknown care home, paramedics, and individuals living with them. In the second group, there were several care home residents and acute medical staff at Cambridge University Hospitals NHS Foundation Trust who cared for at least one resident.

Dr. William Hamilton from the University of Cambridge and CUH said, “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.”

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

This work was funded by COG-UK, Wellcome, the Academy of Medical Sciences, the Health Foundation, and the NIHR Cambridge Biomedical Research Centre.

Journal Reference:
  1. William L Hamilton et al. Genomic epidemiology of COVID-19 in care homes in the East of England. DOI: 10.7554/eLife.64618
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