Commentary: COG-UK Report 5, 7th May 2020

Comment on COG-UK Report 5, 7th May 2020

The 5th report from COG-UK includes analysis of a total of 10,483 SARS-CoV-2 genomes, sequenced before 7th May 2020.

The report also includes analysis of viral genomes sequenced from five care homes in London. The samples were taken from staff and residents between 13th and 15th of April 2020. Of the 210 samples assessed, 91 were positive for SARS-CoV-2. 55 of these samples were of high enough quality for analysis. These data were used for phylogenetic studies within each care home, and for comparison with 277 non-care home viral genomes originating in London.

Analysis of the data suggests that in one care home, there were at least four separate introductions of the virus. A similar pattern of multiple introductions of the virus was observed in two other care homes, although less data were available for these sites. There was also some evidence that following an introduction of the virus, in some cases, there was transmission within a care home.

No common pattern or direction was seen for transmission, either between staff and residents or between symptomatic and asymptomatic people.

Further analysis identified a putative cluster of viral sequences, containing samples from multiple care homes. The presence of similar sequences across different care homes could suggest either transmission of SARS-CoV-2 between care homes, or separate introductions of the same viral lineage to different care homes from the community or other healthcare settings. Since the completion of this report, additional sequence data have been analysed. This analysis indicated that the sequences from care homes are part of a widespread viral lineage and consequently it is not possible to determine which of these scenarios is the case.

The findings highlight the importance of ongoing, larger studies, with additional metadata. Such studies will be vital to study transmission in care settings and inform control strategies.

The researchers anticipate that as the number of genomes sequenced increases, they will be able to provide a high resolution view of viral lineage diversity in the UK. This will make it possible to distinguish dominant local lineages and track viral spread from one part of the UK to another.

In such a fast-moving situation, the consortium members note it is important to consider the limitations of phylogenetic analysis, and the importance of caveats when interpreting data.