Table 6. Outbreak characteristics for 10 care homes with the largest number of SARS-CoV-2 genomes.
Epidemiological characteristics of the 10 care homes with the largest number of genomes are shown. Collectively these comprised 102 cases (102/700 (14%) of the total number of care home cases with genomic data available). ‘Cluster count’ refers to the number of SARS-CoV-2 clusters within each care home defined by transcluster (described in Materials and methods and main text). ‘Major cluster count’ shows the count for the dominant cluster (with the largest number of cases) and its percentage contribution to total case numbers for each care home. ‘Care home date range’ indicates the number of days from first sample to last sample date for residents from each care home. ‘Cluster date range’ indicates the number of days from first sample to last sample date for residents from each cluster within that care home, as defined by the transcluster algorithm, also showing the sample count (n) for each cluster. Sampling dates used collection date if known, or receive date in the diagnostic laboratory if collection date was unknown. The date range for each care home is typically larger than the date range for clusters within care homes, except for single-cluster care homes like CARE0314. This is consistent with the transcluster algorithm defining groups of cases occurring closer together in time. While the care homes frequently had more than one introduction of the virus among residents (i.e. >1 clusters), there was usually a single dominant cluster responsible for the majority of cases. Individual counts of males and females for each care home are not shown as this generally gave counts of less than five, risking patient anonymity. Overall, there were 59/102 (57.8%) females for these 10 care homes.
| Care home code | Sample count | Age (median, IQR, range) |
Ct values (median, IQR, range) |
Cluster count | Major cluster count | Care home date range (days) | Cluster date range (days, sample count) |
|---|---|---|---|---|---|---|---|
| CARE0032 | 7 | 87 (IQR: 81–91, range: 56–93) | 23 (IQR: 22–24, range: 14–26) | 2 | 6/7 (85.7%) | 39 | 0 days, n = 1 10 days, n = 6 |
| CARE0061 | 10 | 88.5 (IQR: 87–92.2, range: 84–97) | 23 (IQR: 21.2–26.5, range: 12–33) | 4 | 7/10 (70%) | 38 | 0 days, n = 1 22 days, n = 7 0 days, n = 1 0 days, n = 1 |
| CARE0063 | 12 | 74.5 (IQR: 67.8–81, range: 42–94) | 23 (IQR: 20.8–27, range: 14–30) | 2 | 11/12 (91.7%) | 21 | 18 days, n = 11 0 days, n = 1 |
| CARE0097 | 7 | 90 (IQR: 82.5–92, range: 73–95) | 23 (IQR: 20.5–24, range: 17–27) | 2 | 6/7 (85.7%) | 28 | 0 days, n = 1 14 days, n = 6 |
| CARE0151 | 7 | 81 (IQR: 77–89, range: 69–96) | 20 (IQR: 19–25.5, range: 17–30) | 4 | 4/7 (57.1%) | 20 | 0 days, n = 1 0 days, n = 4 0 days, n = 1 0 days, n = 1 |
| CARE0173 | 7 | 81 (IQR: 77.5–94, range: 71–95) | 19 (IQR: 17.5–26, range: 15–27) | 3 | 3/7 (42.9%) | 21 | 0 days, n = 1 3 days, n = 3 0 days, n = 3 |
| CARE0263 | 12 | 85.5 (IQR: 81.8–90.5, range: 69–97) | 19.5 (IQR: 18.5–24.8, range: 14–29) | 3 | 9/12 (75%) | 3 | 3 days, n = 9 0 days, n = 2 0 days, n = 1 |
| CARE0264 | 9 | 91 (IQR: 82–95, range: 73–96) | 26 (IQR: 25–27, range: 18–29) | 1 | 9/9 (100%) | 14 | 14 days, n = 9 |
| CARE0277 | 13 | 84 (IQR: 82–89, range: 71–94) | 26 (IQR: 24–27, range: 23–29) | 2 | 12/13 (92.3%) | 13 | 13 days, n = 12 0 days, n = 1 |
| CARE0314 | 18 | 87.5 (IQR: 81.2–90.8, range: 74–97) | 24 (IQR: 22.2–26, range: 14–29) | 1 | 18/18 (100%) | 5 | 5 days, n = 18 |