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. 2021 Mar 2;10:e64618. doi: 10.7554/eLife.64618

Figure 1. Study flow diagram Out of 6600 patients testing positive in the Cambridge Microbiology Public Health Laboratory (CMPHL) during the study period, 1167 were identified as being care home residents from 337 care homes.

(The methodology for assigning care home status is described in main text and Figure 1—figure supplement 1). Out of 1297 samples from 1167 care home residents, 286 samples were assigned for nanopore sequencing on site and 833 samples for sequencing at the Wellcome Sanger Institute (WSI). Of these, 258 and 533 sequences were available and downloaded from the MRC-CLIMB server at the time of running the analysis, respectively. Of these available genomes, 224 and 522 passed sequencing quality control thresholds (described in Materials and methods), respectively. This yielded the final analysis set of 700 high-coverage genomes from care home residents (representing 292 care homes): 197 genomes sequenced on site by nanopore and 503 sequences at WSI by Illumina. * 193 care homes were registered with the CQC as being residential homes without nursing care, referred to as ‘residential homes’ in main text, and 144 had nursing care available, referred to as ‘nursing homes’. ** Samples were selected for nanopore sequencing on site if they were inpatients or healthcare workers at Cambridge University Hospitals NHS Foundation Trust (CUH), where we prioritised rapid turnaround time to investigate hospital-acquired infections, plus a randomised selection of other East of England samples to provide broader genomic context to the CUH cases. The remaining samples not selected for nanopore sequencing on site, where available, were sent to WSI for sequencing.

Figure 1.

Figure 1—figure supplement 1. Flow diagram for identifying care homes from Cambridge-COGUK metadata Steps for identifying care home residents (further details in Materials and methods).

Figure 1—figure supplement 1.

First, the address field in the patient electronic healthcare records was searched for matching terms indicating a care home (e.g. ‘care home’, ‘nursing home’, etc). Second, the patient address field was searched for matching terms from a list of care home names registered to the Care Quality Commission (CQC). The resulting list was manually inspected and every care home included in the study was linked to a registered CQC care home. CQC coding of whether the care home had nursing care available was used (referred to as ‘nursing homes’ if nursing care was available and ‘residential homes’ if not). If the address information was incomplete (no postcode and/or no address line) then the case was excluded as impossible to determine whether or not the patient was from a care home, unless the person was known to be a healthcare worker (HCW), in which case it was assumed they were not a care home resident. This process yielded the final result of 1167 care home residents from 337 care homes; 5246 individuals that were not care home residents, and 187 individuals that were indeterminable.
Figure 1—figure supplement 2. Breakdown of main organisations submitting samples to Cambridge PHE Laboratory over study period per week.

Figure 1—figure supplement 2.

Only showing sites that submitted samples from >50 people with positive test results over study period, otherwise counted as ‘Other’. To maintain patient anonymity, per time interval only showing sites that submitted samples from >5 people with positive test results (otherwise counted as ‘Other’). Data prior to 16 March is amalgamated due to low sample numbers. Note that over the course of the study, some sites changed testing provider from CMPHL as further testing sites became available around the region. This explains some of the variation in the relative proportion of cases submitted from each site. The numbers reported here do not necessarily reflect total case numbers for each hospital or submitting organisation, as tests may have been performed elsewhere or metadata not collected in this study; the numbers are included purely to indicate where the samples included in this study originated from.
Figure 1—figure supplement 3. UK care home testing policy timeline.

Figure 1—figure supplement 3.

(1) 31st January – first recorded case of covid-19 in the UK. (2) 26th February - first case of COVID-19 in the East of England; start date of this study. (3) 12th March – individuals in the community advised to self-isolate for 7 days, without testing. Testing only offered to care homes in the context of a suspected outbreak. (4) 23rd March - UK lockdown officially begins. (5) 15th April – action plan announced to test all symptomatic residents in care homes, plus testing of all residents prior to admission to care home from hospital. (6) 29th April – testing guidance amended to reflect that asymptomatic as well symptomatic residents and staff in care homes may need to be tested as part of an outbreak. (7) Policy for COVID-19 testing prior to discharge to care homes instigated 16th April: https://www.gov.uk/government/publications/coronavirus-covid-19-adult-social-care-action-plan/covid-19-our-action-plan-for-adult-social-care. (8) 10th May - end date of this study. (9) 11th May – national whole care home testing portal (offering a single test to all staff and residents) goes live for care homes with residents aged 65 years and over or dementia patients. (10) 8th June – national whole care home testing portal extends eligibility to care homes with residents aged under 65 years. (11) 3rd July – announcement that regular asymptomatic testing for care home staff and residents will be rolled out through the national whole care home testing portal in July for homes with residents aged over 65 years or dementia patients. References: Public Health England, 2020b; The Health Foundation, 2020.