Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Abstract

Background: The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes.

Aim: To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave.

Methods: A clinical review was performed for all patients discharges from hospitals to care homes from 1^st March 2020 to 31^st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records.

Findings: In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home.

Conclusion: The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine.

Keywords: Care homes; Hospital discharge; Introduction; SARS-CoV-2.

Figure 1

Severe acute respiratory syndrome coronavirus-2 phylogenetic tree output from CIVET displaying sequences from Care Home 20 (CH20) and background data. Green, care home sequences; blue, background community sequences from the COG-UK dataset (location/Sample_ID/date_collected). Care home sequences are from samples collected between 4^th May 2020 and 2^nd June 2020. The sequence circled in red is the patient discharged from hospital, and was collected on 14^th May 2020. The x-axis scale shows genetic divergence [single-nucleotide polymorphisms (SNPs) per genome length]. All CH20 consensus sequences were very closely related and clustered together with pangolin lineage B.1.1.14. There were 19 consensus genomes which were identical, and six consensus genomes displaying two or fewer SNP differences.

Figure 2

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) phylogenetic tree output from CIVET displaying sequences from Care Home 1 (CH1) and background data. In total, it was possible to sequence 10 of 11 SARS-CoV-2-positive cases identified in CH1, including the positive case discharged from hospital. Cluster analysis by CIVET showed nine CH1 sequences clustered with two hospital inpatient cases. The x-axis scale shows genetic divergence [single-nucleotide polymorphisms (SNPs) per genome length]. Blue, care home sequences; green, background sequences; red, patient discharged from hospital; orange, hospital inpatients. Collection dates for these samples are shown in Figure 3. Data used from COG-UK dataset (location/Sample ID/date collected). There was one sequence from CH1 which was a different phylogenetic lineage to the other cases; however, this was the last positive case in the care home, and 12 days apart from the previous positive case.

Figure 3

Timeline of first discharge of patient to Care Home 1 (CH1) and related background cases in hospital. Day 1 is the first hospital admission date for Resident 3 (discharged patient). Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-positive tests are represented by black dots (•), with hospital and care home locations by colour. During the first hospital admission for Resident 3, Inpatient 1 and Inpatient 2 were on the same ward and positive for SARS-CoV-2 at the time. After Resident 3 was discharged back to CH1, a further 10 positive cases were identified at CH1. This figure was created using modified R script (https://github.com/wlhamilton/Patient-ward-movement-timelines). Both inpatients were discharged to private homes after admission. ∗Resident 3 died during their second admission to hospital.