Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes
Cotton S., McHugh MP., Dewar R., Haas JG., Templeton K., Robson SC., Connor TR., Loman NJ., Golubchik T., Martinez Nunez RT., Bonsall D., Rambaut A., Snell LB., Livett R., Ludden C., Corden S., Nastouli E., Nebbia G., Johnston I., Prieto JA., Saeed K., Jackson DK., Houlihan C., Frampton D., Hamilton WL., Witney AA., Bucca G., Pope CF., Moore C., Thomson EC., Cutino-Moguel T., Harrison EM., Smith CP., Rogan F., Beckwith SM., Murray A., Singleton D., Eastick K., Sheridan LA., Randell P., Jackson LM., Ariani CV., Gonçalves S., Fairley DJ., Loose MW., Watkins J., Moses S., Nicholls S., Bull M., Amato R., Smith DL., Aanensen DM., Barrett JC., Kele B., Aggarwal D., Shepherd JG., Curran MD., Parmar S., Parker MD., Williams C., Glaysher S., Underwood AP., Bashton M., Pacchiarini N., Loveson KF., Byott M., Carabelli AM., Templeton KE., Peacock SJ., de Silva TI., Wang D., Langford CF., Sillitoe J., Gunson RN., Cottrell S., O'Grady J., Kwiatkowski D., Lillie PJ., Cortes N., Moore N., Thomas C., Burns PJ., Mahungu TW., Liggett S., Beckett AH., Holden MT., Levett LJ., Osman H., Hassan-Ibrahim MO., Simpson DA., Chand M., Gupta RK., Darby AC., Paterson S., Pybus OG., Volz EM., de Angelis D., Robertson DL., Page AJ., Martincorena I.
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 1st March 2020 to 31st 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.