| Title: |
Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study |
| Authors: |
Meredith, LW; Hamilton, WL; Warne, B; Houldcroft, CJ; Hosmillo, M; Jahun, AS; Curran, MD; Parmar, S; Caller, LG; Caddy, SL; Khokhar, FA; Yakovleva, A; Hall, G; Feltwell, T; Forrest, S; Sridhar, S; Weekes, MP; Baker, S; Brown, N; Moore, E; Popay, A; Roddick, I; Reacher, M; Gouliouris, T; Peacock, SJ; Dougan, G; Török, ME; Goodfellow, I |
| Publisher Information: |
Elsevier |
| Publication Year: |
2021 |
| Collection: |
Oxford University Research Archive (ORA) |
| Description: |
Background The burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures. Methods In this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases. Findings Between March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting. Interpretation We established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community ... |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| DOI: |
10.1016/s1473-3099(20)30562-4 |
| Availability: |
https://doi.org/10.1016/s1473-3099(20)30562-4; https://ora.ox.ac.uk/objects/uuid:1d64d61c-f6e7-412d-96b6-35989e19dc75 |
| Rights: |
info:eu-repo/semantics/openAccess ; CC Attribution (CC BY) |
| Accession Number: |
edsbas.BDCD6E43 |
| Database: |
BASE |