tetano
Editor, Senior Moderator
Lancet Infect Dis
. 2020 Jul 14;S1473-3099(20)30562-4.
doi: 10.1016/S1473-3099(20)30562-4. Online ahead of print.
Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study
Luke W Meredith[SUP] 1 [/SUP], William L Hamilton[SUP] 2 [/SUP], Ben Warne[SUP] 2 [/SUP], Charlotte J Houldcroft[SUP] 3 [/SUP], Myra Hosmillo[SUP] 1 [/SUP], Aminu S Jahun[SUP] 1 [/SUP], Martin D Curran[SUP] 4 [/SUP], Surendra Parmar[SUP] 4 [/SUP], Laura G Caller[SUP] 5 [/SUP], Sarah L Caddy[SUP] 6 [/SUP], Fahad A Khokhar[SUP] 6 [/SUP], Anna Yakovleva[SUP] 1 [/SUP], Grant Hall[SUP] 1 [/SUP], Theresa Feltwell[SUP] 3 [/SUP], Sally Forrest[SUP] 6 [/SUP], Sushmita Sridhar[SUP] 7 [/SUP], Michael P Weekes[SUP] 6 [/SUP], Stephen Baker[SUP] 6 [/SUP], Nicholas Brown[SUP] 4 [/SUP], Elinor Moore[SUP] 8 [/SUP], Ashley Popay[SUP] 9 [/SUP], Iain Roddick[SUP] 9 [/SUP], Mark Reacher[SUP] 9 [/SUP], Theodore Gouliouris[SUP] 10 [/SUP], Sharon J Peacock[SUP] 11 [/SUP], Gordon Dougan[SUP] 6 [/SUP], M Est?e T?r?k[SUP] 12 [/SUP], Ian Goodfellow[SUP] 13 [/SUP]
Affiliations
Abstract
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 settings.
Funding: COVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.
. 2020 Jul 14;S1473-3099(20)30562-4.
doi: 10.1016/S1473-3099(20)30562-4. Online ahead of print.
Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study
Luke W Meredith[SUP] 1 [/SUP], William L Hamilton[SUP] 2 [/SUP], Ben Warne[SUP] 2 [/SUP], Charlotte J Houldcroft[SUP] 3 [/SUP], Myra Hosmillo[SUP] 1 [/SUP], Aminu S Jahun[SUP] 1 [/SUP], Martin D Curran[SUP] 4 [/SUP], Surendra Parmar[SUP] 4 [/SUP], Laura G Caller[SUP] 5 [/SUP], Sarah L Caddy[SUP] 6 [/SUP], Fahad A Khokhar[SUP] 6 [/SUP], Anna Yakovleva[SUP] 1 [/SUP], Grant Hall[SUP] 1 [/SUP], Theresa Feltwell[SUP] 3 [/SUP], Sally Forrest[SUP] 6 [/SUP], Sushmita Sridhar[SUP] 7 [/SUP], Michael P Weekes[SUP] 6 [/SUP], Stephen Baker[SUP] 6 [/SUP], Nicholas Brown[SUP] 4 [/SUP], Elinor Moore[SUP] 8 [/SUP], Ashley Popay[SUP] 9 [/SUP], Iain Roddick[SUP] 9 [/SUP], Mark Reacher[SUP] 9 [/SUP], Theodore Gouliouris[SUP] 10 [/SUP], Sharon J Peacock[SUP] 11 [/SUP], Gordon Dougan[SUP] 6 [/SUP], M Est?e T?r?k[SUP] 12 [/SUP], Ian Goodfellow[SUP] 13 [/SUP]
Affiliations
- PMID: 32679081
- DOI: 10.1016/S1473-3099(20)30562-4
Abstract
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 settings.
Funding: COVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.