ArticleeLife2021
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- Genomic and Phylogenetic Dissection of SARS-CoV-2 Transmission Networks in Healthcare Workers.International journal of microbiology · 2026Article
- The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission.PLoS computational biology · 2025Article
- Article
- The potential of genomic epidemiology: capitalizing on its practical use for impact in the healthcare setting.Frontiers in public health · 2025Article
- SARS-CoV-2 delta variant in African lions (Panthera leo) and humans at Utah's Hogle Zoo, USA, 2021-22.Zoonoses and public health · 2024Article
- A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.Virus evolution · 2024Article
- A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?British journal of health psychology · 2023Article
- SARS-CoV-2 Outbreak Investigation Using Contact Tracing and Whole-Genome Sequencing in an Ontario Tertiary Care Hospital.Microbiology spectrum · 2023Article
- Dynamics of nosocomial SARS-CoV-2 transmissions: Facing the challenge of variants of concern in a Brazilian reference hospital.Journal of medical virology · 2023Article
- Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks.The Journal of hospital infection · 2023Article
- Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.The Journal of hospital infection · 2023Article
- Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias.The Journal of infectious diseases · 2022Article
- Article
- Reactivation/relapse of SARS-CoV-2 in a child following haematopoietic stem cell transplantation, confirmed by whole genome sequencing, following apparent viral clearance.The Journal of infection · 2022Article
- Article
- Unraveling the hurdles of a large COVID-19 epidemiological investigation by viral genomics.The Journal of infection · 2022Article
- Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers.Scientific reports · 2022Article
- Article
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Authors and funding
17 authors.
Funding
Abstract
Background: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult. Methods: We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hr following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020. Results: We analysed data from 326 HOCIs. Among HOCIs with time from admission ≥8 days, the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time from admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%). Conclusions: The methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period. Funding: COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute.
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