Published
02 February 2022
  • Journal article

A2B-COVID: a tool for rapidly evaluating potential SARS-CoV-2 transmission events

Authors
Illingworth, Christopher J.R. ; 
Hamilton, William L. ; 
Jackson, Chris; 
Warne, Ben; 
Popay, Ashley; 
Meredith, Luke W.; 
Hosmillo, Myra; 
Jahun, Aminu S.; 
Fieldman, Tom; 
Routledge, Matthew; 
Houldcroft, Charlotte J.; 
Caller, Laura G.; 
Caddy, Sarah L.; 
Yakovleva, Anna; 
Hall, Grant; 
Khokhar, Fahad A.; 
Feltwell, Theresa; 
Pinckert, Malte L.; 
Georgana, Iliana; 
Chaudhry, Yasmin; 
Curran, Martin D.; 
Parmar, Surendra; 
Sparkes, Dominic; 
Rivett, Lucy; 
Jones, Nick K.; 
Sridhar, Sushmita; 
Forrest, Sally; 
Dymond, Tom; 
Grainger, Kayleigh; 
Workman, Chris; 
Gkrania-Klotsas, Effrossyni; 
Brown, Nicholas M.; 
Weekes, Michael P.; 
Baker, Stephen; 
Peacock, Sharon J.; 
Gouliouris, Theodore; 
Goodfellow, Ian G.; 
De Angelis, Daniela; 
Török, M. Estée
Source
Molecular Biology and Evolution

Abstract

Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust (CUH) during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.

Rights

Available under License Creative Commons Attribution.

Cite as

Illingworth, C., Hamilton, W., Jackson, C., Warne, B., Popay, A., Meredith, L., Hosmillo, M., Jahun, A., Fieldman, T., Routledge, M., Houldcroft, C., Caller, L., Caddy, S., Yakovleva, A., Hall, G., Khokhar, F., Feltwell, T., Pinckert, M., Georgana, I., Chaudhry, Y., Curran, M., Parmar, S., Sparkes, D., Rivett, L., Jones, N., Sridhar, S., Forrest, S., Dymond, T., Grainger, K., Workman, C., Gkrania-Klotsas, E., Brown, N., Weekes, M., Baker, S., Peacock, S., Gouliouris, T., Goodfellow, I., De Angelis, D. & Török, M. 2022, 'A2B-COVID: a tool for rapidly evaluating potential SARS-CoV-2 transmission events', Molecular Biology and Evolution. http://dx.doi.org/10.1093/molbev/msac025

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Topics
Coronavirus (COVID-19)
Keywords
COVID-19 Infectious disease transmission
Funder
COVID- Genomics UK COG-UK Consortium; 
Medical Research Council
Publisher
Oxford University Press
Source repository
University of Glasgow
Last updated: 19 October 2023
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