Illingworth, Christopher J. R., Hamilton, William L., Jackson, Christopher, Warne, Ben, Popay, Ashley, Meredith, Luke, Hosmillo, Myra, Jahun, Aminu, Fieldman, Tom, Routledge, Matthew, Houldcroft, Charlotte J., Caller, Laura, Caddy, Sarah, Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin, Parmar, Surendra, Sparkes, Dominic ORCID: 0000-0002-8475-3864, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom ORCID: 0000-0002-6438-7422, Grainger, Kayleigh, Workman, Chris, Gkrania-Klotsas, Effrossyni ORCID: 0000-0002-0930-8330, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Gouliouris, Theodore ORCID: 0000-0002-2011-1205, Goodfellow, Ian, De Angelis, Daniela and Torok, M. Estee (2022). A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol. Biol. Evol., 39 (3). OXFORD: OXFORD UNIV PRESS. ISSN 1537-1719

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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 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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Illingworth, Christopher J. R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hamilton, William L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jackson, ChristopherUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Warne, BenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Popay, AshleyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Meredith, LukeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hosmillo, MyraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jahun, AminuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fieldman, TomUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Routledge, MatthewUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Houldcroft, Charlotte J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Caller, LauraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Caddy, SarahUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yakovleva, AnnaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hall, GrantUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Khokhar, Fahad A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Feltwell, TheresaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pinckert, Malte L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Georgana, IlianaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chaudhry, YasminUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Curran, MartinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Parmar, SurendraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sparkes, DominicUNSPECIFIEDorcid.org/0000-0002-8475-3864UNSPECIFIED
Rivett, LucyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jones, Nick K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sridhar, SushmitaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Forrest, SallyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dymond, TomUNSPECIFIEDorcid.org/0000-0002-6438-7422UNSPECIFIED
Grainger, KayleighUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Workman, ChrisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gkrania-Klotsas, EffrossyniUNSPECIFIEDorcid.org/0000-0002-0930-8330UNSPECIFIED
Brown, Nicholas M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Weekes, Michael P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Baker, StephenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peacock, Sharon J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gouliouris, TheodoreUNSPECIFIEDorcid.org/0000-0002-2011-1205UNSPECIFIED
Goodfellow, IanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
De Angelis, DanielaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Torok, M. EsteeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-689094
DOI: 10.1093/molbev/msac025
Journal or Publication Title: Mol. Biol. Evol.
Volume: 39
Number: 3
Date: 2022
Publisher: OXFORD UNIV PRESS
Place of Publication: OXFORD
ISSN: 1537-1719
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
GENOMIC SURVEILLANCE; VIRUS; DYNAMICSMultiple languages
Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & HeredityMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/68909

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