Mapping the drivers of within-host pathogen evolution using massive data sets

Duncan S. Palmer; Isaac Turner; Sarah Fidler; John Frater; Dominique Goedhals; Philip Goulder; Kuan-Hsiang Gary Huang; Annette Oxenius; Rodney Phillips; Roger Shapiro; Cloete van Vuuren; Angela R. McLean; Gil McVean

doi:10.1038/s41467-019-10724-w

Nature Communications (Jul 2019)

Mapping the drivers of within-host pathogen evolution using massive data sets

Duncan S. Palmer,
Isaac Turner,
Sarah Fidler,
John Frater,
Dominique Goedhals,
Philip Goulder,
Kuan-Hsiang Gary Huang,
Annette Oxenius,
Rodney Phillips,
Roger Shapiro,
Cloete van Vuuren,
Angela R. McLean,
Gil McVean

Affiliations

Duncan S. Palmer: Department of Statistics, University of Oxford
Isaac Turner: Department of Statistics, University of Oxford
Sarah Fidler: Division of Medicine, Wright Fleming Institute, Imperial College
John Frater: Institute for Emerging Infections, The Oxford Martin School
Dominique Goedhals: HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
Philip Goulder: Division of Infectious Diseases, University of the Free State, and 3 Military Hospital
Kuan-Hsiang Gary Huang: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research
Annette Oxenius: Institute of Microbiology, Swiss Federal Institute of Technology Zurich
Rodney Phillips: Institute for Emerging Infections, The Oxford Martin School
Roger Shapiro: Botswana Harvard AIDS Institute Partnership
Cloete van Vuuren: HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
Angela R. McLean: Institute for Emerging Infections, The Oxford Martin School
Gil McVean: Department of Statistics, University of Oxford

DOI: https://doi.org/10.1038/s41467-019-10724-w
Journal volume & issue: Vol. 10, no. 1
pp. 1 – 14

Abstract

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Various host factors may impact within-host pathogen evolution. Here, the authors develop a Bayesian approach for identifying host-pathogen interactions using large data sets of pathogen diversity, and apply it to investigate HLA-induced selection in the HIV-1 genome.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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