Title: Mapping the drivers of within-host pathogen evolution using massive data sets
Authors: orcid: http://orcid.org/0000-0002-0824-0047
last_name: Palmer
first_name: Duncan S.
name: Duncan S. Palmer
affiliations: label: 1
institution: Department of Statistics, University of Oxford
country: UK
name: Department of Statistics, University of Oxford , 24-29 St Giles’, Oxford OX1 3LB, UK .
label: 2
institution: Wellcome Trust Centre for Human Genetics
country: UK
name: Wellcome Trust Centre for Human Genetics , Roosevelt Drive, Oxford OX3 7BN, UK .
label: 3
institution: Institute for Emerging Infections, The Oxford Martin School
country: UK
name: Institute for Emerging Infections, The Oxford Martin School , Oxford OX1 3BD, UK .
orcid: http://orcid.org/0000-0002-2378-4886
last_name: Turner
first_name: Isaac
name: Isaac Turner
affiliations: label: 1
institution: Department of Statistics, University of Oxford
country: UK
name: Department of Statistics, University of Oxford , 24-29 St Giles’, Oxford OX1 3LB, UK .
label: 2
institution: Wellcome Trust Centre for Human Genetics
country: UK
name: Wellcome Trust Centre for Human Genetics , Roosevelt Drive, Oxford OX3 7BN, UK .
orcid: http://orcid.org/0000-0003-1676-7583
last_name: Fidler
first_name: Sarah
name: Sarah Fidler
affiliations: label: 4
institution: Division of Medicine, Wright Fleming Institute, Imperial College
country: UK
name: Division of Medicine, Wright Fleming Institute, Imperial College , London W2 1PG, UK .
orcid: http://orcid.org/0000-0001-7163-7277
last_name: Frater
first_name: John
name: John Frater
affiliations: label: 3
institution: Institute for Emerging Infections, The Oxford Martin School
country: UK
name: Institute for Emerging Infections, The Oxford Martin School , Oxford OX1 3BD, UK .
label: 5
institution: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research
country: UK
name: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research , Oxford OX1 3SY, UK .
label: 6
institution: Oxford NIHR Biomedical Research Centre
country: UK
name: Oxford NIHR Biomedical Research Centre , Oxford OX3 7LE, UK .
last_name: Goulder
first_name: Philip
name: Philip Goulder
affiliations: label: 7
institution: Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research
country: UK
name: Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research , Oxford OX1 3SY, UK .
label: 8
institution: HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
country: South Africa
name: HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal , Durban, South Africa .
last_name: Goedhals
first_name: Dominique
name: Dominique Goedhals
affiliations: label: 9
institution: Department of Medical Microbiology and Virology, University of the Free State, and National Heath Laboratory Service
country: South Africa
name: Department of Medical Microbiology and Virology, University of the Free State, and National Heath Laboratory Service , Bloemfontein, South Africa .
orcid: http://orcid.org/0000-0003-1910-9367
last_name: Huang
first_name: Kuan-Hsiang Gary
name: Kuan-Hsiang Gary Huang
affiliations: label: 5
institution: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research
country: UK
name: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research , Oxford OX1 3SY, UK .
label: 10
institution: Einstein Medical Center Philadelphia
country: USA
name: 10  Einstein Medical Center Philadelphia , 5501 Old York Road, PA 19141, USA .
orcid: http://orcid.org/0000-0002-2079-2354
last_name: Oxenius
first_name: Annette
name: Annette Oxenius
affiliations: label: 11
institution: Institute of Microbiology, Swiss Federal Institute of Technology Zurich
country: Switzerland
name: 11  Institute of Microbiology, Swiss Federal Institute of Technology Zurich , 8093 Zurich, Switzerland .
last_name: Phillips
first_name: Rodney
name: Rodney Phillips
affiliations: label: 3
institution: Institute for Emerging Infections, The Oxford Martin School
country: UK
name: Institute for Emerging Infections, The Oxford Martin School , Oxford OX1 3BD, UK .
label: 5
institution: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research
country: UK
name: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research , Oxford OX1 3SY, UK .
label: 6
institution: Oxford NIHR Biomedical Research Centre
country: UK
name: Oxford NIHR Biomedical Research Centre , Oxford OX3 7LE, UK .
last_name: Shapiro
first_name: Roger
name: Roger Shapiro
affiliations: label: 12
institution: Botswana Harvard AIDS Institute Partnership
country: Botswana
name: 12  Botswana Harvard AIDS Institute Partnership , Gaborone BO 320, Botswana .
label: 13
institution: Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health
country: USA
name: 13  Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health , Boston, MA 02215, USA .
last_name: van Vuuren
first_name: Cloete
name: Cloete van Vuuren
affiliations: label: 9
institution: Department of Medical Microbiology and Virology, University of the Free State, and National Heath Laboratory Service
country: South Africa
name: Department of Medical Microbiology and Virology, University of the Free State, and National Heath Laboratory Service , Bloemfontein, South Africa .
orcid: http://orcid.org/0000-0002-3386-7888
last_name: McLean
first_name: Angela R.
name: Angela R. McLean
affiliations: label: 3
institution: Institute for Emerging Infections, The Oxford Martin School
country: UK
name: Institute for Emerging Infections, The Oxford Martin School , Oxford OX1 3BD, UK .
label: 14
institution: Zoology Department, South Parks Road, University of Oxford
country: UK
name: 14  Zoology Department, South Parks Road, University of Oxford , Oxford OX1 3PS, UK .
orcid: http://orcid.org/0000-0002-5012-4162
last_name: McVean
first_name: Gil
name: Gil McVean
affiliations: label: 1
institution: Department of Statistics, University of Oxford
country: UK
name: Department of Statistics, University of Oxford , 24-29 St Giles’, Oxford OX1 3LB, UK .
label: 2
institution: Wellcome Trust Centre for Human Genetics
country: UK
name: Wellcome Trust Centre for Human Genetics , Roosevelt Drive, Oxford OX3 7BN, UK .
label: 15
institution: Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery
country: UK
name: 15  Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery , Old Road Campus, Oxford OX3 7LF, UK .
Affiliations: label: 1
institution: Department of Statistics, University of Oxford
country: UK
name: Department of Statistics, University of Oxford , 24-29 St Giles’, Oxford OX1 3LB, UK .
label: 2
institution: Wellcome Trust Centre for Human Genetics
country: UK
name: Wellcome Trust Centre for Human Genetics , Roosevelt Drive, Oxford OX3 7BN, UK .
label: 3
institution: Institute for Emerging Infections, The Oxford Martin School
country: UK
name: Institute for Emerging Infections, The Oxford Martin School , Oxford OX1 3BD, UK .
label: 4
institution: Division of Medicine, Wright Fleming Institute, Imperial College
country: UK
name: Division of Medicine, Wright Fleming Institute, Imperial College , London W2 1PG, UK .
label: 5
institution: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research
country: UK
name: Nuffield Department of Clinical Medicine, University of Oxford, Peter Medawar Building for Pathogen Research , Oxford OX1 3SY, UK .
label: 6
institution: Oxford NIHR Biomedical Research Centre
country: UK
name: Oxford NIHR Biomedical Research Centre , Oxford OX3 7LE, UK .
label: 7
institution: Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research
country: UK
name: Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research , Oxford OX1 3SY, UK .
label: 8
institution: HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal
country: South Africa
name: HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal , Durban, South Africa .
label: 9
institution: Department of Medical Microbiology and Virology, University of the Free State, and National Heath Laboratory Service
country: South Africa
name: Department of Medical Microbiology and Virology, University of the Free State, and National Heath Laboratory Service , Bloemfontein, South Africa .
label: 10
institution: Einstein Medical Center Philadelphia
country: USA
name: 10  Einstein Medical Center Philadelphia , 5501 Old York Road, PA 19141, USA .
label: 11
institution: Institute of Microbiology, Swiss Federal Institute of Technology Zurich
country: Switzerland
name: 11  Institute of Microbiology, Swiss Federal Institute of Technology Zurich , 8093 Zurich, Switzerland .
label: 12
institution: Botswana Harvard AIDS Institute Partnership
country: Botswana
name: 12  Botswana Harvard AIDS Institute Partnership , Gaborone BO 320, Botswana .
label: 13
institution: Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health
country: USA
name: 13  Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health , Boston, MA 02215, USA .
label: 14
institution: Zoology Department, South Parks Road, University of Oxford
country: UK
name: 14  Zoology Department, South Parks Road, University of Oxford , Oxford OX1 3PS, UK .
label: 15
institution: Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery
country: UK
name: 15  Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery , Old Road Campus, Oxford OX3 7LF, UK .
Field: Immunology and Microbiology
Document type: preprint
Year: 2017