Prof Anthony Scott

Professor of Vaccine Epidemiology

United Kingdom

I am a clinician and epidemiologist with an interests in infectious diseases and vaccinology. I trained in Infectious Diseases in London and Newcastle and in Epidemiology at LSHTM. Since 1993 I have worked almost continuously at the KEMRI-Wellcome Trust Research Programme in Kilifi, Kenya both as researcher and clinician. Between 1998-1999 I spent two years at the Respiratory Diseases Branch of the US CDC in Atlanta. Between 1998 and 2012 I was based at the Nuffield Department of Clinical Medicine in Oxford; since 2013 I have been based at the School. Since 2016 I have been supporting the development of a new research centre, the Hararghe Health Research partnership, in Harar, Ethiopia - a collaboration between LSHTM and Haramaya University. I have directed the NIHR Health Protection Research Unit in Immunisation since 2014 and, from 2013-2023, I was a member of the UK vaccine policy committee, JCVI. I continue to do vaccine policy work on the WHO strategic advisory group of experts in vaccines and immunisation.


Department of Infectious Disease Epidemiology and International Health
Faculty of Epidemiology and Population Health


Vaccine Centre
Antimicrobial Resistance Centre


Each summer, since 2014, I have co-directed a two week intensive short course with Stefan Flasche under the title: "Epidemiological Evaluation of Vaccines: Efficacy, Safety and Policy". I lecture on infectious diseases, surveillance, disease burden assessment, pneumonia and pneumococcal diseases on a variety of MSc modules including Epidemiology of Infectious Diseases, Clinical Bacteriology and Vaccine Immunology.


Since the early 1990s I have researched the aetiology of pneumonia in adults and children and the causes of death in children, with a focus on East Africa. I have measured the impact of new conjugate vaccines for H. influenzae type b and Pneumococcus against invasive bacterial disease, meningitis and pneumonia. I have used carriage studies and modelling to understand the transmission of pneumococci and the indirect effects of conjugate vaccines. I have also undertaken Phase I/II vaccine studies of new vaccines against pneumococcus and non-typhoidal salmonella and studied the immunogenicity of pneumococcal conjugate vaccines given to newborn children, and given in fractional doses to older children. In Eastern Ethiopia, I have described the causes of death in children aged <5 years and in Kenya I have followed the long term mortality impacts of new vaccines and the COVID-19 pandemic in the Kilifi HDSS. I have used seroepidemiological studies to define population immunity to pneumococcus and SARS-CoV-2. In the UK I have overseen a programme of policy-relevant research to assist JCVI, UKHSA and NHS England to introduce new vaccines and optimise existing vaccine programmes.

Research Area
Infectious disease policy
Serology, vaccines
Disease and Health Conditions
United Kingdom
Sub-Saharan Africa (developing only)

Selected Publications

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors.
Uyoga, S; ADETIFA, IM O; Karanja, HK; Nyagwange, J; Tuju, J; Wanjiku, P; Aman, R; Mwangangi, M; Amoth, P; Kasera, K; Ng'ang'a, W; Rombo, C; Yegon, C; Kithi, K; Odhiambo, E; Rotich, T; Orgut, I; Kihara, S; OTIENDE, M; BOTTOMLEY, C; Mupe, ZN; Kagucia, EW; GALLAGHER, KE; Etyang, A; VOLLER, S; ... Warimwe, GM.
Effect of strikes by health workers on mortality between 2010 and 2016 in Kilifi, Kenya: a population-based cohort analysis.
Ong'ayo, G; OOKO, M; Wang'ondu, R; BOTTOMLEY, C; Nyaguara, A; Tsofa, BK; Williams, TN; Bejon, P; SCOTT, JA G; Etyang, AO;
The Lancet Global Health
Sustaining pneumococcal vaccination after transitioning from Gavi support: a modelling and cost-effectiveness study in Kenya.
OJAL, J; Griffiths, U; Hammitt, LL; ADETIFA, I; Akech, D; Tabu, C; SCOTT, JA G; FLASCHE, S;
The Lancet Global Health
Effect of Previous Exposure to Malaria on Blood Pressure in Kilifi, Kenya: A Mendelian Randomization Study.
Etyang, AO; Kapesa, S; Odipo, E; Bauni, E; Kyobutungi, C; Abdalla, M; Muntner, P; Musani, SK; Macharia, A; Williams, TN; Cruickshank, JK; SMEETH, L; SCOTT, JA G;
Journal of the American Heart Association
Effect of 10-valent pneumococcal conjugate vaccine on the incidence of radiologically-confirmed pneumonia and clinically-defined pneumonia in Kenyan children: an interrupted time-series analysis.
Silaba, M; OOKO, M; BOTTOMLEY, C; Sande, J; Benamore, R; Park, K; Ignas, J; Maitland, K; Mturi, N; Makumi, A; OTIENDE, M; Kagwanja, S; Safari, S; Ochola, V; Bwanaali, T; Bauni, E; Gleeson, F; Deloria Knoll, M; ADETIFA, I; Marsh, K; Williams, TN; Kamau, T; Sharif, S; Levine, OS; Hammitt, LL; ... SCOTT, JA G.
The Lancet Global Health
Effect of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya: a longitudinal surveillance study.
Hammitt, LL; Etyang, AO; Morpeth, SC; OJAL, J; Mutuku, A; Mturi, N; Moisi, JC; ADETIFA, IM; Karani, A; Akech, DO; OTIENDE, M; Bwanaali, T; Wafula, J; Mataza, C; Mumbo, E; Tabu, C; Knoll, MD; Bauni, E; Marsh, K; Williams, TN; Kamau, T; Sharif, SK; Levine, OS; SCOTT, JA G;
Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4.
Gilchrist, JJ; Rautanen, A; Fairfax, BP; Mills, TC; Naranbhai, V; Trochet, H; Pirinen, M; MUTHUMBI, E; Mwarumba, S; Njuguna, P; Mturi, N; Msefula, CL; Gondwe, EN; MacLennan, JM; Chapman, SJ; Molyneux, ME; Knight, JC; Spencer, CC A; Williams, TN; MacLennan, CA; SCOTT, JA G; Hill, AV S;
Nature communications
Prospective Observational Study of Incidence and Preventable Burden of Childhood Tuberculosis, Kenya.
Brent, AJ; Nyundo, C; Langat, J; Mulunda, C; Wambua, J; Bauni, E; Sande, J; Park, K; Williams, TN; Newton, CR J; Levin, M; SCOTT, JA G; KIDS TB Study Group,;
Emerging infectious diseases
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