Dr Stephane Hue

Associate Professor in Epidemiology

London School of Hygiene & Tropical Medicine
Keppel Street
London
SE11 4BY
United Kingdom

Email
Stephane

I am a computational biologist specialised in pathgen genomics and the molecular epidemiology of infectious diseases. My research activity focuses on the reconstruction of pathogen transmission for surveillance or in outbreak situations.

After graduating at the University Paul Sabatier in Toulouse, France, I moved to the United Kingdom to complete a Masters in Medical Molecular Microbiology at the University of Nottingham. This was followed by a PhD in the molecular epidemiology of HIV-1 at University College London. After completing postdoctoral positions at the University of Oxford and University College London, I have joined LSHTM in 2014, where I am currently holding an associate professor position.

Affiliations

Department of Infectious Disease Epidemiology and Dynamics

Faculty of Epidemiology and Population Health

Centres

Centre for Mathematical Modelling of Infectious Diseases

Teaching

I have been teaching viral evolution, molecular epidemiology and phylogenetics to undergraduate and postgraduate students since 2008.

At LSHTM, I am teaching a range of lectures and practical sessions for the MSc Epidemiology (Introduction to Molecular Epidemiology, Introduction of Omics in Epidemiology, Omics Applications to Communicable Diseases, Genomics in the age of COVID-19, Molecular Epidemiology of Infectious Diseases, Introduction to Phylogenetics), for the MSc Health Data Science (Genetic Variation, Pathogen Genomics, Disease Outbreak Studies), for the MSc Medical Microbiology (HIV Drug Resistance, Molecular Epidemiology of Viruses) and for the short course 'Introduction to the Modelling of Infectious diseases' (Introduction to Phylodynamics).

I am the co-organiser of the MSc modules 'Epidemiology and Omics' (2484) and 'Genomic Health Data' (2492).

Research

I primarily study pathogen transmission through the joint analysis of epidemiological and gene sequence data. My work involves the implementation of statistical models in phylogenetic studies, particularly in the context of reconstructing time and spatial trends of viral transmissions.

While my research activity was primarily oriented towards the study of HIV-1, I am applying my skills to a range of other viruses and bacteria, including Dengue virus, Hepatitis Delta Virus, SARS-CoV-2 and Streptococcus pneumonia.

Research Area

Bioinformatics

Genomics

Molecular epidemiology

Virology

Disease and Health Conditions

HIV/AIDS

Dengue

Hepatitis

Emerging infectious diseases

Respiratory diseases

Country

United Kingdom

Vietnam

Gambia

Region

European Union

East Asia & Pacific (developing only)

Sub-Saharan Africa (all income levels)

Selected Publications

Emergence of Novel Norovirus GII.4 Variant.

Chhabra, P; TULLY, DC; Mans, J; Niendorf, S; Barclay, L; Cannon, JL; Montmayeur, AM; Pan, C-Y; Page, N; Williams, R; Tutill, H; Roy, S; Celma, C; Beard, S; Mallory, ML; Manouana, GP; Velavan, TP; Adegnika, AA; Kremsner, PG; Lindesmith, LC; Hué, S; Baric, RS; Breuer, J; Vinjé, J;

2023

Emerging infectious diseases

Reconstructing the phylodynamic history and geographic spread of the CRF01_AE-predominant HIV-1 epidemic in the Philippines from PR/RT sequences sampled from 2008 to 2018.

Polotan, FG M; Salazar, CR P; Morito, HL E; Abulencia, MF B; Pantoni, RA R; Mercado, ES; Hué, S; Ditangco, RA;

2023

Virus evolution

Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea.

ROBERT, A; Tsui Lok Hei, J; Watson, CH; Gsell, P-S; Hall, Y; Rambaut, A; Longini, IM; Sakoba, K; KUCHARSKI, AJ; Touré, A; Danmadji Nadlaou, S; Saidou Barry, M; Fofana, TO; Lansana Kaba, I; Sylla, L; Diaby, ML; Soumah, O; Diallo, A; Niare, A; Diallo, A; EGGO, RM; Caroll, MW; Henao-Restrepo, AM; EDMUNDS, WJ; Hué, S;

2023

Virus evolution

Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022.

KANTEH, A; Jallow, HS; Manneh, J; SANYANG, B; Kujabi, MA; Ndure, SL; JARJU, S; Sey, AP; Damilare K, D; Bah, Y; Sambou, S; Jarju, G; Manjang, B; Jagne, A; Bittaye, SO; Bittaye, M; FORREST, K; Tiruneh, DA; Samateh, AL; Jagne, S; Hué, S; MOHAMMED, N; AMAMBUA-NGWA, A; KAMPMANN, B; D'Alessandro, U; ... SESAY, AK.

2023

The Lancet Global health

Dengue virus type 4 isolate DET-P-0428-1 polyprotein (POLY) gene, complete cds; and sfRNA2 lncRNA gene, partial sequence

Ashall, J; SHAH, S; Biggs, JR; Chang, J-NR; Jafari, Y; Brady, OJ; Mai, HK; Lien, LT; Do Thai, H; Nguyen, HA T; Anh, DD; Iwasaki, C; Kitamura, N; Van Loock, M; Herrera-Taracena, G; Rasschaert, F; Van Wesenbeeck, L; Yoshida, L-M; HAFALLA, JC R; HUE, S; HIBBERD, ML;

2023

National Center for Biotechnology Information

A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains.

Ashall, J; SHAH, S; BIGGS, JR; Chang, J-NR; Jafari, Y; BRADY, OJ; Mai, HK; Lien, LT; Do Thai, H; Nguyen, HA T; Anh, DD; Iwasaki, C; Kitamura, N; Van Loock, M; Herrera-Taracena, G; Rasschaert, F; Van Wesenbeeck, L; Yoshida, L-M; HAFALLA, JC R; HUE, S; HIBBERD, ML;

2023

Virus evolution

Dengue virus type I isolate DEN-P-1098-1 polyprotein (POLY) gene, partial cds

2023

National Center for Biotechnology Information

Emergence and pandemic spread of small ruminant lentiviruses.

Carrozza, M-L; Niewiadomska, A-M; Mazzei, M; Abi-Said, MR; Hué, S; Hughes, J; Gatseva, A; Gifford, RJ;

2023

Virus evolution

Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis.

Baxter, J; Langhorne, S; Shi, T; TULLY, DC; Villabona-Arenas, CJ; Hué, S; Albert, J; Leigh Brown, A; ATKINS, KE;

2023