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Department of Genetics

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Infectious disease dynamics


epidemiology; public health; disease dynamics; antigenic and genetic evolution; 

Research Interests: 

Outbreaks of infectious pathogens remain common and widespread.  There remains a poor understanding of how pathogens are propagated and maintained in communities. This information is needed to help optimize intervention efforts. A complex interplay of host factors (e.g., human mobility), local environmental factors (e.g., environmental suitability) and viral factors (e.g., transmissibility) contribute to determine spread. In addition, where pathogens circulate endemically, local host immunity profiles, often built up over decades of continuous circulation have a fundamental role in determining which lineages can persist and which ones die out. However, as immune profiles at both individual and population levels are rarely measured, its impact on viral circulation patterns remains largely unknown. To disentangle the competing drivers of pathogen emergence and maintenance, including the role of immunity, we need high quality detailed data from the same pathogen system. In addition, we need new methods, which can integrate these different data sources and allow appropriate inferences about what is causing the observed patterns of disease. 
The focus of Henrik Salje’s group is on applied public health research, especially with regards to the spread of infectious pathogens. This research program sits at the interface of mathematical modelling, genetics, population biology, big data, public health and field-based epidemiology. By integrating the knowledge base and expertise available from these different fields, he seeks to generate a more complete understanding of the different drivers of disease transmission and optimize our chances of controlling spread.


Selected Publications:

Ruchusatsawat, Kriangsak, Pattara Wongjaroen, Arisara Posanacharoen, Isabel Rodriguez-Barraquer, Somchai Sangkitporn, Derek A. T. Cummings, and Henrik Salje. 2019. “Long-Term Circulation of Zika Virus in Thailand: An Observational Study.” The Lancet Infectious Diseases, February.
Salje, Henrik, Derek A. T. Cummings, Isabel Rodriguez-Barraquer, Leah C. Katzelnick, Justin Lessler, Chonticha Klungthong, Butsaya Thaisomboonsuk, et al. 2018. “Reconstruction of Antibody Dynamics and Infection Histories to Evaluate Dengue Risk.” Nature 557 (7707): 719–23.
Salje, Henrik, Justin Lessler, Irina Maljkovic Berry, Melanie C. Melendrez, Timothy Endy, Siripen Kalayanarooj, Atchareeya A-Nuegoonpipat, et al. 2017. “Dengue Diversity across Spatial and Temporal Scales: Local Structure and the Effect of Host Population Size.” Science 355 (6331): 1302–6.

Salje, Henrik, Kishor Kumar Paul, Repon Paul, Isabel Rodriguez-Barraquer, Ziaur Rahman, Mohammad Shafiul Alam, Mahmadur Rahman, Hasan Mohammad Al-Amin, James Heffelfinger, and Emily Gurley. 2019. “Nationally-Representative Serostudy of Dengue in Bangladesh Allows Generalizable Disease Burden Estimates.” eLife 8 (April).

Contact Details

Group leader : Dr Henrik Salje

Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge CB2 3EH,
United Kingdom


Group Members

See Group Members here

Group Website