Title: Viruses at the human-livestock interface: improved genomic detection and prediction of zoonotic viruses that harm Kenyan pastoralists.
Funder: The Academy of Medical Sciences

Abstract: Zoonotic viruses cause severe human disease, and occasionally initiate pandemics. Zoonotic viruses that circulate in livestock particularly threaten sub-Saharan Africans, because most keep livestock. Spillover events will occur increasingly frequently as climate change, population growth and farming production continue to intensify. Livestock-mediated zoonotic viruses are severely underreported in Africa because they typically cause few symptoms in livestock, and because high burden of other diseases within affected communities obscures human illness. Our poor understanding of the maintenance and spread of zoonotic viruses within livestock, and their subsequent emergence to humans, limits our ability to predict and control outbreaks. Portable genomic sequencing and genomic epidemiology offer new opportunities to detect zoonotic viruses and use virus genomes to reconstruct unobserved outbreak dynamics, even in resource-limited settings. I will exploit these recent advances for improved prediction and prevention of livestock-mediated zoonotic virus outbreaks in Africa. I will investigate whether zoonotic viruses contribute to unexplained illness amongst Kenyan pastoralist. I will use network and phylodynamic approaches to determine whether the distribution and dispersal of human-specific viruses in pastoralists could help predict virus spread amongst their livestock. I will develop improved sequencing approaches that will enhance our ability to conduct genomic surveillance of zoonotic viruses alongside surveillance for other human and livestock viruses. My research will underpin new genomic strategies to predict zoonotic virus outbreaks. The new data and methods generated will strengthen our ability to establish novel surveillance approaches, and inform targeted vaccination and control strategies.

Lay abstract: Zoonotic viruses that jump from animals can cause severe human disease, and occasionally initiate pandemics. Transmission events occur increasingly frequently because of climate change, farming intensification and population growth. Viruses that spread from livestock particularly threaten people in sub-Saharan Africa, because most people keep livestock. Rare case detection and frequent misdiagnosis of infection means that we know little about zoonotic virus circulation in African livestock reservoirs or their subsequent emergence to humans. This severely limits our ability to prevent human disease. Breakthroughs in virus genome sequencing and analysis offer new opportunities to detect zoonotic viruses and reconstruct their spread. My goal is to exploit these new approaches to improve our understanding of livestock-mediated zoonoses in Africa. Focusing on pastoralist households in Kenya, I will determine whether zoonotic viruses can explain reported human or livestock illness. I will investigate whether circulation of human-specific viruses amongst pastoralists could be used to predict the hidden circulation of zoonotic viruses amongst their livestock. I will develop an improved sequencing method that allows us to improve our understanding of zoonotic virus emergence and spread more efficiently, by piggybacking off growing efforts to sequence non-zoonotic viruses. My research will improve prediction and control of zoonotic virus outbreaks, particularly in low-resource countries in Africa. In addition, it will improve our understanding of non-zoonotic viruses that nevertheless harm rural Kenyan pastoralists and their livestock. My methods will strengthen ability to establish novel surveillance approaches, and generate genomes that underpin improved vaccines and targeted strategies to control spread.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION