Fraser Pathogen Dynamics Group

About Us

We are a group of scientists with expertise in infectious disease epidemiology, phylogenetics, mathematical modelling, maths, virology and outbreak response, led by Christophe Fraser. We spent the last few years working on HIV and COVID and have recently started two new reserach programmes in pandemic preparedness. Please see below for further information on our projects.

An overview of current projects is below. Please also visit our project-specific webpages for ore information:

DIGITAL CONTACT TRACING              PANGEA-HIV               BEEHIVE               AMPHEUS

PRESTO

PRESTO stands for "PREpare using Simulated Trial Optimisation" and is a CEpI-funded project to accelerate the estimation of vaccine efficacy and real-world effectiveness by simulating vaccine trial and study designs. PRESTO is building a comprehensive modelling framework to recommend vaccine trial designs for epidemic or pandemic versions (“X” versions) of the seven CEPI priority pathogens (Chikungunya virus, Ebola virus disease, Lassa virus, MERS-Cov, Nipah virus, Rift Valley fever virus and an unknown virus). One novel feature of the modelling framework will be its ability to take into account logistic and ethical considerations.

Digital pandemic preparedness

The Oxford Martin Programme on Digital Pandemic Preparedness is a collaboration between different groups in Oxford. It will generate a blueprint for digital health systems that can be deployed during pandemics, create a funding model for implementation, and work with public health agencies to develop the next generation of pandemic-ready digital tools. The team will explore the relationship between the common good and other values, including human rights, as well as the foundations of an ethical digital response, by examining the moral basis for using certain technologies in managing pandemics and developing ways to use data analytics in a manner that protect people's privacy.

Digital contact tracing

In early 2020, we proposed to slow the spread of COVID-19 by using a contact-tracing app on mobile phones (Ferretti & Wymant et al, Science 2020). This led to the development of a contact tracing app by the NHS, the national health service in England and Wales. We went on to develop an individual-based simulation of interventions against COVID-19 including manual and digital contact tracing which is open source and available on Github (see also Hinch et al, PLoS Computational biology 2021) Since then, we have published a number of studies on how to design and evaluate succesful contact tracing apps.

Please visit our COVID-19 website, which contains a list of all publications, blogs and other documents.

PANGEA-HIV

PANGEA (Phylogenetics and Networks for Generalised HIV Epidemics in Africa) uses molecular epidemiology and phylodynamics of HIV sequences to study transmission dynamics in HIV epidemics in Southern Africa. In recent years, anti-retroviral therapy and preventive therapy has become more readily available in Africa, but tools to assess the efficacy of current interventions and improvements in care are missing. Understanding how and in which groups of a population the virus is spreading will not only help to monitor epidemics, but also enable policy makers to design intervention programmes and assess their impact. To collect the data for this ambitious analysis, partners across Africa, the United States and Europe have come together to generate and analyse over 30,000 full-genome or near full-genome HIV sequences from five sub-Saharan African countries.

Please see the PANGEA-HIV website for further details.

HPTN-071 and PopART Phylo

HPTN-071 - PopART (Population Effects of Antiretroviral Therapy to reduce HIV Transmission) is the largest HIV trial conducted to date, with over 1.2 million participants in 21 communities in South Africa and Zambia. In these communities, 15 to 30% of the population is HIV positive, which reflects the fact that despite the availability of antiretroviral therapy (ART), HIV incidence rates remain high in many parts of southern Africa. PopART assessed which treatment strategies are effective and evaluated not only access to ART, but also a package of additional interventions like HIV counselling and home visits by community workers. Our group was responsible for the mathematical modelling of the epidemic in the study communities. The aim was to assess the effectiveness of the preventions and calculate the costs for rolling them out on a larger scale.

PopART Phylogenetics is an ancillary study to the main PopART study. It uses phylogenetic techniques to analyse approximately over 5000 samples obtained from the PopART patient communities in Zambia. The aims are to estimate the proportion of transmission events that occur during acute and early HIV infection (and therefore before the start of treatment) and identify demographic, clinical and epidemiological factors that contribute to HIV transmission. Using phylogenetic methods will also allow us to estimate the proportion of transmission events that occur within and outside the PopART communities.

Publications PopART (selection): Cori et al 2014, Hayes, Ayles et al 2015, Hayes, Fidler et al 2015, Bond et al 2018, Floyd et al 2018, Hayes et al 2019, Seeley et al 2019

Publication PopART Phylo: Hall et al, Lancet Microbe 2023

BEEHIVE

BEEHIVE (Bridging the Epidemiology and Evolution of HIV in Europe) is a cross-European study of HIV genomics and virulence amongst seroconverters. It builds on the discovery that virus levels found after the infection has become established (set-point viral load) is similar in patients which have been infected by the same source. This suggests that set-point viral load and, by association, severity of disease are at least partly determined by the viral genome. BEEHIVE aims to assemble 4500 viral sequences from HIV patients across Europe and use this data to discover and characterise viral mutations or combinations of mutations that influence the severity of disease. The quality of the sequences will allow us to study viral diversity in single patients while the quality of the associated metadata will allow for the identification of sub-epidemics and risk factors for onward transmission.

Publications: Fraser et al 2014; Blanquart et al 2017; Wymant, Hall et al 2017; Wymant et al 2018; Wymant et al, Science 2022

Please see the BEEHIVE website for further details.

AMPHEUS

AMPHEUS stands for Analytics and Microbiology for Precision Health and Epidemiology - A Unified Solution. Funded by the Bill and Melinda Gates Foundation, AMPHEUS will deliver a single integrated platform for clinical microbiology, real-time epidemiology and intervention research to fight infectious pathogens in low income settings. The project has developed a scalable laboratory infrastructure for rapid diagnostics and whole genome viral sequencing, initially in Zambia. The lab will link to digital technologies to broaden access to molecular diagnostics while informing public health efforts aimed at prevention and improved clinical outcomes.

Publications: Bonsall, Golubchik et al 2019

Please see the AMPHEUS website for further details.