MRes Infectious & Tropical Diseases - Disease Control

ID	Title	Overview
DC1	Delayed Malaria Following Perennial Malaria Chemoprevention in Côte d'Ivoire (London)	Perennial malaria chemoprevention (PMC) is a WHO-recommended strategy that reduces malaria morbidity in young children through the provision of sulfadoxine-pyrimethamine at health system contact points. In endemic areas, repeated Plasmodium falciparum exposure leads to gradual acquisition of protective immunity, first against severe disease, then uncomplicated malaria, and finally infection. When effective interventions reduce exposure during critical periods of immune development in children, protected children may experience increased susceptibility once the intervention is withdrawn. The PMC Plus Project provides an opportunity to examine delayed malaria in the context of programmatically-delivered PMC with expanded dosing. You will carry out a systematic review of delayed malaria and a quantitative data analysis of a recently completed impact evaluation of PMC in Côte d'Ivoire.
DC2	Genomic Characterization & Transmission Dynamics of Mpox Virus in Uganda: A Multi-Platform Approach (Uganda)	Mpox virus (MPXV) is a global threat with sustained human transmission. Uganda, bordering the DRC, faces Clade Ib introductions and local spread. Surveillance gaps persist in genomic & platform utility. Using samples available at the MRC Unit, you will integrate multi-platform NGS and bioinformatics to enhance MPXV surveillance and address the follow research question and aims. Question: How does multi-platform NGS improve detection of emerging lineages and understanding of viral adaptation? Aims: (1) Characterization: generate near-full genomes to differentiate Clades Ia & Ib. (2) Evolutionary Analysis: identify APOBEC3 mutations and their associations with fitness/diagnostic escape. (3) Evaluation: compare Oxford Nanopore (ONT) and Illumina for rapid surveillance. You will use MiSeq/MinION sequencing and analyses including assembly, phylogenetics, molecular clock modeling and platform benchmarking. Through this framework you will contribute to enhancing epidemic preparedness in Uganda.
DC3	Paratyphi Mykrobe – a tool for enhanced genomic epidemiology of enteric fever pathogens (London)	Enteric fever, caused by the bacteria Salmonella Typhi & Paratyphi A, drives >14 million illnesses annually of which >100,000 are associated with mortality. Control of enteric fever is complicated by the emergence of antimicrobial resistance (AMR). In 2021, the Global Typhoid Genomics Consortium (GTGC) was established to facilitate sharing of pathogen genome data, and extraction of metrics of public health utility such as pathogen genotypes (lineages) and molecular determinants of AMR for public health benefit. Building on the existing Paratype genotyping scheme, and the Typhi Mykrobe analysis tool, you will leverage >3,000 Paratyphi A genomes curated by the GTGC to develop Paratyphi Mykrobe, an analysis tool for typing Paratyphi A genomes by genotype, plasmid markers, and AMR determinants for enhanced genomic epidemiology and surveillance. Prior experience in genomics or coding is desirable but not essential.
DC4	New Tools for TB screening (Zambart, Zambia)	TB remains the leading infectious disease killer in the world today. TB screening is recommended by WHO in high burden areas but the optimal way to screen is unknown. Tools for screening and diagnosis of TB are urgently needed and there is a current explosion of ideas, many involving artificial intelligence, that may be useful. We have several projects running in our Zambian field site examining tools such as point-of-care ultrasound using AI interpretation, AI-interpreted digital stethoscopes, AI-interpreted cough sounds application, near point-of-care tests for TB, and lung flutes to aid sputum expectoration. In this project you will explore the utility of some of these new tools in a high TB, high HIV burden setting.
DC5	Development of a multivalent poultry vaccine to prevent Campylobacter and Salmonella infection (London and The Gambia)	Diarrhoeal disease remains a major threat to global health. Among the most common bacterial causes, Campylobacter is greatly under-reported and is a serious WHO concern. Campylobacter mainly enters the food chain through the consumption and handling of infected poultry, and a Campylobacter poultry vaccine would considerably reduce pathogen in the food chain. This project will be part of a Wellcome funded consortium (the Campylobacter Control Campaign) involving The Gambia and several African countries to culture Campylobacter, undertake genomics and vaccinate poultry to reduce Campylobacter. You will carry out research visits to The Gambia and integrate omics data and modelling approaches to digitally engineer optimized vaccines. The project will piggy-back Campylobacter antigens onto an existing Salmonella live attenuated vaccine to produce low-cost glycoconjugate livestock vaccines that simultaneously protect against Campylobacter and Salmonella.
DC6	Rural–urban residence and parasitic infections in yellow fever vaccine waning in Ugandan adolescents (Uganda)	Yellow fever vaccination is recommended as a single lifetime dose; however, emerging evidence suggests that vaccine-induced immunity may wane more rapidly in some settings. Chronic exposure to parasitic infections such as malaria and helminths may modulate immune function and influence the durability of vaccine responses. You will investigate the long-term persistence of yellow fever vaccine–induced neutralising antibody responses among Ugandan adolescents, comparing participants from rural (POPVAC B) and urban (POPVAC C) settings. Participants previously enrolled in these trials will be traced for follow-up. Archived and newly collected samples will be analysed to characterise antibody trajectories over time. Neutralising antibody titres, measured by plaque reduction neutralisation tests (PRNT), will serve as the primary outcome, with ELISA-measured IgG as the secondary outcome. We hypothesise that adolescents in rural settings with higher parasitic exposure will exhibit faster waning of vaccine-induced antibody responses.
DC7	Malaria parasite infection measurements to understand temporal changes in endemic populations (London)	Malaria inflicts a high global burden which is very unequally distributed, with most cases occurring in West and Central Africa. National surveys are important to track variation within and between countries, monitor trends over time, and guide control of this disease. Most surveys consider infection prevalence, but there is likely to be additional value in measurements of densities of parasites in the blood, detection of sexual parasite transmission stages, and parasite species-specific trends. You will statistically analyse such data from examinations of blood slides from more than 40,000 children under five years of age in national surveys in Nigeria between 2010 and 2025. Variation in temporal trends in different parts of the country will be investigated alongside related indices including haemoglobin levels in a subset of children over the years. Your findings will highlight critical changes as indicators of progress and also inform design of measurements in future surveys.
DC8	Developing Multiplex Tools for Detecting Invasive Vectors and Pathogens in Field Settings (London and Ghana)	Climate change is driving the northward expansion of disease-carrying vectors species into previously temperate regions, including northern Europe. Two Aedes vector species are now established across much of southern/central Europe and have been detected in England. These species have caused arbovirus (e.g. Dengue) outbreaks in many European countries, and local arbovirus transmission in the UK is increasingly plausible. Field-deployable surveillance tools to detect pathogens in vectors and detect the presence of vectors in environmental DNA samples are needed to support early warning systems, yet current methods rely on laboratory PCR infrastructure that is poorly suited for field use. This project combines wet-lab, including nucleic acid extraction, assay optimization, and sequencing, with computational analysis and statistics. Together, these components will deliver field-ready surveillance tools capable of rapid and sensitive pathogen and vector detection.
DC9	The role of economic development in historical success stories of malaria elimination (London)	When a country has just eliminated malaria, the bulk of the credit is typically given to malaria-specific interventions. But often we realise later, with hindsight, that success was assisted by broader multi-sectoral processes – environmental, social and economic. In other words, we succeeded partly because the wind of development was behind us. The elimination stories in North America, Northern and Southern Europe, Central and east Asia all appear to contain elements that illustrate this point of view. How much did these contribute to elimination? You will review the scientific literature, and assess the evidence concerning whether and how such development-driven changes contributed to success in those cases, and whether there are lessons for Africa in these stories. The output will be a published systematic scoping review.

Title

Overview

DC1

Delayed Malaria Following Perennial Malaria Chemoprevention in Côte d'Ivoire

(London)

Perennial malaria chemoprevention (PMC) is a WHO-recommended strategy that reduces malaria morbidity in young children through the provision of sulfadoxine-pyrimethamine at health system contact points. In endemic areas, repeated Plasmodium falciparum exposure leads to gradual acquisition of protective immunity, first against severe disease, then uncomplicated malaria, and finally infection. When effective interventions reduce exposure during critical periods of immune development in children, protected children may experience increased susceptibility once the intervention is withdrawn.

The PMC Plus Project provides an opportunity to examine delayed malaria in the context of programmatically-delivered PMC with expanded dosing. You will carry out a systematic review of delayed malaria and a quantitative data analysis of a recently completed impact evaluation of PMC in Côte d'Ivoire.

DC2

Genomic Characterization & Transmission Dynamics of Mpox Virus in Uganda: A Multi-Platform Approach

(Uganda)

Mpox virus (MPXV) is a global threat with sustained human transmission. Uganda, bordering the DRC, faces Clade Ib introductions and local spread. Surveillance gaps persist in genomic & platform utility.

Using samples available at the MRC Unit, you will integrate multi-platform NGS and bioinformatics to enhance MPXV surveillance and address the follow research question and aims.

Question: How does multi-platform NGS improve detection of emerging lineages and understanding of viral adaptation?

Aims: (1) Characterization: generate near-full genomes to differentiate Clades Ia & Ib. (2) Evolutionary Analysis: identify APOBEC3 mutations and their associations with fitness/diagnostic escape. (3) Evaluation: compare Oxford Nanopore (ONT) and Illumina for rapid surveillance.

You will use MiSeq/MinION sequencing and analyses including assembly, phylogenetics, molecular clock modeling and platform benchmarking. Through this framework you will contribute to enhancing epidemic preparedness in Uganda.

DC3

Paratyphi Mykrobe – a tool for enhanced genomic epidemiology of enteric fever pathogens

(London)

Enteric fever, caused by the bacteria Salmonella Typhi & Paratyphi A, drives >14 million illnesses annually of which >100,000 are associated with mortality. Control of enteric fever is complicated by the emergence of antimicrobial resistance (AMR). In 2021, the Global Typhoid Genomics Consortium (GTGC) was established to facilitate sharing of pathogen genome data, and extraction of metrics of public health utility such as pathogen genotypes (lineages) and molecular determinants of AMR for public health benefit.

Building on the existing Paratype genotyping scheme, and the Typhi Mykrobe analysis tool, you will leverage >3,000 Paratyphi A genomes curated by the GTGC to develop Paratyphi Mykrobe, an analysis tool for typing Paratyphi A genomes by genotype, plasmid markers, and AMR determinants for enhanced genomic epidemiology and surveillance. Prior experience in genomics or coding is desirable but not essential.

DC4

New Tools for TB screening

(Zambart, Zambia)

TB remains the leading infectious disease killer in the world today. TB screening is recommended by WHO in high burden areas but the optimal way to screen is unknown. Tools for screening and diagnosis of TB are urgently needed and there is a current explosion of ideas, many involving artificial intelligence, that may be useful.

We have several projects running in our Zambian field site examining tools such as point-of-care ultrasound using AI interpretation, AI-interpreted digital stethoscopes, AI-interpreted cough sounds application, near point-of-care tests for TB, and lung flutes to aid sputum expectoration.

In this project you will explore the utility of some of these new tools in a high TB, high HIV burden setting.

DC5

Development of a multivalent poultry vaccine to prevent Campylobacter and Salmonella infection

(London and The Gambia)

Diarrhoeal disease remains a major threat to global health. Among the most common bacterial causes, Campylobacter is greatly under-reported and is a serious WHO concern. Campylobacter mainly enters the food chain through the consumption and handling of infected poultry, and a Campylobacter poultry vaccine would considerably reduce pathogen in the food chain. This project will be part of a Wellcome funded consortium (the Campylobacter Control Campaign) involving The Gambia and several African countries to culture Campylobacter, undertake genomics and vaccinate poultry to reduce Campylobacter.

You will carry out research visits to The Gambia and integrate omics data and modelling approaches to digitally engineer optimized vaccines. The project will piggy-back Campylobacter antigens onto an existing Salmonella live attenuated vaccine to produce low-cost glycoconjugate livestock vaccines that simultaneously protect against Campylobacter and Salmonella.

DC6

Rural–urban residence and parasitic infections in yellow fever vaccine waning in Ugandan adolescents

(Uganda)

Yellow fever vaccination is recommended as a single lifetime dose; however, emerging evidence suggests that vaccine-induced immunity may wane more rapidly in some settings. Chronic exposure to parasitic infections such as malaria and helminths may modulate immune function and influence the durability of vaccine responses.

You will investigate the long-term persistence of yellow fever vaccine–induced neutralising antibody responses among Ugandan adolescents, comparing participants from rural (POPVAC B) and urban (POPVAC C) settings. Participants previously enrolled in these trials will be traced for follow-up. Archived and newly collected samples will be analysed to characterise antibody trajectories over time. Neutralising antibody titres, measured by plaque reduction neutralisation tests (PRNT), will serve as the primary outcome, with ELISA-measured IgG as the secondary outcome. We hypothesise that adolescents in rural settings with higher parasitic exposure will exhibit faster waning of vaccine-induced antibody responses.

DC7

Malaria parasite infection measurements to understand temporal changes in endemic populations

(London)

Malaria inflicts a high global burden which is very unequally distributed, with most cases occurring in West and Central Africa. National surveys are important to track variation within and between countries, monitor trends over time, and guide control of this disease. Most surveys consider infection prevalence, but there is likely to be additional value in measurements of densities of parasites in the blood, detection of sexual parasite transmission stages, and parasite species-specific trends.

You will statistically analyse such data from examinations of blood slides from more than 40,000 children under five years of age in national surveys in Nigeria between 2010 and 2025. Variation in temporal trends in different parts of the country will be investigated alongside related indices including haemoglobin levels in a subset of children over the years. Your findings will highlight critical changes as indicators of progress and also inform design of measurements in future surveys.

DC8

Developing Multiplex Tools for Detecting Invasive Vectors and Pathogens in Field Settings

(London and Ghana)

Climate change is driving the northward expansion of disease-carrying vectors species into previously temperate regions, including northern Europe. Two Aedes vector species are now established across much of southern/central Europe and have been detected in England. These species have caused arbovirus (e.g. Dengue) outbreaks in many European countries, and local arbovirus transmission in the UK is increasingly plausible. Field-deployable surveillance tools to detect pathogens in vectors and detect the presence of vectors in environmental DNA samples are needed to support early warning systems, yet current methods rely on laboratory PCR infrastructure that is poorly suited for field use.

This project combines wet-lab, including nucleic acid extraction, assay optimization, and sequencing, with computational analysis and statistics. Together, these components will deliver field-ready surveillance tools capable of rapid and sensitive pathogen and vector detection.

DC9

The role of economic development in historical success stories of malaria elimination

(London)

When a country has just eliminated malaria, the bulk of the credit is typically given to malaria-specific interventions. But often we realise later, with hindsight, that success was assisted by broader multi-sectoral processes – environmental, social and economic. In other words, we succeeded partly because the wind of development was behind us.

The elimination stories in North America, Northern and Southern Europe, Central and east Asia all appear to contain elements that illustrate this point of view. How much did these contribute to elimination?

You will review the scientific literature, and assess the evidence concerning whether and how such development-driven changes contributed to success in those cases, and whether there are lessons for Africa in these stories. The output will be a published systematic scoping review.