Health Diagnostics

Solomon Langat of the Kenya Medical Research Institute in Kenya will develop a targeted viral enrichment protocol to improve the sensitivity of metagenomic sequencing for detecting known and novel vector-borne and viral hemorrhagic fever viruses. Infectious disease outbreaks caused by arboviruses and other viral infectious pathogens are common, particularly in Kenya. Current methods for diagnosing these infections have limited sensitivity and only detect known pathogens.

Ida Viktoria Kolte of Fiocruz in Brazil will employ metagenomic next generation sequencing (mNGS) for the analysis of sputum and blood samples from Indigenous patients to identify the causes of severe lung infection in the rural Amambai district. Brazil's one million Indigenous people suffer a disproportionate burden of infectious and respiratory diseases. Lung infections are challenging to diagnose because they can be caused by viral, bacterial and fungal pathogens and are often associated with co-infections.

Volga Ana Iñiguez Rojas of the Fundación para el Desarrollo de la Ecología in Bolivia will use metagenomic next generation sequencing to determine the diversity of viruses circulating in wild and domestic mammals and humans in two highly contrasting regions in Bolivia: The Amazon and the Andean Highlands. Emerging infectious diseases from zoonotic pathogens are a major public health threat. Bolivia is a hotspot for zoonotic diseases because of its highly diverse mammalian species and extensive deforestation.

Karifa Kourouma of the Centre National de Formation et de Recherche en Santé Rurale (CNFRSR) de Maferinyah in Guinea will integrate metagenomic sequencing into an existing viral hemorrhagic fever surveillance platform in Guinea to enable identification of a broad range of known and unknown infectious pathogens. Guinea is a hotspot for viral hemorrhagic fevers such as Ebola and dengue. The current platform uses PCR-based diagnostics but these lack sensitivity and can only detect a handful of known viruses.

Jennifer Fitzpatrick of Zambart in Zambia will design and implement a one-step multiplex whole genome sequencing platform for the diagnosis of female genital schistosomiasis (FGS), sexually transmitted infections (STIs) and vaginal microbiome analysis in Zambia. FGS is caused by Schistosoma haematobium and affects around 56 million women in sub-Saharan Africa. Current diagnostic capabilities for STIs and FGS are inadequate and many patients are either incorrectly treated, overtreated or receive no treatment at all.

Yoke-Fun Chan of the University of Malaya in Malaysia will deploy metagenomic next generation sequencing to identify regional, rare and novel pathogens associated with neuroinfection in Malaysia. Neuroinfection can be caused by many different pathogens and around 60-80% of cases remain undiagnosed. Malaysia is a hotspot for viruses associated with encephalitis and an ideal location for establishing global pathogen surveillance.

Victor Tunje Jeza of the Technical University of Mombasa in Kenya will apply metagenomic next generation sequencing to identify the etiology of febrile illness not associated with malaria, chikungunya or dengue in coastal and Western Kenya, to help design more effective interventions for prevention and treatment. Febrile illnesses are caused by diverse pathogens and are common among children in the coastal and western regions, where malaria is also endemic.

Kanny Diallo of the Centre Suisse de Recherches Scientifiques en Côte d'Ivoire will use metagenomic sequencing to investigate the etiological diversity of meningitis in Mali, Guinea, and Côte d’Ivoire, three countries in the so-called African meningitis belt, to improve diagnosis and public health responses. The African meningitis belt stretches from Senegal to Ethiopia and has the highest burden of meningitis worldwide. Meningitis can be caused by many different types of pathogens (bacteria, virus, fungi, and parasites), which vary between countries.

Rajpal S. Kashyap of the Central India Institute of Medical Sciences in India will use metagenomic next generation sequencing (mNGS) to investigate the etiology of undiagnosed meningoencephalitis cases in tertiary care hospitals in India. Meningoencephalitis is a central nervous system disease associated with substantial morbidity and mortality in India. Up to 75% of cases remain undiagnosed because current tests are unable to identify the wide range of causative pathogens.

Elizabeth Batty of the University of Oxford in the United Kingdom will use metagenomic next generation sequencing to identify pathogens in patient samples that are negative by all other diagnostics, to better understand the causes of febrile illness in South and Southeast Asia. Although studies have identified a broad spectrum of pathogens underlying non-malarial febrile illness, the cause of fever remains unknown in more than half of patients.