Awards

James Beeson of Burnet Institute in Australia, Melissa Kapulu of Health Research Operations Kenya Limited in Kenya, Isaac Ssewanyana of Infectious Diseases Research Collaboration in Uganda, Faith Osier of Imperial College London in the U.K. and Pras Jagannathan of Stanford University in the U.S., will analyze clinical samples using an antibody functional assay platform with malaria antigen arrays to identify antigens targeted by protective antibodies for next-generation malaria vaccines. They will identify antigen-specific functional antibodies that strongly correlate with protective immunity to malaria observed in clinical studies with two populations: Kenyan adults after controlled experimental challenge infection with Plasmodium falciparum and children followed longitudinally who were naturally exposed in Uganda and in Papua New Guinea. They will then use biostatistical modeling approaches to identify antigen and functional antibody types that most frequently occur in protective combinations, identifying additive and synergistic combinations of responses and responses most predictive of protective immunity across age groups and populations. This will enable prioritization of antigens and their combinations for malaria vaccine candidates.

Rajshekhar Karpoormath of the University of KwaZulu-Natal in South Africa will test a set of potential anti-TB hit compounds against clinically relevant TB strains, using the results to generate optimized hit compounds for development of new anti-TB drugs. They will screen the potential hits against susceptible, monodrug-resistant, multidrug-resistant, and extensively drug-resistant TB strains as well as other Mycobacterium strains. The screening results will inform structure-based drug design to generate optimized hit compounds. Potential lead hits will be screened again, with the most promising evaluated against intracellular bacteria in macrophages, tested for in vitro cytotoxicity, and evaluated for mechanism of action in bioassays including carbon-isotope tracing metabolomics and an in vitro granuloma assay.

Moses Obimbo Madadi of the University of Nairobi in Kenya and Aida Sivro of the University of Manitoba in Canada will determine the molecular epidemiology of human papillomavirus (HPV) in cervical cancer cases in Kenya to enable monitoring of changes in the prevalence of HPV types targeted by current vaccines and detect possible replacement with other types. They will perform a cross-sectional study on Kenyan women being followed-up for cervical cell abnormalities at hospitals in Nairobi and in rural Kenya. Outcome measures will include prevalence of HPV genotypes by age, geographic location, and HIV status. HPV genotypes will be stratified by cervical diagnosis to determine the top genotypes associated with cervical cancer. This research will provide robust and standardized statistics on the burden and genetics of oncogenic HPV infection in Kenyan women.

Wambui Nyabero of Medevice Kenya in Kenya and Vibhav Joshi of InnAccel Technologies Pvt Ltd in India will pilot test Fetal Lite, a fetal monitor for early detection of fetal distress to reduce intrapartum mortality. The monitor is designed for ease of use and patient comfort. It measures fetal and maternal heart rate and uterine activity, has automated data analysis with audio and visual alerts, and has a built-in electronic partogram and AI-based pregnancy risk scoring. It is cloud-enabled with a central web dashboard for report sharing and trend monitoring. They will deploy devices in medical facilities associated with the University of Nairobi, measuring the quality of the auto-generated analysis compared to blinded expert annotation and the ease of use by nursing staff. They will also capture the associated birth outcomes, the guidance provided through remote monitoring, and the number of detected fetal distress cases and referrals.

Daniel Muema of the KAVI Institute of Clinical Research, University of Nairobi in Kenya and Marit J. van Gils of the University of Amsterdam in the Netherlands will characterize the B cell immune repertoire in defined African populations to inform the use of an HIV vaccine with a germline-targeted immunogen. This clinically advanced, HIV envelope glycoprotein immunogen, BG505 SOSIP GT1.1, is engineered to guide the development of naïve B cells to produce broadly neutralizing antibodies (bnAbs) against HIV. They will determine the baseline frequencies of bnAb-precursor naïve B cells and bnAb-like memory B cells that recognize this immunogen in uninfected, adult sex workers highly exposed to HIV and in adults living with HIV. This will determine if the immunogen will be effective in these populations for HIV prophylaxis and functional cure, informing the design of vaccine clinical trials.

Seth Bloom of Massachusetts General Hospital and Margaret Kasaro of the University of North Carolina Global Projects Zambia in Zambia will validate metabolite biomarkers of clinically-relevant, vaginal microbiota community state types (CSTs) for development of diagnostics for research and clinical care. Different CSTs confer distinct risks for diseases linked to bacterial vaginosis, including risk of preterm birth and HIV infection. They will validate in a Zambian cohort the CST metabolite biomarkers that they previously identified in a South African cohort. They will grow pure cultures of individual bacteria to identify species and candidate enzymes responsible for vaginal CST biomarker production or consumption to inform development of a diagnostic assay. An inexpensive, real-time, point-of-care, diagnostic assay for use in low-resource settings would remove the need for slower, costlier DNA sequencing methods. Such a diagnostic test for vaginal microbiota-associated diseases will improve diagnosis, prediction of clinical risk, and monitoring of responses to therapy.

Digby Warner of the University of Cape Town in South Africa and Catherine Blish of Stanford University in the U.S. will explore human precision-cut lung slices (hPCLS) as an Mtb bioaerosol detection platform and model system for infection. Such a platform would provide an immediate read-out of Mtb infectivity and give insights into the initial Mtb-host interaction. They will determine the feasibility and reproducibility of using the hPCLS platform with samples containing extremely low numbers of Mtb bacilli, monitoring bacterial infectivity, replication, and dissemination by time-lapse fluorescence microscopy and examining key early events by cytometric and single-cell molecular assays. The platform could be used to answer specific questions, including whether Mtb organisms released during coughing by symptomatic TB patients are more infectious than those aerosolized during normal respiratory activities by asymptomatic individuals. It could also be applied at the site of aerosol sampling to guide and monitor preventative and therapeutic interventions.

Leon Tshilolo of the Institut de Recherche Biomédicale 1-Health in the Democratic Republic of Congo and Johnny Mahlangu of University of the Witwatersrand in South Africa will perform a pilot study using a mobile laboratory to conduct sickle cell disease (SCD) screening and patient follow-up in hard-to-reach and rural areas of the DRC. A mobile laboratory could lead to broader and earlier detection of SCD, enabling treatment sooner, and help ensure continued treatment, together reducing mortality and improving health outcomes. Sickle cell carriers will also be identified, with the study contributing to a more accurate epidemiological map of SCD to guide national healthcare strategy and advocacy efforts.

Erica Andersen-Nissen of Hutchinson Center Research Institute of South Africa and Gerhard Walzl of Stellenbosch University, both in South Africa, will perform bronchoalveolar lavage in volunteers receiving the BCG or MTBVAC vaccine intradermally in the HVTN 605 clinical trial to delineate vaccine-induced lung immune responses and identify correlates of protection. Lavage will be performed pre- and post-vaccination, and cells isolated from the lavage fluid will be analyzed for protein expression and by transcriptional profiling. They will compare the lung immune response they detect with the blood immune response identified in the large datasets available as part of the trial. Correlations between them could identify human blood biomarkers of lung T-cell responses that protect against TB. Such biomarkers will inform ongoing and future studies of immune correlates of efficacious TB vaccines.

Rajeev Shrestha of Dhulikhel Hospital Kathmandu University Hospital in Nepal with the Institute of Tropical Medicine Antwerp in Brussels and Paul Pronyk of National University of Singapore in Singapore will establish an integrated surveillance platform to speed the detection of dengue and the response to dengue outbreaks in Nepal. The platform will encompass dengue surveillance at multiple levels. Ecological and community-based surveillance will incorporate population-based, longitudinal dengue serosurveys to identify dengue hotspots. Hotspot mapping will integrate meteorological data for targeted mosquito vector surveillance, including serotype-specific detection of dengue virus in mosquitoes. Hospital-based surveillance will combine PCR-based dengue detection with information on clinical outcomes at sites across diverse geographical locations in Nepal, and genomic profiling will be performed for a subset of these circulating dengue strains. The integrated platform will serve national health authorities and policymakers, while setting the stage for similar platforms targeting additional emerging infectious diseases.

Jo-Ann Passmore of the University of Cape Town in South Africa and Elizabeth Bukusi of KEMRI in Kenya will determine the effects of the antibiotic metronidazole on bacterial vaginosis (BV)-associated microbes to guide the development of a live biotherapeutic product (LBP). BV is treated with antibiotics like metronidazole (MTZ), but recurrence is high, and an LBP could sustainably interrupt BV. They will compare temporal changes in abundance of BV-associated bacteria in women from Kenya and South Africa receiving MTZ treatment, and they will evaluate the impact of MTZ treatment on cervicovaginal inflammatory profiles. They will also compare antibiotic resistance prevalence and profiles for BV-associated bacterial strains isolated from these women, before and after MTZ treatment. The results will guide the interpretation of ongoing and future LBP efficacy studies, as well as generating a panel of BV-associated bacterial strains that can be screened to help select new candidate LBP strains.

George Wamukoya of African Group of Negotiators Experts Support (AGNES) in Kenya and Seyram Agbemenya of Africa Capacity Building Foundation in Ghana will establish an African hub of technical support for country teams to develop proposals for climate change adaptation projects fundable by the public and private sectors and philanthropies. They will pilot the approach through proposal writing workshops bringing together teams across at least three countries. The teams will include experts from the government, private sector, and academia. Together, they will profile the risks as described in the climate policy documents for their respective countries to build a business case, while analyzing the international climate finance landscape to identify aligned funding opportunities. They will take a portfolio approach to identify a strategic pipeline of projects to accelerate climate change adaption in Africa.

Jacqueline Weyer of the National Institute for Communicable Diseases in South Africa and Jinal Bhiman of Wits Health Consortium (Pty) Ltd also in South Africa will leverage a rapid monoclonal antibody (mAb) isolation and screening pipeline to develop diagnostics that differentiate between pathogens to support epidemic responses. Africa’s burden of many zoonoses and vector-borne diseases (VBD), such as Lassa fever and yellow fever, remains largely unknown, mainly due to diagnostic costs and limited access to reagents. They will leverage an existing screening pipeline, with infrastructure established by the Global Immunology and Immune Sequencing for Epidemic Response - South Africa (GIISER-SA) project, using a mouse model as a more readily available source of pathogen-specific B cells to identify mAbs that detect three ebolavirus species. These mAbs will be tested for sensitivity and specificity using patient samples and can be used to develop immunoassays, including rapid lateral flow assays, which are important for rapid, field-based diagnosis.

Anne Lee of Brigham and Women's Hospital in the U.S. and Yasir Shafiq of Aga Khan University in Pakistan will develop geospatial models to predict risks of undernutrition among adolescent girls and pregnant and lactating women in settings affected by conflict, climate and COVID-19 to help target interventions. Globally, around 30–40 million pregnant women and 50 million adolescent girls are underweight. Risks of undernutrition have recently been amplified by numerous armed conflicts, climatic shocks such as flooding and the COVID-19 pandemic. However, real-time data shortages prevent interventions, such as balanced energy-protein supplements, from reaching the highest-risk groups. Using Bayesian Hierarchical Spatial modeling, they will develop geospatial models for countries vulnerable to conflict and climate change, such as Ethiopia and Yemen. By incorporating socio-demographic and economic indicators, and climate-related and conflict-related shocks from national databases, they can estimate risks based on exposure and predict outcomes, such as undernutrition and anemia.

Margaret Kasaro and Soumya Benhabbour of the University of North Carolina at Chapel Hill in the U.S. will evaluate 3D-printed intravaginal ring (IVR) prototypes in Zambia to identify the design most acceptable to women for long-term use against unplanned pregnancy and HIV infection. In Zambia, HIV prevalence remains particularly high among women, and 41% of pregnancies are unplanned. IVRs are an effective, well-tolerated, and women-controlled contraceptive and HIV-preventative; however, their performance has suffered in large-scale clinical trials because of poor adherence. They have exploited a state-of-the-art 3D-printing process to rapidly engineer IVRs in a cost-effective, single-step process enabling the controlled release of multiple drugs for HIV prevention and contraception. They will recruit around 16 women, aged 18–45 from Kampala Health Centre, and use focus groups to evaluate their views on the proposed 90-day timeframe of use for four different IVR prototypes to guide the final design.

Yasir Shafiq of Aga Khan University in Pakistan and Anne Lee of Brigham and Women's Hospital in the U.S. will develop geospatial models to predict risks of undernutrition among adolescent girls and pregnant and lactating women in settings affected by conflict, climate and COVID-19 to help target interventions. Globally, around 30–40 million pregnant women and 50 million adolescent girls are underweight. Risks of undernutrition have recently been amplified by numerous armed conflicts, climatic shocks such as flooding and the COVID-19 pandemic. However, real-time data shortages prevent interventions, such as balanced energy-protein supplements, from reaching the highest-risk groups. Using Bayesian Hierarchical Spatial modeling, they will develop geospatial models for countries vulnerable to conflict and climate change, such as Ethiopia and Yemen. By incorporating socio-demographic and economic indicators, and climate-related and conflict-related shocks from national databases, they can estimate risks based on exposure and predict outcomes, such as undernutrition and anemia.

Raghavan Varadarajan in collaboration with Sudha Kumari, both of the Indian Institute of Science in India and Nico Callewaert of the VIB-UGent Center for Medical Biotechnology in Belgium will modify the microorganism, Pichia pastoris, used to produce lower-cost vaccines in low-resource settings, to generate more effective vaccines. Many vaccines are composed of pathogen-derived proteins that require production inside other cells. Although P. pastoris can produce these antigens at a lower cost than mammalian or insect cells, the viral proteins it produced for the SARS-CoV-2 vaccine were hyperglycosylated and poorly immunogenic, unlike those produced in mammalian cells. They will express different antigen forms in mammalian cells, and in different Pichia hosts, to determine whether altering glycosylation and protein size affects immunogenicity. They will also glycoengineer Pichia hosts to determine whether they can produce more effective vaccines. Ultimately, this approach could improve vaccine production for COVID-19 and other viruses.

Jinal Bhiman of Wits Health Consortium (Pty) Limited in South Africa and Jacqueline Weyer of the National Institute for Communicable Diseases also in South Africa will leverage a rapid monoclonal antibody (mAb) isolation and screening pipeline to develop diagnostics that differentiate between pathogens to support epidemic responses. Africa's burden of many zoonoses and vector-borne diseases (VBD), such as Lassa fever and yellow fever, remains largely unknown, mainly due to diagnostic costs and limited access to reagents. They will leverage an existing screening pipeline, with infrastructure established by the Global Immunology and Immune Sequencing for Epidemic Response - South Africa (GIISER-SA) project, using a mouse model as a more readily available source of pathogen-specific B cells to identify mAbs that detect three ebolavirus species. These mAbs will be tested for sensitivity and specificity using patient samples and can be used to develop immunoassays, including rapid lateral flow assays, which are important for rapid, field-based diagnosis.

Simon Kariuki of the Liverpool School of Tropical Medicine, Kenya in Kenya and Holden Maecker of Stanford University in the U.S. will determine whether probiotics and synbiotics can boost infant immune responses to vaccines. Diarrhea is the second leading cause of death in young children, with rotavirus a leading culprit. Oral rotavirus vaccines are routinely administered in low- and middle-income countries (LMIC) but are only 50% effective compared to 85–98% effectivity in high-income countries. One major cause could be environmental enteric dysfunction (EED), which is pervasive in children in LMIC. Their clinical trial of 600 newborns from western Kenya indicated that administering weekly probiotics and synbiotics (Lactobacilli and Bifidobacteria) up to age six months improved gut health and prevented EED-associated inflammation. They will use stored plasma samples and vaccination records to determine the impact of EED and systemic inflammation, as well as pro- and synbiotic effects on rotavirus vaccine efficacy.

Georgia Tomaras and Nathanial Chapman of Duke University and Girija Goyal and Don Ingber of the Wyss Institute at Harvard University, both in the U.S., will test whether Organ-on-a-Chip technology can inform how antibodies protect humans from pathogen infections to design more effective vaccines. Identifying protective vaccine features and validating them in human clinical trials is time-consuming and costly. An alternative is to use primary human organ chips that reproduce human physiology in vitro. They will stimulate peripheral blood mononuclear cells on the human lymph-node-on-a-chip with existing COVID vaccines and extensively characterize the resultant antibodies, including evaluating epitope specificity, and isotype and glycan profiling. They will also assess the capacity of these antibodies to prevent or reduce SARS-CoV-2 infection using the lung-on-a-chip technology. This approach can ultimately be applied to other pathogens, such as those causing malaria.

Cameron Myhrvold of Princeton University and Mireille Kamariza of the University of California, Los Angeles, both in the U.S., will develop an assay to rapidly detect multiple drug resistance mutations in Plasmodium falciparum and Mycobacterium tuberculosis for malaria and tuberculosis (TB) surveillance, respectively. Malaria and TB are two of the world's deadliest infectious diseases. Rapid and accurate drug resistance testing can save lives but current assays are slow or difficult to scale. Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN) is a CRISPR-based diagnostic test that detects nucleic acid biomarkers, such as those in pathogens, with high specificity and throughput. They have developed microfluidic CARMEN (mCARMEN), which produces results in under five hours, and will use an algorithm to design assays that detect the top ten drug-resistant P. falciparum mutations from blood samples, and M. tuberculosis mutations from saliva samples that confer resistance to two first-line TB drugs.

Maurício Barreto and colleagues of Fiocruz in Brazil, together with Alexa Heeks and colleagues of the Health Foundation of South Africa in South Africa, will employ real-world data from two large countries of the Global South to develop a common data model of infectious diseases affecting pregnant women to identify causes and aid intervention development. Centro de Integração de Dados e Conhecimentos para Saúde (CIDACS), together with the Western Cape Provincial Health Data Centre (WCPHDC), have built data systems to utilize routinely collected health data for exploring disease impacts. They will leverage these data systems to explore the impact of gestational syphilis in Bahia, Brazil, and tuberculosis in the Western Cape province of South Africa, and the coverage and effects of screening interventions. Teams will include data curators, analysts and scientists, who will perform data discovery and processing, alongside epidemiologists, clinicians and public health specialists, who will perform epidemiological analyses and community engagements.

Alexa Heeks and colleagues of the Health Foundation of South Africa in South Africa, together with Maurício Barreto and colleagues of Fiocruz in Brazil, will employ real-world data from two large countries of the Global South to develop a common data model of infectious diseases affecting pregnant women to identify causes and aid intervention development. Centro de Integração de Dados e Conhecimentos para Saúde (CIDACS), together with the Western Cape Provincial Health Data Centre (WCPHDC), have built data systems to utilize routinely collected health data for exploring disease impacts. They will leverage these data systems to explore the impact of gestational syphilis in Bahia, Brazil, and tuberculosis in the Western Cape province of South Africa, and the coverage and effects of screening interventions. Teams will include data curators, analysts and scientists, who will perform data discovery and processing, alongside epidemiologists, clinicians and public health specialists, who will perform epidemiological analyses and community engagements.

Seth Adu-Afarwuah of the University of Ghana in Ghana and Julie Croff of Oklahoma State University Center for Health Sciences in the U.S. will assess the effects of nutritional supplementation on adolescent brain development in low-resource settings to support interventions. Nutritional behavior majorly impacts the rapid stage of adolescent neurodevelopment, which in turn impacts future generations through effects on maternal and paternal nutritional status, cognition and parenting. However, little is known about typical adolescent neurodevelopment in low- and middle-income countries, where 90% of the world’s adolescents live. They will recruit 40–60 post-pubertal adolescents in Accra, Ghana, measure their corticolimbic system development over nine months, and assess their problem-solving, planning and cognitive functioning. In another cohort of 40–60 post-pubertal adolescents, they will measure adherence to an eight-month twice-daily micronutrient supplementation program and associated nutritional outcomes.

Julie Croff of Oklahoma State University Center for Health Sciences in the U.S. and Seth Adu-Afarwuah of the University of Ghana in Ghana will assess the effects of nutritional supplementation on adolescent brain development in low-resource settings to support interventions. Nutritional behavior majorly impacts the rapid stage of adolescent neurodevelopment, which in turn impacts future generations through effects on maternal and paternal nutritional status, cognition and parenting. However, little is known about typical adolescent neurodevelopment in low- and middle-income countries, where 90% of the world’s adolescents live. They will recruit 40–60 post-pubertal adolescents in Accra, Ghana, measure their corticolimbic system development over nine months, and assess their problem-solving, planning and cognitive functioning. In another cohort of 40–60 post-pubertal adolescents, they will measure adherence to an eight-month twice-daily micronutrient supplementation program and associated nutritional outcomes.

Brigida Rusconi of Washington University in the U.S. will determine whether female infants develop long-lived antibodies against gut bacteria that subsequently both protect against bacterial infections and promote healthy gut immune and microbiota development in their offspring. Enteric bacterial infections are leading causes of infant morbidity in low- and middle-income countries. Using their mouse model, they found that mothers lacking IgG antibodies, which normally develop before weaning, are unable to provide passive protection against enteric infections to their pups. They will adapt their microbial flow cytometry to test whether maternal serum IgGs react more strongly to infant gut bacteria, suggesting establishment in infancy, and whether they provide passive immunity during pregnancy. They will also analyze plasma from two-year-old infants to identify those with weak IgG reactivity and potential causes. Finally, using a malnutrition cohort in Pakistan, they will train local bioinformaticians and assess whether malnutrition inhibits anti-gut commensal IgG responses.

Daniel Kiboi of the Jomo Kenyatta University of Agriculture and Technology in Kenya will assess whether a novel mutation in the human malaria parasite, Plasmodium falciparum, can be used as a marker to identify drug-resistant malaria and protect key antimalarial drugs. Emerging P. falciparum variants resistant to the three frontline drugs kill millions of people annually but are hard to detect. A better understanding of how these variants resist the actions of existing drugs can help to develop more effective drugs. They previously used a mouse malaria model to produce Plasmodium parasites resistant to all three main drugs and identified the candidate mutated protein likely causing this resistance. They will use in silico bioinformatics analysis, CRISPR/Cas9 approaches, and in vitro drug susceptibility assays to evaluate and validate this mutant protein and determine its role in drug resistance in the human malaria parasite.

Yingda Xie of Rutgers New Jersey Medical School in the U.S. and Joaniter Nankabirwa of Makerere University in Uganda will use CRISPR-based technology to monitor respiratory, food-borne and antimicrobial-resistant pathogens in Ugandan wastewater. A recent Ebola outbreak in Uganda highlights the need for routine multi-pathogen surveillance. However, the vast quantities and diversities of microbes in wastewater make it hard to identify those that might cause deadly outbreaks. They will combine CRISPR-based diagnostics with the recently developed multiplex assay, Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), which enables highly sensitive and specific detection of over 150 nucleic acid sequences from dozens of samples in parallel. They will assess the performance of a field-deployable CRISPR assay to monitor specific pathogens in hospital sewage lines of Mulago Hospital. They will also leverage CARMEN to broadly survey for high-priority outbreak pathogens, including Ebola and yellow fever, in Kampala’s regional wastewater sources.

Carl Lachat of Ghent University in Belgium and Firehiwot Workneh of Addis Continental Institute of Public Health in Ethiopia will assess nutrient gaps in adolescent girls and the feasibility of providing supplements to break intergenerational cycles of poor growth and development in Burkina Faso and Ethiopia. Annually, around 21 million adolescent girls in low- and middle-income countries become mothers, with their infants at increased risk of impaired development. This may be caused by nutrient competition as both pregnancy and adolescence are nutrient-demanding phases. Supplementation with balanced energy-protein (BEP) during pregnancy increases birth weight with sustained benefits during infancy, but how this intervention could be tailored to adolescent girls is unclear. They will use a probability of adequacy approach to evaluate the diets and nutrition of 200 adolescent girls. They will also assess adolescent girls’ acceptability of paying for and taking BEP supplements in rural settings using group discussions and questionnaires.

Herman Pontzer of Duke University in the U.S. and Patricia Ukegbu of the Michael Okpara University of Agriculture in Nigeria will track the daily energy expenditures and requirements, and nutritional statuses of adolescent girls in rural Nigeria to help support their growth and development. Low- and middle-income countries suffer greatly from undernutrition, poor dietary practices and food insecurities, but are also experiencing increased obesity and unhealthy weight gain. Adolescents are particularly vulnerable to poor nutritional health but often neglected in nutritional program planning due to a lack of accurate data. To address this, they will recruit fifty female adolescents aged 13–18 from selected urban and rural schools in Abia State and measure their daily energy expenditure (kcal/d) and body composition (fat%) using the gold-standard doubly-labeled water method. This will be combined with dietary, food security and physical activity assessments to develop an accurate evaluation of nutritional health.

Kathryn Holt of the London School of Hygiene and Tropical Medicine in the United Kingdom and Senjuti Saha of the Child Health Research Foundation (CHRF) in Bangladesh, along with FTIR experts Luísa Peixe and Angela Novais from the University of Porto, will establish Fourier-Transform infrared (FTIR) spectroscopy in a pediatric microbiological diagnostics laboratory in Bangladesh to support clinical and infection control decisions. FTIR is a relatively low-cost, reagent-free technique that can discern different pathogen strains when combined with attenuated total reflection (ATR). They will set up a Spectrum Two FTIR-ATR instrument, on loan from PerkinElmer at the CHRF, train personnel, and use it to acquire spectra from approximately 1,500 isolates from their biobank to identify three clinically important pathogens: Klebsiella, Acinetobacter, and Salmonella. They will assess reproducibility across different users and laboratories on a validation set of 100 sequenced isolates, and finally test whether FTIR can identify pathogens directly in blood to produce more rapid results.

Rose Hayeshi of North-West University in South Africa will test whether humanized mouse models harboring selected gene variants specific to indigenous African populations can be used to identify novel therapeutics that will be effective in this population before advancing into clinical trials. Most medicines are developed and tested in European and Asian populations, which can lead to approved drugs that cause adverse reactions or are ineffective in African populations. Cytochrome P450 (CYP) enzyme allelic variants are common in African populations and may affect drug responses. She will use humanized mouse models expressing CYP2B6 and the CYP2B6*6 allelic variant, which is common in African populations, to test whether they can recapitulate specific drug responses observed in vitro and in humans using physiologically-based pharmacokinetic (PBPK) modeling.

Marion Jourdan of Danone Nutricia Research in the Netherlands together with Michael Zimmermann of ETH Zürich in Switzerland will test an approach to enhance iron absorption from food in children in Kenya by providing them with live food-grade bacteria to release phytate-bound iron from popular foods such as cereal flour. Phytates bind strongly to iron and inhibit its absorption. Their previous work identified different bacterial strains containing phytases that could grow in milk, degrade phytates, and release nutritionally-relevant levels of free iron in vitro. They will test different strain combinations for their phytate-degrading activity under different conditions, such as in specific foods and in an environment mimicking the upper GI tract, and select the best one for producing a fermented food product. This will then be tested to assess its effect on iron absorption in a cohort of 22 iron-deficient Kenyan school-aged children.

Jurriaan de Steenwinkel of the Erasmus Medical Center Rotterdam in the Netherlands together with Eric Nuermberger of Johns Hopkins University in the U.S. will combine expertise to develop a robust, preclinical mouse model of latent tuberculosis (TB) together with a molecular assay for measuring candidate drug activity to boost drug development. Reducing latent TB infections is essential to meet the goal of the World Health Organization’s End TB Strategy but current drugs have limited effect and measuring the activity of candidate compounds in latent infections is challenging. Successfully developing new drugs also requires improved preclinical models that identify drug candidates more likely to be effective in the clinic. They will combine their paucibacillary murine TB model with their first-in-class RS ratio assay, which quantifies rRNA synthesis in the causative Mycobacterium tuberculosis, and test its value for identifying new drugs that can more rapidly and effectively cure patients also with latent infections.

Rakhi Dandona of the Public Health Foundation of India will examine gender disparities in national health programs in India by harnessing existing large-scale gender-specific data for disease burden and their risk factors from the Global Burden of Disease Study to help address gender-based health inequities in India. Males and females are affected differently by many diseases. The researchers will examine three national health programs in India covering various age-groups, specifically adolescent health, the elderly, and mental health, for gender-specific disease and risk estimates to assess where more focus is needed on girls and women. This would facilitate gender-specific health interventions within the existing national health programs and identify potential new programs to achieve better health outcomes for women and girls.

Munyaradzi Musvosvi of the University of Cape Town in South Africa will determine whether a valuable biomarker of tuberculosis (TB) can be measured in small volumes of blood collected by finger-prick together with an automated, low-cost processing approach to accelerate diagnoses in low-resource settings. Individuals with TB have higher levels of a specific activation marker on the surface of some of their T cells, which could be a valuable diagnostic target. However, current methods to measure levels requires trained health and laboratory professionals to draw the blood, perform the assay, and analyze the results. As a more practical approach for resource-limited settings, they will test whether the biomarker can be reliably measured in low volumes of blood. They will also develop a microfluidic device to automatically process blood samples for flow cytometry analysis, and novel staining reagents as an alternative to expensive antibodies.

Rachel Chikwamba of the Council for Scientific and Industrial Research in South Africa together with Kerry Love of Sunflower Therapeutics in the U.S. will establish local manufacturing capacity in South Africa to increase access to protein-based biologic drugs including antibodies and vaccines, which are used for treating many different diseases. Access to biologics is unevenly distributed across the globe, and the conventional manufacturing practices are expensive and require substantial physical space and operational know-how. They have established low-cost, automated and modular manufacturing systems that can be easily adapted to different biologics and changing market needs. They will determine current local and regional needs and capabilities associated with biologics, identify five initial products for development, and produce business models for commercialization that can be used as a roadmap for the successful local deployment of their biologics manufacturing technology.

Sana Syed of the University of Virginia in the U.S. together with Imran Nisar of Aga Khan University in Pakistan will utilize metabolic modeling of patient-derived ‘omics data from pre-existing maternal and pediatric cohorts to identify new biomarkers and therapeutic targets for environmental enteropathy (EE), which is associated with impaired childhood growth and development and vaccine responses. They will leverage a computational, flux-balance analysis-based approach to analyze large transcriptomic and proteomic datasets from pregnant mothers and infants with EE to identify disease-associated metabolic signatures. The signatures derived from pregnant mothers might precede the development of EE and reveal pharmaceutical targets for prevention. They will also develop a duodenal enteroid cell culture model derived from biopsies of children with EE to test whether the identified infant-derived metabolic signatures can be disrupted with existing pharmacological agents as potential new treatments.

Adriana Bonomo of Fiocruz in Brazil together with Penny Moore of the National Institute for Communicable Diseases in South Africa will identify solutions for combating new SARS-CoV-2 variants by developing an in vitro assay to predict new variants and identifying broad specificity antibodies for use as new drugs and diagnostics. Despite the success of vaccines and antibody therapies, the continual emergence of new viral variants, which thwart our immune defenses and therapies, remains a major challenge of the pandemic. They will develop a virus training assay by culturing existing variants with hyper-immune sera from infected individuals in South Africa and Brazil to drive selection of new mutations and identify potential new variants. They will also isolate new monoclonal antibodies directed to conserved cleavage sites of the viral spike protein, which are essential for it to infect cells, that could be used as treatments to block infection by a wide range of variants.

Seth Bloom of Massachusetts General Hospital in the U.S. together with Sinaye Ngcapu of the Center for the AIDS Programme of Research (CAPRISA) in South Africa will investigate how bacterial vaginosis (BV) and non-Lactobacillus-dominated vaginal microbiota elevate the risk of contracting HIV-1 to help develop preventative therapies. South Africa has high rates of BV and microbiota-associated vaginal HIV transmission but the underlying mechanisms are unknown, which makes it difficult to prevent. The researchers will combine samples from South African cohorts with innovative in vitro assays to test their hypothesis that bacterially-produced putrescine, which is a BV-associated metabolite, in the cervicovaginal mucosa enhances HIV risk by increasing the post-translational modification and thereby activation of a molecule involved in promoting HIV protein production. They will also test existing inhibitors of this pathway as novel, pre-clinical HIV prevention candidates to establish the groundwork for a clinical trial.

Penny Moore of the National Institute for Communicable Diseases in South Africa together with Adriana Bonomo of Fiocruz in Brazil will identify solutions for combating new SARS-CoV-2 variants by developing an in vitro assay to predict new variants and identifying broad specificity antibodies for use as new drugs and diagnostics. Despite the success of vaccines and antibody therapies, the continual emergence of new viral variants, which thwart our immune defenses and therapies, remains a major challenge of the pandemic. They will develop a virus training assay by culturing existing variants with hyper-immune sera from infected individuals in South Africa and Brazil to drive selection of new mutations and identify potential new variants. They will also isolate new monoclonal antibodies directed to conserved cleavage sites of the viral spike protein, which are essential for it to infect cells, that could be used as treatments to block infection by a wide range of variants.

Peter van Heusden of the University of the Western Cape in South Africa together with Placide Mbala of the Institut National de Récherche Biomedicale in the DRC will establish in-house pathogen sequencing capabilities at a research institute in the DRC to enable rapid responses to meningitis outbreaks and improve patient outcomes. Despite the success of vaccines, meningitis outbreaks caused by diverse bacterial species still cause substantial fatalities across Africa. Diagnosis of the latest outbreak in the DRC was delayed for several months because samples had to be transported out of the country for genomic sequencing. They will leverage a field-portable sequencer with bioinformatics processor to build a platform with a user-friendly interface for use in a low-infrastructure setting. They will also train local scientists to extract DNA from patient samples, run the sequencer, and interpret the results so that they can provide rapid surveillance of meningitis-causing pathogens directly in the DRC.

Nicole Stoffel of the University of Oxford in the United Kingdom together with Pattanee Winichagoon of Mahidol University in Thailand will perform a double-blind randomized controlled trial to test whether providing iron-fortified food to iron-deficient women in Thailand improves their immune response to vaccination. Vaccines underperform in low- and middle-income countries, which may be caused by poor nutrition. Iron deficiency is common, and iron may play a key role in adaptive immunity and vaccine response. Preliminary data from their earlier study in Kenya showed that women given intravenous iron one week before a vaccine produced significantly more antibodies. To translate this to low-resource settings, they will perform a trial of 180 women in northeastern Thailand and provide half of them with a wheat-flour-based baked snack fortified with iron for forty days and test its effect on their immune response to two vaccine types: an intramuscular influenza vaccine and an oral typhoid vaccine.

Nitin Baliga of the Institute for Systems Biology in the U.S. together with Google Applied Science will combine systems biology with machine learning and artificial intelligence to accelerate the discovery of more effective and affordable treatments for tuberculosis. Tuberculosis kills 1.5 million people annually, but developing novel treatments is expensive using current methods and complicated by the different physiological states and sub-populations of the causative Mycobacterium tuberculosis. To address this, they will use a new modelling approach that leverages transcriptome data and a novel algorithm to identify more robust protein targets that are valid across bacterial states and populations. These targets will then be screened using DNA-encoded small molecule libraries (DELs), which is lower-cost than traditional high-throughput screens. Screening results will be used to train a machine learning model to identify small molecule compounds with favorable drug-like properties and high probabilities of inhibiting the target. The anti-bacterial activity of selected compounds will then be tested experimentally.

Lye McKinnon of the University of Manitoba in Canada together with Ali Ssetaala of the Uganda Virus Research Institute in Uganda will determine whether nasal mucosal immune responses induced by COVID-19 vaccines and natural infection can help prevent infection and transmission. Although COVID-19 mRNA vaccines effectively prevent severe disease, they are less effective at preventing transmission, which is critical for protecting vulnerable populations particularly against emerging, highly transmissible variants. Boosting nasal immunity may locally inhibit replication of the SARS-CoV-2 virus and thereby limit both infection and transmission. To test this, they will perform a two-site longitudinal study in Winnipeg, Canada and Kampala/Entebbe, Uganda of fully vaccinated individuals with and without breakthrough Omicron infections to determine whether existing nasal immunity is protective. They will also test whether Omicron breakthrough boosts virus-specific IgA and T cell responses in the nasal mucosa, which may further protect against transmission. The results may strengthen the case for nasal-delivered vaccines to better contain the COVID-19 pandemic.

Jesse Gitaka of Mount Kenya University in Kenya in collaboration with David Anderson of Burnet Institute in Australia, will develop a diagnostic device for iron deficiency anemia that is suitable for resource-limited settings. Iron deficiency anemia can cause maternal death, prematurity and stunting. Current diagnostic tests require expensive equipment or are not specific enough to distinguish between the different causes of anemia. They will develop a device that detects the low levels of hemoglobin found in immature red blood cells, called reticulocytes. The device will use magnetic beads and microfluidics to physically separate reticulocytes from whole blood, and then absorbance to measure the red color of hemoglobin and thereby determine levels. They will use samples from healthy donors to develop algorithms that can calculate the amount of hemoglobin per reticulocyte to provide an accurate diagnosis.

Maurício Barretto of Fiocruz in Brazil will integrate COVID-19 data from Brazil into existing harmonized datasets from over 500 million people across the world, to better inform public health strategies. International data on COVID-19 is needed to help lift the world out of the pandemic. However, there is little real-world data from South Asia or Brazil. They will map data from the COVID-19 surveillance database for the State of Bahia, which covers a population of 15 million people, to the common data model known as OMOP, which brings together disparate data into a common format. They will run analytical tools on these mapped data to characterize COVID-19 forms and disease outcomes, to quantify the use of COVID-19 treatments in routine practice and to identify risk factors that can be used to predict disease severity and help better manage patients.

Haroon Hafeez of Shaukat Khanum Memorial Cancer Hospital and Research Centre in Pakistan will integrate COVID-19 data from Pakistan into existing harmonized datasets from over 500 million people across the world, to better inform public health strategies. International data on COVID-19 is needed to help lift the world out of the pandemic. However, there is little real-world data from South Asia or Brazil. They will map the anonymized electronic medical records from over 7.8 million people, including over 20,000 COVID-19 positive patients, from a hospital in Lahore to the common data model known as OMOP, which brings together disparate data into a common format. They will run analytical tools on these mapped data to characterize COVID-19 forms and disease outcomes, to quantify the use of COVID-19 treatments in routine practice and to identify risk factors that can be used to predict disease severity and help better manage patients.

Lyle McKinnon of the University of Manitoba in Canada will test whether a specific type of immune cell known as tissue resident memory T cells, which are found in the nasal cavity during SARS-CoV-2 infection, help limit disease severity and viral replication. The nasal mucosa is the first place in the body that is exposed to the SARS-CoV-2 virus. However, little is known about the local immune response and how this may influence disease progression, which varies dramatically between people. They have developed a nasal sampling protocol and will use it to characterize nasal T cells from COVID-19 positive patients in three sites in Winnipeg, Canada, and Nairobi, Kenya, to see if it correlates with clinical outcomes. They will also compare the activation of these nasal tissue T cells in uninfected individuals before and after SARS-CoV-2 vaccination to determine their role in vaccination-mediated immunity.

Jed Sundwall of Open Imagery Network Inc. in the U.S. will collect and curate high-quality agricultural mapping data from drone imagery in Kenya that has commercial value and can also be openly accessed for public good purposes. High quality and timely geospatial data is often only collected in the commercial sector, which makes it too expensive for the public and philanthropic sectors to access and use to address development challenges. To resolve this, they will develop a minimum viable product to demonstrate the potential for collecting high-quality, annotated agricultural data that has commercial value and can also be openly accessed. The imaging data will be obtained from an approximately 40 square kilometre area, annotated to identify field boundaries and building footprints, and made available through their partner, PLACE, who have digital infrastructure and a data trust for providing commercial licenses.

Fatma Guerfali of Institut Pasteur de Tunis in Tunisia and Jesse Gitaka of Mount Kenya University in Kenya, will implement wastewater SARS-CoV-2 surveillance in diverse sanitation settings in Kenya and Tunisia to help determine the true number of people infected with SARS-CoV-2, which is currently underestimated. The detection of SARS-CoV-2 RNA in sewage can be used to monitor virus circulation in the population. However, this is more challenging in settings with diverse sanitation practices, such as in many parts of Africa. They will quantify SARS-CoV-2 RNA in untreated wastewater from diverse sanitation settings and correlate them with clinical testing to determine their accuracy. They will also develop epidemiological models using a web-based informatics platform, which integrates geo-spatial, temporal and SARS-CoV-2 RNA analysis, to test the performance of longitudinal SARS-CoV-2 RNA wastewater surveillance from hospitals and public sanitation systems.

Geoffrey Siwo of the University of Notre Dame in the U.S. will use a computational approach to identify broad-spectrum antiviral drugs that trigger an innate immune response and could be used against a range of viruses. Traditional drug discovery approaches target viral proteins, but this requires prior knowledge of the virus and can lead to the development of resistance. In contrast, compounds that trigger the host’s natural biological defense mechanism inside each cell are less likely to cause resistance, and can be used for treating novel viruses as well as for vaccine adjuvants. They will develop an artificial intelligence (AI) approach that uses predicted broad-spectrum antivirals to generate a large variety of related molecules. These will be compared with a library of approved drugs to identify compounds with similar chemistries. The top 100 compounds will be tested for broad anti-viral activity in multiple human cell lines.

Danielle Ehret of the Vermont Oxford Network in the U.S. in collaboration with Krista Donaldson of Equalize Health also in the U.S. and Mahlet Abayneh of the Ethiopian Pediatrics Society, will develop a web-based clinical training course to train staff in neonatal intensive care units in Ethiopia to better recognize respiratory distress syndrome in preterm infants, and to safely deliver continuous positive airway pressure (CPAP) to reduce mortality rates. Respiratory distress syndrome causes almost half of all preterm deaths in neonatal units in Ethiopia. These would be preventable if the staff had received adequate clinical training. However, the recent pandemic forced a halt to the national hands-on training program that was planned in 2020. As an alternative, they will host monthly training webinars focused on diagnosis and treatment, and develop an observation checklist to assess the quality of CPAP delivery. They will evaluate their approach by quantifying staff training rates, diagnoses of respiratory distress syndrome, and treatment and mortality rates.

Iwnetim Abate and Loza Tadesse of SCIFRO Inc with Manu Prakash of Stanford University both in the U.S. will develop an education platform to inspire and equip African college students to solve local health problems through science using simple, inexpensive tools such as paper-based centrifuges and chemistry kits. Less than 8% of sub-Saharan Africans get to attend tertiary education, and there are limited options for pursuing a career in science. This means that even with the recent rise in inexpensive scientific equipment, many local problems of Africans remain unsolved. They will develop easy-to-follow pedagogy and teaching kits and use them to conduct a pilot study by holding a month-long summer workshop for 100 Ethiopian college students in Addis Ababa. The workshop will demystify the scientific process and motivate the students to begin tackling local projects, which will be monitored online. They will also invite 20 college instructors to participate and provide them with kits to distribute to their local schools and colleges.

Yasmin Chandani of inSupply Health Limited and Pratap Kumar of Health-E-net Limited both in Kenya will develop a simple digital health tool to support the maternal and child health supply chains for low-literate, nomadic communities spread sparsely across Kenya. Counties in semi-arid lands have poor maternal and child health indicators caused by vast distances, low literacy rates, no fixed health facilities, and no data on supply chains. To address this, they will develop software to combine paper-based methods with feature-phone cameras for community health workers to easily record data on stocks and supplies. The recorded data will be integrated into existing workflows to inform supply chain managers and support ordering and resupply decisions. They will perform a twelve-month pilot study in Turkana County that will involve training community health workers to use the tool, and they will evaluate its performance in accurately recording stocks dispensed and received during resupply. They will also collect qualitative feedback from health workers to help improve the tools design.

Rudolph Gleason of Georgia Institute of Technology in the U.S. and Abebbaw Fekadu of CDT-Africa in Ethiopia will develop a low-cost, wearable device that wirelessly monitors the vital signs of neonates in low-resource settings to help lower mortality rates. In Ethiopia, and many other regions, the leading causes of neonatal deaths are respiratory distress, infection, and asphyxia. However, the key warning signs of these conditions - temperature, heart rate, respiratory rate, and blood oxygen concentration - are difficult to monitor in low-resource settings that often lack sufficient technical resources and medical staff. They have built a first-generation device that they will test on 50 neonates over seven days in a hospital in Addis Ababa to assess its performance in the clinic and gather user feedback from nurses and parents. Using the results, they will employ a user-centered design approach and engage Ethiopian engineering students to improve the device design and perform a market analysis and cost assessments for local manufacturing.

Zaza Ndhlovu of the Africa Health Research Institute in South Africa and Fekadu Tafesse of Oregon Health & Science University (OHSU) will identify the molecular mechanisms enabling HIV to survive in humans to help develop new therapies to fully eradicate the disease. Potent antiretroviral therapies have rendered HIV a manageable chronic disease, but it is still incurable. Needing daily medication over a lifetime makes this approach ultimately expensive and also challenging to maintain in low-resource settings. The virus is thought to evade existing therapies by locating to lymph nodes where it is protected from being destroyed by CD8 T cells. CD8 T cells are banned from lymph nodes because they don't express the CXCR5 protein. They have discovered several epigenetic mechanisms that regulate CXCR5 levels. To follow up, they will screen 471 compounds that target epigenetic processes and may also upregulate CXCR5 in human primary CD8 T cells, and they will also test a known regulator of CXCR5 expression. Their results could lead to a gene therapy-based approach to cure HIV.

Mohlopheni Marakalala of the Africa Health Research Institute in South Africa and Eric Rubin of the Harvard TH Chan School of Public Health in the U.S. will use a genetic screening tool, Tn-seq, to identify the specific bacterial genes protecting Mycobacterium tuberculosis (MTB) from immune destruction that could be used to develop new therapeutic approaches to fight tuberculosis, which causes over 1.5 million deaths annually. BCG is the only approved tuberculosis vaccine, but its effect is limited, particularly in adults. This may be because BCG induces a memory-like innate immune response mediated by macrophages, so-called ‘trained immunity’, which the bacterium somehow evades. To find out how, they will use transposon-mediated mutagenesis to mutate every non-essential gene in MTB and use these mutant strains to infect BCG-trained monocytes isolated from vaccinated humans. The genes that enable MTB to survive under these conditions will then be identified by whole genome sequencing and validated using genetic and chemical approaches. This could ultimately lead to the development of targeted drugs to support BCG vaccinations.

Justin Lessler of the International Vaccine Access Center, Baltimore of the Johns Hopkins University Bloomberg School of Public Health in the U.S. and Anthony Ahumibe of Nigeria Centre for Disease Control in Nigeria will launch a West African disease surveillance network for cholera to leverage local pathogen genome sequencing efforts for disease control and ultimately elimination. New genome sequencing technologies at substantially decreased costs have opened up the opportunity for laboratories in low-resource settings to monitor local disease by sequencing the genomes of the causative pathogens, which is critical for understanding disease epidemiology and guiding control efforts. However, these laboratories often lack the ability to analyze complex sequencing data. To address this, they will hold sequencing training workshops; provide equipment, reagents, and ongoing bioinformatic support; and establish a cross-country peer network using online collaborative tools. In addition, in response to the COVID-19 pandemic, support for SARS-CoV-2 sequencing will be provided to selected sites in the disease surveillance network.

Lemu Golassa of Addis Ababa University in Ethiopia and Laurent Dembele of University of Science, Techniques and Technology of Bamako in Mali will analyze the malaria-causing parasite Plasmodium vivax to identify molecules that enable it to transform into a dormant hypnozoite form in the liver, which is thought to be the key obstacle to malaria elimination. In many regions, P. vivax has become the dominant species causing malaria, resisting eradication due to this dormant liver stage of infection where it is resistant to most existing drugs and still a major cause of disease. Understanding how P. vivax forms hypnozoites could help develop more effective malaria drugs. They will isolate P. vivax from human blood and use cultured liver cells to evaluate their ability to form hypnozoites. Transcriptional profiling on these different isolates should reveal the molecular markers that enable P. vivax to form hypnozoites, which could be used as drug targets.

Clare Wenham of the London School of Economics and Political Science in the United Kingdom and colleagues will study whether considering gender in the design and operation of mosquito-control programs can help them to sustainably eliminate vector-borne diseases such as Zika. Brazil has eliminated disease-causing mosquitoes several times, but they keep returning. Data from Africa have shown that malaria control programs purposefully involving women have longer-lasting effects, which may translate to other countries and for other diseases. To test this, they will analyze how women impact vector control programs, as well as how they are specifically affected by them, by conducting fieldwork, including interviewing local community health workers and vector control agents, and analyzing existing data. This evidence will be used to produce a gender-mainstreamed vector control policy for piloting to test whether gender is a valuable determinant of the success of disease-control programs.

Lyle McKinnon of the University of Manitoba in Canada and Nicola Mulder of the University of Cape Town in South Africa will study the cause of bacterial vaginosis, which is linked to reproductive health complications and increased risk of HIV, to help identify new treatments. Bacterial vaginosis (BV) is characterized by harmful vaginal populations of anaerobic bacteria, often recurs, and is more common in Black and Latina women, suggesting that there could be a genetic component involved. Indeed, their previous genome-wide association study in South African women identified two human genetic variants associated with BV. These genes are involved in the epithelial-to-mesenchymal transition whereby epithelial cells lose their adhesion properties to become more like mesenchymal cells. To test whether this process is key to BV, and can thus be used to develop new treatments, they will expand their genome-wide association study and use in vitro cell models to analyze the role of the epithelial-to-mesenchymal transition in promoting the growth of harmful types of bacteria.

Sunday Ekesi of the International Centre of Insect Physiology and Ecology in Kenya and Josh Tewskbury of Future Earth in the U.S. will model the effects of climate change on major food crops and their insect pests to better forecast crop yields and inform intervention strategies. The changing climate will likely have a multitude of effects on both insect-pest populations, by affecting their size and activity, and on crop physiology, which together will affect yield. They will dissect these complex interactions focusing on maize, which is the main staple food in Kenya, and a major maize-pest, and use a phytotron (enclosed research greenhouse) to evaluate the effects of the current climate, and a range of projected climates, on insect feeding rates and crop levels. These data will then be used in a process-based dynamic modelling approach to develop robust mathematical models that can make accurate predictions on crop loss caused by the climate.

Philip Roessler of The College of William & Mary and Laiah Idelson of ETR both in the U.S. will test whether promoting cooperative mobile phone use in families in low-resource settings can improve household income and welfare. In their recent study, they found that providing a cost-free smartphone to poor households in Tanzania had a significant, positive impact on their economic state. The impact appeared to be catalyzed when both the male and female members of the household shared the smartphone and abolished when male members monopolized it. To investigate this, they will conduct a field study in Tanzania with 300 married young women. Two hundred women will be provided with smartphones, with half of those receiving specifically joint training also for their spouse on the use of digital banking and mobile money, to encourage cooperative use and knowledge-sharing within families. After 10-12 months, they will conduct surveys to evaluate whether cooperative use enhances economic status and health.

Seth Cochran of Operation Fistula in the U.S. and Nick Bennett of Simprints in the United Kingdom will incorporate facial recognition technology from Simprints into their existing automated patient registry to better track and support women with obstetric fistula in low-resource settings. Obstetric fistula is caused during childbirth and leads to the uncontrolled release of bodily wastes. It is estimated that more than 2 million young women live with untreated obstetric fistula in Asia and sub-Saharan Africa. They have set up a program to end fistula for every woman that has included developing a tablet or phone-based patient tracking and performance management system, which has been expanded to 15 countries. The challenge has been to accurately track individual patients from their initial identification through treatment to their managed reintegration into society. To address this, they will integrate and test two biometric technologies, fingerprinting and facial recognition, and evaluate their ability to accurately identify patients across different settings and people’s reactions to the technologies.

Hamed Alemohammad of Open Imagery Network Inc. in the U.S. and Ernest Mwebaze of Google AI Research Center in Ghana will generate synthetic imaging data to train machine learning algorithms to better interpret satellite images in low-resource settings to monitor crops and increase food security. The increase in global satellite observations at different spatial and temporal scales has led to the development of sophisticated analytical methods such as machine learning for a variety of applications. For agricultural applications, the optimal performance of these methods requires ground reference data from field visits, which is time-consuming, expensive, and challenging in remote areas. To circumvent this need, they will generate a time series of realistic, fully synthetic images for around 8000 plots of major crops in Kenya using a generative adversarial networks approach, which involves developing two neural network models that compete against each other. They will then compare the synthetic imaging data with their existing ground reference data to see how well they can improve the classification of crop types using machine learning methods.

Stephan Sieber of the Technical University of Munich in Germany will work together with Véronique Dartois of Hackensack Meridian Health in the U.S. to test whether his new antibiotic, which uniquely activates, as well as inactivates, molecular pathways to destroy certain pathogenic bacteria, can be adapted to kill the related Mycobacterium tuberculosis (Mtb), which causes tuberculosis. Current antibiotic treatments are lengthy, and it remains difficult to completely destroy all the bacteria in the body. More worryingly is that Mtb has been developing resistance to these antibiotics, which all work in similar ways, so in some patients they are useless. They have discovered a new antibiotic that works differently: it inactivates bacterial menaquinone biosynthesis but also uniquely activates a signal peptidase to boost its secretory function. In the laboratory, this antibiotic notably bypasses the development of resistance and even kills dormant bacteria, likely by its activating mechanism. They will investigate its mechanism of action in Mtb using affinity-based protein profiling and use that knowledge to select related compounds that might work better in people. These will then be tested in a mouse model of tuberculosis as a first step towards clinical development.

Anne CC Lee and Mandy Brown Belfort of Brigham and Women's Hospital in the U.S. along with Stéphane Sizonenko and Petra Huppi of the University of Geneva in Switzerland will test whether lactoferrin, a breast milk nutrient, can promote growth and reduce injury in the developing infant brain. Of the 15 million annual preterm births, almost a million of the surviving babies have severe neurological defects such as cerebral palsy. However, there are limited treatments available. Breast milk has a positive effect on the infant brain, but the mechanisms for this are unclear. Their preliminary data showed that lactoferrin, a glycoprotein found in breast milk, has a neuroprotective effect in several rat models of neonatal brain injury. They will build on this to study the effect of different concentrations of lactoferrin in the rat models, as well as assaying candidate inflammation, cell death, and neurotrophic factors to identify the molecular mechanisms involved. They will perform a human observational study to associate the different levels of lactoferrin found in breast milk samples from a cohort of mothers of preterm infants at Brigham and Women's Hospital with the infant's brain development as assessed by magnetic resonance imaging. They will also measure lactoferrin levels in samples collected from 100 mothers in Bangladesh to see how they compare. Together, they will generate essential data on lactoferrin for future human clinical trials in low- to middle-income countries.

Alison Bentley of the National Institute of Agricultural Botany and Ari Sadanandom of the University of Durham both in the United Kingdom will examine whether a new molecular link that they found explaining the increase in plant diseases (biotic factors) associated with high nutrient levels (abiotic factors) can be exploited to maximize wheat crop yield with minimal negative impact on the environment. Wheat, one of the first domesticated food crops, has been grown for over 10,000 years and is critically important to global food supply. Traditionally, crop yields are maximized by applying nitrogen fertilizer to stimulate growth, and fungicides and pesticides to prevent disease. These approaches are expensive and can harm the environment. Another complication is that increasing amounts of nitrogen fertilizer also increases the occurrence of disease. They have identified a group of transcription factors (TFs) - proteins that control expression of specific genes – that appear to protect plants against the fungus Septoria specifically under varying nitrogen levels. To investigate this, they will create transgenic wheat to increase or decrease each TF and explore the effect on disease resistance and growth in different concentrations of nitrogen. Understanding this relationship will allow them to boost plant resistance to disease under high growth conditions, and thereby optimize crop yield with maximal economic gain and minimal environmental impact.

David Hughes of Pennsylvania State University, John Corbett of aWhere, and Rhiannan Price of DigitalGlobe, in the U.S. will develop a software platform comprising prediction algorithms that leverage artificial intelligence to predict where and when plant diseases and pests will occur from weather and satellite data to alert farmers to check their crops. Pests and diseases are moving targets, however most current surveillance methods monitor only their presence or absence. Predicting when and where they are likely to occur would be more valuable for preventing them. This has recently been made possible by studies on how environmental factors influence the emergence and behaviour of crop pests and diseases. They will use a systems approach that incorporates these new predictors along with historical data and couples them with an artificial intelligence component that learns from ground observations recorded using smartphones to improve accuracy. They will combine their existing agricultural intelligence platform and smartphone application with their prototype predictive model and test their approach with maize and cassava crops on farms across seven different counties in Kenya. The platform will produce location-specific forecasts that can be acted upon immediately by farmers.

David Aanensen from the University of Oxford and the Wellcome Sanger Institute in the United Kingdom and Maria van Kerkhove of the World Health Organization in Switzerland will combine next generation DNA sequencing technology with a simple, web-based data collection, processing, and distribution platform to better track the global spread of deadly infectious diseases including Middle East Respiratory Syndrome (MERS-CoV). MERS - also known as camel flu - is a viral disease that causes fever, cough, diarrhea, and shortness of breath, and is transmitted from camels to humans. One third of people diagnosed with the disease die. Next generation sequencing (NGS) technology allows rapid, inexpensive detection of pathogens as they spread. However, laboratories in different member states use different formats for sequencing data, and there is no mechanism for sharing it in real time. This limits the value of the technology for stopping outbreaks. To address this, they will establish routine sequencing protocols for both human and camel samples, and develop an interactive web platform on which the sequencing and epidemiological data can be shared. This will help develop more effective, real-time medical and non-medical interventions at local, national, and international levels. Once established, the protocols developed here may be applied to outbreaks of other diseases.

Achim Hoerauf of IMMP in Germany will apply artificial intelligence (AI) to speed the development of treatments for onchocerciasis, which is an infectious disease commonly known as River Blindness caused by a parasitic worm. The parasites are spread by affected blackflies, and the worm larvae accumulate in the skin and eyes, causing irritation and sometimes blindness. Nearly 21 million cases occur each year, and 99% of affected people live in Africa. The drug currently used for treatment kills only worm larvae, and studies are ongoing to identify more effective drugs that target adult worms. However, evaluating these drug candidates requires manual analysis using microscopy of samples of irritated skin from patients after treatment. This process is time consuming and slows drug development. To address this, they will use samples that have already been manually annotated to train an AI system to automatically analyze future samples to recognize worm body parts, gender, vitality, and stage of development. Once established, the AI system will be tested with samples from a new clinical trial - tissues from patients treated with the new drug will be analyzed in parallel by human and computer. Once optimized, the AI system will take over the analysis, and the much slower human analysis will only be needed as a quality control system.

Yingda Xie of Rutgers, The State University of NJ and JoAnne Flynn of the University of Pittsburgh, both in the U.S., will develop a non-invasive approach for testing candidate anti-tuberculosis compounds in animal models and patients using positron emission tomography-x-ray computed tomography (PET/CT). Tuberculosis (TB) is a leading cause of death in developing countries, and rates are sustained by the causative bacterium, Mycobacterium tuberculosis, developing resistance to current drugs. To circumvent this, new drugs are being designed to target human cells and proteins rather than those of the bacteria. To test these drugs, new tools are also needed to monitor TB in patients. 18 Fluorodeoxyglucose (FDG)-PET/CT is a non-invasive imaging tool that uses radioactively-labelled glucose to light up areas of metabolic activity in the body such as the lesions formed by M. tuberculosis and immune cells that play a critical role in infection. They have histopathological sections and cell and chemical data of TB lesions from non-human primate models and will use them to quantify the different lesions. Then, by using the available PET-CT scans of the lesions, they will search for quantitative signatures that can predict a specific type of lesion. The accuracy of these PET/CT signatures will be tested in a separate group of animals. Their study will reveal details of the TB immune response across different lesions, which could help design new treatments, and the signatures can be used to test the activity of new drug candidates in animal models and humans.

Alain Labrique of Johns Hopkins Bloomberg School of Public Health in the U.S. and Meghan Azad of the University of Manitoba in Canada will study the impact of prelacteals - fluids or solids given before breastfeeding is established - on the populations of bacteria in the newborn gut (the microbiome), and how it may affect development. Immediate and exclusive breastfeeding helps maintain healthy growth in infants and protects them against infections, which are also influenced by their gut microbiome. However, in Bangladesh and many other low-resource countries, it is common practice to give newborns ritual foods, like honey or sugar water, before breastfeeding begins, which may impede development. They hypothesize a link between prelacteal use and newborn development mediated by the gut microbiome. To test this, they will use an ongoing population-based study in rural Bangladesh and compare the types and amounts of bacteria in the gut using stool samples of 300 prelacteal-fed and exclusively breastfed infants at 7 days, 28 days and 3 months of life. They will also analyze the composition of the prelacteals being used, including the presence of any toxic contaminants, and of the breastmilk of the mothers, for correlating with any changes in gut microbial populations. The study will enable them to quantify the potentially negative impact of this widespread cultural practice, common to over a billion people across the Gangetic floodplain.

Eric Kaduru of KadAfrica Estate Limited and John Onekalit of the Kitgum Concerned Women's Association both in Uganda will provide a 12-month, integrated life skills and agricultural training program along with land and seedlings to young refugee women out of school in Uganda to begin their own sustainable passion fruit farming cooperatives. Uganda has accepted many refugees, but also has the world's youngest population and very high unemployment. As a result, particularly girls have very limited employment opportunities if they even manage to finish school, and instead often work in the sex industry or immediately get married. This in turn leads to increased teenage pregnancies and rates of HIV. They will provide a cooperative start-up kit including training in sustainable passion fruit farming, which has a guaranteed market, access to land through a community-based land lease model, and passion fruit seedlings. The girls will also be taught about finance, nutrition, and sexual and reproductive health. They will test their approach in two refugee camps with 180 adolescent girls between 14- and 22-years old who are out of school. The success of the project will be assessed in terms of the effect on poverty and health.

Ruth Müller of the Institute of Tropical Medicine in Belgium and Meghnath Dhimal of the Nepal Health Research Council will provide entomological training for health science students and medical professionals and increase community awareness of vector-borne diseases (VBDs) in Nepal to better equip the population to deal with disease outbreaks. VBDs like those caused by the dengue, zika, or chikungunya viruses cause more than 700,000 deaths annually, mostly in poor countries with limited public health resources and tropical climates. Climate change has expanded the affected areas as warmer temperatures facilitate survival of the insect vectors. They will establish the EntoCAP team to enhance entomological capacity to fight these diseases. The team will hold five-day workshops for 300 health science students and health care professionals on surveillance and control of vector populations, and monitoring of disease outbreaks. They will also increase community interest in VBDs by hosting science labs for children to teach them how to recognize mosquitoes at various developmental stages and understand the dangers of VBDs. In addition, they will begin building a reference collection using DNA barcoding technology to catalog insect vectors by species for studying biodiversity and microevolution of disease vectors.

Elena Levashina of the Max Planck Institute for Infection Biology in Germany and Kelly Lee of the University of Washington in the U.S. will use cryoelectron tomography to image the three-dimensional ultrastructure of a protein on the surface of the malaria-causing parasite Plasmodium falciparum to help design better vaccines. Malaria kills half a million people annually, but there are still no highly effective vaccines available. One of the parasite's coat proteins, CSP, is a prime target for vaccine development. However, not much is known about its natural structure on the live parasite, which is how inhibitory antibodies produced in response to a vaccine will be able to recognize and destroy it. One of the best ways to observe the natural structure of a protein at high resolution is to immobilize it in non-crystalline ice and image it under very low (< −150 °C) temperatures. They will develop protocols to isolate large numbers of highly pure parasites directly from mosquitoes and carefully cryopreserve them on grids to maintain their natural form and enable clearer imaging. They will also use this high-resolution imaging technique to study how antibody binding affects the parasite. Their results will help design new vaccines that can produce highly active, inhibitory antibodies.

Eric Ochomo of the Kenya Medical Research Institute (KEMRI) in Kenya and Luc Djogbenou of the University of Abomey (UAC) in Benin will develop a curriculum to teach African scientists how to use genetic approaches to combat insecticide resistance in the fight against malaria. Malaria is a disease that kills almost 500,000 people annually, most in sub-Saharan Africa. People become infected when bitten by mosquitoes that transmit the disease-causing parasites. Insecticide treatment of bed nets and indoor areas are effective methods of disease control, but mosquitoes are becoming resistant. Varying the types of insecticides used and applying them in different combinations can help fight resistance, but it's difficult to know the most effective approach before resistance develops without the help of genetic markers. They will teach African scientists techniques to identify genetic resistance markers including sample collection and preservation, transcriptomic and whole-genome sequencing, and bioinformatics using online and hands-on approaches. This will ensure timely changes to insecticide application to better combat resistance. They will also encourage local scientists to establish industry partnerships to ensure that resistance monitoring can continue long-term.

Sophie Mower of The Centre for Global Equality in the United Kingdom will establish a collaborative program for technology students at Bahir Dar University in Ethiopia using expertise and support from a number of other centers in Africa and beyond to provide training and financial resources for them to research and develop their own innovative solutions to local challenges. Students at the university work on creative solutions such as mapping applications particularly in areas of agriculture and health. However, advancing their ideas is limited by the lack of professional networks and material resources. They will provide a dedicated space at the university and work with the Centre for Global Equality (CGE) and companies in the Cambridge Cluster, both in the United Kingdom, and an African innovation hub. Together, they will provide training for 30 students on co-creating their solutions with end-users to increase their impact. They will also hold an ideation hackathon to generate design ideas, and award $2000 to the six most competitive projects. These will be supported through to prototype development using methods from an incubator approach established at the CGE.

Cambria Finegold, Richard Shaw and Roger Day of the Centre for Agriculture and Bioscience International in collaboration with Katherine Denby of the University of York and Sarah Gurr of the University of Exeter all in the United Kingdom, will design a platform - GBCrop - to collect, analyze and disseminate data on the global impact of crop pests and disease. The fact that 40% of crops are lost to pests impacts both the global food supply and local economies. Despite this, little is known about why and how crop pests and diseases occur. The extent of the problem was acknowledged by the UN declaring 2020 the Year of the Plant. They will design GBCrop to collect large quantities of high-quality data and apply advanced analytical methods to generate results that can then be used to direct research and policy development, and to predict the impact of emerging diseases. The program is modeled after Global Burden of Disease, which has transformed health policy agendas over the last 25 years. They will begin by consulting with key experts, and then include policy makers, private industry representatives, government organizations, potential funders and scientific experts. Together they will decide what data to collect and how it can best be used to accurately predict the impact of emerging crop diseases. They will launch their plan-of-action in the Year of the Plant and aim to make their first recommendations in 2023 on how to maximize crop gains.

Mohlopheni Marakalala of the Africa Health Research Institute in South Africa will study the role of specific proteins associated with immune cell death in tuberculosis patients to better understand how the disease progresses and help develop new diagnostics and therapies. Tuberculosis (TB) is a bacterial disease that causes 1.5 million deaths per year, mostly in poor countries. Understanding how the human immune system responds to TB infection could help develop more effective, host-targeted treatments. Granulomas - tissues that form as a result of inflammation - are commonly seen in the lungs of TB patients. Their characteristics change as the disease progresses and they can cause severe lung damage. Granulomas are thought to be formed by the death of white blood cells called neutrophils, which are also abundant in the airways of patients. He will study granulomas isolated from patients at different stages of the disease to identify proteins linked to neutrophil cell death and see if they are linked with lung damage and disease progression. He will then determine whether the levels of these proteins in the blood can be used as disease biomarkers for the early detection of TB. Lastly, he will use molecular genetic techniques to reduce the level of these proteins in neutrophils and evaluate the effect on TB infection to see if the approach could be exploited as a potential therapy.

Iruka Okeke of the University of Ibadan, College of Medicine in Nigeria and Kat Holt of Monash University in Australia will set-up a remote laboratory that uses nanopore sequencing as a low-cost, portable method to monitor the spread of antimicrobial resistance in rural areas of Africa and combine it with genome editing tools for more rapid diagnosis and improved treatment. Antimicrobial resistance (AMR) occurs when pathogens are able to survive treatments that previously would have killed them. Infection persists in these patients and spreads to others in the community, increasing both the risk of serious complications and the economic costs. To combat AMR, it needs to be tracked locally and quickly enough to inform treatment. However, traditional tracking methods are slow, and difficult to use in rural settings because of limited resources. Nanopore sequencing technology is a highly portable method of sequencing DNA that is suitable for resource-poor settings. They will setup a prototype minimal bacterial genomics lab at a provincial hospital laboratory in Africa, and use nanopore sequencing to catalog pathogens collected from patients and monitor AMR. They will also combine the sequencing with a genome editing tool - CRISPR-Cas - to enrich for known resistant pathogens and enable much faster diagnosis directly from blood or stool samples. Once optimized in the initial location, the remote lab can be recreated in other areas of Africa.

Caroline Stefani of the Benaroya Research Institute at Virginia Mason and Yongxing (Leon) Zhao of Carnegie Mellon University both in the U.S. will build an imaging platform combining expansion microbiology and confocal virtual reality to visualize complex host-pathogen interactions in infected tissues to help develop new diagnostics and therapeutics. It is the molecular interactions between the host and the pathogen, both in tissues and inside cells, that ultimately dictate whether an infection takes hold or is destroyed. Identifying these interactions could help develop new treatments. However, they remain difficult to study in sufficient resolution. They have developed a new method for three-dimensional visualization of confocal microscopy images using commercial virtual reality technology to pinpoint the subcellular localization of host-pathogen interactions. They will combine this with a new technique, expansion microscopy optimized for microbiology (ExMicro), which visualizes nanoscale details of dozens of different molecules in infected tissue by embedding it in a polyacrylate-based polymer that can be expanded in pure water to improve resolution. They will develop protocols and software to optimize both methods for studying host-pathogen interactions, and build a platform to share their new toolset with the scientific community.

Pia Wintermark of McGill University in Canada and Cally Tann of the London School of Hygiene & Tropical Medicine in the United Kingdom will establish a pilot cohort in Uganda of term newborns who suffered from asphyxia at birth, which means that their brain and other organs did not receive enough blood or oxygen, and conduct a clinical test of a novel neurorestorative agent (i.e., to repair brain injuries) to see if it can improve early brain development in this setting. Birth asphyxia and the resulting neonatal encephalopathy is the third leading cause of mortality in infants under five and leads to significant brain damage and long-term neurodevelopmental morbidities. In a rat model of term neonatal brain damage, they found that a compound, sildenafil, reduced brain damage and inflammation, and increased nerve cell growth. This compound has already proven safe for use in humans for other purposes. They will first assemble a pilot cohort of 100 neonates with neonatal encephalopathy in Uganda, and clinically evaluate them over the first three months of age to better characterize the disease in this setting. From this cohort, 30 newborns will be selected to test whether daily treatment of sildenafil from day 2 to day 9 of life can improve brain growth and development and is a feasible and acceptable neurorestorative treatment strategy in this setting.