Awards

Orapan Sripichai of the National Institute of Health of Thailand in Thailand will engage a national network of laboratories for the genomic surveillance of Salmonella, involving sequencing clinical isolates to characterize strains, virulence factors and mechanisms of antimicrobial resistance. Salmonella infection is prevalent in Thailand and can be life-threatening. The emergence of multidrug-resistant Salmonella strains in Southeast Asia is an additional major concern. They will collect approximately 1,500 clinical isolates from 77 provincial hospitals across Thailand over one year, and train local laboratory scientists and bioinformaticians to produce and analyze genomics data. The data will be uploaded to a standard repository in the National Center for Biotechnology Information (NCBI) and will help to guide prevention and control measures.

Rifky Waluyajati Rachman of the West Java Provincial Health Laboratory in Indonesia will employ targeted next-generation sequencing (NGS) to support genomic surveillance of drug-resistant tuberculosis (TB) in Indonesia. Indonesia has the second highest number of TB cases globally and a growing burden of largely undetected multidrug-resistant TB, yet no drug resistance surveillance in place. They will perform targeted NGS on over 5,000 positive sputum samples to more accurately estimate drug-resistant TB prevalence. They will also conduct whole genome sequencing at the community level to understand transmission patterns and help guide public health interventions. To build capacity, they will provide tailored training on the experimental, bioinformatic, public health, and epidemiological aspects of infectious disease surveillance. They will also establish a public center of expertise for pathogen surveillance in West Java, which has a population of 48 million.

Pragya Yadav of the Indian Council of Medical Research - National Institute of Virology in India will strengthen genomic and epidemiological surveillance in different locations across India to enhance preparedness against high-risk viral diseases. With India's extreme geo-climatic diversity, it is under constant threat of emerging and reemerging viral infections. They will enhance surveillance of endemic diseases in India, including Zika and Dengue, by establishing a network of seven laboratories and training staff in molecular diagnostic techniques, including sequencing, data analysis, and biosafety. They will also select surveillance sites for collecting samples and expand next-generation sequencing capacity to identify variants.

Audrey Dubot-Pérès of the Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU) in Lao PDR will establish a pilot respiratory syncytial virus (RSV) genomic surveillance system to determine disease burden and monitor strain circulation in Lao PDR. RSV is the leading cause of viral pneumonia in young children in low-income countries. Accurate data on disease burden, transmission and viral evolution are critical to successfully introduce emerging vaccines and therapies. Leveraging their experience as a national center for SARS-CoV-2 genomic surveillance, they will develop an RSV genomic sequencing protocol using samples collected from children at two central and four provincial hospitals. They will also investigate whether RSV RNA can be purified directly from rapid diagnostic tests to improve surveillance in remote areas. The data will be displayed on a national health dashboard. If successful, their approach could be expanded into a national surveillance system.

This grant is one of three grants that are funded and administered by the Programme for Research in Epidemic Preparedness and Response (PREPARE) in Singapore.

Chhorvann Chhea of the National Institute of Public Health in Cambodia will expand Cambodia’s Severe Acute Respiratory Infections (SARI) surveillance network by integrating metagenomic next-generation sequencing to better diagnose and monitor severe respiratory infections. Pneumonia is the leading cause of death globally in children under five years old, with the majority of severe cases classified as viral. To successfully develop treatments and vaccines, a comprehensive understanding of viral genetic diversity is required; however, this remains largely uncatalogued for common respiratory viruses, such as respiratory syncytial virus (RSV). They will collect oropharyngeal swabs, blood culture isolates, or lower respiratory tract samples from adults and children with SARI at nine sites. They will extract RNA and leverage pandemic sequencing infrastructure for sequencing, taxonomic identification and phylogenetic analyses to guide molecular epidemiology and outbreak investigations. The data will be integrated with a country-wide genomic surveillance strategy, currently under development.

This grant is one of three grants that are funded and administered by the Programme for Research in Epidemic Preparedness and Response (PREPARE) in Singapore.

Mai Le of the National Institute of Hygiene and Epidemiology in Vietnam will expand Vietnam’s systematic surveillance and sequencing capacities to detect potential pandemic pathogens, including influenza and coronaviruses, and incorporate agnostic sequencing of conventionally undiagnosed pathogens. They will build on the existing infrastructure of the influenza-like illnesses sentinel surveillance network, which collects samples from four outpatient clinics, to include testing for both influenza A and B and SARS-CoV-2 viruses, with the possibility to expand. They will also revive the hospital-based Severe Acute Respiratory Infections (SARI) surveillance network, which works with three hospital emergency departments and ICUs, to focus on 12 pathogens and incorporate an agnostic sequencing component. Their activities will include training health workers in sample collection and scientists in directed and agnostic sequencing of respiratory pathogens and bioinformatics analysis. The data produced will be shared in real-time on an online dashboard.

This grant is one of three grants that are funded and administered by the Programme for Research in Epidemic Preparedness and Response (PREPARE) in Singapore.

Pontiano Kaleebu of the Uganda Virus Research Institute in Uganda will expand their genome surveillance platform to monitor the circulation of SARS-CoV-2 variants in Uganda to help inform timely public health decisions and the development of diagnostics and vaccines. They will obtain geographically-representative COVID-19 patient samples for genomic sequencing, as well as samples from strategic sites including points of entry, where several variants have emerged. They are also collecting blood samples and nasopharyngeal swabs from patients, some of whom have been vaccinated, to determine their ability to neutralize viral variants and to produce monoclonal antibodies for potential use as diagnostics or for vaccine design. The methods and capacity established during this project will also be used for immunological surveillance of other infectious diseases.

Christian Happi of Redeemer's University in Nigeria will assess the impact and risks of emerging SARS-CoV-2 virus variants in Africa, which are threatening vaccination efforts. They will produce viral pseudotypes using genomic sequences of around ten SARS-CoV-2 variants-of-concern that are dominant in Africa. These pseudotypes will be used in high-throughput neutralization assays with Vero cells in the presence of serum samples taken from over 400 vaccinated or previously-infected Nigerians, which contain many different types of antibodies, to evaluate their ability to neutralize the viral variants. This will reveal how well protected the population is against viral variants, and inform vaccine and immunization strategies. The serum samples that strongly protect against a range of SARS-CoV-2 variants will be subjected to single-cell immunoglobulin gene sequencing to identify neutralizing monoclonal antibodies for designing more effective vaccines.

Charles Sande of the African Research Collaboration for Health (ARCH) in Kenya will build on their existing SARS-CoV-2 genomic surveillance work covering the six counties of Coastal Kenya to identify new SARS-CoV-2 variants and evaluate their sensitivity to existing vaccines. Daily naso- and oropharyngeal samples from suspected COVID 19 cases will be processed for PCR testing and genome sequencing to identify any new SARS-CoV-2 variants. They will then evaluate the potential impact of these new variants on the Kenyan population by measuring the neutralizing activity of antibody-containing plasma obtained from a cohort of vaccinated adults. Using established channels, they will rapidly communicate their results to local and national health ministries, and across the African continent, to inform pandemic control strategies. Selected samples will be preserved for future monoclonal antibody development to target new variants.

Peter Quashie of the University of Ghana, West African Centre for Cell Biology of Infectious Pathogens in Ghana will determine the impact of SARS-CoV-2 viral variants and their susceptibility to neutralization by vaccine-induced and naturally-acquired immunity to better manage pandemic control in Ghana. They will evaluate over 600 existing plasma samples taken at multiple timepoints from both vaccinated and unvaccinated COVID-19 patients with associated SARS-CoV-2 sequencing data to identify the viral variants, and additional samples as new variants emerge. They will use ELISA and Luminex assays to screen these samples for anti-viral antibodies. Positive samples will then be used in neutralization assays to measure their ability to protect against different viral variants. Plasma with strong broad or selective neutralization activity will be processed for single cell sequencing to identify monoclonal antibodies for potential therapeutic use. Their pipeline can also be applied to other viral outbreaks such as HIV or Ebola.