This type of analysis transformed the way coronavirus was tracked during the pandemic. With new funding, it will be extended to track a wide range of other pathogens.
University of Birmingham experts will be collaborating with Scripps Research, and the National Institute for Communicable Disease in South Africa to develop and implement the new technologies.
Dr Josh Quick, in the School of Biosciences, said: “Birmingham has been leading the field of viral surveillance since 2015 when Professor Nick Loman and I established the first real-time genomic surveillance of the West African Ebola outbreak. Development of the ARTIC sequencing protocol and the CLIMB computing infrastructure enabled the U.K. to establish a world-leading national surveillance system for tracking Coronavirus.
“This grant will support the development of cutting-edge methods for environmental surveillance from wastewater, increasing capacity worldwide and training the next generation of scientists to perform genomic surveillance."
“This grant will support the development of cutting-edge methods for environmental surveillance from wastewater, increasing capacity worldwide and training the next generation of scientists to perform genomic surveillance."Dr Josh Quick, School of Biosciences
The process of identifying different pathogens using wastewater genomic surveillance, is complex, as wastewater samples contains tiny quantifies of viruses of interest. The approach developed by the team uses hundreds of computationally designed primers to amplify the pathogen signal into something usable. Sequencing it then allows researchers to identify the pathogen and even determine the specific type which is valuable for monitoring outbreaks and the effectiveness of testing and vaccination programs.
Most analysis tools used to identify pathogens are developed for clinical samples (like swabs or blood tests) but for a wastewater application they must be able to untangle complex mixtures of species or even mixtures of types of the same species. Wastewater surveillance has been successfully used as an early-warning system for the emergence of new Covid variants in a country or region.
The research team will use laboratory techniques and computational tools developed by Dr Quick and Professor Loman and extend them to monitor more pathogens, including Measles, Rubella, Influenza and Hepatitis viruses.
The two-year project will have a particular focus on delivering affordable solutions that can be implemented in lower middle-income countries where there may be large surveillance gaps.