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Sanger hopes to track respiratory pathogens with single nose swab

Image: Dan Ross/Wellcome Sanger Institute

Wellcome Sanger Institute set to develop routine genomic surveillance and monitor for emerging viruses

A new initiative to track respiratory viruses in the UK has been launched today by the Wellcome Sanger Institute.

The genomics and genetics research institute said the initiative aims to develop the capability for routine genomic surveillance of respiratory viruses and monitor for emerging ones.

During the coronavirus pandemic, the institute was involved in the Covid-19 Genomics UK Consortium, which used genomic sequencing to track the spread of the virus and the emergence of new variants. The network has been praised for its impact on the country’s Covid-19 response.

The new Respiratory Virus and Microbiome Initiative will look at viruses including the influenza virus, respiratory syncytial virus, adenoviruses and rhinovirus. It will be led by researchers at the Wellcome Sanger Institute, in partnership with the UK Health Security Agency, other public health bodies and academic institutes.

Susan Hopkins, chief medical adviser at the UK Health Security Agency, said the initiative “is an exciting development in expanding the UK pathogen genomics capability that has been so vital to our health protection activity in recent years.

“Genomic sequencing has been crucial in the response to the Covid-19 pandemic and will continue to be pivotal in global efforts to address all kinds of threats to health in the future.”

Researchers behind the initiative will first establish combined genome sequencing of Sars-CoV-2, influenza, respiratory syncytial virus and other common respiratory viruses in a single test. But the goal is to eventually determine all of the genes and species—including viruses, bacteria and fungi—present in a single nose swab sample.

The results are expected to give a baseline of the respiratory virus dynamics in the UK and will result in “an extensive viral genome dataset” that will be publicly available.

‘A better understanding of pathogens’

The Wellcome Sanger Institute said the initiative will lead to a better understanding of common pathogens in the UK, act as an early warning system for new viruses, support public health responses, and enable research into the transmission and evolution of respiratory organisms.

The data generated by the initiative are expected to lead to a better understanding of common respiratory viruses in the UK, which will help to generate new vaccines and ensure existing ones offer good protection.

Over time, the aim is to scale up and adapt the platforms, technologies and methodologies so they can be used globally for genomic surveillance programmes.

Gordon Dougan, director of infectious disease at Wellcome, said the initiative is an “important step in building monitoring systems in the UK, and could help track outbreaks of viruses such as influenza and RSV [respiratory syncytial virus].

“This approach is an example of how science can be used to detect rising levels of infectious diseases, and identify [their] sources and drivers. It could also become a blueprint to strengthen virus-tracking in other countries. Preventing future pandemics depends on countries around the world working together to ensure early intervention on infectious disease rise and spread.”

As part of the initiative, researchers will also carry out work into the dynamics of the respiratory microbiome, which is all the organisms in our nose, throat and lungs.

The team will study how the microbiome changes during infection and how this relates to severity of illness. The data generated will allow researchers to track antimicrobial resistance.