Canary in a coal mine: genomic surveillance could provide early warning for future pandemics

BioTechniques News
Aisha Al-Janabi

Researchers are developing a cheap, easy-to-use and scalable genomic technology for conducting global surveillance of respiratory viruses.

A group of scientists at the Wellcome Sanger Institute (Cambridgeshire, UK) in collaboration with the UK Health Security Agency (UKHSA; London, UK) are currently creating genomic tools to track and understand emerging and circulating respiratory viruses, as reported by The Guardian. The project, known as the Respiratory Virus and Microbiome Initiative (RVI), aims to provide a global genomic surveillance strategy that could be incorporated by public health departments all over the world to act as an early warning for potential outbreaks.

Building upon expertise gained during the COVID-19 pandemic when the Sanger Institute sequenced millions of SARS-CoV-2 genomes in collaboration with the COVID-19 Genomics UK (COG-UK) Consortium, the RVI team aims to use lessons from COVID-19 to develop a standardized approach to sequencing multiple respiratory viruses in a single assay. Such an approach could be used in any laboratory.

“In many labs around the world, people have smaller sequencing machines and cannot sequence as many samples as we can at the Sanger. So, we want the system to work equally well on those machines as it does here on our large volume devices,” explained the leader of the Sanger Institute’s genomic surveillance unit, John Sillitoe [1]. Project leader Ewan Harrison went on to add “the crucial point is that we have got to develop a system that uses inexpensive reagents, does not require teams of highly-trained technicians and can be used at scale. Then we can really make a difference.”

The technology being developed includes a targeted assay that can detect co-infections of multiple common respiratory viruses from a single nasal swab, including influenza, respiratory syncytial virus (RSV) and coronaviruses.

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The team is also working on a shotgun metagenomics approach to identify all of the genes and fungal, viral and bacterial species present in a sample. Such an approach would allow the team to establish a baseline of the respiratory virus dynamics in the UK, and to generate an extensive viral genome dataset that would be publicly available. Harrison recently told the Observer that three different versions of the technology are currently being tested, with hopes of developing a hybrid technology and a usable system that will be operational within a year.

“The systems we develop are intended to be the canary in the coal mine,” said Harrison [2]; a standardized global genomic surveillance technology is valuable to identifying emerging variants of concern and novel viruses, providing an early warning and a critical opportunity to intervene.

The technology will also provide critical insights into the transmission and evolution of respiratory viruses, including the emergence and distribution of antimicrobial resistance, and will inform vaccine design and modification.

As summarized by Gordon Dougan, the Director of Infectious Disease at Wellcome, “preventing future pandemics depends on countries around the world working together to ensure early intervention on infectious disease rise and spread.” [3].

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