The pandemic showed the power of viral sequencing. Now the U.K. plans to decode other respiratory bugs

Building on the global boom in viral surveillance during the pandemic, U.K. scientists on Tuesday unveiled an initiative to expand sequencing of the common seasonal respiratory bugs that have received comparatively little attention.

The Respiratory Virus & Microbiome Initiative, launched and funded by the Wellcome Sanger Institute, will track the evolution not just of SARS-CoV-2, the coronavirus that causes Covid-19, but also other coronaviruses, different flu families, RSV, and other pathogens that typically just cause the sniffles but collectively lead to waves of illness every year. Researchers hope the initiative will enable them to better monitor viruses in the U.K. as they change, alert them to any worrisome mutations, and get tipped to the emergence of new viruses.

“The ability to track and look for these events early is obviously something that’s really important,” said Ewan Harrison, the head of the initiative.

The program, a collaboration with the U.K. Health Security Agency and other scientists, hopes to generate tons of data for academics and public health officials to use in their work, and also aims to “supercharge” research that could ultimately lead to the development of vaccines and therapeutics, Harrison said. It’s also simply about better understanding these viruses. While flu has attracted lots of research over the years, some of the other bugs — like rhinovirus or adenovirus — are not as well-monitored. Scientists don’t even understand their transmission dynamics all that well, he said.

Viral sequencing exploded during the pandemic, with global efforts helping detect variants like Delta and Omicron (and all the Omicron sublineages) and guiding response strategies. A major moment in the pandemic was when, in early January 2020, scientists publicly released the genome of the virus, which allowed responders around the world to start developing diagnostic tests and served as a starter’s pistol for vaccine development. From there, scientists shared millions of sequences on public trackers.

More recently, the number of Covid infections being sequenced has collapsed as much of the world has moved past the emergency phase — a trend public health officials globally have lamented.

It’s not just the detection of major new variants that sequencing can enable. Sequencing viruses can help scientists track routes of transmission, whether in a hospital or from country to country. When combined with lab studies or epidemiological research, it can answer questions about the virus’s basic biology, whether the virus is becoming more transmissible, or whether the impact of an infection is changing — like how the Delta variant seemed to cause more severe disease. It’s also a tool that can help track how well vaccines are holding up against evolving viruses.

Expanding routine sequencing is the type of research that could come in handy with other viruses. In the United States, for example, experts are trying to figure out why an anticipated wave of a rare polio-like condition that can occur after an infection with a common enterovirus never materialized last fall, despite a surge of those enterovirus infections. Researchers are exploring the virus’ genome to see if it changed in some way.

The new initiative is designed to build an infrastructure that becomes part of routine viral surveillance, but also one that can be deployed during the next epidemic or pandemic, Harrison said. During the pandemic, researchers got their first experience with sequencing data helping inform responses to a public health crisis.

“It’s now something we now think is really important to build upon,” Harrison said.

As the team develops the techniques and tools they’ll use in their project, one goal is to keep it as low-cost as possible, with the idea that other research teams around the world could adopt such protocols. All of their methods and computational software will be made freely available.

“Sequencing know-how is incredibly widespread now, so I think the opportunity for this to happen globally is there,” said Judith Breuer, a professor of virology at University College London and one of the researchers involved in the new program.

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