Genetic tracking scheme for cold and flu viruses could warn of dangerous outbreaks

New efforts to routinely sequence the genes of viruses that cause severe respiratory infections such as influenza and respiratory syncytial virus could lead to better treatments and vaccines

To Michael Le Paige

Virus samples from people with severe respiratory infections such as influenza and respiratory syncytial infections in the UK are routinely tested by DNA sequencing in projects that could lead to better treatments and vaccines. It also provides early warning of dangerous new outbreaks.

The team behind the project, called the Respiratory Virus and Microbiome Initiative, says it is not aware of similar plans elsewhere in the world, but hopes other countries will adopt the same approach. To facilitate this, we make all methods and data freely available.

Ewan Harrison of the Wellcome Sanger Institute in Cambridge, UK, who is leading the project, said:

Sequencing viral genomes has been possible for decades, but it was only during the covid-19 pandemic that many countries began routinely sequencing thousands of samples. more than I thought. Among other things, this genomic surveillance allowed researchers to detect the first omicron variants and accurately predict that they would cause a huge wave of cases worldwide.

“For the first time in human history, large-scale genomics has allowed governments and policy makers to know in advance what will happen in an epidemic. I think this is a very important and profound change.” Harrison says. “This is something that we think is really important to build on.”

Many other viruses, such as RSV, can also cause serious respiratory infections, he says, but our understanding of them is very limited. There’s really no regular genomic surveillance of these other viruses, other than genome sequencing,” Harrison says.

Tests commonly used today to identify viruses that cause severe infections reveal only the type of virus, such as rhinovirus or adenovirus, says Judith, a virologist at University College London. Breuer said.

Sequencing the entire viral genome will reveal more information and help in many ways. First and foremost, it helps ensure that people receive the most effective treatment. For example, some antibody treatments for covid-19 may be less effective against newer variants, so doctors should Alternative treatment can be performed immediately.

It could also lead to better vaccines. SARS-CoV-2 sequencing revealed that omicron variants have spread and become dominant worldwide, so mRNA booster shots have been updated to include two of these variants and vaccines is now more effective against them.

Gene sequencing can also reveal how viruses are spread, which can help contain them. If so, we don’t know if they got it in the hospital or in the community, Breuer says. Sequencing will tell us if they carry the exact same virus and therefore if hospital infection control measures need to be improved.

Finally, Harrison wants to catch emerging new diseases early. If other countries also have regular genomic surveillance, they are much more likely to do so.

Sequencing a dozen or so viruses that may be present in a sample is simply sequencing one, especially if the aim is to do so using cheap tests that are available anywhere in the world. technically more difficult than This is why Harrison and his team are using stored swabs to perfect their approach before working with the UK Health Security Agency to start testing fresh swabs from critically ill patients. is expected to extend surveillance beyond critically ill patients and other types of viruses.

For now, the researchers also plan to sequence all the genetic material present in some swab samples. Fungi can now be identified and the airway microbiome can be studied.

“The methods and techniques that Ewan and Sanger are developing will be very helpful,” says Breuer. “This is a surprisingly important initiative.”

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