Genetic tracking system for cold and influenza viruses can warn of serious disease outbreaks

A new effort to sequence the genes of viruses that cause acute respiratory infections, such as influenza and RSV, could lead to better treatments and vaccines.


January 10, 2023

Electron microscope image of SARS-CoV-2 coronavirus particles

Electron microscope image of SARS-CoV-2 coronavirus particles

NIAID-RML/National Institutes of Health/Science Picture Library

Virus samples from people with acute respiratory infections, such as influenza and RSV, will be routinely tested in the UK by DNA sequencing in a project that could lead to better treatments and vaccines, as well as an early warning of serious new outbreaks. The technology will be trialled on stored nasal swabs from COVID-19 tests starting later this year, before being rolled out more widely next year.

The team behind the project, called the Respiratory Virus and Microbiome Initiative, says it is not aware of any similar plan anywhere else in the world, but hopes other countries will adopt the same approach. And to encourage this, it will make all methods and data freely available.

He says “hopefully it can be used globally” Ewan Harrison at the Wellcome Sanger Institute in Cambridge, UK, who is leading the project.

While the viral genome could have been sequenced for decades, it was only during the COVID-19 pandemic that several countries began routinely sequencing thousands of samples, revealing how SARS-CoV-2, the virus behind the disease, was evolving. Faster. than expected. Among other things, this genetic monitoring enabled researchers to discover the first Omicron variants and correctly predict that they would cause a huge wave of cases around the world.

“For the first time in human history, large-scale genomics has provided governments and policymakers with advance warning of what will happen in a pandemic situation, and I think this is a really important and profound change,” says Harrison. “It’s something we think is really important to continue to build on.”

He says many other viruses, such as RSV, can also cause serious respiratory infections, but our understanding of them is very limited. “Other than a small amount of genome sequencing in influenza cases, there really isn’t any routine genetic monitoring for these other viruses,” says Harrison.

For now, the tests usually used to identify viruses causing severe infections reveal only their type, such as rhinovirus or adenovirus, she says. Judith Brewera virologist at University College London.

Sequencing the complete genome of the virus reveals more information, which can be useful in several ways. For starters, it can help ensure people get the most effective treatments. Some antibody treatments for covid-19 May be less effective against newer variantsFor example, doctors can immediately offer alternative therapies if they know someone has one of these variants.

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

Genetic sequencing can also reveal how viruses spread and thus help contain them. For example, if you only knew that two people in intensive care had rhinovirus infections, you would have no idea if they were infected in the hospital or in the community, Brewer says. Sequencing can tell us if they have the exact same virus, and therefore if a hospital’s infection control measures need to be improved.

Last but not least, Harrison hopes to catch emerging new diseases early. The odds of doing so would be much greater if other countries also carried out routine genome surveillance.

Sequencing any of the dozens of different types of viruses that may be present in a sample is technically more difficult than sequencing just one, especially when the goal is to do so with a cheap test that can be used anywhere in the world. This is why Harrison and his team will perfect their approach using stored swabs before starting to test new swabs from critically ill patients in collaboration with the UK’s Health Security Agency. In the long term, the hope is to expand surveillance beyond those in critical condition and other types of viruses.

For now, the researchers also plan to sequence all of the genetic material found in a few swab samples. This approach, known as metagenomics, would enable them to identify every type of virus, bacteria and fungus present, allowing them to study the microbiome of the respiratory tract.

“The methods and techniques that Ewan and Sanger are developing will be very useful,” Brewer says. “This is an amazingly important initiative.”

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