Genetic virus tracking scheme could warn of dangerous outbreaks

New efforts to routinely sequence the genes of viruses that cause severe respiratory infections such as influenza and RSV could lead to more effective treatments and vaccines.

Virus samples from people with severe respiratory infectionssuch as influenza and RSV in the UK will be routinely tested by DNA sequencing in a project that could lead to improved treatments and vaccines, as well as earlier warning of dangerous new outbreaks. The technology will be trialled on stored nasal swabs from COVID-19 tests starting later this year and rolled out more widely next year.

The team behind the project, called the Respiratory Viruses and Microbiomes Initiative, says they are not aware of any similar plan elsewhere in the world, but hopes other countries will take the same approach. To encourage this, all methods and data will be available free of charge.

“We hope it can be used worldwide,” says Ewan Harrison at the Wellcome Sanger Institute in Cambridge, UK, who is leading the project.

Although it has been possible to sequence viral genomes for decades, it was not until the COVID-19 pandemic that many countries began to routinely sequence thousands of samples, showing how SARS-CoV-2, the virus that causes the disease, was developing faster than expected. Among other things, this genomic observation allowed researchers to discover the first omicron variants and correctly predict that they will cause a huge wave of diseases around the world.

“For the first time in human history, large-scale genomics has provided governments and politicians with a warning of what will happen during an epidemic, and I think this is a really important and profound change,” says Harrison. “That’s what we think is really important for further development.”

Many other viruses such as RSV, can also cause serious respiratory infections, he says, but our understanding of them is extremely limited. “Apart from a bit of genome sequencing in influenza cases, there really isn’t any routine genomic surveillance for these other viruses,” says Harrison.

Currently, the tests commonly used to identify viruses that cause severe infections only show what type they are, such as rhinovirus or adenovirus. Judith Breyervirologist at University College London.

Whole genome sequencing of a virus provides much more information that can be useful in many ways. First, it can help provide the most effective treatment for people. Some treatments with antibodies against covid-19 may be less effective against newer variantsfor example, so that doctors can immediately prescribe an alternative treatment if they know someone has one of those options.

It could also lead to better vaccines. Since SARS-CoV-2 sequencing has shown that omicron variants have spread around the world and become dominant, Updated mRNA boosters. include two of these options to make vaccines more effective against them.

Genetic sequencing can also reveal how viruses spread and therefore help contain them. For example, if you only know that two people in intensive care have a rhinovirus infection, you can’t tell if they got it in the hospital or in the community, Breuer says. Sequencing can tell us if they have exactly the same virus, and therefore if infection control measures in the hospital need improvement.

Last but not least, Harrison hopes to catch new diseases at an early stage. The chances of doing so will be much higher if other countries also conduct routine genomic surveillance.

Sequencing any of the dozen or so different types of viruses that might be present in a sample is technically more difficult than just sequencing one, especially when the goal is to do it with a cheap test that can be used anywhere in the world. That’s why Harrison and his team will refine their approach using stored swabs before moving on to testing fresh swabs from critically ill patients, in collaboration with the UK’s Health Security Agency. In the long term, there is hope for increased surveillance apart from those in critical condition and other types of viruses.

For now, the researchers also plan to sequence all of the genetic material present in multiple swab samples. This approach, known as metagenomics, will allow them to identify all kinds of viruses, bacteria and fungi present, allowing them to study the respiratory microbiome.

“The methods and technologies that Yuen and Sanger are developing will be extremely useful,” says Breuer. “This is a surprisingly important initiative.”

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