At the height of the Covid pandemic, UK labs were sequencing thousands of SARS-CoV-2 genomes daily to track circulating variants, and identify any new ones that emerged.
Now researchers at the Sanger Institute are launching a project that could eventually achieve something similar for the many other respiratory viruses that make us sick – and fill UK hospital beds – every year.
The Respiratory Viruses and Microbiome Initiative will lay the foundation for large-scale genetic surveillance of multiple respiratory viruses, including influenza, RSV, adenovirus, and rhinoviruses, as well as monitoring of emerging threats.
“It comes from the simple idea that what we did for Covid, we should now do for all respiratory viruses, because if we can build a better understanding of these viruses, we can be in a better place to understand their transmission and how to develop vaccines against them,” said Dr Ewan. Harrison of the Wellcome Sanger Institute, who is leading the initiative.
His team is developing genome-sequencing methods that could enable a single respiratory sample to be taken from any NHS patient, and to quickly identify which virus or viruses are present – something Harrison believes could be possible, at least in a limited capacity, by the fall. .
“This is hugely important, massive and a much-needed step change in how we monitor or test for infections,” said Dr Catherine Hyams of the University of Bristol, who is studying how the Covid-19 pandemic has affected the spread of respiratory viruses.
Current surveillance programs in the UK track some viruses, such as influenza and Covid, by testing a representative sample of patients with respiratory infections using virus-specific PCR (polymerase chain reaction) tests. But PCR tests work by checking the known sequence of DNA from specific viruses. If you are not looking for this virus – or it has altered DNA sequence – it will not be detected.
Patients may also be tested for specific viruses if their symptoms are severe enough to warrant hospitalization, to help direct their care. However, there is currently no single test that can detect all respiratory viruses, and patients can develop more than one infection at a time, which means other infections may be missed.
So-called “metagenomic sequencing” gets around this problem by reading the sequences of all genes in a sample, with no assumptions about what to expect. These sequences are then compared to genetic databases to identify the organisms present.
It allows you to detect known viruses, but possibly also new viruses or viruses that have mutated and are therefore no longer picked up by [standard PCR tests]Dr Antonia Hu, Consultant Infectious Diseases and Senior Clinical Lecturer at the University of Glasgow’s Center for Virology Research, said MRC.
Sanger’s team will work closely with partners at the UK’s Health and Security Agency and other public health bodies to translate this real-time data into strategies that can help keep people healthy and reduce pressure on NHS beds.
Knowing what bugs or errors are causing someone’s illness can help guide their individual treatment, but even the greatest benefits of this data have to come at a population level.
For one thing, it can ensure that existing vaccines are as protective as possible. “The public health impact of this should not be underestimated and has been clearly demonstrated by the Covid-19 vaccine programme. This approach can also be used to monitor the effectiveness of vaccine programs and, if combined with data on disease severity, will be particularly powerful,” Hyams said. .
Monitoring new strains that could escape existing treatments or vaccines should also enable scientists to develop new strategies to contain their spread, including better tests, modified treatments and vaccines.
Researchers will also study the data to better understand the transmission and evolution of respiratory viruses, as well as seek to identify novel viruses and potential pandemic threats. Doing so will lead to a better understanding of how these viruses interact with each other, and could serve as an early warning system for new viruses.
“Understanding which particular strains of each virus cause disease in patients, and whether multiple strains or viruses are present simultaneously, will dramatically change our understanding of how viruses lead to disease, which viruses tend to coexist, and which viruses tend to co-exist,” Hyams said. The severity of the disease caused by each virus. This will allow us to understand the mechanisms by which different viruses cause disease as well as identify patient groups that may be at risk of severe disease due to a particular infection.”
The ultimate goal is to identify all genes and all species — including viral, bacterial and fungal species — found in a single nasal swab sample. Doing so could shed new light on the microbial ecosystem in the lungs, and how it affects someone’s risk of infection.
Ho said: “We know that chest infections are often not caused by a single virus or bacteria, and often it is some kind of ecosystem that can be disturbed by infection, antibiotics, or a change in temperature. There is also a growing understanding that viruses may They interact with each other, so if there is a high spread of one virus, it may prevent you from catching another virus – or it may make you more susceptible to infection.
“The opportunity to understand this ecosystem, and how viruses and bacteria interact with each other, is very exciting.”
If the initiative is successful, it could become a blueprint for boosting virus tracing in other countries – essential for preventing future pandemics.
Professor Gordon Duggan, Director of Infectious Diseases at Wellcome, said: “Genomic sequencing offers a fantastic opportunity to track viruses globally. It can give researchers and policymakers a finger on the pulse of where and how they are trading. This is vital information for setting up healthcare and research systems.”