Health officials in the UK have drawn up plans for a “genomics transformation” that aims to detect and deal with outbreaks of infectious diseases faster and more effectively in the light of the Covid pandemic.
Information gleaned from the genetics of Covid proved crucial as the virus swept around the globe, revealing how the pathogen spread, evolved, and responded to a succession of vaccines and medicines developed to protect people.
The UK Health Security Agency (UKHSA) now aims to build on the lessons of the pandemic by embedding genomics into routine public health practice. The move intends to bolster surveillance for outbreaks, drive down cases of infections such as TB, measles, hepatitis C and HIV/Aids, and predict the course of future threats, such as avian flu and diseases borne by mosquitoes and ticks as they gain ground in a warming climate.
“We changed our thinking about genomics during Covid,” said Dr Meera Chand, director of clinical and emerging infections at the UKHSA. “It’s not that we need to generate huge numbers of genomes all the time, it’s that we can use the data to change what we’re doing. Genomics gives you information you can act on, it’s not just a research tool.”
The boost for genomics is central to the UKHSA’s 10-year science strategy released on Tuesday. Among the plans, which cover infections, radiation protection, the health impact of the climate crisis, and vaccine development, is a commitment to the “100 Days Mission”, which aims to have diagnostic tests, drugs and vaccines ready to deploy within 100 days of a new pandemic threat emerging.
One way of detecting outbreaks early is to monitor the genomes of viruses and bacteria circulating in the population. Any sharp shift in the normal pattern of a pathogen can indicate that a particular strain is surging, perhaps because it has evolved to evade frontline drugs.
The same approach can highlight when apparently sporadic infections belong to a cluster. Rather than waiting for a pattern of sick patients to emerge from GP or hospital records, genomic analyses of bugs, for example listeria and salmonella, can identify cases driven by the same source. Last year, UK health officials triggered a global recall of Kinder Surprise eggs after genomics revealed a cluster of antibiotic-resistant Salmonella infections linked to a chocolate factory in Belgium. “We’ll always need shoe-leather epidemiology, there’s no escape from that, but genomics can support it to make it fast, highly accurate and make us respond quicker and more definitively,” said Chand.
Another strategy could turn hospital intensive care units into an early warning system for dangerous outbreaks. Instead of testing patients only for common infections, such as influenza, scientists could use genomics to identify all of the pathogens in a patient’s lung swab. While the data can be hard to interpret – many bugs will not be important – the approach can spot new and emerging infections that would otherwise be missed. A similar “pathogen agnostic” genomics strategy helped uncover how different viruses combined to fuel an increase in cases of life-threatening hepatitis in vulnerable children last year.
Chand said that not knowing what the next infection would be presented a challenge. “In all likelihood, it’ll be a pathogen we didn’t expect, or possibly that we’ve never seen, and we need to have this kind of approach in play to support us.”
According to the UKHSA strategy, humans have been hit by more than 330 new and emerging infectious diseases since the 1940s, nearly two-thirds of which appear to have spread from animals. The likelihood of more coming after Covid, Sars, Mers and mpox is increasing, the report adds, given the greater contact between humans and animals and the ease of spread as a result of global trade and travel.
Here again, health officials hope to bring genomics to bear. The devastating outbreak of avian flu has killed tens of thousands of wild birds in the UK and the virus has been detected in mammals such as foxes. Through genomics, scientists can monitor how the virus evolves. “That’s a very active area for us,” said Chand. “We take international data every week and try and understand what we are seeing in the data and what the implications might be.”
