Viral Genetic Surveillance, the canary in the coal mine for emerging diseases – a look at avian flu

With the current pandemic of bird flu – avian influenza – there is a growing concern around diseases spilling over from animals to humans. The COVID-19 pandemic highlighted the devastating impact such spillover events can have, and bird flu, with its ability to infect multiple species, could pose a similar threat. Since it first emerged in late 2020, this particular type of bird flu has infected a wide array of bird species, about 20 mammal species and some humans. 

The current bird flu outbreak has had a devastating impact on both domestic and wild birds and has been detected in over 100 wild bird species worldwide. In domestic poultry, millions of birds have been culled to control the spread, leading to significant economic losses for the poultry industry. With birds confined to living indoors in attempts to limit the spread of the virus, poultry welfare is also suffering. Wild birds are being severely affected, with many species experiencing high mortality rates. Limiting the spread in wild birds is almost impossible, so the spread of the virus will continue and the risk of spillover in humans will continue.  

The potential for bird flu viruses to cause widespread illness and death makes them a public health concern. Whilst the risk to humans in close contact with birds is currently low, and the risk of human-to-human transmission rare, this could change. Genetics is revolutionising how we monitor and understand the spread of viruses and could provide a much needed early-warning system on how they are changing including whether it is evolving to be more likely to infect people. The virus’s global reach has disrupted ecosystems and biodiversity, highlighting the urgent need for effective surveillance and control measures to protect both animal and human health.

Bird to human transmission

Human infections typically occur through direct or close contact with infected birds or contaminated environments. Whilst currently a low risk to humans, this could change as the virus changes and adapts to new species. Activities such as handling infected poultry, cleaning bird cages, or visiting live bird markets increase the risk of transmission. Mild symptoms may include eye infections, upper respiratory symptoms, and mild flu-like symptoms. However, severe cases can lead to pneumonia, acute respiratory distress syndrome, multi-organ failure, and even death. 

In the UK there have been no reported cases of bird flu in humans, whilst in the United States 14 human cases with no deaths have been reported since March 2024, all were after exposure to farm animals. Since January 2024, 93 laboratory confirmed cases of H5N6 and H3N8 with 36 deaths have been reported in the WHO Western Pacific region – a region of 27 countries including Japan, New Zealand, Mongolia, China and many of the Pacific Ocean islands. Genetic testing is being used to identify the strains and monitoring the virus for any changes. 

Human-to-human transmission

While human-to-human transmission of bird flu viruses is rare, it is not impossible. There have been instances where the virus has spread between people, usually among close contacts such as family members or healthcare workers. However, these cases have not led to sustained human-to-human transmission. There are indications that human biology is limiting the risk of human-to-human transmission. A human gene – BTN3A3 (butyrophilin subfamily 3 member A3) – which is expressed in human airways was shown in a study to block the replication of avian flu in human cells. However, viruses are constantly changing and can potentially overcome barriers by mutating. If that were to occur there are indications that older populations might be more protected than younger ones because of past exposure to various influenzas. The concern remains that the virus could mutate to become more easily transmissible among humans, potentially leading to a pandemic. Genetic surveillance will provide clues if this is occurring.

Genetic monitoring of pathogens

Genetic analysis plays a crucial role in understanding the evolution and spread of bird flu. Genetic tools have become central in the fight against bird flu, providing valuable insights into the virus’s evolution, aiding in early detection, and guiding surveillance efforts in both birds and humans. This information helps in predicting potential outbreaks by understanding how the virus adapts to different hosts as well as identify any mutations that may increase its transmissibility or virulence. For instance, genetic studies have shown how the H5N1 strain has evolved to infect a wide range of bird species and even some mammals. Surveillance programmes are essential for monitoring bird flu. 

Just as canaries once warned miners of invisible dangers, active surveillance and the use of genomics now acts as our modern-day sentinel, detecting emerging diseases before they can spread widely. The UK Health Security Agency (UKHSA) has implemented an asymptomatic avian influenza surveillance programme to monitor the virus in both birds and humans. This programme includes collecting samples from individuals who are at high risk of exposure, such as poultry workers, to detect the presence of the virus. 

As we continue to face the threat of pandemics and epidemics, such as mpox, chikungunya and dengue, leveraging genetic technology with active surveillance will be key to safeguarding public health. Ongoing surveillance, genetic monitoring, and public health preparedness are essential to monitor these risks and prevent future pandemics.