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There's a lot you can tell from extracting and sequencing the DNA footprint of a barn, but we've always known RNA is a critical part of the picture. Thanks to support from a FFAR grant, we've made steady progress, and RNA detection is ready to be launched this fall. We're excited to start working with our early adopters, and a broader roll-out to come by the end of this year.
Most living things carry their genetic instructions in DNA. Some viruses, however, use RNA (think DNA’s close cousin) instead, including Influenza, Infectious Bronchitis Virus (IBV), Avian Metapneumovirus (aMPV), Newcastle disease and reovirus.
Our DNA sequencing reads the bacteria, fungi, parasites, and DNA viruses in your barn. But to continue the literary metaphors from previous blogs, it's like reading a library where some of the books are printed in a second alphabet. The RNA viruses were on the shelf the whole time; we just couldn't read them. RNA sequencing adds that second alphabet.
The viruses we will be able to watch for
These are the RNA viruses our customers ask about most, and why each one matters.
- Avian influenza (HPAI): Can wipe out a flock within days and triggers depopulation. Earlier warning means earlier action.
- Avian metapneumovirus (aMPV): Subtype A and B arrived in the US around 2023–2024. Both cause respiratory disease and decreased egg production, and many flocks have little immunity to either one.
- Infectious bronchitis virus (IBV): The most common respiratory disease in broilers. Variant strains, like DMV/1639, slip past vaccines that don't match them. Additionally, pullets infected with IBV in early life may develop false layer syndrome.
- Avian reovirus: Variant strains cause lameness and tendon damage. The virus is hardy and hard to clear from a barn.
- Retroviruses (ALV-J, REV): Avian leukosis and reticuloendotheliosis cause tumors and weaken the immune system, often with few early signs.
- Duck-associated viruses: Duck hepatitis virus, duck astroviruses, west nile virus, and duck reoviruses hit commercial ducks. Wild ducks also carry avian influenza without getting sick.
- PRRS: Obviously not a poultry pathogen, but one of the most costly diseases in US swine production, causing reproductive failure in sows and respiratory disease in piglets. We started swine pilots this summer - stay tuned for more here!
Why RNA is the closest proxy to an active infection
Our DNA results are best read as trends. RNA virus results are closer to a snapshot of what's happening in the flock right now.
Not all bacteria need a bird. Many bacterial pathogens can survive in litter, dust and on barn surfaces, and some can even grow there. Their DNA also lingers after they die. On top of that, birds can carry bacteria for diseases, such as spotty liver disease (Campylobacter hepaticus) or Mycoplasma gallisepticum, without showing signs of illness. That’s why we can detect them in barns with no sick birds, and why one DNA detection may not mean an active outbreak. What typically matters is if the amount is increasing, which may indicate an active outbreak or increase risk of a secondary infection if a primary insult occurs.
Viruses do. Viruses can only replicate inside a living host. They can't multiply in litter or on surfaces, and their RNA generally doesn’t persist as long as bacterial DNA once it's shed. So when we find an RNA virus, it most likely came from birds that were infected and shedding relatively recently. That makes it the closest environmental signal we have to an active infection.
A couple of considerations. As with DNA, our results show what's in the barn, not a diagnosis of individual birds, so results are best read with context and veterinarian support. And because many flocks get live vaccines for IBV, aMPV, Newcastle disease and reovirus, a detection may reflect vaccine virus. We can't (yet!) tell vaccine strains from field strains.
Looking ahead
Longer term, RNA also opens the door to new insights. Messenger RNA (mRNA), for example, shows which genes microbes are actively switching on, which could tell us not just who is in the barn but what they're doing. This could be useful for spotting when a pathogen switches on disease-causing genes, confirming whether harmful bacteria are active after a cleanout, or providing evidence that probiotic species are enhancing gut nutrition.
Get in touch
RNA detection will work on the same boot sock samples you already collect, so there's no change to your routine on the farm. If you’re interested in RNA surveillance when it’s ready to launch, please reach out at hello@barnwellbio.com to get in touch!
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