WASHINGTON — Pandemics aren’t just for humans, as all farmers know too well. Pathogens can wreak havoc on crops, farm and domestic animals, damaging economies and, sometimes, taking a heavy human toll. The potato blight of the 19th century, for instance, destroyed the country’s most important staple crop, resulting in more than 2 million deaths from famine. Rice blast fungus destroys enough rice annually to feed 60 million people.
In recent years, highly pathogenic avian influenza (HPAI) has become a global crisis within the poultry market, requiring the slaughter of hundreds of millions of domestic birds since the virus emerged, disrupting global trade and causing many billions of dollars in losses. According to the USDA, the number of domestic birds affected by the 2022-23 avian flu outbreak is approaching 70 million birds, breaking the record set during the 2015 season of 50 million birds affected and causing up to $4 billion in losses. This makes 2022-23 the worst avian flu season yet for the U.S. poultry industry. These are significant losses. The poultry industry employs 300,000 people across 30 states, generating $45 billion annually, according to Senator Chris Coons, chair of the Senate Chicken Caucus.
And the ramifications of HPAI aren’t limited to agriculture. There are potentially serious implications for human health as well, should the virus mutate to enable the spread easily from person to person.
Testing: The first line of defense
Containing and controlling the spread of agricultural pathogens begins with testing. You can’t stop what you can’t see. The earlier farmers and authorities can detect an infection, the faster they can take action. And while there are tests for most major agricultural pathogens available, they each have disadvantages.
These tests are mostly one of two basic types: lab-based PCR, which stands for polymerase chain reaction, and lateral flow tests (LFTs) commonly known as antigen tests. Let’s take each in turn.
In a PCR test, a sample must be collected and then sent to a lab. There, the sample undergoes DNA amplification, which requires a series of thermal cycles where the genetic material is repeatedly heated and cooled. The process requires a lab environment and a trained technician to perform, and, while the test is extremely precise, it can take days or even more than a week to return results if the lab is over capacity.
In the case of HPAI, the disease acts quickly. As soon as one bird shows symptoms of the disease, the entire flock of thousands can die within days. What’s more, the longer an infection is allowed to rampage through a flock, the longer humans are in contact with infected birds. The H5N1 variant of HPAI does not transmit effectively among people, but there have been 244 documented human cases as of October 2023, and in 56% of these cases, the person died. The more time the disease has to mutate in poultry and the greater the exposure humans have to infected birds, the more likely it becomes that H5N1 will develop the ability to spread among human populations, potentially sparking a pandemic far worse than the one caused by COVID-19.
Antigen tests are an alternative to PCR, a test that can be conducted in the field and provide rapid results. But these tests are less precise than PCR and produce a significant number of false negatives — which means a farmer may think that the flock is safe from infection, when, in fact, a pathogen is silently spreading. To get accurate results with antigen tests, multiple tests must be performed 24 hours apart, which removes antigen tests’ greatest advantage: speed of results. Again, with HPAI, it’s critical to get precise results because the virus quickly causes so much damage.
Tracking and predicting the spread: Surveillance and monitoring
Beyond the tests themselves, it’s critical for authorities to have access to current test data as soon as possible so they can understand and predict a pathogen’s spread to protect additional farms. Data collection for avian influenza is currently a largely manual process. There’s often a significant delay in reporting results, which means authorities are working from data reflecting conditions from days, even weeks ago — that’s plenty of time for many pathogens to have spread much further afield, infecting many other crops and livestock on other farms.
Testing is also important for global trade. For example, France has recently begun vaccinating ducks against HPAI, which, while it protects them against death and severe disease, does not provide sterilizing immunity. This means that poultry can contract the virus and spread it to other birds without showing any symptoms. As a result, the United States has placed a ban on importation of some French poultry, because it’s no longer readily apparent which birds may be infected. Testing with current methods won’t address the issue, because PCR takes too long to turn around a result, and antigen isn’t precise enough.
There is a novel and innovative application of an established technology that could fill this testing gap by providing rapid, accurate results on-site, at affordable pricing, without having to send samples to a lab.
LAMP: An established technology with new promise
Loop-mediated isothermal amplification, better known as LAMP, is a DNA amplification technology like PCR, but unlike PCR it does not require thermal cycling, and instead keeps the sample at a constant temperature. It’s an established technology that has recently come off of patent, which opens up LAMP for additional innovation.
The presence of a pathogen is typically detected in one of two ways. The first is the optical turbidity or fluorescence approach, where a positive result will cloud the liquid, preventing light from passing through it. The other uses electrical detection, in which an electrical field is used to determine the presence of the pathogen. Electrical detection has the advantage of being able to detect a pathogen even in the presence of some turbidity in the sample. It’s possible to apply LAMP technology for in-the-field tests and obtain precise results within a half hour or less
Additionally, there’s no reason test results need to be manually reported in an age where high-speed connectivity is so widespread. The technology is available for a testing device to automatically send accurate molecular testing results specific to the actual strain, to the cloud along with metadata such as geotagging, time and the identity of the test purchaser. With this information, authorities can track fast-moving pathogens in near real-time and, even more importantly, accurately model future spread. Authorities can institute measures to contain the disease and limit the damage it causes.
The world is increasingly a smaller place where climate change and global trade are accelerating the spread of existing and novel pathogens that can have a catastrophic impact on agriculture. The first step to controlling these diseases is to gather accurate, timely information. In this way, farmers can treat the disease and take action to reduce its spread. And authorities can enact effective measures on a larger scale to prevent localized infections from running rampant across entire countries or continents.
Current testing measures are not up to the challenge. Agriculture needs a new testing paradigm to provide accurate yet affordable rapid results in the field with fast, automated reporting.
Shaun Holt is the CEO of Alveo Technologies.
—Shaun Holt, CEO, Alveo Technologies