Leveraging CleanPlex Technology for H5N1 Virus Surveillance and Research

Leveraging CleanPlex Technology for H5N1 Virus Surveillance and Research

H5N1, commonly known as bird flu, is a highly pathogenic avian influenza (HPAI) virus that primarily affects birds. However, it has shown the potential to infect mammals, including humans. The virus was first detected in geese in Asia in 1996 and has since led to multiple outbreaks worldwide.¹ While human infections remain rare, the mortality rate for those infected is high, raising concerns about its potential to evolve into a more transmissible strain.

What are the Symptoms in Cows?

Unlike poultry, where H5N1 causes severe illness and high mortality, infected cattle have exhibited milder symptoms, making the detection of the virus more challenging.⁶ Reported symptoms in cows include:

• Reduced milk production
• Thickened milk or discolored milk
• Fever
• Lethargy
• Nasal discharge

Because symptoms in cattle can be subtle, undetected infections in cattle could facilitate further viral evolution and potential spillover events to humans or other species.

1. https://www.sciencedirect.com/science/article/abs/pii/S0168170213001743?via%3Dihub
2. https://www.cdc.gov/bird-flu/situation-summary/data-map-wild-birds.html
3. https://www.cdc.gov/bird-flu/situation-summary/data-map-commercial.html
4. https://www.aphis.usda.gov/livestock-poultry-disease/avian/avian-influenza/hpai-livestock
5. https://www.cdc.gov/bird-flu/situation-summary/index.html
6. https://www.cdc.gov/bird-flu/prevention/farm-workers.html#:~:text=Cows%20typically%20experience%20mild%20illness,sporadic%20cases%20of%20human%20infection

How is H5N1 Being Spread?

The spread of highly pathogenic avian influenza H5N1 has raised concerns due to its ability to jump between species. While the virus primarily affects birds, recent detections in dairy cattle highlight new transmission risks that could have broader implications for agriculture and public health.

Transmission Among Birds

H5N1 has been circulating in wild birds for years, with waterfowl acting as natural reservoirs. The virus spreads through:

• Direct contact with infected birds
• Contaminated water sources (virus is shed in bird droppings)
• Aerosol transmission in dense poultry farms
• Fomites (contaminated feed, equipment, or clothing)

In poultry farms, once introduced, the virus spreads rapidly, leading to high mortality rates and forcing culling measures to prevent further outbreaks.

How H5N1 Reached Dairy Cattle

As mentioned, the detection of H5N1 in U.S. dairy cows is a significant shift in the virus’s host range. While investigations are still ongoing, several potential transmission routes have been identified:

• Contaminated feed or water: Wild birds carrying the virus could have introduced it to dairy farms.
• Contact with infected birds: Livestock facilities near infected bird populations could be at higher risk.
• Fomites: Farm equipment, workers’ clothing, or vehicle movement between farms could have spread the virus.
• Milk from infected cows: Although pasteurization kills the virus, unpasteurized milk has tested positive for H5N1, raising concerns about viral shedding.

Potential for Cross-Species Transmission

The expansion of H5N1 to mammals increases concerns about viral adaptation. If the virus mutates in a way that allows more efficient human-to-human transmission, it could pose a pandemic risk.

• Close monitoring of cattle-to-cattle and cattle-to-human transmission is necessary to assess public health risks.
• Rapid detection and containment efforts can help slow the spread and prevent further cross-species transmission.
• Next-Generation Sequencing is important for tracking viral mutations and further understanding how the virus is adapting.

What Testing is Being Done for H5N1 and Why It Matters

Testing for H5N1 is an important component of disease control efforts, particularly as the virus has now spread to U.S. dairy cattle. The USDA, in collaboration with Federal, State, and industry partners, is implementing comprehensive testing strategies to contain the outbreak and prevent further transmission.⁷

The USDA’s Animal and Plant Health Inspection Service (APHIS) oversees all H5 livestock testing through the National Animal Health Laboratory Network (NAHLN) and National Veterinary Services Laboratories (NVSL). Testing is provided free of charge, with samples collected through various programs, including:

• Milk testing under the December 2024 Federal Order and the National Milk Testing Strategy
• Testing prior to interstate movement as required by the April 2024 Federal Order
• Dairy Herd Status Program monitoring
• State-designed testing programs tailored to local regulations
• Testing before livestock participate in fairs, exhibitions, or sales as part of State-led surveillance programs

These measures help with early detection, allowing authorities to track the virus’s spread, identify potential risks, and minimize economic and public health impacts.

Advancing H5N1 Surveillance with CleanPlex Technology

As H5N1 continues to evolve and spread, robust genomic surveillance is extremely important to understanding its transmission dynamics and preventing further outbreaks. CleanPlex NGS Sequencing Panels empower researchers with a rapid, scalable, and cost-effective tool to analyze viral genomes, track emerging variants, and support public health efforts.

By leveraging CleanPlex technology, scientists can stay ahead of viral evolution and enhance global preparedness against H5N1 and other infectious diseases. By providing high-resolution genetic data, NGS allows researchers to:

• Detect and track viral mutations in real-time
• Analyze viral evolution and identify genetic markers of increased transmissibility
• Conduct surveillance of wildlife, livestock, and human cases to monitor potential outbreaks
• Develop targeted interventions to slow the spread of H5N1

Given the rapid spread and cross-species transmission of H5N1, high-throughput sequencing solutions are important for staying ahead of viral evolution and mitigating public health risks.

7. https://www.aphis.usda.gov/livestock-poultry-disease/avian/avian-influenza/hpai-livestock

Why Choose CleanPlex NGS Sequencing Panels for H5N1 Research?

Paragon Genomics’ CleanPlex Technology offers an ultra-high-performance PCR amplicon-based targeted sequencing approach, ideal for researchers monitoring and analyzing H5N1. CleanPlex Custom NGS Panels provide:

• Fast Turnaround Time: Receive your custom NGS panels in less than four weeks from design acceptance to shipment, allowing you to quickly adapt to emerging viral mutations.
• Cost-Effective Sequencing: Achieve high on-target performance and uniform coverage, minimizing sequencing costs while maximizing data quality.
• Ultra-High Multiplexing: Sequence up to 20,000+ amplicons per pool, enabling comprehensive viral genome analysis with a simplified workflow.
• Scalability and Flexibility: Easily update your custom NGS panels as new variants and genetic markers emerge.
• High Performance: CleanPlex panels are designed with high first-pass success rates and optimized target design to ensure accuracy and efficiency.
• Expert Support: Our team of PhD-level scientists provides full support throughout the design and ordering process, providing a seamless implementation in your research.

By integrating CleanPlex NGS technology into H5N1 research, scientists can enhance disease monitoring, improve outbreak response, and support long-term mitigation efforts against emerging influenza threats.