$950 per sick cow. $737,500 per herd. The audit that protects you from those numbers? Most farms aren’t ready.

Executive Summary: H5N1 has swept through more than 700 dairy herds across 16 states since March 2024—and it’s quietly determining which operations keep access to export markets worth $2.32 billion annually. Cornell University researchers documented the toll: $950 per clinically affected cow, with one Ohio herd losing $737,500 in a single outbreak. Biosecurity audits are emerging as the new gatekeepers. Pass with proper documentation, and you’re positioned for export-oriented milk flows and federal assistance. Fall short, and your operation risks being confined to domestic commodity channels. What’s encouraging: most early audit failures stemmed from paperwork gaps, not actual biosecurity problems—a 90-day preparation approach can put most farms ahead of the requirements. The operations moving now aren’t overreacting; they’re running the numbers.

If you’ve spent any time at industry meetings this fall, you’ve probably heard the conversations shifting. Producers are talking about biosecurity audits differently than they were six months ago. Some still view them as bureaucratic overhead—and given everything else competing for attention, that’s an understandable reaction. But something interesting is happening among operations that have lived through H5N1 outbreaks or watched neighbors go through them. They’re starting to see these audits less as paperwork and more as a stress test for whether their business model can handle what’s coming.

That shift matters. These audits are quietly becoming gatekeepers for federal support, signals to processors about supply-chain reliability, and—whether we anticipated it or not—a dividing line between herds positioned for export markets and those that aren’t.

Understanding The Disease Picture

Let’s ground this in what we actually know, because the science has moved pretty quickly.

When USDA confirmed on March 24, 2024, that H5N1 had jumped from birds into lactating dairy cows—first appearing in Texas and Kansas—most of us expected a contained situation. That’s not what happened. By November 2024, federal trackers showed more than 440 confirmed cases across 16 states, rising to more than 700 by year’s end, according to USDA APHIS case summaries. California, Colorado, Michigan, and Idaho—major dairy regions—got hit. In California alone, somewhere between 70-75% of the state’s dairies were affected after August 2024, according to DairyReporter. (For a deeper dive into how this outbreak evolved, see our coverage in “H5N1 Crisis One Year Later: What Dairy Farmers Need to Know.”)

But here’s what really changes the planning conversation: we’re now dealing with multiple H5N1 genotypes in cattle. In early 2025, USDA’s National Veterinary Services Laboratories documented a second genotype—D1.1—genetically distinct from the B3.13 strain that drove the initial wave, as reported by WeCAHN. D1.1 had already become predominant in many wild-bird flyways and has been linked to severe human cases, including at least one fatal infection, according to CDC situation summaries.

What does this mean practically? Repeated spillovers from wild birds are likely to continue. Cow-to-cow transmission works efficiently in certain housing systems—particularly large freestalls and dry lots with frequent animal movement. This has shifted from a temporary outbreak to an endemic-risk backdrop for the industry. And while researchers are investigating vaccine candidates, no approved H5N1 vaccine for dairy cattle currently exists, leaving biosecurity as the primary management tool.

Dr. Keith Poulsen, DVM, PhD, DACVIM, who directs the Wisconsin Veterinary Diagnostic Laboratory, captured the stakes in comments to Brownfield Ag News: “A national effort to eliminate the B313 variation of the H5N1 virus is important for cow and human health, and to prevent disrupting dairy export markets, which account for 40% of U.S. production.”

That 40% figure is worth sitting with for a moment.

What The Research Tells Us About Herd-Level Impact

We’re fortunate to have solid economic data now. A study published in Nature Communications in July 2025 by Cornell University researchers followed a 3,876-cow Holstein herd in Ohio through an H5N1 outbreak. The findings got my attention—and we covered them extensively in “Bird Flu Bombshell: Dairy Cows Losing a Full Ton of Milk.”

Here’s what they documented:

About one in five cows showed clear clinical signs—sharp milk drop, fever, reduced feed intake. Those clinically affected cows produced roughly 900 kilograms less milk than expected over approximately 60-67 days. When the Cornell team tallied milk losses, elevated culling, and increased mortality, they arrived at an economic loss of about $950 per clinically affected cow. Total losses for that single herd came to around $737,500.

Field observations from affected Central Valley herds suggest these findings track with what producers and veterinarians are seeing: the effects linger longer than expected. Fresh cow performance, butterfat levels, rebreeding rates—these stay suppressed for weeks after cows appear to recover. It’s not a quick bounce-back.

What’s also noteworthy is that serology showed high exposure across the entire Ohio herd, despite only 20% of the herd displaying clinical signs. The Cornell team found that 89% of sampled cows had been exposed, but about three-quarters of those never showed symptoms—they just kept milking at normal levels despite carrying the virus. That’s how quietly this thing can move through a freestall or dry-lot operation while still impacting your shipped solids.

How These Audits Actually Work

Let’s be honest: nobody wants another clipboard in the barn. Most of us got into dairy because we like working with cows, not wrestling with paperwork. But here’s the reality—these audits aren’t going away, and understanding them now beats scrambling later.

The USDA APHIS HPAI Biosecurity Audit Tool is publicly available at aphis.usda.gov. Originally designed for poultry, it’s been adapted for dairy through state programs and “Secure Our Herds” guidance. Penn State Extension and University of Minnesota Extension have both published dairy-specific biosecurity planning guides worth reviewing. (Our “Battle Plan: How to Protect Your Dairy Herd from HPAI” breaks down the practical steps in detail.)

Auditors evaluate three main areas:

First, your written biosecurity plan. They want something farm-specific, not a generic template. That means a premises map showing your Lines of Separation, entry points, housing areas, manure routes, and Personal Biosecurity Areas. Plus written procedures for cleaning, disinfection, visitor control, and response protocols.

Second, personnel understanding. Auditors talk to your people—milkers, calf feeders, hospital-pen crew—and ask them to explain basic concepts. Where’s the LOS? When do you change boots? What would you do if you noticed unusual symptoms? Training logs help, but the conversations matter.

Third, visual verification. They walk through the operation and compare what they see to what’s documented. Are footbaths where the map says? Are they properly maintained? Do traffic patterns match what’s written?

California’s experience with their Biosecurity Compliance Audit Program has been instructive. CDFA reported that most initial shortfalls involve documentation and staff understanding, not an absence of biosecurity practices. Many farms had decent practices but failed early audits because their written plans were too generic, their premises maps missed key features, or their training records were inconsistent.

We don’t have national pass/fail statistics yet. But the pattern from early-adopting states is clear: demonstrating what you do matters as much as doing it.

Running The Numbers

This is where the conversation gets practical. Here’s how the economics stack up at different scales:

Factor	200-Cow Tie-Stall (Northeast)	500-Cow Freestall (Upper Midwest)	3,000-Cow Dry-Lot (Southwest)
Monthly Milk Revenue	~$88,000	~$265,000	~$1.6 million
60-Day Revenue at Risk	~$176,000	~$530,000	~$3.2 million
Estimated Outbreak Cost (20% clinical rate @ $950/cow)	~$38,000	~$95,000	~$570,000
Typical Compliance Investment	$10,000–$25,000	$25,000–$45,000	$75,000–$150,000
Annual Consumables/Staff Time	$5,000–$10,000	$10,000–$20,000	$25,000–$40,000
Quarantine Period	30–60 days	30–60 days	30–60 days

Calculations based on $22/cwt milk price, 80 lbs/cow/day production, Cornell University research benchmarks, and extension cost estimates. Actual figures vary by region and existing infrastructure.

A few things jump out from this table. First, the compliance investment looks much more reasonable when compared to potential outbreak exposure—we’re talking tens of thousands versus hundreds of thousands (or millions at larger scales). Second, that quarantine period hits everyone the same way, regardless of size. Minnesota’s guidance describes 30-day quarantines from the last positive test, often extending to 60 days for multiple negative bulk-tank samples.

The decision point becomes clearer when you lay it out this way.

Understanding Federal Assistance

So here’s the question that always comes up: doesn’t USDA assistance offset this risk? It helps meaningfully, but doesn’t eliminate the exposure.

The ELAP program was expanded in June 2024 for H5N1 milk losses. Per the FSA fact sheet, payments assume a 21-day period of no production when a cow is removed, followed by seven days at 50% production.

The benefit covers about 90% of calculated milk loss—Secretary Vilsack announced this in June 2024, as reported by Brownfield Ag News.

Four practical considerations:

First, ELAP addresses milk loss only—not culling costs, lost pregnancies, or suppressed components over subsequent months.

Second, payments arrive after the fact, sometimes months later. DairyReporter noted that 43% of payments went to dairies that were reimbursed multiple times over a six-month window.

Third, access depends on good records. Incomplete documentation makes navigating these programs considerably harder.

Fourth, most standard livestock mortality and business interruption policies weren’t written with HPAI in mind. Coverage varies—worth discussing with your agent before you need to find out.

What Market Signals Are Telling Us

The regulatory dimension is only part of the picture.

Mexico provides the clearest illustration. In 2023, Mexico imported roughly $2.32 billion in U.S. dairy products—about one-quarter of total exports —and that share grew to 29% by September 2024, according to USDA-FAS data cited by Dairy Global. Mexico relies on U.S. suppliers for over 80% of its imported dairy. (We explored the strategic importance of this relationship in “How USMCA Boosted U.S. Dairy Exports to Mexico by 59%” and more recently in “Your Biggest Dairy Customer is About to Ditch You.”)

CoBank’s December 2024 analysis called Mexico “America’s most reliable dairy customer.” Japan, South Korea, and Southeast Asian markets are also watching how we manage this.

When detections occur, some countries temporarily restrict imports or require additional attestations. While pasteurization inactivates the virus, international buyers want to see systematic on-farm risk management.

Processors are responding by asking more questions about farm-level HPAI testing during contract discussions and encouraging alignment with enhanced biosecurity programs.

What this points toward is an informal tiered system—operations with documented biosecurity positioned for export-oriented flows, while those with weaker documentation may find themselves confined to domestic commodity channels.

The Hidden Benefits

Beyond market positioning and outbreak prevention, there’s something else worth considering. When farms implement these biosecurity protocols—even reluctantly—they often discover unexpected improvements in day-to-day herd health.

Extension materials and producer experiences suggest considerable overlap between HPAI compliance measures—maintained footbaths, defined traffic patterns, separate calf-barn equipment, consistent hospital-area sanitation—and practices addressing environmental mastitis, digital dermatitis, and calf scours.

Operations maintaining strict separation protocols often report fewer diarrhea and pneumonia treatments in youngstock over time. When farms systematically map who and what crosses between zones, they frequently uncover unexpected pathogen risks—shared tools between hospital pens and fresh-cow groups, rendering routes near commodity storage.

We don’t have controlled studies quantifying the relationship between “audit completion equals X% SCC reduction.” But the overlap between audit-ready practices and proven herd-health management is substantial enough that many producers see two benefits from one investment.

A Practical 90-Day Approach

For operations deciding to move forward, here’s what’s working for progressive herds. (For additional technical guidance, our “HPAI H5N1: The 2025 Science-Based Dairy Farm Survival Guide” provides comprehensive protocols.)

Days 1-30: Establish Your Baseline

Model your outbreak scenario. Use actual shipments and current prices to estimate 30- or 60-day disruption impact. Apply Cornell benchmarks at whatever attack rate seems realistic for your system.

Develop a compliance budget. For a 200-cow tie-stall, expect $10,000-$20,000; for 500-1,000 cows, $25,000-$50,000.

Consult advisors. Vets can reality-check risk assumptions. Lenders can evaluate phasing investments.

Days 31-60: Build Your Framework

Create detailed premises maps. Mark entries, housing, pens, storage, and routes. Add LOS boundaries.

Install control points. Automatic footbaths, boot stations, permanent markers, and clear signage.

Establish simple documentation. Clipboards at stations, low-friction compliance.

Seasonal timing matters. Wisconsin or Minnesota farms often prioritize infrastructure before freeze-up, then focus on documentation through winter. In warmer regions, summer heat might push work to milder months.

Days 61-90: Validate Your Systems

Conduct a mock audit. Download the USDA tool, walk your place as an inspector would.

Address gaps. Make correct behavior the path of least resistance.

Organize records. One binder or folder, readily accessible.

Conversations Worth Having

With your processor: Are formal requirements coming? Will audit-ready status influence relationships?

With your vet: Can you walk our premises before an outside auditor? What’s working for similar operations?

With your lender: Concentrated investment or phasing? How would quarantine affect debt service?

With your insurance agent: Does current coverage address HPAI losses? What documentation would be required?

Different Valid Approaches

Not every operation is approaching this identically—and that’s appropriate. A 220-cow Vermont family operation faces different exposure than a 5,000-cow Texas Panhandle dry-lot. Pacific Northwest operations contend with seasonal bird migration; Southeast herds deal with year-round humidity challenges.

Some view HPAI as a temporary disruption—manage it if it arrives. Others see it as structural evolution—dairy moving toward formalized supply-chain partnerships.

Neither approach is right or wrong. They reflect different assessments and risk tolerances. Operations moving earliest tend to already think in multi-year cycles—plant relationships, replacements, genetics, environmental compliance, and now biosecurity as connected pieces.

The Bottom Line: 

H5N1 has infected more than 700 dairy herds across 16 states, with documented losses of $950 per clinically affected cow according to Cornell research. USDA biosecurity audits are becoming gatekeepers for federal assistance and export market access. A 90-day preparation approach can position operations ahead of coming requirements.

KEY TAKEAWAYS:

• H5N1 isn’t going away: 700+ herds infected across 16 states, two genotypes now circulating, no vaccine in sight—this is the new baseline for dairy risk planning
• The economic toll is documented: Cornell research: $950 per clinically affected cow, $737,500 lost in one Ohio herd. Peer-reviewed numbers you can use for your own math
• Audits now decide market access: Documented biosecurity positions you for export channels worth $2.32B annually. Missing paperwork risks confining your milk to domestic commodity pricing
• Most farms fail on paperwork, not practices: Early audit shortfalls were documentation gaps and training records—you’re likely closer to compliant than you realize
• A 90-day approach works at any scale: Three phases—baseline, build, validate—with realistic costs from $10K for a 200-cow tie-stall to $150K for a 3,000-cow dry lot

Complete references and supporting documentation are available upon request by contacting the editorial team at editor@thebullvine.com.

Learn More:

• The Biosecurity Changes That Stuck: What Dairy Producers Say Actually Works (And Pays) – Discover why neighbors and simple habits—not expensive gates—are the most effective biosecurity tools. This guide reveals low-cost, high-compliance protocols that staff actually follow, ensuring your farm passes the “personnel understanding” portion of USDA audits.
• Record Dairy Exports Hide a Brutal Truth: You’re Selling at a Loss – While audits secure market access, this analysis challenges whether those markets are profitable. It exposes the dangerous spread between export volumes and production costs, helping you evaluate if your compliance investment unlocks high-margin opportunities or just moves milk at a loss.
• Digital Dairy Detective: How AI-Powered Health Monitoring is Preventing $2,000 Losses Per Cow – Move beyond manual visual checks. This article demonstrates how automated health monitoring systems provide the verifiable, data-driven “visual verification” auditors demand, while simultaneously catching costly health events days before clinical signs appear.

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