Mass Depopulated Poultry Farms Remain Non-Operational for ~4 Months After H5N1 Pooled PCR Detections

Current biosecurity protocols prevent separating healthy birds from infected ones, resulting in “stamping out” entire flocks and disrupting the food supply chain.

By Nicolas Hulscher, MPH

Diagnostic testing for H5N1 in poultry relies on pooled-PCR (polymerase chain reaction). APHIS surveillance guidelines suggest to take two pooled samples of up to 11 birds each per poultry house​. In practice, an examiner might swab 11 birds (one swab per bird) and combine those swabs into one tube as a “pool,” and do this twice (total ~22 birds tested) for a flock. Since individual birds aren’t tracked post-test, swabbed chickens are generally returned to their flock unmarked. With this method, it’s impossible to isolate healthy birds from infected ones. Moreover, depending on the cycle threshold (Ct) values used, values may be false positive, leading to unnecessary control measures.

When a pooled PCR test for H5N1 returns positive, the facility undergoes immediate quarantine and “stamping out” of the flock. All birds on the infected premises are depopulated (culled) as quickly as possible (the USDA’s goal is within 24–48 hours of detection)​. This whole-flock culling policy is standard – all poultry on an infected farm are destroyed, even healthy-appearing birds. The farm then remains non-operational for an extended period while cleanup and testing are conducted.

A farm can be out of operation for several months following a mass cull. Cleaning and virus elimination is labor-intensive, and the required waiting period and testing add weeks. For example, during the large 2014–2015 HPAI outbreak, commercial farms took about 111 days on average from the date HPAI was confirmed to the point they were cleared to restock​. That is roughly 3.5 to 4 months of downtime, which can deliver significant blows to the food supply chain.

As I highlighted a few weeks ago, these protocols have not only failed to contain the current outbreak, but resulted in human infections and 45-year-high egg prices:

Mass, healthy animal depopulation is not a sustainable solution given the pervasive nature of the current H5N1 outbreak. Replacement flocks are likely to be reinfected by migratory waterfowl, perpetuating the cycle of transmission and viral adaptation without evolving herd immunity. Given the scale and complexity of the current H5N1 outbreak, a more strategic and sustainable approach is needed:

Nicolas Hulscher, MPH

Epidemiologist and Foundation Administrator, McCullough Foundation

www.mcculloughfnd.org

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