#Influenza A Virus detection in Bulk Tank and Pen Level #Milk from #Dairies Affected by Highly Pathogenic Avian Influenza #H5N1

 

Abstract

Highly pathogenic avian influenza virus H5N1 has been infecting dairy herds in the U.S. since its initial incursion into cows in early 2024. Although national strategies have aimed to detect affected herds, the best way to surveil herds for the H5N1 virus has not been formally studied and we also do not understand herd-level patterns of infection. To understand infection patterns of H5N1 in dairy herds over time, we conducted early surveillance of non-affected farms in California in the Fall of 2024 in an observational study. Daily bulk tank milk (BTM) samples were submitted from each herd and tested for influenza A (IAV) via rRt-PCR. In a subset of herds, IAV testing of multiple excretion types from cattle of different classes and pen-level daily milk was also completed soon after BTM detection. Daily detections of IAV occurred in BTM for a minimum of 33 days, with some herds continuing to have detection beyond a 75-day window. BTM Ct nadirs were seen between 1-3 weeks of detection. In herds that were tested, virus was detected in the milk from all pens of cattle within a very short time frame after BTM detection, or prior to the initiation of pen level sampling. A very low percentage (2.8%) of individual cow samples tested positive for IAV when collected soon after BTM detection, and although the virus was found in all excretion types, a majority of positive samples were from milk. This suggests that BTM may be the best early indicator of herd infection, and that movement of the virus to all lactating pens of cattle after herd incursion is relatively quick. These results also suggest that surveillance strategies with a long interval between BTM testing days may miss herds with short infection windows. Because most herds experienced test days where some submitted BTM samples had virus detected while others did not, and virus was detected in pen level milk samples when the BTM from the herd had become test negative, this work also highlights the necessity of studying the test sensitivity of IAV rRt-PCR detection in aggregate milk samples.

Competing Interest Statement

The authors have declared no competing interest.

Funding Statement

This project was completed using Federal funds provided through the United States Department of Agriculture, Cooperative Agreement 25-9419-0731 and the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. 75N93021C00016.

Source: MedRxIV, https://www.medrxiv.org/content/10.1101/2025.10.26.25338833v1

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