Establishing methods to monitor H5N1 influenza virus in dairy cattle milk

  1. Elyse Stachler
  2. Andreas Gnirke
  3. Kyle McMahon
  4. Michael Gomez
  5. Liam Stenson
  6. Charelisse Guevara-Reyes
  7. Hannah Knoll
  8. Toni Hill
  9. Sellers Hill
  10. Katelyn S. Messer
  11. Jon Arizti-Sanz
  12. Fatinah Albeez
  13. Elizabeth Curtis
  14. Pedram Samani
  15. Natalia Wewior
  16. David H. O’Connor
  17. William Vuyk
  18. Sophia Khoury
  19. Matthew K. Schnizlein
  20. Nicole C. Rockey
  21. Zachariah Broemmel
  22. Michael Mina
  23. Lawrence C. Madoff
  24. Shirlee Wohl
  25. Lorraine O’Connor
  26. Catherine M. Brown
  27. Al Ozonoff
  28. Daniel J. Park
  29. Bronwyn L. MacInnis
  30. Pardis C. Sabeti

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Abstract

Highly Pathogenic Avian Influenza strain H5N1 has caused a multi-state outbreak among US dairy cattle, spreading across 15 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk from 20 states for methods development, we found that H5N1 concentrations by digital PCR strongly correlated with qPCR cycle threshold (Ct) values, with dPCR exhibiting greater sensitivity. We also found that metagenomic sequencing after hybrid selection was best for higher concentration samples while amplicon sequencing performs best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to test bulk milk samples monthly from all cattle dairy farms within Massachusetts, which remain negative to date. The methods, workflow, and recommendations described here provide a framework for others aiming to conduct H5N1 surveillance efforts.

Article activity feed

  1. Rapid Reviews Infectious Diseases

    Connor Bamford

    Review 2: "Establishing Methods to Monitor H5N1 Influenza Virus in Dairy Cattle Milk"

    While recommending minor clarifications and exploring cost implications, the reviewers emphasize the significance of this research in shaping policies for routine H5N1 monitoring in dairy herds and advancing non-clinical diagnostic approaches for infectious diseases.

  2. Rapid Reviews Infectious Diseases

    Timm Harder

    Review 1: "Establishing Methods to Monitor H5N1 Influenza Virus in Dairy Cattle Milk"

    While recommending minor clarifications and exploring cost implications, the reviewers emphasize the significance of this research in shaping policies for routine H5N1 monitoring in dairy herds and advancing non-clinical diagnostic approaches for infectious diseases.

  4. Version published to 10.1101/2024.12.04.24318491v1 on medRxiv