Positivity as of August 30, 2024

Merge pull request #41 from dholab/proposals

Added recent results

Positivity as of June 25, 2024

This release contains the latest data from David H. O'Connor's laboratory at University of Wisconsin - Madison. This release brings the tally of confirmed dairy product HPAI-positives to 87. The dairy products used to isolate these positives come from 20 U.S. states.

Initial Release - 2024-05-15

First Release

This is the first release in what will be an actively updated repository reporting positive Highly Pathogenic Avian Influenza detections in dairy products. Interested contributors should use the proposals branch to add rows to the DETECTION_RESULTS.tsv dataset.

Before submitting a pull request from the proposals branch to the main branch, please refer to the proposal instructions at proposal_instructions.md in the repository docs/ folder.

Repository Overview

HPAI (high-pathogenic avian influenza) RNA has been detected in consumer dairy products in the United States. Many labs around the country have been using these products to monitor the extent of the ongoing H5N1 outbreak in dairy cattle. Due to the dual threat this outbreak poses to public health and industry, it is imperative that HPAI positivity data for dairy products is shared in both a transparent and responsible manner. The purpose of this repository is to gather and make available dairy product HPAI PCR and sequencing data to coordinate monitoring efforts while also setting a standard for sensitive metadata stewardship.

Sampling Dairy Products for HPAI RNA

Dairy products can be easily obtained from grocery stores and/or other vendors. All dairy products registered on the FDA Interstate Milk Shippers List have an Interstate Milk Shippers (IMS) code that can be used to trace each unit back to the dairy plant where it was processed. IMS codes consist of a two letter state code and a four letter plant code separated by a hyphen. This code, used in tandem with the website whereismymilkfrom.com, can help inform sampling strategy. While IMS codes identify the exact locations of specific dairy processing plants, it is mandatory that only state-level information is shared on this repository (see Metadata Stewardship).

This repository is intended for dairy samples only. Other sample types are outside the scope of this project.

Extracting HPAI RNA from Dairy Products

Milk and Cream

We have published an HPAI RNA extraction protocol tested on milk and cream on protocols.io: protocol

Metadata Stewardship

This repository aims to share information about broad trends in HPAI across the US milk supply, not to investigate individual plants, brands, or farms. Please keep this aim in mind as you name your samples. Any pull requests that include geographic information at a level below state, plant IDs, or brand abbreviations will not be approved.

Geolocation Data

Because the following states have less than three dairy processing plants, to avoid identifying individual plants please replace the following states with “NA” in the “processing_plant_state” column: AK, AR, GA, LA, MS, ND, SC, WV. Again, do not include ANY sample geolocation information below state level in any submission column.

Naming Conventions

In the “sample” column, "carton" column, or any other column, DO NOT include:

• Geolocation information below state level (or state level info from one of the states specifically mentioned under Geolocation Data)
• Any reference to the brand of dairy product tested
• Any reference to the type of dairy product tested (this is to protect dairy producers that may be the only location in their state to process a specific product)
• Any code (such as the IMS code) that can be used to identify a specific brand, product, or location

Data Submission

We invite any labs able to test dairy products for HPAI and willing to abide by our metadata standards to submit their PCR and sequencing data to this repository. Further information on how to submit your data can be found in the proposal_instructions.md.