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Corrected primer asset names in DETECTION_RESULTS.tsv and assets fold… #35

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Corrected primer asset names in DETECTION_RESULTS.tsv and assets fold… #35

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50 changes: 25 additions & 25 deletions DETECTION_RESULTS.tsv
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sample carton date_purchased date_expiration assay average_cycle_threshold isolate_average_copies_per_uL dairyproduct_average_copies_per_mL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed
dholab_30081_01 dholab_carton_0001 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_02 dholab_carton_0002 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_03 dholab_carton_0003 2024-04-24 2024-06-05 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_04 dholab_carton_0004 2024-04-24 2024-05-30 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_05 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 32.435 19 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_06 dholab_carton_0006 2024-04-24 2024-05-19 qPCR 33.055 13 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_07 dholab_carton_0007 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_08 dholab_carton_0008 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_09 dholab_carton_0009 2024-04-24 2024-05-02 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_10 dholab_carton_0010 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_11 dholab_carton_0011 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_12 dholab_carton_0012 2024-04-24 2024-05-02 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_13 dholab_carton_0013 2024-04-24 2024-05-07 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_14 dholab_carton_0014 2024-04-24 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_15 dholab_carton_0015 2024-04-26 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30114_01 dholab_carton_0016 2024-05-02 2024-05-17 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE VA dholab 2024-05-14
dholab_30114_02 dholab_carton_0017 2024-05-02 2024-06-06 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE NY dholab 2024-05-14
dholab_30114_03 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30114_04 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 33.52 10 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14
dholab_30114_06 dholab_carton_0020 2024-05-02 2024-06-27 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE CO dholab 2024-05-14
dholab_30114_07 dholab_carton_0021 2024-05-02 2024-06-04 qPCR 31.17 46 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE TX dholab 2024-05-14
dholab_30114_08 dholab_carton_0022 2024-05-02 2024-05-16 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE UT dholab 2024-05-14
dholab_30114_09 dholab_carton_0023 2024-05-02 2024-05-30 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IN dholab 2024-05-14
dholab_30114_10 dholab_carton_0024 2024-05-02 2024-07-11 qPCR 26.29 1145 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE MI dholab 2024-05-14
dholab_30114_14 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 31.34 40 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-05-14
dholab_30081_01 dholab_carton_0001 2024-04-24 2024-05-08 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_02 dholab_carton_0002 2024-04-24 2024-05-01 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_03 dholab_carton_0003 2024-04-24 2024-06-05 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_04 dholab_carton_0004 2024-04-24 2024-05-30 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14
dholab_30081_05 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 32.435 19 AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_06 dholab_carton_0006 2024-04-24 2024-05-19 qPCR 33.055 13 AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14
dholab_30081_07 dholab_carton_0007 2024-04-24 2024-05-08 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_08 dholab_carton_0008 2024-04-24 2024-05-08 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_09 dholab_carton_0009 2024-04-24 2024-05-02 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_10 dholab_carton_0010 2024-04-24 2024-05-01 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_11 dholab_carton_0011 2024-04-24 2024-05-01 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_12 dholab_carton_0012 2024-04-24 2024-05-02 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_13 dholab_carton_0013 2024-04-24 2024-05-07 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30081_14 dholab_carton_0014 2024-04-24 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14
dholab_30081_15 dholab_carton_0015 2024-04-26 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14
dholab_30114_01 dholab_carton_0016 2024-05-02 2024-05-17 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE VA dholab 2024-05-14
dholab_30114_02 dholab_carton_0017 2024-05-02 2024-06-06 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE NY dholab 2024-05-14
dholab_30114_03 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30114_04 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 33.52 10 AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14
dholab_30114_06 dholab_carton_0020 2024-05-02 2024-06-27 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE CO dholab 2024-05-14
dholab_30114_07 dholab_carton_0021 2024-05-02 2024-06-04 qPCR 31.17 46 AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE TX dholab 2024-05-14
dholab_30114_08 dholab_carton_0022 2024-05-02 2024-05-16 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE UT dholab 2024-05-14
dholab_30114_09 dholab_carton_0023 2024-05-02 2024-05-30 qPCR NA AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IN dholab 2024-05-14
dholab_30114_10 dholab_carton_0024 2024-05-02 2024-07-11 qPCR 26.29 1145 AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE MI dholab 2024-05-14
dholab_30114_14 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 31.34 40 AVRLVS_fluMgene_primers.fasta AVRLVS_fluMgene_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-05-14
dholab_30125_1 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE OH dholab 2024-05-14
dholab_30125_2 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14
dholab_30125_3 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 28.97 468 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE KY dholab 2024-05-14
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7 changes: 6 additions & 1 deletion README.md
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[![Still Validation](https://github.com/dholab/dairy-hpai-monitoring/actions/workflows/validate.yml/badge.svg)](https://github.com/dholab/dairy-hpai-monitoring/actions/workflows/validate.yml)

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.
HPAI (highly-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.

To submit results of your own, read over our [proposal instructions](docs/proposal_instructions.md) and then open [a new issue](https://github.com/dholab/dairy-hpai-monitoring/issues/new).
## Table of Contents
Expand All @@ -11,6 +11,7 @@ To submit results of your own, read over our [proposal instructions](docs/propos
- [Sampling Dairy Products for HPAI RNA](#sampling-dairy-products-for-hpai-rna)
- [Extracting HPAI RNA from Dairy Products](#extracting-hpai-rna-from-dairy-products)
- [Milk and Cream](#milk-and-cream)
- [Quantifying and Sequencing HPAI RNA from Dairy Products](#quantifying-and-sequencing-hpai-rna-from-dairy-products)
- [Metadata Stewardship](#metadata-stewardship)
- [Geolocation Data](#geolocation-data)
- [Naming Conventions](#naming-conventions)
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We have published an HPAI RNA extraction protocol tested on milk and cream on protocols.io: [protocol](https://www.protocols.io/view/rna-extraction-from-milk-for-hpai-surveillance-dczp2x5n.html)

### Quantifying and Sequencing HPAI RNA from Dairy Products

We have published an HPAI 250bp tiled amplicon sequencing protocol compatible with Oxford Nanopore and Illumina sequencing platforms on protocols.io: [protocol](https://www.protocols.io/view/whole-genome-sequencing-of-h5n1-from-dairy-product-dev43e8w.html)

## 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.
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0 assets/AVRLVS_universalflu_primers.fasta → assets/AVRLVS_fluMgene_primers.fasta
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0 assets/AVRLVS_universalflu_probe.fasta → assets/AVRLVS_fluMgene_probe.fasta
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