Evidence map›Paper›PMID 39677482›Full record

ArticlemedRxiv : the preprint server for health sciences2024

Establishing methods to monitor H5N1 influenza virus in dairy cattle milk.

Elyse Stachler, Andreas Gnirke, Kyle McMahon, Michael Gomez, Liam Stenson, Charelisse Guevara-Reyes, Hannah Knoll, Toni Hill, Sellers Hill, Katelyn S Messer and 20 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

30 authors.

Elyse StachlerBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0002-4961-1983
Andreas GnirkeBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0001-5324-6387
Kyle McMahonBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Michael GomezBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Liam StensonBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Charelisse Guevara-ReyesBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Hannah KnollBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Toni HillBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Sellers HillBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Katelyn S MesserBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Jon Arizti-SanzBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0002-4092-9952
Fatinah AlbeezBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Elizabeth CurtisBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Pedram SamaniBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Natalia WewiorBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
David H O'ConnorBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0003-2139-470X
William VuykUniversity of Wisconsin-Madison, Madison, Wisconsin, USA.
Sophia KhouryThe University of Texas at Austin, Austin, Texas, USA.
Matthew K SchnizleinMichigan State University, East Lansing, MI, USA.
Nicole C RockeyDuke University, Durham, NC, USA.
Zachariah BroemmelDuke University, Durham, NC, USA.
Michael MinaImmune Observatory, Boston, Massachusetts, USA.
Lawrence C MadoffMassachusetts Department of Public Health, Boston, Massachusetts.ORCID 0000-0003-2589-7777
Shirlee WohlMassachusetts Department of Public Health, Boston, Massachusetts.ORCID 0000-0002-0311-3348
Lorraine O'ConnorMassachusetts Department of Agricultural Resources, Boston, Massachusetts.
Catherine M BrownMassachusetts Department of Public Health, Boston, Massachusetts.
Al OzonoffBoston Children's Hospital, Boston, Massachusetts, USA.ORCID 0000-0003-4233-5899
Daniel J ParkBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0001-7226-7781
Bronwyn L MacInnisBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0003-0082-968X
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.ORCID 0000-0002-9843-1890

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI NEAFSEY, DANIEL E · 2014 to 2024
$66.5M
West African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2M
NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI110818
6 · The paper itself

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.

Identifiers

PMID39677482
PMCPMC11643214

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.