Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA
Year: 2025
Type: article
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.
Source: Emerging infectious diseases
Authors: Elyse Stachler, Andreas Gnirke, Kyle McMahon, Michael Gomez, Liam Stenson, Charelisse Guevara-Reyes, Hannah Knoll, Toni Hill, Sellers Hill, Katelyn S. Messer, Jon Arizti-Sanz, Fatinah Albeez, Elizabeth Curtis, Pedram Samani, Natalia Wewior, David H. O’Connor, William Vuyk, Sophia Khoury, Matthew K. Schnizlein, Nicole C. Rockey, Zachariah Broemmel, Michael Mina, Lawrence C. Madoff, Shirlee Wohl, Lorraine O’Connor, Catherine M. Brown, Al Ozonoff, Daniel J. Park, Bronwyn L. MacInnis, Pardis C. Sabeti
Institutions: Broad Institute, University of Puerto Rico at Río Piedras, Harvard University, University College London, University of Wisconsin–Madison, The University of Texas at Austin, Michigan State University, Duke University, Massachusetts Department of Public Health, University of Massachusetts Chan Medical School, Brigham and Women's Hospital, Boston Children's Hospital, Howard Hughes Medical Institute
Language: English
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Open Access status: diamond
Awards: G10969003, G1943808918, G4733222645, G5393839250, G5621676343, NEW ENGLAND PATHOGEN GENOMICS CENTER OF EXCELLENCE - THE MASSACHUSETTS DEPARTMENT OF PUBLIC HEALTH (MADPH) IS PROPOSING THE FORMATION OF THE NEW ENGLAND PATHOGEN GENOMICS CENTER OF EXCELLENCE (THE CENTER) IN RESPONSE TO THE US PUBLIC HEALTH PATHOGENS GENOMICS CENTERS OF EXCELLENCE (CDC-RFA-CK22-2204) FUNDING OPPORTUNITY. THIS APPLICATION IS FOR THE MANDATORY COMPONENTS (CORE, RESPONSE IMPLEMENTATION) AND ALSO INCLUDES THE OPTIONAL COMPONENT (LEAD PGCOE FOR EDUCATION). THE CENTER’S MISSION IS TO ENHANCE REGIONAL CAPACITY FOR THE GENERATION, ANALYSIS, AND INTEGRATION INTO PUBLIC HEALTH RESPONSE OF PATHOGEN GENOMIC DATA, INCREASING THE SCALE, SPEED, SENSITIVITY, AND QUALITY OF DATA GENERATED. THE CENTER LEVERAGES THE COMPLEMENTARY STRENGTHS OF ITS REGIONAL AND ACADEMIC PARTNERS, INCLUDING PUBLIC HEALTH, GENOMICS, DATA VISUALIZATION, CLINICAL MEDICINE, AND EDUCATION. IT WILL BE LED BY MADPH, WITH THE BROAD INSTITUTE OF MIT AND HARVARD AS LEAD ACADEMIC PARTNER AND OTHER MEMBERS FROM MASSACHUSETTS AND CONNECTICUT. TO SERVE ALL OF NEW ENGLAND, IT WILL DRAW ON EXISTING LINKS BETWEEN STATE HEALTH DEPARTMENTS, MADPH’S ROLE LEADING THE REGIONAL NETWORK OF THE CDC’S BIOINFORMATICS REGIONAL RESOURCE CAPACITY-BUILDING PROGRAM, AND A RANGE OF COOPERATIVE EFFORTS DURING THE SARS-COV-2 (SC2) PANDEMIC. MORE BROADLY, THE TEAM IS DEEPLY INVOLVED IN NATIONAL AND INTERNATIONAL EFFORTS TO BUILD PUBLIC HEALTH CAPACITY FOR PATHOGEN GENOMICS. IN THE FIRST YEAR, THE CENTER WILL ADDRESS TWO PRIORITY PATHOGEN TYPES, RESPIRATORY PATHOGENS AND SEXUALLY TRANSMITTED INFECTIONS, WITH THE LATTER FOCUSED ON NEISSERIA GONORRHOEAE INFECTIONS. WE WILL COMBINE UNBIASED AND TARGETED APPROACHES TO 1) DIFFERENTIATE THE UNDERLYING CAUSE AND MONITOR THE TRANSMISSION DYNAMICS OF INFECTIONS; 2) DEVELOP TOOLS TO IDENTIFY PATHOGEN GENOMIC RISK PROFILES RELATED TO DRUG RESISTANCE; AND 3) IMPLEMENT RAPID DETECTION AND GENOTYPING TECHNOLOGIES. TO SUPPORT SUCH PATHOGEN-SPECIFIC USE CASES, THE CENTER WILL WORK TO CODIFY WORKFLOWS AND STANDARDIZE DATA AND ITS TRANSLATION FOR PUBLIC HEALTH DECISION MAKING. WE WILL STREAMLINE SAMPLE ACCESS AND HANDLING (PHYSICAL AND REGULATORY); DEVELOP SEQUENCING FOR NEW SAMPLE TYPES; IMPROVE UNBIASED METAGENOMIC SEQUENCING FOR USE IN PUBLIC HEALTH LABS; DEVELOP STANDARDIZED DATA VISUALIZATION AND REPORTING; AND ADVANCE CLIA-GRADE SEQUENCING FOR CLINICAL APPLICATIONS. WE AIM TO DEVELOP METHODS, PROCESSES, AND TOOLS THAT ARE SCALABLE, GENERALIZABLE, AND APPLICABLE TO USERS DOMESTICALLY AND ABROAD. IN PARALLEL, THE CENTER WILL PREPARE FOR RAPID DEPLOYMENT OF TOOLS AND PROCESSES TO RESPOND TO AN EMERGING INFECTIOUS THREAT. THIS WILL REQUIRE CREATING FLEXIBLE PLANS TO DEPLOY AVAILABLE RESOURCES FOR SCALABLE SEQUENCING AND APPROPRIATE DATA ANALYSIS, VISUALIZATION, AND REPORTING TOOLS FOR INTEGRATION OF INFORMATION INTO PUBLIC HEALTH RESPONSE; THESE WILL BE BASED ON EXPERIENCE WITH LOCAL (MUMPS), REGIONAL (HEPATITIS A), AND INTERNATIONAL (ZIKA/SC2) OUTBREAKS. TO OVERCOME POTENTIAL REGULATORY DELAYS, MULTI-INSTITUTIONAL AND INTERSTATE IRB PROTOCOLS AND MTAS WILL BE ESTABLISHED IN ADVANCE. THE CORE EDUCATION COMPONENTS OF THE CENTER WILL FOCUS ON PRACTICAL TRAINING IN THE TOOLS DESCRIBED ABOVE. INITIAL GOALS WILL INCLUDE TRAINING IN BIOINFORMATICS ANALYSIS THROUGH THE TERRA.BIO PLATFORM AND SUPPORT FOR EFFORTS LIKE THE MASSCPR VIRAL VARIANTS CALL SERIES THAT BRINGS TOGETHER BASIC AND TRANSLATIONAL RESEARCHERS AND PUBLIC HEALTH PRACTITIONERS. ADDITIONAL GOALS WILL BE IDENTIFIED THROUGH A NEEDS ASSESSMENT OF PUBLIC HEALTH PROFESSIONALS. FOR THE NATIONAL TRAINING LEAD CENTER, WE PROPOSE 1) A COMPREHENSIVE LANDSCAPE ANALYSIS OF NEEDS IN GENOMIC TRAINING AND CAPACITY; 2) A DEDICATED PGCOE PORTAL, ACCREDITATION PROGRAM, AND CURATED ONLINE TRAINING OFFERINGS; AND 3) NEW OPPORTUNITIES FOR ADVANCED AND NONTRADITIONAL LEARNING., G8014130074, G9000020611, G9000059902
OpenAlex ID: W4408937780