Year: 2025
Type: preprint
Abstract: Avian influenza viruses (AIVs) are zoonotic pathogens that pose an increasing global threat due to their potential for significant economic losses in agriculture, spillover into humans, and the risk of a pandemic should human-to-human transmission occur. These concerns underscore the need for rapid, sensitive and specific tools to detect and differentiate circulating AIV subtypes and clades. Current AIV diagnostic methods rely on specialized equipment and trained personnel, limiting their use in the field and in low-resource settings. Here, we extended SHINE (Streamlined Highlighting of Infections to Navigate Epidemics), a CRISPR-based platform, to detect and subtype AIVs. We designed, optimized, and validated SHINE assay for the H5 AIV detection using both fluorescence and lateral flow readout, achieving 100% specificity with PCR-based assays when tested on seasonal influenza-positive clinical samples, and a limit of detection of 121.7 copies/μL on vaccine-derived H5 viral seedstocks. To expand the scope of avian influenza detection, we also designed and validated a SHINE assay targeting the 2.3.4.4b A(H5N1) lineage, in response to the ongoing H5N1 outbreak in cattle in the United States, and a SHINE assay specific to Eurasian H7 lineage to discriminate against North American H7 lineage. Together, these SHINE assays offer a promising platform for AIV diagnosis and surveillance, particularly in settings with limited laboratory infrastructure.
Source: medRxiv
Institutions: Princeton University, Massachusetts General Hospital
Language: English
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Open Access status: green
Awards: Development of a highly-multiplexed CRISPR-based TB drug susceptibility test, G4733222645, G5520316217, 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.
OpenAlex ID: W4413722684