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A KEY CHALLENGE IN CONTROLLING PRRSV IN THE U.S. IS THE RAPID EVOLUTION OF NEW GENETIC AND ANTIGENIC VARIANTS. AN UNTAPPED OPPORTUNITY TO ADDRESS THIS CHALLENGE LIES IN USING LARGE-SCALE GENETIC SEQUENCE DATABASES GENERATED BY DIAGNOSTIC LABORATORIES AS PART OF ROUTINE MONITORING BY THE INDUSTRY. RETROSPECTIVE ANALYSIS OF SUCH DATASETS HAS REVEALED A CYCLIC PATTERN OF STRAIN EMERGENCE AND TURNOVER, WITH STRAINS DIFFERING IN KNOWN ANTIGENIC SITES WITHIN THE ORF5 REGION. HOWEVER, BETTER TOOLS ARE NEEDED TO VISUALIZE, ANALYZE, AND INTERPRET SUCH DATA AS PART OF ONGOING GENOMIC SURVEILLANCE FOR VARIANTS. IN ADDITION, OUR ABILITY TO CORRELATE VARIANTS' GENETIC SEQUENCES TO ANTIGENIC PHENOTYPES IS LIMITED, WHICH HINDERS THE APPLICABILITY OF SEQUENCE DATA TO DISEASE MANAGEMENT. LASTLY, WHILE WHOLE-GENOME SEQUENCING PRESENTS AN OPPORTUNITY TO ELUCIDATE ANTIGENIC PHENOTYPES, TOOLS TO VISUALIZE AND INTERPRET WGS DATA ARE NEEDED TO FACILITATE INDUSTRY-WIDE ADOPTION. HERE, OUR OBJECTIVE IS TOQUANTIFY AND PREDICT ANTIGENIC DISTANCE BETWEEN CONTEMPORARY PRRSV VARIANTS. USING CROSS-NEUTRALIZATION AND B-CELL RECEPTOR ASSAYS, ANTIGENIC CARTOGRAPHY, AND MACHINE LEARNING, WE WILL BUILD ALGORITHMS TO PREDICT ANTIGENIC PHENOTYPES FROM GENETIC SEQUENCES IN SILICO. WE ALSO PROPOSE TO ESTABLISH A VISUALIZATION PLATFORM TO TRACK THE EVOLUTION AND PREDICTED ANTIGENICITY OF DIFFERENT VARIANTS TO PROMOTE RESEARCH COMMUNICATION TO INDUSTRY PLAYERS AND ENHANCE DISEASE MANAGEMENT. THROUGH WORKSHOPS, SEMINARS, AND STAKEHOLDER MEETINGS, WE INTEND TO EQUIP STAKEHOLDERS WITH THE SKILLS TO UNDERSTAND GENETIC AND ANTIGENIC ASSOCIATIONS OF VIRUSES ISOLATED ON FARMS. THUS, STAKEHOLDERS CAN MAKE DATA-INFORMED DECISIONS WHEN USING VACCINES/LVI AND ALSO PREEMPT INTERVENTIONS TO CONTAIN NEW VARIANTS MINIMIZING LOSSES.

$277,215FY2022National Institute of Food and AgricultureUSDA

Regents Of The University Of Minnesota

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A KEY CHALLENGE IN CONTROLLING PRRSV IN THE U.S. IS THE RAPID EVOLUTION OF NEW GENETIC AND ANTIGENIC VARIANTS. AN UNTAPPED OPPORTUNITY TO ADDRESS THIS CHALLENGE LIES IN USING LARGE-SCALE GENETIC SEQUENCE DATABASES GENERATED BY DIAGNOSTIC LABORATORIES AS PART OF ROUTINE MONITORING BY THE INDUSTRY. RETROSPECTIVE ANALYSIS OF SUCH DATASETS HAS REVEALED A CYCLIC PATTERN OF STRAIN EMERGENCE AND TURNOVER, WITH STRAINS DIFFERING IN KNOWN ANTIGENIC SITES WITHIN THE ORF5 REGION. HOWEVER, BETTER TOOLS ARE NEEDED TO VISUALIZE, ANALYZE, AND INTERPRET SUCH DATA AS PART OF ONGOING GENOMIC SURVEILLANCE FOR VARIANTS. IN ADDITION, OUR ABILITY TO CORRELATE VARIANTS' GENETIC SEQUENCES TO ANTIGENIC PHENOTYPES IS LIMITED, WHICH HINDERS THE APPLICABILITY OF SEQUENCE DATA TO DISEASE MANAGEMENT. LASTLY, WHILE WHOLE-GENOME SEQUENCING PRESENTS AN OPPORTUNITY TO ELUCIDATE ANTIGENIC PHENOTYPES, TOOLS TO VISUALIZE AND INTERPRET WGS DATA ARE NEEDED TO FACILITATE INDUSTRY-WIDE ADOPTION. HERE, OUR OBJECTIVE IS TOQUANTIFY AND PREDICT ANTIGENIC DISTANCE BETWEEN CONTEMPORARY PRRSV VARIANTS. USING CROSS-NEUTRALIZATION AND B-CELL RECEPTOR ASSAYS, ANTIGENIC CARTOGRAPHY, AND MACHINE LEARNING, WE WILL BUILD ALGORITHMS TO PREDICT ANTIGENIC PHENOTYPES FROM GENETIC SEQUENCES IN SILICO. WE ALSO PROPOSE TO ESTABLISH A VISUALIZATION PLATFORM TO TRACK THE EVOLUTION AND PREDICTED ANTIGENICITY OF DIFFERENT VARIANTS TO PROMOTE RESEARCH COMMUNICATION TO INDUSTRY PLAYERS AND ENHANCE DISEASE MANAGEMENT. THROUGH WORKSHOPS, SEMINARS, AND STAKEHOLDER MEETINGS, WE INTEND TO EQUIP STAKEHOLDERS WITH THE SKILLS TO UNDERSTAND GENETIC AND ANTIGENIC ASSOCIATIONS OF VIRUSES ISOLATED ON FARMS. THUS, STAKEHOLDERS CAN MAKE DATA-INFORMED DECISIONS WHEN USING VACCINES/LVI AND ALSO PREEMPT INTERVENTIONS TO CONTAIN NEW VARIANTS MINIMIZING LOSSES. · GrantIndex