PURPOSE OF THIS WORK. INFECTIOUS DISEASES OF LIVESTOCK AND POULTRY ARE A PERSISTENT THREAT TO ANIMAL HEALTH, AGRICULTURAL PRODUCTIVITY, AND FOOD SECURITY. LONG ISLAND IS HOME TO DIVERSE SMALLSCALE CATTLE FARMS AND POULTRY OPERATIONS, WHICH ARE VULNERABLE TO OUTBREAKS OF VIRAL AND PARASITIC DISEASES. THIS PROJECT AIMS TO CONDUCT COMPREHENSIVE MOLECULAR AND SEROLOGICAL SURVEILLANCE OF MAJOR INFECTIOUS DISEASES AFFECTING CATTLE AND POULTRY ON LONG ISLAND. TARGETED CATTLE PATHOGENS WILL INCLUDE INFECTIOUS BOVINE RHINOTRACHEITIS VIRUS, BOVINE RESPIRATORY SYNCYTIAL VIRUS, BOVINE CORONAVIRUS, BOVINE ROTAVIRUS, AND SOME PARASITES SUCH AS THE GASTROINTESTINAL PARASITE HAEMONCHUS CONTORTUS. FOR POULTRY, SURVEILLANCE WILL INCLUDE INFECTIOUS BRONCHITIS VIRUS AND INFECTIOUS LARYNGOTRACHEITIS VIRUS, WHICH ARE HIGHLY SIGNIFICANT VIRAL RESPIRATORY PATHOGENS OF CHICKENS. THE PREVALENCE, GENETIC DIVERSITY, AND EPIDEMIOLOGICAL TRENDS OF THESE PATHOGENS WILL BE DETERMINED USING MOLECULAR DIAGNOSTICS, SEROLOGICAL ASSAYS, AND SEQUENCING. THE DATA WILL STRENGTHEN PREVENTIVE STRATEGIES, IMPROVE HERD AND FLOCK HEALTH MANAGEMENT, AND SUPPORT LOCAL ONE HEALTH INITIATIVES. THE LONG-TERM GOAL OF THIS PROPOSAL IS TO ESTABLISH A SUSTAINABLE, GENOMICS-DRIVEN SURVEILLANCE PLATFORM FOR INFECTIOUS DISEASES OF LIVESTOCK AND POULTRY ON LONG ISLAND THAT CAN SERVE AS A MODEL FOR OTHER REGIONS. OUR SPECIFIC OBJECTIVES INCLUDE: 1) ESTABLISH THE PREVALENCE AND SEROPOSITIVITY OF MAJOR CATTLE AND POULTRY VIRUSES USING MOLECULAR AND SEROLOGICAL ASSAYS; 2) EVALUATE GASTROINTESTINAL PARASITISM IN CATTLE, WITH EMPHASIS ON HAEMONCHUS CONTORTUS; 3) EMPLOY NEXT-GENERATION SEQUENCING TO DECODE FULL-LENGTH GENOMES OF VIRAL AND PARASITIC PATHOGENS DETECTED IN LONG ISLAND HERDS AND FLOCKS; 4) PERFORM COMPREHENSIVE COMPARATIVE GENOMIC ANALYSIS AND GENOME MINING TO IDENTIFY MARKERS OF VIRULENCE, IMMUNE EVASION, AND VACCINE ESCAPE. II. ACTIVITIES TO BE PERFORMED WITH THE FUNDS FROM THIS AWARD. SAMPLES WILL BE COLLECTED FROM THE REGIONAL DAIRY HERDS AND POULTRY FARMS. BLOOD, NASAL SWABS, FECAL, AND MILK SAMPLES WIL BE COLLECTED FROM CATTLE, AND OROPHARYNGEAL/CLOACAL SWABS, AND BLOOD COLLECTED FROM POULTRY. PCR/RT-PCR WILL BE USED TO DETECT THE LISTED VIRUSES. ILLUMINA AND/OR OXFORD NANOPORE WILL BE USED FOR SEQUENCING TO OBTAIN COMPLETE GENOMES OF THE VIRAL AND PARASITIC PATHOGENS. BIOINFORM ATIC GENOME MINING WILL BE USED TO IDENTIFY ANTIGENIC DETERMINANTS, VIRULENCE FACTORS, AND MARKERS RELEVANT TO VACCINE EFFICACY. ELISA AND NEUTRALIZATION ASSAYS WILL BE USED TO IDENTIFY ANTIBODIES TO VIRUSES AND PARASITES. FECAL EGG COUNTS AND LARVAL CULTURE WILL BE USED TO IDENTIY PARASITES. III. DELIVERABLES AND EXPECTED OUTCOMES FROM THESE ACTIVITIES. THE PREVALENCE AND SEROPOSITIVITY RATES FOR THE SELECTED VIRUSES AND PARASITES OF CATTLE AND BIRDS ACROSS SAMPLED LONG ISLAND FARMS WILL BE DETERMINED. HIGH-QUALITY, ANNOTATED GENOMES FOR REPRESENTATIVE ISOLATES OF VIRAL AND PARASITIC PATHOGENS WILL BE DEPOSITED IN GENBANK AND OTHER PUBLIC REPOSITORIES. GENES ENCODING VIRULENCE FACTORS, ANTIGENIC DRIFT MUTATIONS, AND NOVEL EPITOPES RELEVANT FOR VACCINE AND DIAGNOSTIC DEVELOPMENT WILL BE IDENTIFIED. THE DISTRIBUTION OF PATHOGENS ACROSS LONG ISLAND FARMS WILL BE MADE AVAILABLE FOR VETERINARIANS AND POLICYMAKERS. AT LEAST 2-3 PEER-REVIEWED MANUSCRIPTS IN INTERNATIONAL JOURNALS ARE EXPECTED TO BE PUBLISHED. THIS WORK WILL BE PRESENTED AT CONFERENCES, AND NECESSARY REPORTS WILL BE MADE AVAILABLE FOR FARMERS, VETERINARIANS, AND LOCAL AGRICULTURAL AUTHORITIES. GRADUATE STUDENTS AND TECHNICIANS WILL BE TRAINED IN MOLECULAR DIAGNOSTICS, SEQUENCING, AND BIOINFORMATICS ANALYSIS. IV. INTENDED BENEFICIARIES OF THE ACTIVITIES WILL INCLUDE LOCAL FARMERS AND LIVESTOCK/POULTRY PRODUCERS, VETERINARIANS, THE RESEARCH AND ACADEMIC COMMUNITY, POLICY MAKERS, AGRICULTURAL AUTHORITIES, AND THE WIDER PUBLIC. V. SUBRECIPIENT ACTIVITIES. NONE.