Industry-wide surveillance of Marek's disease virus on commercial poultry farms: underlying potential for virulence evolution and vaccine escape

Marek9s disease virus is a herpesvirus of chickens that costs the worldwide poultry industry over 1 billion USD annually. Severity of disease has increased over the last half century due to evolution of the virus, a trajectory accompanied by reduced efficacy of two generations of Marek9s disease vaccines. Whether continued evolution will erode the efficacy of current vaccines is an open question. We conducted a three-year surveillance study to assess the prevalence of Marek9s disease virus on commercial poultry farms, determine the effect of various factors on virus prevalence, and document virus dynamics on broiler chicken houses over short (weeks) and long (years) timescales. We extracted DNA from dust samples collected from commercial chicken and egg production facilities in Pennsylvania, USA. Quantitative polymerase chain reaction (qPCR) was used to assess wild-type virus detectability and concentration. Using data from 1018 dust samples with Bayesian generalized linear mixed effects models, we determined the factors that correlated with virus incidence. Maximum likelihood and autocorrelation function estimation on 3727 dust samples were used to document and characterize virus concentrations within houses over time. Overall, wild-type virus was detectable at least once on 36 of 104 farms at rates that varied substantially between farms. Virus was detected in 1 of 3 broiler-breeder operations (companies), 4 of 5 broiler operations, and 3 of 5 egg layer operations. Marek9s disease virus detectability differed by production type, bird age, day of the year, operation (company), farm, house, flock, and sample. Operation (company) was the most important factor, accounting for between 12% and 63.4% of the variation in virus detectability. Within individual houses, virus concentration often dropped below detectable levels and reemerged later. The data presented here characterize Marek9s disease virus dynamics, a prerequisite in determining whether current vaccine protection will be eroded by future virus evolution.