Andrew F Read | Search bioRxiv

bioRxiv2016

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

Mareks disease virus is a herpesvirus of chickens that costs the worldwide poultry industry over 1 billion USD annually. Two generations of Mareks disease vaccines have shown reduced efficacy over the last half century due to evolution of the virus. Understanding where the virus is present may give insight into whether continued reductions in efficacy are likely. We conducted a three-year surveillance study to assess the prevalence of Mareks disease virus on commercial poultry farms, determine the effect of various factors on virus prevalence, and document virus dynamics in 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 prevalence across farms. Maximum likelihood and autocorrelation function estimation on 3727 additional 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. Mareks 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. These data characterize Mareks disease virus dynamics, which are potentially important to the evolution of the virus.

Epidemiology↗

bioRxiv2016

DNA from dust: comparative genomics of large DNA viruses in field surveillance samples

Mareks disease (MD) is a lymphoproliferative disease of chickens caused by airborne gallid herpesvirus type 2 (GaHV-2, aka MDV-1). Mature virions are formed in the feather follicle epithelium cells of infected chickens from which the virus is shed as fine particles of skin and feather debris, or poultry dust. Poultry dust is the major source of virus transmission between birds in agricultural settings. Despite both clinical and laboratory data that show increased virulence in field isolates of MDV-1 over the last 40 years, we do not yet understand the genetic basis of MDV-1 pathogenicity. Our present knowledge on genome-wide variation in the MDV-1 genome comes exclusively from laboratory-grown isolates. MDV-1 isolates tend to lose virulence with increasing passage number in vitro, raising concerns about their ability to accurately reflect virus in the field. The ability to rapidly and directly sequence field isolates of MDV-1 is critical to understanding the genetic basis of rising virulence in circulating wild strains. Here we present the first complete genomes of uncultured, field-isolated MDV-1. These five consensus genomes were derived directly from poultry dust or single chicken feather follicles without passage in cell culture. These sources represent the shed material that is transmitted to new hosts, vs. the virus produced by a point source in one animal. We developed a new procedure to extract and enrich viral DNA, while reducing host and environmental contamination. DNA was sequenced using Illumina MiSeq high-throughput approaches and processed through a recently described bioinformatics workflow for de novo assembly and curation of herpesvirus genomes. We comprehensively compared these genomes to one another and also to previously described MDV-1 genomes. The field-isolated genomes had remarkably high DNA identity when compared to one another, with few variant proteins between them. In an analysis of genetic distance, the five new field genomes grouped separately from all previously described genomes. Each consensus genome was also assessed to determine the level of polymorphisms within each sample, which revealed that MDV-1 exists in the wild as a polymorphic population. By tracking a new polymorphic locus in ICP4 over time, we found that MDV-1 genomes can evolve in short period of time. Together these approaches advance our ability to assess MDV-1 variation within and between hosts, over time, and during adaptation to changing conditions.

Microbiology↗