RT Journal Article
SR Electronic
T1 DNA from dust: the first field-isolated genomes of MDV-1, from virions in poultry dust and chicken feather follicles
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 039479
DO 10.1101/039479
A1 Utsav Pandey
A1 Andrew S. Bell
A1 Daniel Renner
A1 David Kennedy
A1 Jacob Shreve
A1 Chris Cairns
A1 Matthew Jones
A1 Patricia Dunn
A1 Andrew Read
A1 Moriah L. Szpara
YR 2016
UL http://biorxiv.org/content/early/2016/02/12/039479.abstract
AB Marek’s 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.