RT Journal Article
SR Electronic
T1 DNA from dust: comparative genomics of large DNA viruses in field surveillance samples
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 A. Kennedy
A1 Jacob Shreve
A1 Chris L. Cairns
A1 Matthew J. Jones
A1 Patricia A. Dunn
A1 Andrew F. Read
A1 Moriah L. Szpara
YR 2016
UL http://biorxiv.org/content/early/2016/09/01/039479.abstract
AB The intensification of the poultry industry over the last sixty years facilitated the evolution of increased virulence and vaccine breaks in Marek’s disease virus (MDV-1). Full genome sequences are essential for understanding why and how this evolution occurred, but what is known about genome-wide variation in MDV comes from laboratory culture. To rectify this, we developed methods for obtaining high quality genome sequences directly from field samples without the need for sequence-based enrichment strategies prior to sequencing. We applied this to the first characterization of MDV-1 genomes from the field, without prior culture. These viruses were collected from vaccinated hosts that acquired naturally circulating field strains of MDV-1, in the absence of a disease outbreak. This reflects the current issue afflicting the poultry industry, where virulent field strains continue to circulate despite vaccination, and can remain undetected due to the lack of overt disease symptoms. We found that viral genomes from adjacent field sites had high levels of overall DNA identity, and despite strong evidence of purifying selection, had coding variations in proteins associated with virulence and manipulation of host immunity. Our methods empower ecological field surveillance, make it possible to determine the basis of viral virulence and vaccine breaks, and can be used to obtain full genomes from clinical samples of other large DNA viruses, known and unknown.