RNA-seq analysis of viral gene expression in the skin of Marek’s disease virus infected chickens

Marek’s disease virus (MDV), a highly cell-associated oncogenic avian α-herpesvirus, is the causative agent of malignant transformation of T cells in domestic chickens. The latently infected CD4+CD8− T cells carry the virus through the blood stream and establish lymphomas in the skin, visceral organs and peripheral nerves. The feather follicle epithelium (FFE) is the only anatomical site where fully infectious enveloped virions are produced and eventually disseminated into the environment to infect contact birds. Therefore, skin and FFE play a critical role as being the common source of re-infection of birds sharing the same habitat. The molecular mechanism involved in the replication and assembly of MDV in the FFE leading to the production and release of cell-free infectious virus particles is unknown and to date no viral or host gene has been implicated in the process. To examine alterations in the expression pattern of viral genes, we performed RNA-seq on the skin samples of Marek’s disease virus-infected susceptible chickens at 10, 20, and 30 days post infection. For comparative analysis of the expression patterns of viral genes between the skin and spleen of the MD-susceptible and resistant lines, Real-Time RT-PCR was employed. In total, RNA-seq based analysis identified 42 viral genes that were differentially expressed in the skin of infected birds. Majority of the identified genes are involved in DNA replication, capsid, tegument, and envelop formation. Comparative analysis between the skin and spleen of MD-susceptible and resistant chicken lines, revealed significantly higher expression of the genes in the skin of either lines than the spleen. Furthermore, much higher expression of the genes was observed in the skin of the susceptible line than the resistant line.