Differentially expressed genes following persistent infection with infectious pancreatic necrosis virus in vitro and in vivo

The mechanisms of viral persistence of infectious pancreatic necrosis virus (IPNV) are not well understood. In this study we have used a model of IPNV persistently infected CHSE (Chinook salmon embryonic) cells as correlate of persistent infection in fish focusing on differentially expressed genes using subtractive hybridization (SSH). Selected genes were also analyzed by quantitative real-time PCR (qPCR) in persistently infected parr of Atlantic salmon. Persistent infection was established by growing CHSE cells surviving an IPNV infection. Infection in rescued cells was non-lytic with a virus yield of 103–105 TCID50/ml of supernatant, resembling what can be found during a persistent infection in vivo. By comparing gene expression in persistently infected cell vs. non-infected cells we found an upregulation of genes involved in direct interaction or degradation of viral proteins, proteasome activating subunit 3, and of ATRX (X-linked alpha-thalassemia/mental retardation syndrome), a transcription repressor, which may indicate a repression of viral replication through reduced transcription. Further ephrin B1 (signal-transduction group) was found strongly up-regulated, and receptors for various ephrins are used for cell interaction and as entry points for other viruses in higher vertebrates. Endonuclease/reverse transcriptase 1 (RVT1) was also found highly up-regulated in persistently infected cells. The comparison of persistently infected cells to in vivo infected fish showed that the expression profiles found in CHSE cells give corresponding results for selected genes, as ATRX, ephrin B1 and RVT-1. We observed similar results by use of two independent methods (SSH and qPCR) for 8 out of 15 genes analyzed and the transcript profile of persistently IPNV-infected cells involve upregulation of genes encoding proteins involved in viral protein degradation and translation inhibition. The understanding is that this may contribute to keep the number of virus particles low during viral persistence.