A 2.5-Kilobase Deletion Containing a Cluster of Nine MicroRNAs in the Latency-Associated-Transcript Locus of the Pseudorabies Virus Affects the Host Response of Porcine Trigeminal Ganglia during Established Latency

The alphaherpesvirus Pseudorabies virus (PrV) establishes latency primarily in neurons of trigeminal ganglia when only transcription of the latency-associated transcript (LAT) locus is detected. Eleven microRNAs (miRNAs) cluster within LAT, suggesting a role in establishment and/or maintenance of latency. We generated a mutant PrV (M) deleted of nine miRNA genes which displayed almost identical properties with the parental PrV (WT) during propagation in vitro. Fifteen pigs were experimentally infected with either WT, M or mock infected. Similar levels of virus excretion and host antibody response were observed in all infected animals. At 62 days post infection trigeminal ganglia were excised and profiled by deep sequencing and RT-qPCR. Latency was established in all infected animals without evidence of viral reactivation demonstrating that miRNAs are not mandatory for this process. Lower levels of Large Latency Transcript (LLT) were found in ganglia infected by M compared to WT PrV. All PrV miRNAs were expressed, with highest expression found for prv-miR-LLT1, prv-miR-LLT2 (in WT-ganglia) and prv-miR-LLT10 (in both WT and M-ganglia). No evidence of differentially expressed porcine miRNAs was found. Fifty-four porcine genes were differentially expressed between WT, M and control ganglia. Both viruses triggered a strong host immune response, but in M- ganglia gene upregulation was prevalent. Pathway analyses indicated that several biofunctions, including those related to cell-mediated immune response and migration of dendritic cells, were impaired in M- ganglia. These findings are consistent with a function of the LAT locus in the modulation of host response for maintaining a latent state.