Viral microRNA Profile in Acute White Spot Syndrome Virus (WSSV) Infection

Both viral and host microRNAs (miRNAs) play vital roles in virus-host interactions.  Shrimp white spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture, which has a large double strand DNA genome and is reported to express high density of miRNAs in the early stage of its infection.  Yet no previous deep sequencing work reported any WSSV miRNA.  By comparing small RNA deep sequencing profiles between acute and latent stages of infected Chinese Shrimp (Fenneropenaeus chinensis), we identified 16 virial miRNAs, which were surprisingly different from the early stage miRNAs reported previously.  RT-PCR assay showed that most the viral miRNAs’ expression kept increasing till 48 hours post infection and some miRNAs were expressed differently betwwen the stomach and the lymphoid (Oka) organ.  Integrating miRNA and cDNA transcriptome data, we found miRNA transcripts (primary miRNAs) for 14 of the 16 miRNAs, and predicted both viral and host target genes of WSSV miRNAs.  Enrichment analysis of target genes indicated that viral miRNAs may alter immune related processes such as chemokine signaling pathway, Ras signaling pathway, melanogenesis and phagocytosis, indicating their pivotal roles in acute infection stage.  This study provided the first deep sequencing evidence of WSSV miRNAs and presented a comprehensive regulatory network between viral miRNAs and their target gene transcriptions.