Cyprinid herpesvirus 3 genome and microtranscriptome sequencing

Koi herpesvirus disease (KHVD) is an emerging disease that causes mass mortality in koi and common carp, Cyprinus carpio L. Its causative agent is Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV). Although data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. In this context, a specific enrichment procedure for sequencing full-length CyHV-3 genomes directly from tissues of infected fish was developed and evaluated. Full sequences from 8 specimens could be recovered from gill samples containing as little as 5,000 CyHV-3 copies, with a high depth (>100x) almost all along the genome. This study also aimed to identify potential miRNAs involved in the lytic cycle of CyHV-3 and monitor their expression for up to ten days post-infection. To confirm their involvement in the lytic cycle, the expression profiles of these miRNAs were compared at two different temperatures: a permissive temperature (22 degrees Celsius) and a non-permissive temperature (30 degrees Celsius).This should help shed new light on the evolution patterns and virulence factors of this deadly virus.