Abstract
Cyprinid herpesvirus-3 (CyHV-3), or koi herpesvirus (KHV), is responsible for high mortalities in aquacultureof both common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi) worldwide. Thecomplete genomes of three CyHV-3 isolates showed more than 99% of DNA sequence identity, with themajority of differences located in short tandem repeats, also called VNTR (variable number of tandemrepeats). By targeting these variations, eight loci were selected for genotyping CyHV-3 by multiple locusVNTR analysis (MLVA). CyHV-3 strains obtained after sequential in vivo infections exhibited identicalMLVA profiles, whereas samples originating from a single isolate passaged 6 and 82 times in vitro exhibitedmutations in two of the eight loci, suggesting a relatively slow genetic evolution rate of the VNTRs.The method was subsequently applied on 38 samples collected in Indonesia, France and the Netherlands.Globally, the isolates grouped in two main genetic clusters, each one divided in two subgroups includingeither CyHV-3-U/I or CyHV3-J. Interestingly, Indonesian strains were rather distant from CyHV-3-J isolate.The results of the present study indicate that these VNTR molecular markers are efficient in estimating thegenetic diversity among CyHV-3 isolates and are therefore suitable for further molecular epidemiologicalstudies.