No abstract

Structural variation turnovers and defective genomes: key drivers for the in vitro evolution of the large double-stranded DNA koi herpesvirus (KHV), Peer Community Journal, 2: e44.

Cyprinid herpesvirus-3 (CyHV-3) is the etiological agent of koi herpesvirus disease (KHVD) in common and koi carp farming. This highly contagious pathogen has a 295-kb genome that harbours 156 open reading frames. Recent in vitro experimental evolution studies highlighted strong dynamics of genomic structural variations (SVs), in particular in the region of ORF150, an ORF potentially involved in virus multiplication and host inflammatory response. Among these SVs, a 1363-bp deletion could be associated with a loss of virulence. The present study aimed at investigating the genomic variations in the ORF150 region, and especially the deletion, in viruses isolated from carp populations of Indonesia. A screening of 236 fish from 43 different farms revealed a high prevalence of CyHV-3 (nearly 70%), both in symptomatic and asymptomatic common carp. However, in contrast with the results obtained in vitro, long read sequencing of the ORF150 region revealed a low level of genetic variations and the absence of the 1363-pb deletion. The complex interactions between the virus, the environment and the host, particularly the immune system, probably play an important role in this reduced variability.

Structural variations (SVs) constitute a significant source of genetic variability in virus genomes. Yet knowledge about SV variability and contribution to the evolutionary process in large double-stranded (ds)DNA viruses is limited. Cyprinid herpesvirus 3 (CyHV-3), also commonly known as koi herpesvirus (KHV), has the largest dsDNA genome within herpesviruses. This virus has become one of the biggest threats to common carp and koi farming, resulting in high morbidity and mortalities of fishes, serious environmental damage, and severe economic losses. A previous study analyzing CyHV-3 virulence evolution during serial passages onto carp cell cultures suggested that CyHV-3 evolves, at least in vitro, through an assembly of haplotypes that alternatively become dominant or under-represented. The present study investigates the SV diversity and dynamics in CyHV-3 genome during 99 serial passages in cell culture using, for the first time, ultra-deep whole-genome and amplicon-based sequencing. The results indicate that KHV polymorphism mostly involves SVs. These SVs display a wide distribution along the genome and exhibit high turnover dynamics with a clear bias towards inversion and deletion events. Analysis of the pathogenesis-associated ORF150 region in ten intermediate cell passages highlighted mainly deletion, inversion and insertion variations that deeply altered the structure of ORF150. Our findings indicate that SV turnovers and defective genomes represent key drivers in the viral population dynamics and in vitro evolution of KHV. Thus, the present study can contribute to the basic research needed to design safe live-attenuated vaccines, classically obtained by viral attenuation after serial passages in cell culture.