Investigating pathogenicity of Spring Viraemia of Carp virus (SVCV) and the development of diagnostic tools

Abstract

Spring viraemia of carp virus (SVCV) is an OIE listed, notifiable disease affecting carp aquaculture. Disease outbreaks can lead to mass mortality events which poses significant economic threats to farmers and fishery owners. However, SVCV research has been limited due to the lack of full-genome sequences available for isolates from all genogroups, as well as limited information on SVCV pathogenicity. This study performed full-genome sequencing on several SVCV isolates from each of the recognised genogroups. Phylogenetic analysis of these sequences confirmed that isolates fall into 4 genogroups Ia-Id, which had been previously reported in literature. Interestingly, there was an additional sequence complementary to the grass carp thymosin beta-a gene in the 3’ non-coding region of the G gene of a few of the Asian strains (Ia) that could influence the virus replication in that host. A conventional RT-PCR assay was designed to study the prevalence and distribution of the unusual additional sequence. Sequence alignments were used to design a new SVCV-specific TaqMan RT-qPCR assay based on the polymerase (L) gene. Testing of this assay on representative isolates from genogroups Ia-Id showed it was highly specific; detecting all SVCV isolates tested at low virus loads and did not cross-react with other closely related Spriviviruses. An in vitro investigation into differences in the innate immune response to isolates from different genogroups revealed that the Ia genogroup may be able to evade the immune response to promote their own replication whereas isolates from the Ib genogroup induced a strong anti-viral response that could play a role in reducing their pathogenicity. This study has also made good progress towards the development of a reverse genetics reporter system for SVCV and VHSV, incorporating green fluorescent protein (GFP) as a reporter gene. This information can be used going forward to develop a complete reverse genetics system for SVCV in which viable virus is generated from DNA, and then through genetic mutation allow us to learn more about the mechanisms involved in SVCV pathogenicity.