Genomic evidence of homologous recombination in spring viremia of carp virus: A negatively single stranded RNA virus

•A new SVCV strain SVCV-265 was isolated from koi in China, 2013.•The isolate was shown to be of low virulence to koi.•Complete genome sequencing revealed SVCV-265 was clustered into Asian clade.•P gene of SVCV-265 was clustered differently to G gene.•Homologous recombination was detected in SVCV for the first time.

A new strain of spring viraemia of carp virus, denominated SVCV-265, was isolated from an ornamental common carp (Cyprinus carpio) in Shanghai, China, 2013. The isolate could produce obvious cytopathic effects on EPC cells, while was shown to be of low virulence for juvenile koi. Complete genome sequencing revealed the genome of the SVCV-265 strain is 11,029 nucleotides in length and phylogenetic analysis showed the isolate was clustered within Asia clade but was divergent from Chinese A1, A2 and BJ0505-2 strains. Previous report indicated that the G and P gene of SVCV shared similar topologies of evolutionary trees. In this study, phylogenetic analysis based on the P gene sequences showed the SVCV-265 was clustered into Iai subgroup and divergent from Chinese isolates A1, A2 and BJ0505-2, which were clustered into Iaii group. However, sequence alignment of the G gene showed the SVCV-265 has a close relationship with A1, A2 and BJ0505-2 isolates. Recombination analysis of all the whole sequences of SVCV available revealed isolates A2 and BJ0505-2 were likely the homologous recombination descendants of the A1 and SVCV-265. The crossover regions were located between 3845-6387 nt for A2 and 3573-6444 nt for BJ0505-2, respectively. Phylogenetic analysis of the crossover region further confirmed these findings. This current study describes the molecular characterization of the new isolate SVCV-265 from China and is the first report of homologous recombination in SVCV.