Abstract: Three pairs of overlapped primers were designed to amplify the coding sequences (CDS) of spring virernia of carp virus (SVCV) (designated as SVCV-shlj4) genome according to genome of SVCV-A2 (DQ491000.1) strain in the GenBank to analyze the complete genomic sequence of a current SVCV isolated in northern China. RACE Kit was used to clone the non-coding regions of the genome 5′ untranslated region (UTR) and 3′ UTR. The total genomic sequences of SVCV-shlj4 were spliced by DNAstar software, and phylogenetic analysis was performed based on the genome and its encoded matrix protein, glycoprotein and phosphoprotein by Lasergene and MEGA5.1 software. The complete genome of SVCV-shlj4 strain was shown to be 11 029 bp in length, and to code five structural proteins from the 3′ end to the 5′ end, encoding nuclear proteins (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA polymerase (L). The phylogenetic analysis of complete genomic sequence showed that SVCV-shlj4 had the maximal genome similarity of 99.0% with that of a Chinese SVCV-A2 strain, and had the minimal genome similarity of 93.0% with a European SVCV VR-1390 strain. The phylogenetic analysis based on the N protein, G protein and P protein revealed that the SVCV-shlj4 strain clustered into the Asian branch, belonged to the Iaii subgenogroups within the Ia genogroup. Compared with the Chinese strain SVCV-A1, SVCV-shlj4 lacked 1 bp in the 1357, 1364 and 1376 nt sites of the N protein gene coding region, and two gene fragments (44 bp and 31 bp) were deleted from the 4630 and 4639 nt sites in the 3′ non-coding region of the G gene. SVCV-shlj4 inserted a 10 bp gene fragment in the 3′ non-coding region of the G gene (4637 nt site) compared with the European strain VR-1390, and lacked 18 bp in the coding region of the L protein gene (5822 nt site) compared with the Chinese SVCV BJ0505-2 strain. In present experiment, the molecular genetic characteristics of the current prevalent strain (SVCV-shlj4) in northern China were systematically analyzed which provided data support with the research on the molecular evolution of SVCV.
林婧楠, 徐黎明, 赵景壮, 任广明, 卢彤岩. 一株鲤春病毒血症病毒SVCV-shlj4全基因组序列分析[J]. 大连海洋大学学报, 2020, 35(5): 707-713.
LIN Jingnan, XU Liming, ZHAO Jingzhuang, REN Guangming, LU Tongyan. Complete genomic sequence of a spring virernia of carp virus SVCV- shlj4 isolated from common carp Cyprinus carpio in China. Journal of Dalian Ocean University, 2020, 35(5): 707-713.
2020, Vol. 35 
