Fitzner Andrzej, Niedbalski Wieslaw
Department of Foot and Mouth Disease, National Veterinary Research Institute, Wodna 7, 98-220, Zduńska Wola, Poland.
Arch Virol. 2017 Oct;162(10):3197-3203. doi: 10.1007/s00705-017-3476-0. Epub 2017 Jul 12.
The aim of this study was to characterise the nucleotide and amino acid sequence of complete genomes (7.5 kb) from RHDV strains isolated in Poland and estimate the genetic variability in different elements of the viral RNA. In addition, the sequence of Polish RHDV isolates isolated from 1988-2015 was compared with the sequences of other European RHDV, including the RHDVa and RHDV2/RHDVb subtypes. The complete sequence was developed by the compilation of partial nucleotide sequences. This sequence consisted of approximately 7428 nucleotides. For comparison of nucleotide sequences and the development of phylogenetic trees of Polish RHDV isolates and reference RHDV strains representing the main phylogenetic groups of classical RHDV, RHDVa and RHDV2 as well as the non-pathogenic rabbit lagovirus RCV, the BLAST software with blastn and MEGA6 with neighbour-joining method was applied. The complete nucleotide sequence of Polish isolates of RHDV has also been entered into GenBank. For comparative analysis, nineteen complete sequences representing the main RHDV genetic types available in GenBank were used. The results of phylogenetic analysis of Polish RHDV strains reveals the presence of three classical RHDV genogroups (G2, G4 and G5) and an RHDVa variant (G6). The oldest RHDV isolates (KGM 1988, PD 1989 and MAL 1994) belong to genogroup G2. It can be assumed that the elimination of these strains from the environment probably occurred at the turn of 1994 and 1995. Genogroup G2 was replaced by the phylogenetically younger BLA 1994 and OPO 2004 strains from genogroup G4, which probably originated from the G3 lineage, represented by the Italian strains BS89. The last representatives of classical RHDV in Poland are isolates GSK 1988 and ZD0 2000 from genogroup G5. A single clade contains the Polish RHDV strains from 2004-2015 (GRZ 2004, KRY 2004, L145 2004, W147 2005, SKO 2013, GLE 2013, RED1 2013, STR 2012, STR2 2013, STR 2014, BIE 2015) identified as RHDVa, which clustered into genogroup G6, as represented by the RHDV strain Triptis 1996. All recent isolated RHDV isolates belong exclusively to RHDVa and no RHDV2 was diagnosed in Poland.
本研究的目的是对从波兰分离出的兔出血症病毒（RHDV）毒株的完整基因组（7.5 kb）的核苷酸和氨基酸序列进行特征分析，并估计病毒RNA不同元件中的遗传变异性。此外，将1988 - 2015年从波兰分离出的RHDV毒株序列与其他欧洲RHDV的序列进行比较，包括RHDVa和RHDV2/RHDVb亚型。完整序列是通过拼接部分核苷酸序列得到的。该序列由大约7428个核苷酸组成。为了比较核苷酸序列并构建波兰RHDV分离株以及代表经典RHDV、RHDVa和RHDV2主要系统发育组的参考RHDV毒株以及非致病性兔杯状病毒RCV的系统发育树，应用了带有blastn的BLAST软件和采用邻接法的MEGA6软件。波兰RHDV分离株的完整核苷酸序列也已提交至GenBank。为进行比较分析，使用了GenBank中19个代表主要RHDV基因类型的完整序列。对波兰RHDV毒株的系统发育分析结果显示存在三个经典RHDV基因组（G2、G4和G5）以及一个RHDVa变体（G6）。最古老的RHDV分离株（KGM 1988、PD 1989和MAL 1994）属于基因组G2。可以推测这些毒株在1994年和1995年之交可能已从环境中消失。基因组G2被来自基因组G4的系统发育上较年轻的BLA 1994和OPO 2004毒株所取代，这些毒株可能起源于以意大利毒株BS89为代表的G3谱系。波兰经典RHDV的最后代表是来自基因组G5的GSK 1988和ZD0 2000分离株。一个单独的分支包含2004 - 2015年的波兰RHDV毒株（GRZ 2004、KRY 2004、L145 2004、W147 2005、SKO 2013、GLE 2013、RED1 2013、STR 2012、STR2 2013、STR 2014、BIE 2015），这些毒株被鉴定为RHDVa，它们聚集成基因组G6，以RHDV毒株Triptis 1996为代表。所有最近分离的RHDV毒株仅属于RHDVa，在波兰未诊断出RHDV2。
