Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China.
Department of Molecular Genetics and Development, University of Montreal, Montreal, QC H3T 1J4, Canada.
Viruses. 2023 Mar 23;15(4):815. doi: 10.3390/v15040815.
Rabbit haemorrhagic disease virus (RHDV), European brown hare syndrome virus (EBHSV), rabbit calicivirus (RCV), and hare calicivirus (HaCV) belong to the genus of the family that causes severe diseases in rabbits and several hare () species. Previously, Lagoviruses were classified into two genogroups, e.g., GI (RHDVs and RCVs) and GII (EBHSV and HaCV) based on partial genomes, e.g., VP60 coding sequences. Herein, we provide a robust phylogenetic classification of all the Lagovirus strains based on full-length genomes, grouping all the available 240 strains identified between 1988 and 2021 into four distinct clades, e.g., GI.1 (classical RHDV), GI.2 (RHDV2), HaCV/EBHSV, and RCV, where the GI.1 clade is further classified into four (GI.1a-d) and GI.2 into six sub-clades (GI.2a-f). Moreover, the phylogeographic analysis revealed that the EBHSV and HaCV strains share their ancestor with the GI.1, while the RCV shares with the GI.2. In addition, all 2020-2021 RHDV2 outbreak strains in the USA are connected to the strains from Canada and Germany, while RHDV strains isolated in Australia are connected with the USA-Germany haplotype RHDV strain. Furthermore, we identified six recombination events in the VP60, VP10, and RNA-dependent RNA polymerase (RdRp) coding regions using the full-length genomes. The amino acid variability analysis showed that the variability index exceeded the threshold of 1.00 in the ORF1-encoded polyprotein and ORF2-encoded VP10 protein, respectively, indicating significant amino acid drift with the emergence of new strains. The current study is an update of the phylogenetic and phylogeographic information of Lagoviruses that may be used to map the evolutionary history and provide hints for the genetic basis of their emergence and re-emergence.
兔出血症病毒（RHDV）、欧洲褐兔综合征病毒（EBHSV）、兔杯状病毒（RCV）和野兔杯状病毒（HaCV）属于杯状病毒科的属，可引起兔和几种野兔物种的严重疾病。以前，根据部分基因组（如 VP60 编码序列），将 Lagoviruses 分为两个基因群，GI（RHDV 和 RCV）和 GII（EBHSV 和 HaCV）。在此，我们基于全长基因组对所有 Lagovirus 株进行了稳健的系统发育分类，将 1988 年至 2021 年间鉴定的所有 240 株可用菌株分为四个不同的分支，如 GI.1（经典 RHDV）、GI.2（RHDV2）、HaCV/EBHSV 和 RCV，其中 GI.1 分支进一步分为四个（GI.1a-d）和 GI.2 分为六个亚分支（GI.2a-f）。此外，系统地理分析表明，EBHSV 和 HaCV 株与 GI.1 的祖先共享，而 RCV 与 GI.2 的祖先共享。此外，美国 2020-2021 年的所有 RHDV2 暴发株都与加拿大和德国的菌株有关，而澳大利亚分离的 RHDV 株与美国-德国 RHDV 株有关。此外，我们在全长基因组中使用六个重组事件在 VP60、VP10 和 RNA 依赖性 RNA 聚合酶（RdRp）编码区中鉴定了六个重组事件。氨基酸变异分析表明，ORF1 编码的多蛋白和 ORF2 编码的 VP10 蛋白的变异指数分别超过了 1.00 的阈值，表明新菌株的出现导致氨基酸漂移显著。本研究是对 Lagoviruses 的系统发育和系统地理信息的更新，可用于绘制进化史，并为它们的出现和再次出现提供遗传基础的线索。
