Origin and Phylodynamics of Rabbit Hemorrhagic Disease Virus
Origin and Phylodynamics of Rabbit Hemorrhagic Disease Virus
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DOI：
10.1128/jvi.01523-09
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发表时间：
2009-12-01
影响因子：
5.4
通讯作者：
Holmes, Edward C.
中科院分区：
文献类型：
--
作者：
Kerr, Peter J.;Kitchen, Andrew;Holmes, Edward C.
为了确定兔出血症病毒（RHDV）的起源，系统发育关系和进化动力学，我们检查了210个部分和完整的衣壳基因核苷酸序列。使用贝叶斯马尔可夫链蒙特卡罗方法，我们估计这些序列以每年每个位点3.9 × 10（-4）至11.9 × 10（-4）核苷酸替换的速率进化。这一比率在数据子集中是一致的，对重组的反应是稳健的，并对20世纪50年代至70年代分离的病毒株的来源产生了怀疑，这些病毒株与现代分离株具有很强的序列相似性。使用相同的分析，我们推断RHDV和兔杯状病毒序列联合组的最近共同祖先的时间是< 550年前，而自1984年以来在世界各地传播的RHDV分离株的时间是< 150年前。重要的是，在1984年中国大规模爆发之前，RHDV的多个谱系明显流行，这一发现表明RHDV毒力的早期进化。将RHDV分为4个系统发生群，并分别进行了分析。每个群体在20世纪60年代中期或更早的时候都有一个共同的祖先，并且每个群体都在1984年之前开始人口扩张。值得注意的是，以抗原变体RHDVa为特征的组具有最大的遗传多样性，与升高的适应性相容。总的来说，我们认为RHDV的高毒力可能在世纪早期进化过一次，远早于1984年有文献记载的兔出血性疾病的出现。
To determine the origin, phylogenetic relationships, and evolutionary dynamics of rabbit hemorrhagic disease virus (RHDV), we examined 210 partial and complete capsid gene nucleotide sequences. Using a Bayesian Markov chain Monte Carlo approach, we estimated that these sequences evolved at a rate of 3.9 x 10(-4) to 11.9 x 10(-4) nucleotide substitutions per site per year. This rate was consistent across subsets of data, was robust in response to recombination, and casts doubt on the provenance of viral strains isolated from the 1950s to the 1970s, which share strong sequence similarity to modern isolates. Using the same analysis, we inferred that the time to the most recent common ancestor for a joint group of RHDV and rabbit calicivirus sequences was < 550 years ago and was < 150 years ago for the RHDV isolates that have spread around the world since 1984. Importantly, multiple lineages of RHDV were clearly circulating before the major Chinese outbreak of 1984, a finding indicative of an early evolution of RHDV virulence. Four phylogenetic groups within RHDV were defined and analyzed separately. Each group shared a common ancestor in the mid-1960s or earlier, and each showed an expansion of populations starting before 1984. Notably, the group characterized by the antigenic variant RHDVa harbors the greatest genetic diversity, compatible with an elevated fitness. Overall, we contend that the high virulence of RHDV likely evolved once in the early part of the 20th century, well before the documented emergence of rabbit hemorrhagic disease in 1984.