Full genome-based classification of rotaviruses reveals a common origin between human Wa-like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains
Full genome-based classification of rotaviruses reveals a common origin between human Wa-like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains
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DOI：
10.1128/jvi.02257-07
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发表时间：
2008-04-01
影响因子：
5.4
通讯作者：
Van Ranst, Marc
中科院分区：
文献类型：
--
作者：
Matthijnssens, Jelle;Ciarlet, Max;Van Ranst, Marc
目前，A组轮状病毒的分类是基于两种外层蛋白VP7和VP4以及中间层蛋白VP6的分子特性。由于所有11个轮状病毒基因片段的重组在自然界轮状病毒多样性的产生中起着关键作用，因此需要一个基于所有轮状病毒基因片段的分类系统，以确定哪些基因影响轮状病毒的宿主范围限制、复制和毒力，以及研究轮状病毒的流行病学和进化。为了建立这样的分类系统，我们在数据库现有的基础上，确定了不同G和P基因型的人和动物轮状病毒株的VP1 ~ VP3、VP6和NSP1 ~ NSP5的基因序列，并利用它们来确定所有轮状病毒基因之间的系统发育关系。基于这些系统发育分析，为每个基因确定了适当的识别截止值。对于VP4基因，80%的核苷酸识别截断值与27个已建立的P基因型完全相关。对于VP7基因，80%的核苷酸识别切断值与已建立的G基因型基本一致，但鉴定出另外四种不同的基因型，包括鼠或禽轮状病毒株。对VP1 ~ VP3、VP6和NSP1 ~ NSP5基因的系统发育分析显示，分别存在4、5、6、11、14、5、7、11和6个基因型，核苷酸同源截断值分别为83%、84%、81%、85%、79%、85%、85%、85%和91%。根据这些数据，提出了一种修订的轮状病毒毒株命名法。新的分类系统允许鉴定：(1)不同的基因型，它们可能遵循不同的进化路径；（ii）种间传播和大量的再组合事件；以及（iii）某些基因序列显示(a)人类类华轮状病毒毒株与猪轮状病毒毒株之间具有共同起源，以及(b)人类类ds -1轮状病毒毒株与牛轮状病毒毒株之间具有共同起源。人类和动物轮状病毒之间的这些密切进化联系强调有必要同时密切监测动物和人体内的轮状病毒。
Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans.