The use of RNA-dependent RNA polymerase for the taxonomic assignment of Picorna-like viruses (order Picornavirales) infecting Apis mellifera L. populations
The use of RNA-dependent RNA polymerase for the taxonomic assignment of Picorna-like viruses (order Picornavirales) infecting Apis mellifera L. populations
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DOI：
10.1186/1743-422x-5-10
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发表时间：
2008-01-22
期刊：
影响因子：
4.8
通讯作者：
Schroeder, Declan C.
中科院分区：
文献类型：
--
作者：
Baker, Andrea C.;Schroeder, Declan C.
背景：单链RNA病毒，感染欧洲蜜蜂.已知在蜂群中以低水平存在，在蜜蜂中通常没有观察到明显的感染迹象。RNA依赖的RNA聚合酶（RdRp）的区域的逆转录- PCR（RT-PCR）经常被用于诊断它们在养蜂场中的存在并且也用于对检测到的病毒类型进行分类。结果：对新定义的目的，小核糖核酸病毒目的成员进行RdRp保守结构域的分析;特别关注已知保守的氨基酸残基和基序。使用迄今为止公布的部分和完整的蜜蜂病毒序列编译共有序列。在RdRp保守结构域上，伊弗拉病毒属的某些成员，如变形翅病毒（DWV）、卡久戈病毒（KV）和狄斯瓦螨病毒（VDV）;以及双顺反子病毒属的某些成员，如急性蜜蜂麻痹病毒（ABPV）、以色列麻痹病毒（IAPV）和克什米尔蜜蜂病毒（KBV），分别具有大于98%和92%的同源性。RdRp被验证为一个合适的分类标记的目的小核糖核酸病毒目的成员分配，与其他遗传或表型标记独立使用的潜力。尽管目前使用的RdRp作为一种遗传标记，用于检测特定的蜜蜂病毒，我们提供了压倒性的证据表明，应小心与引物组的设计。我们证明了DWV、VDV和KV，或ABPV、IAPV和KBV分别是彼此的最近后代或变体，这意味着当使用当前RdRp引物组时，在确定这些病毒中任何一种的存在或不存在时应谨慎。此外，更有可能的是，一些引物组（无论使用什么基因）过于特异，从而低估了蜜蜂病毒的多样性。
Background: Single- stranded RNA viruses, infectious to the European honeybee, Apis mellifera L. are known to reside at low levels in colonies, with typically no apparent signs of infection observed in the honeybees. Reverse transcription- PCR ( RT- PCR) of regions of the RNA- dependent RNA polymerase ( RdRp) is often used to diagnose their presence in apiaries and also to classify the type of virus detected.Results: Analysis of RdRp conserved domains was undertaken on members of the newly defined order, the Picornavirales; focusing in particular on the amino acid residues and motifs known to be conserved. Consensus sequences were compiled using partial and complete honeybee virus sequences published to date. Certain members within the iflaviruses, deformed wing virus ( DWV), Kakugo virus ( KV) and Varroa destructor virus ( VDV); and the dicistroviruses, acute bee paralysis virus ( ABPV), Israeli paralysis virus ( IAPV) and Kashmir bee virus ( KBV), shared greater than 98% and 92% homology across the RdRp conserved domains, respectively.Conclusion: RdRp was validated as a suitable taxonomic marker for the assignment of members of the order Picornavirales, with the potential for use independent of other genetic or phenotypic markers. Despite the current use of the RdRp as a genetic marker for the detection of specific honeybee viruses, we provide overwhelming evidence that care should be taken with the primer set design. We demonstrated that DWV, VDV and KV, or ABPV, IAPV and KBV, respectively are all recent descendents or variants of each other, meaning caution should be applied when assigning presence or absence to any of these viruses when using current RdRp primer sets. Moreover, it is more likely that some primer sets ( regardless of what gene is used) are too specific and thus are underestimating the diversity of honeybee viruses.