Aphids (order Hemiptera) are important insect pests of crops and are also vectors of many plant viruses. However, little is known about aphid-infecting viruses, particularly their diversity and relationship to plant viruses. To investigate the aphid viromes, we performed deep sequencing analyses of the aphid transcriptomes from infested barley plants in a field in Japan. We discovered virus-like sequences related to nege/kita-, flavi-, tombus-, phenui-, mononega-, narna-, chryso-, partiti-, and luteoviruses. Using RT-PCR and sequence analyses, we determined almost complete sequences of seven nege/kitavirus-like virus genomes; one of which was a variant of the Wuhan house centipede virus (WHCV-1). The other six seem to belong to four novel viruses distantly related to Wuhan insect virus 9 (WhIV-9) or Hubei nege-like virus 4 (HVLV-4). We designated the four viruses as barley aphid RNA virus 1 to 4 (BARV-1 to -4). Moreover, some nege/kitavirus-like sequences were found by searches on the transcriptome shotgun assembly (TSA) libraries of arthropods and plants. Phylogenetic analyses showed that BARV-1 forms a clade with WHCV-1 and HVLV-4, whereas BARV-2 to -4 clustered with WhIV-9 and an aphid virus, Aphis glycines virus 3. Both virus groups (tentatively designated as Centivirus and Aphiglyvirus, respectively), together with arthropod virus-like TSAs, fill the phylogenetic gaps between the negeviruses and kitaviruses lineages. We also characterized the flavi/jingmen-like and tombus-like virus sequences as well as other RNA viruses, including six putative novel viruses, designated as barley aphid RNA viruses 5 to 10. Interestingly, we also discovered that some aphid-associated viruses, including nege/kita-like viruses, were present in different aphid species, raising a speculation that these viruses might be distributed across different aphid species with plants being the reservoirs. This study provides novel information on the diversity and spread of nege/kitavirus-related viruses and other RNA viruses that are associated with aphids.

中文翻译：

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侵染大麦田的蚜虫种群的病毒组分析：两类新的 Nege/Kita 样病毒和其他新的 RNA 病毒的发现。

蚜虫（半翅目）是农作物的重要害虫，也是许多植物病毒的载体。然而，人们对蚜虫感染病毒知之甚少，特别是它们的多样性以及与植物病毒的关系。为了研究蚜虫病毒组，我们对日本田间受感染的大麦植物的蚜虫转录组进行了深度测序分析。我们发现了与 nege/kita-、flavi-、tombus-、phenui-、mononega-、narna-、chryso-、partiti- 和 uteoviruses 相关的病毒样序列。使用 RT-PCR 和序列分析，我们确定了 7 个 nege/kitavirus 样病毒基因组的几乎完整序列；其中之一是武汉蜈蚣病毒（WHCV-1）的变种。另外六种似乎属于与武汉昆虫病毒9（WhIV-9）或湖北尼格样病毒4（HVLV-4）有远亲关系的四种新型病毒。我们将这四种病毒命名为大麦蚜RNA病毒1至4（BARV-1至-4）。此外，通过对节肢动物和植物的转录组鸟枪组装（TSA）文库的搜索发现了一些nege/kitavirus样序列。系统发育分析表明，BARV-1 与 WHCV-1 和 HVLV-4 形成一个分支，而 BARV-2 至 -4 与 WhIV-9 和蚜虫病毒 Aphis sweetines 病毒 3 聚类。两个病毒组（暂定为 Centivirus 和Aphiglyvirus，分别）与节肢动物病毒样 TSA 一起，填补了 negeviruses 和 kitaviruses 谱系之间的系统发育空白。我们还对 flavi/jingmen-like 和 tombus-like 病毒序列以及其他 RNA 病毒进行了表征，包括六种假定的新型病毒，称为大麦蚜 RNA 病毒 5 至 10。有趣的是，我们还发现了一些与蚜虫相关的病毒，包括 nege/kita 样病毒，存在于不同的蚜虫物种中，这引发了人们的猜测，即这些病毒可能分布在不同的蚜虫物种中，而植物是宿主。这项研究提供了有关 nege/kitavirus 相关病毒和其他与蚜虫相关的 RNA 病毒的多样性和传播的新信息。