Entamoeba and Giardia parasites implicated as hosts of CRESS viruses
Entamoeba and Giardia parasites implicated as hosts of CRESS viruses
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DOI：
10.1038/s41467-020-18474-w
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发表时间：
2020-09-15
影响因子：
16.6
通讯作者：
Van der Hoek, Lia
中科院分区：
文献类型：
--
作者：
Kinsella, Cormac M.;Bart, Aldert;Van der Hoek, Lia
元基因组学技术已经使得无需在细胞培养中分离就能对未知病毒进行基因组测序，但是关于病毒宿主的信息往往缺乏，从而阻碍了病毒特征的描述。能够仅根据基因组数据识别病毒宿主的高通量方法将有助于评估其医学或生物学相关性。在这里，我们通过将人类粪便样本中三个病毒家族的宏基因组发现与可能宿主的确定联系起来来解决这一问题。病毒之间的重组提供了一个共享宿主的证据，在这个宿主中发生了基因交换。我们利用病毒重组网络来划分病毒-宿主集群，然后利用(1)与临床样本中的宿主生物的统计关联，(2)宿主基因组中的内源性病毒元素，以及(3)宿主对这些元素的小RNA反应的证据，将病毒-宿主集群固定在特定的宿主上。这一分析表明，CRESS病毒有两个科（纳雅病毒科和内雅病毒科）感染内阿米巴寄生虫，而第三个科（维雅病毒科）感染十二指肠贾第虫。这三种病毒补充了已知感染真核生物的五个CRESS病毒家族，将CRESS病毒宿主范围扩大到原生动物。系统发育分析表明，感染多细胞生命的CRESS病毒至少在三种情况下独立进化。
Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluation of their medical or biological relevance. Here, we address this by linking metagenomic discovery of three virus families in human stool samples with determination of probable hosts. Recombination between viruses provides evidence of a shared host, in which genetic exchange occurs. We utilise networks of viral recombination to delimit virus-host clusters, which are then anchored to specific hosts using (1) statistical association to a host organism in clinical samples, (2) endogenous viral elements in host genomes, and (3) evidence of host small RNA responses to these elements. This analysis suggests two CRESS virus families (Naryaviridae and Nenyaviridae) infect Entamoeba parasites, while a third (Vilyaviridae) infects Giardia duodenalis. The trio supplements five CRESS virus families already known to infect eukaryotes, extending the CRESS virus host range to protozoa. Phylogenetic analysis implies CRESS viruses infecting multicellular life have evolved independently on at least three occasions.