Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs

被引:385
作者
Wu, Qingfa [1 ]
Luo, Yingjun [1 ]
Lu, Rui [1 ]
Lau, Nelson [2 ]
Lai, Eric C. [3 ]
Li, Wan-Xiang [1 ]
Ding, Shou-Wei [1 ]
机构
[1] Univ Calif Riverside, Dept Plant Pathol & Microbiol, Inst Integrat Genome Biol, Riverside, CA 92521 USA
[2] Brandeis Univ, Dept Biol, Waltham, MA 02454 USA
[3] Sloan Kettering Inst, Dept Dev Biol, New York, NY 10065 USA
基金
美国国家卫生研究院;
关键词
arboviruses; piRNAs; siRNAs; viral immunity; massively parallel sequencing; ANTIVIRAL IMMUNITY; INTERFERING RNAS; DROSOPHILA; GENE; SUPPRESSION; INDUCTION; MECHANISM; INFECTION; NODAVIRUS; DEFENSE;
D O I
10.1073/pnas.0911353107
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
In response to infection, invertebrates process replicating viral RNA genomes into siRNAs of discrete sizes to guide virus clearance by RNA interference. Here, we show that viral siRNAs sequenced from fruit fly, mosquito, and nematode cells were all overlapping in sequence, suggesting a possibility of using siRNAs for viral genome assembly and virus discovery. To test this idea, we examined contigs assembled from published small RNA libraries and discovered five previously undescribed viruses from cultured Drosophila cells and adult mosquitoes, including three with a positive-strand RNA genome and two with a dsRNA genome. Notably, four of the identified viruses exhibited only low sequence similarities to known viruses, such that none could be assigned into an existing virus genus. We also report detection of virus-derived PIWI-interacting RNAs (piRNAs) in Drosophila melanogaster that have not been previously described in any other host species and demonstrate viral genome assembly from viral piRNAs in the absence of viral siRNAs. Thus, this study provides a powerful culture-independent approach for virus discovery in invertebrates by assembling viral genomes directly from host immune response products without prior virus enrichment or amplification. We propose that invertebrate viruses discovered by this approach may include previously undescribed human and vertebrate viral pathogens that are transmitted by arthropod vectors.
引用
收藏
页码:1606 / 1611
页数:6
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