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

Authors: Wu, Q.; Luo, Y.; Lu, R.; Lau, N.; Lai, E. C.; Li, W. X.; Ding, S. W.
Article Title: Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs
Abstract: 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.
Keywords: nonhuman; animals; cell line; rna, small interfering; vertebrata; molecular sequence data; virus rna; rna viruses; base sequence; caenorhabditis elegans; drosophila melanogaster; virus genome; virus detection; virus transmission; rna, viral; rna sequence; invertebrata; virus assembly; arthropoda; mosquito; arboviruses; massively parallel sequencing; pirnas; sirnas; viral immunity; culicidae; genome, viral; arbovirus
Journal Title: Proceedings of the National Academy of Sciences of the United States of America
Volume: 107
Issue: 4
ISSN: 0027-8424
Publisher: National Academy of Sciences  
Date Published: 2010-01-01
Start Page: 1606
End Page: 1611
Language: English
DOI: 10.1073/pnas.0911353107
PUBMED: 20080648
PROVIDER: scopus
PMCID: PMC2824396
Notes: --- - "Cited By (since 1996): 18" - "Export Date: 20 April 2011" - "CODEN: PNASA" - "Source: Scopus"
Citation Impact
MSK Authors
  1. Eric C Lai
    140 Lai