Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

Barzon, Luisa; Lavezzo, Enrico; Militello, Valentina; Toppo, Stefano; Palù, Giorgio

Another interesting strategy to discover arthropod-borne viruses exploits the property of invertebrates to respond to infection by processing viral RNA genomes into siRNAs of discrete sizes. A recent study on small RNA libraries sequenced by NGS platforms [37] showed that viral small silencing RNAs produced by invertebrate animals are overlapping in sequence and can assemble into long contiguous fragments of the invading viral genome. Based on this finding, an approach of virus discovery in invertebrates by deep sequencing and assembly of total small RNAs was developed and applied to the analysis of contigs (i.e., a contiguous length of genomic sequences in which the order of bases is known to a high confidence level) assembled from published small RNA libraries. Five previously undescribed viruses from cultured Drosophila cells and adult mosquitoes were discovered, including three with a positive-strand RNA genome and two with a dsRNA genome [37] . This strategy for virus discovery based on deep sequencing of small RNAs has been also successfully used in plant virology [38] .