|Nandety, R. S.|
|Fofanov, V. Y.|
|Falk, B. W.|
Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/6/2013
Publication Date: 6/12/2013
Citation: Nandety, R., Fofanov, V., Koshinsky, H., Stenger, D.C., Falk, B. 2013. Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis. Virology. 442:12-19. Interpretive Summary: Infected hosts respond to viral infection via production of small RNAs corresponding to the viral genome sequence. Here, populations of small RNAs, accumulating in the glassy-winged sharpshooter in response to infection by two unrelated viruses, were analyzed using Next Generation Sequencing methodology. Most small RNAs corresponding to viral sequences were 21 nucleotides in length, indicating a common mechanism of biosynthesis. Small RNAs corresponding to the single-stranded plus-sense virus Homalodisca coagulata virus-1 (HoCV-1) mapped to the positive sense RNA, and with the exception of a few minor hot-spots, were distributed across the entire genome of HoCV-1. In contrast, small RNAs corresponding to the double-stranded, multi-segmeted virus Homalodisca vitripennis reovirus (HoVRV) mapped to both positive and negative sense strands, with most significant hotspots occurring near RNA ends. These data suggest that taxonomically different viruses in the same host offer different targets for RNA-antiviral defense.
Technical Abstract: Next generation sequencing was used to analyze virus-derived small RNA (vsRNA) profiles for two taxonomically unrelated viruses infecting Homalodisca vitripennis, the glassy winged sharpshooter. Homalodisca coagulata virus-1 (HoCV-1), family Dicistroviridae, and Homalodisca vitripennis virus (HoVRV), family Reoviridae, commonly co-infect H. vitripennis. The vsRNAs were mapped against the monopartite genome of HoCV-1 and all 12 genome segments of HoVRV from doubly-infected insects. The most common size vsRNAs for both viruses was 21 nt, indicating a Dicer-2 mediated processing of vsRNAs. However, strikingly contrasting patterns for vsRNA mapping against the HoCV-1 and HoVRV genomic RNAs were observed. For HoCV-1, the majority of vsRNAs mapped to the genomic positive-strand RNA compared to complementary negative-strand and, although minor hotspots were observed, vsRNAs mapped across the entire HoCV-1 genome. In contrast, HoVRV vsRNAs mapped to both positive and negative-sense strands for all genome segments, but different genomic segments showed distinct patterns. HoVRV vsRNAs were enriched for 5' and 3' regions along with subtle enrichments on negative-sense strands of some HoVRV segments. HoVRV vsRNAs mapping patterns, corresponding to positive and negative-sense strands of HoVRV segment 1, were further validated using quantitative northern blots. These data suggest that taxonomically different viruses in the same host offer different targets for RNA-antiviral defense.