We have used multiplexed high-throughput sequencing to characterize changes in small RNA populations that occur during viral infection in animal cells. Small RNA-based mechanisms such as RNA interference (RNAi) have been shown in plant and invertebrate systems to play a key role in host responses to viral infection. Although homologs of the key RNAi effector pathways are present in mammalian cells, and can launch an RNAi-mediated degradation of experimentally targeted mRNAs, any role for such responses in mammalian host-virus interactions remains to be characterized. Six different viruses were examined in 41 experimentally susceptible and resistant host systems. We identified virus-derived small RNAs (vsRNAs) from all six viruses, with total abundance varying from “vanishingly rare” (less than 0.1% of cellular small RNA) to highly abundant (comparable to abundant micro-RNAs “miRNAs”). In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host miRNA profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We also found evidence for populations of vsRNAs that exist as duplexed siRNAs with zero to three nucleotide 3′ overhangs. Using populations of cells carrying a Hepatitis C replicon, we observed strand-selective loading of siRNAs onto Argonaute complexes. These experiments define vsRNAs as one possible component of the interplay between animal viruses and their hosts.

The widespread class of RNA viruses that utilize internal ribosome entry sites (IRESs) for translation include poliovirus and Hepatitis C virus. To identify host factors required for IRES-dependent translation and viral replication, we performed a genome-wide RNAi screen in Drosophila cells infected with Drosophila C virus (DCV). We identified 66 ribosomal proteins that, when depleted, specifically inhibit DCV growth, but not a non-IRES-containing RNA virus. Moreover, treatment of flies with a translation inhibitor is protective in vivo. Finally, this increased sensitivity to ribosome levels also holds true for poliovirus infection of human cells, demonstrating the generality of these findings.[Keywords: Drosophila C virus; Drosophila; ribosome; translation; picornavirus; dicistroviridae] Supplemental material is available at http://www.genesdev.org.

It has been known for a long time that infection of cultured cells with poliovirus results in the overall inhibition of transcription of most host genes. We examined whether selected host genes can escape transcriptional inhibition by thiouridine marking newly synthesized host mRNAs during viral infection. Using cDNA microarrays hybridized to cDNAs made from thiolated mRNAs, a small set of host transcripts was identified and their expression verified by quantitative PCR and Northern and Western blot analyses. These transcripts were synthesized from genes that displayed enrichment for NF-B binding sites in their promoter regions, suggesting that some NF-B-regulated promoters can escape the virus-induced inhibition of transcription. In particular, two negative regulators of NF-B, IBa and A20, were upregulated during viral infection. Depletion of A20 enhanced viral RNA abundance and viral yield, arguing that cells respond to virus infection by counteracting NF-B-induced proviral effects.

Summary Classified as Critically Endangered, the Ultramarine Lorikeet Vini ultramarina is one of the world’s most threatened lorikeet species. Endemic to the Marquesas Islands in French Polynesia, the species was formerly distributed over most islands in the archipelago, but is today found primarily on the island of Ua Huka, its range having contracted significantly in recent decades. Habitat alteration and loss, and over-exploitation of natural resources, are cited as impacting the Ultramarine Lorikeet, but the influence of introduced black rats Rattus rattus as predators has been implicated as the primary threat to the species. To assess population status and document aspects of the species biology, including habitat preferences and diet, we conducted the first systematic surveys of the species during two independent surveys spaced seven years apart (2002 and 2009). Population estimates of 2,011 ± 284 (in 2002) and 1,922 (in 2009) individuals on Ua Huka suggest the population was relatively healthy and stable between these periods. However, surveys and searches of other islands in the species’ contemporary range, where black rats occur, either failed to document the species or noted very few individuals. These findings highlight the critical importance of Ua Huka as a rat-free refuge and the value of our surveys as baseline estimates of the population status of the species. We discuss the conservation implications of our findings and propose recommendations to secure the species’ future survival.

It has recently come to our attention that there were errors in the assembly of Fig. 2B. We apologize for these errors and make the following changes. Page 10103, column 2, lines 18 to 19: "IER3, A20, IFIT2, IL-6, and CCL2" should read "IER3, A20, IL-6, and CCL2." Page 10105, Fig. 2B, row OCIAD1: Northern blot data represented by the four panels of row OCIAD1 are correct, but there appears to have been a duplication in the figure assembly. We have a paper copy of the original Northern blot data, but we do not have a digital image file of OCIAD1. The four panels of row OCIAD1 have been deleted. Page 10105, Fig. 2B, row ACT: The 2nd panel of row ACT was incorrectly reversed during figure assembly. This panel has been reversed so that the orientation is correct. Page 10105, Fig. 2B, row A20: Northern blot data represented by the four panels of row A20 are correct, but there appears to have been a duplication in the figure assembly. The four panels of row A20 have been replaced using an original digital image file of the A20 Northern blot. Page 10105, Fig. 2B, row IFIT2: Northern blot data represented by panels 3 and 4 of row IFIT2 are correct, but we cannot locate a Northern blot digital image file for panels 1 and 2. The four panels of row IFIT2 have been deleted. Figure 2B should appear as shown below.