Identification of evolutionarily conserved pro-viral and anti-viral host factors from worms to mammals

ABSTRACT Viruses are obligate intracellular parasites that have evolved to co-exist with their hosts. As such, they have the ability to both hijack the necessary host machinery to promote viral proliferation as well as to antagonize host immune defenses. Despite extensive research in these areas there are still significant gaps in our knowledge of the repertoire of host genes that function in either pro-viral or anti-viral manner. A novel strategy to identify host genes that are important for mammalian virus infection takes advantage of the model organism C. elegans. Due to its simplicity and the fact that ~40% of its genes (~7500) are conserved with humans, C. elegans has played a key role in many fundamental discoveries in biology. However, its use in the study of virology had been limited by the lack of known viruses capable of naturally infecting C. elegans until the discovery in 2011 of Orsay Virus. Orsay virus is a non-enveloped positive sense RNA virus related to viruses in the families Picorna-, Calici- and Astroviridae, and thus it can serve as a model for many pathogenic mammalian viruses. Several published studies have demonstrated clear proof of concept that the Orsay virus-C. elegans model can be used to identify novel genes important for infection by mammalian viruses. For some genes that are absolutely required for Orsay virus infection in C. elegans, knockouts of the orthologous gene in human cell culture result in up to ~1,000-fold reductions in virus titers for viruses like encephalomyocarditis virus (EMCV) and Coxsackie Virus B3 (CVB3). To systematically identify genes that promote or antagonize Orsay virus infection in C. elegans, a large-scale RNAi screen will be performed. RNAi in C. elegans is both more facile and robust than corresponding siRNA screening in mammalian cells, and it is complementary to CRISPR screens in cell culture. The goals of this project are: (1) To systematically identify host factors that impact Orsay virus infection in C. elegans by performing RNAi against the ~ 7500 C. elegans genes with human orthologs. (2) Determine whether the human orthologs of genes identified in Aim 1 play roles in infection by a panel of mammalian viruses. This study will identify, in an unbiased fashion, novel genes with pro-viral and anti-viral functions.