In silico reconstruction of rapidly evolving genomes from small RNAs improves viral-derived siRNA profiling

Understanding the interaction between insects and viruses is a prerequisite to develop strategies limiting the transmission of insect-borne viral diseases to the human. Research performed in Drosophila1-4 showed that RNA interference (RNAi) is an essential component of the insect antiviral response. One of the landmarks of the antiviral RNAi response is the production of 21nt-long viral-derived small interfering RNAs (vsiRNAs) from viral double-stranded RNA (dsRNA) molecules. The profiling of vsiRNAs sequences obtained by deep-sequencing technologies has been extensively used as a surrogate to determine the nature of the viral dsRNA molecules exposed to and processed by the RNAi machinery. Importantly, the accuracy of these profiles, and therefore the conclusions drawn from them, strongly depends on the reference sequence used to align the vsiRNA reads. As RNA viruses accumulate mutations at high frequency5, their consensus sequence constantly evolves entailing the re-sequencing of the virus being used. Here we propose a one-step-script, named Paparazzi, that reconstructs from the sample being tested the full-length viral genomes from viral-derived small RNA reads and the vsiRNA profiles. We discuss the possible applications of Paparazzi in viral genome re-sequencing and viral discovery.