Influenza is a common illness that affects about 20 million people in the US. Its effects can vary depending on age group, vaccination status and pre-existing conditions of those affected, with symptoms ranging from mild cold-like symptoms, to respiratory complications that can be lethal. Though vaccines and antivirals have been developed to control influenza infectivity, there are still significant gaps in our understanding o influenza replication that need to be filled to be able to improve current treatments. Upon entering the cell, the influenza virus co-opts the host replication and translation machinery to replicate itself and produce new virions. An essential part of this process is the ability of the vral polymerase complex (vPOL) to produce capped viral messenger RNAs that can be translated by the host. The influenza genome does not encode a capping enzyme, but instead relies on a unique mechanism called cap-snatching whereby vPOL cleaves host mRNAs 10-15nt downstream from the 5' cap and uses these fragments to prime vmRNA synthesis. The cap-snatching mechanism confers the viral mRNA resistance against degradation by RNases, promotes its binding to the Cap Binding Complex for export out of the nucleus; and aids in its recognition by the ribosome for translation of the viral proteins. The mechanism of cap-snatch has previously been studied biochemically and structurally, but in the absence of a technique to profile cap-snatch events during infection, its impact on the host cell remains largely unknown. I have developed a novel Next Generation Sequencing approach that allows us to do a genome-wide analysis of the composition of human, viral, and hybrid RNAs throughout the influenza infection timeline. Using this novel approach we have already been able to elucidate cap-snatching sequence preference and show that it targets specific host sequences to favor infectivity. Our proposed studies of influenza cap-snatching will shed further light on the mechanism's selectivity and its importance to infection beyond simply producing capped vmRNAs. Importantly, improved understanding of the basis of cap-snatch sequence preferences may ultimately lead to the development of novel drugs that target this essential process.
Influenza is a pervasive virus that can produce a wide range of effects, ranging from mildly symptomatic to death. With the use of innovative next-generation sequencing techniques, I will characterize how viral transcription initiation leads to changes in cellular and viral gene expression and how it favors infectivity.
