Evolutionary significance and function of influenza A virus genome packaging signals

The threat of an influenza pandemic is ever present and the prospect of the current strain of bird flu achieving pandemic status is truly alarming. Influenza viruses can evolve rapidly by swapping genes amongst strains of viruses from different hosts. However, key aspects of the processes that govern this ?pick and mix? process are not understood. This grant aims at clarifying the molecular details of influenza evolution with the ultimate aim of being able to predict which combinations of viruses might be more dangerous.

Influenza A virus is a formidable pathogen that has the potential to cause global pandemics with mortality figures in millions. Pandemics are initiated when a strain of virus jumps from wild birds to man. Evolution of novel pandemic viruses is facilitated by the segmented nature of the virus genome which permits reassortment of individual virus genes between viruses from different host species. This mechanism can produce antigenically novel strains of virus with avian-derived haemagglutinin (HA) and neuraminidase (NA) glycoproteins but the majority of other genes from an already human-adapted strain. Such processes provoked the 1957 and 1968 pandemics and the prospect of a similar event occurring between the currently circulating H5N1 avian virus and human-adapted H1N1 or H3N2 strains is alarming. Genome segmentation does however complicate the process of virus assembly, as for a single virus particle to be infectious it must contain at least one copy of all eight segments. This is achieved through a specific packaging mechanism; cis-acting sequences necessary for efficient packaging of each segment have been mapped but at present the mechanism by which these RNA signals function is unclear. We recently employed a bioinformatics approach to better identify evolutionarily conserved packaging sequences in the virus genome at the nucleotide level and significantly, proposed that packaging signals vary between virus strains and thus affect the process of reassortment. Importantly, segment 4 (encoding the HA) and segment 8 (encoding the virulence/interferon antagonist factor NS1) are the prime candidates for such strain-specific variation; a finding with clear implications for the evolution of potentially human pandemic viruses. Accordingly this proposal is aimed at improving our understanding of the evolutionary significance and function of influenza A virus packaging signals. We will directly test the hypothesis that packaging signals in the HA and NS genes show subtype-specific differences that affect reassortment, use virus genetics to probe intra- and inter-segment interactions between packaging signals, examine where in infected cells individual segments interact and test hypotheses for how the packaging signals operate.