Understanding the pathways by which antiviral resistance mutations in influenza emerge and take hold is important for developing effective responses to the virus. Resistance mutations are typically not maintained in a population after drug treatment ceases, given their evolutionary benefit to the virus when challenged by antivirals generally carries some cost to viral fitness. However, this is not always the case where the restoration of fitness can be achieved with compensatory mutations. To help understand the origins and dynamic nature of the influenza resistance mutations, we have developed and employed a new and innovative phylonumerics approach that avoids the need for either gene or protein sequences.
Protein mass maps or fingerprints are extensively used for protein identification in proteomics applications. We have shown that they can also be used to study the evolutionary history of organisms through the construction of so-called mass trees from sets of masses (i.e numbers) that reflect a protein’s sequence. Furthermore, single point amino acid mutations can be identified from mass differences alone and displayed along branches of these mass trees in this phylonumerics approach.
Frequent ancestral and descendant mutations that precede and follow the manifestation of antiviral resistance mutations in influenza neuraminidase are identified. In the case of N2 neuraminidase, the majority of mutations drive hydrophilicity changes around the active site, primarily through the incorporation or loss of hydroxyl groups, though do not impact the catalytic active site residues. These mutations either aid or restrict the entry and subsequent binding of a sialic acid or antiviral inhibitor.
Recent results from the application of the phylonumerics approach will be presented where mutations ancestral and descendant to resistance mutations will be discussed in terms of their mechanistic consequences in relation to H1N1 and H3N2 influenza strains.