Genetic drift of influenza virus genomic sequences occurs through the combined effects of sequence alterations introduced by a low fidelity polymerase and the varying selective pressures experienced as the virus migrates through different host environments. While traditional phylogenetic analysis is useful in tracking the evolutionary heritage of these viruses, the specific genetic determinants that dictate important phenotypic characteristics are often difficult to discern within the complex genetic background arising through evolution. Here we describe a novel Influenza Sequence Feature Variant Type (Flu-SFVT) approach, made available through the public Influenza Research Database resource (www.fludb.org), in which variant types (VTs) identified in defined influenza protein sequence features (SFs) are used for genotype-phenotype association studies. Since SFs have been defined for all influenza proteins based on known structural, functional and immune epitope recognition properties, the Flu-SFVT approach allows for the rapid identification of the molecular genetic determinants of important influenza virus characteristics and their connection to underlying biological functions. We demonstrate the use of the SFVT approach to obtain statistical evidence for effects of NS1 protein sequence variations in dictating influenza virus host range restriction.