Influenza A virus(H1N1),a genetic reassortment of endemic strains of human,avian and swine flu,has crossed species barrier to human and apparently acquired the capability of human to human transmission.Some strains of H5N1 subtype are highly virulent because NS1 protein inhibits antiviral interferon α/β production.Another protein NS2 mediates export of viral ribonucleoprotein from nucleus to the cytoplasm through export signal.In this paper,we have studied structure-function relationships of these proteins of H1N1 subtype and have determined the cause of their pathogenicity.Our results showed that non-conservative mutations slightly stabilized or destabilized structural domains of NS1 or NS1-dsRNA complex,hence slightly increased or decreased the function of NS1 protein and consequently enhanced or reduced the pathogenicity of the H1N1 virus.NS2 protein of different strains carried non-conservative mutations in different domains,resulting in slight loss of function.These mutations slightly decreased the pathogenicity of the virus.Thus,the results confirm the structure-function relation-ships of these viral proteins.