Development and implementation of influenza a virus subtyping and detection of genotypic resistance to neuraminidase inhibitors

Ruiz‐Carrascoso, Guillermo; Casas, Inmaculada; Pozo, Francisco; Pérez‐González, Carmen; Reina, Jordi; Pérez‐Breña, Pilar

Influenza virus hemagglutinin and neuraminidase, surface glycoproteins with an essential role in viral pathogenesis, are important antigen determinants and essential markers for epidemiological surveillance. Neuraminidase is also a suitable target for designing antiviral drugs. The introduction into clinical practice of neuraminidase inhibitors and the development of random point mutations have increased the emergence of drug‐resistant viruses. A universal RT nested PCR‐based system has been developed for subtyping H1, H3, N1 and N2, in influenza A viruses of human or animal origin. The subsequent sequencing and analysis of the hemagglutinin and neuraminidase templates reveal antigenic and receptor binding changes in the HA1 subunit and mutations of clinical relevance concerning resistance to neuraminidase inhibitors. The specificity and sensitivity of the method were evaluated using 113 influenza A isolates, 105 influenza A positive respiratory samples obtained from patients and 29 prototype strains of both human and animal origin. The resulting analytical sensitivity of the subtyping techniques is one to at least 100 molecules of cloned DNA product in a final reaction volume of 50 µl. In the course of implementing the method, two H1N1 isolates with the H274Y mutation in the neuraminidase segment have been detected and their molecular features analyzed. The emergence of influenza virus resistance makes the neuraminidase genetic characterization and surveillance activities to detect antiviral resistance necessary. J. Med. Virol. 82: 843–853, 2010. © 2010 Wiley‐Liss, Inc.