Detection of hemagglutinin variants of the pandemic influenza a (H1N1) 2009 virus by pyrosequencing

Marnie Levine, Tiffany G. Sheu, Larisa V. Gubareva, Vasiliy P. Mishin

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

For influenza viruses, pyrosequencing has been successfully applied to the high-throughput detection of resistance markers in genes encoding the drug-targeted M2 protein and neuraminidase. In this study, we expanded the utility of this assay to the detection of multiple receptor binding variants of the hemagglutinin protein of influenza viruses directly in clinical specimens. Specifically, a customized pyrosequencing protocol that permits detection of virus variants with the D, G, N, or E amino acid at position 222 in the hemagglutinin of the 2009 pandemic influenza A (H1N1) virus was developed. This customized pyrosequencing protocol was applied to the analysis of 241 clinical specimens. The use of the optimized nucleotide dispensation order allowed detection of mixtures of variants in 10 samples (4.1%) which the standard cyclic nucleotide dispensation protocol failed to detect. The optimized pyrosequencing protocol is expected to provide a more accurate tool in the analysis of virus variant composition.

Original languageEnglish (US)
Pages (from-to)1307-1312
Number of pages6
JournalJournal of Clinical Microbiology
Volume49
Issue number4
DOIs
StatePublished - Apr 2011

ASJC Scopus subject areas

  • Microbiology (medical)

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