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

Authors
Type
Published Article
Journal
Journal of Clinical Microbiology
1098-660X
Publisher
American Society for Microbiology
Publication Date
Volume
49
Issue
4
Pages
1307–1312
Identifiers
DOI: 10.1128/JCM.02424-10
PMID: 21307217
Source
Medline
License
Unknown

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.

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