Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry
ARMY MEDICAL RESEARCH INST OF INFECTIOUS DISEASES FORT DETRICK MD
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Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCRelectrospray ionization mass spectrometry RT -PCRESI-MS technology. Methods and Principal Findings Analysis of base compositions ofRT-PCR amplicons from influenza core gene segments PB 1, PB2, P A, M, NS, NP are used to provide sub-species identification and infer influenza virus Hand N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different Hand N types, including 29 avian H5Nl isolates.Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period 1999-2006 showed correct identification of the viral species andsubtypes 97 sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100 concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons 2005-2006 showedevidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1 of these recentsamples providing a view into viral evolution. ConclusionSignificance Thus, rapid R T PCRESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identifY mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high throughput method promises to become an integral component of influenza surveillance.
- Medicine and Medical Research