Dataset Information

Global surveillance of emerging Influenza virus genotypes by mass spectrometry.

ABSTRACT:

Background

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 PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.

Methods and principal findings

Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 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 and subtypes with >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) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution.

Conclusion/significance

Thus, rapid RT-PCR/ESI-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.

SUBMITTER: Sampath R

PROVIDER: S-EPMC1876795 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature

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Publications

Global surveillance of emerging Influenza virus genotypes by mass spectrometry.

Sampath Rangarajan R Russell Kevin L KL Massire Christian C Eshoo Mark W MW Harpin Vanessa V Blyn Lawrence B LB Melton Rachael R Ivy Cristina C Pennella Thuy T Li Feng F Levene Harold H Hall Thomas A TA Libby Brian B Fan Nancy N Walcott Demetrius J DJ Ranken Raymond R Pear Michael M Schink Amy A Gutierrez Jose J Drader Jared J Moore David D Metzgar David D Addington Lynda L Rothman Richard R Gaydos Charlotte A CA Yang Samuel S St George Kirsten K Fuschino Meghan E ME Dean Amy B AB Stallknecht David E DE Goekjian Ginger G Yingst Samuel S Monteville Marshall M Saad Magdi D MD Whitehouse Chris A CA Baldwin Carson C Rudnick Karl H KH Hofstadler Steven A SA Lemon Stanley M SM Ecker David J DJ

PloS one 20070530 5

<h4>Background</h4>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 PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.<h4>Methods and principal findings</h4>Analysis of base com ...[more]

PMID: 17534439

Similar Datasets

Project description:BACKGROUND: Highly pathogenic avian influenza A(H5N1) viruses are an important health problem in many Asian and African countries. The current increase in human cases demonstrates that influenza A(H5N1) is still a significant global pandemic threat. Many health organizations have recognized the need for new strategies to improve influenza global surveillance. Specifically, the World Health Organization through the global technical consultation for influenza surveillance have called for a detailed picture of the current limitations, especially at the nation level, to evaluate, standardize and strength reporting systems. The main goal of our study is to demonstrate the value of genetic surveillance as part of a strategic surveillance plan. As a proof of concept, we evaluated the current situation of influenza A(H5N1) in Asian and Africa. RESULTS: Our analysis revealed a power-law distribution in the number of sequences of A(H5N1) viruses analyzed and/or reported to influenza surveillance networks. The majority of the Asian and African countries at great risk of A(H5N1) infections have very few (approximately three orders of magnitude) sequenced A(H5N1) viruses (e.g. hemagglutinin genes). This suggests that countries under pandemic alert for avian influenza A(H5N1) have very limited participation (e.g. data generation, genetic analysis and data share) in avian influenza A(H5N1) surveillance. More important, this study demonstrates the usefulness of influenza genetic surveillance to detect emerging pandemic threat viruses. CONCLUSIONS: Our study reveals that some countries suffering from human cases of avian influenza have limited participation (e.g. genetic surveillance or data share) with global surveillance networks. Also, we demonstrate that the implementation of genetic surveillance programs could increase and strengthen worldwide epidemic and pandemic preparedness. We hope that this work promotes new discussions between policy makers and health surveillance organizations to improve current methodologies and regulations.

Dataset Information

Global surveillance of emerging Influenza virus genotypes by mass spectrometry.

Background

Methods and principal findings

Conclusion/significance

Publications

Global surveillance of emerging Influenza virus genotypes by mass spectrometry.

Similar Datasets

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