Global surveillance of emerging influenza virus genotypes by mass spectrometry

Rangarajan Sampath, Kevin L. Russell, Christian Massire, Mark W. Eshoo, Vanessa Harpin, Lawrence B. Blyn, Rachael Melton, Cristina Ivy, Thuy Pennella, Feng Li, Harold Levene, Thomas A. Hall, Brian Libby, Nancy Fan, Demetrius J. Walcott, Raymond Ranken, Michael Pear, Amy Schink, Jose Gutierrez, Jared DraderDavid Moore, David Metzgar, Lynda Addington, Richard Rothman, Charlotte A Gaydos, Samuel Yang, Kirsten St George, Meghan E. Fuschino, Amy B. Dean, David E. Stallknecht, Ginger Goekjian, Samuel Yingst, Marshall Monteville, Magdi D. Saad, Chris A. Whitehouse, Carson Baldwin, Karl H. Rudnick, Steven A. Hofstadler, Stanley M. Lemon, David J. Ecker

Research output: Contribution to journalArticle

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 subspecies 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.

Original languageEnglish (US)
Article numbere489
JournalPLoS One
Volume2
Issue number5
DOIs
StatePublished - May 30 2007

Fingerprint

Orthomyxoviridae
Viruses
Mass spectrometry
Mass Spectrometry
reverse transcriptase polymerase chain reaction
Genotype
influenza
mass spectrometry
Human Influenza
Polymerase Chain Reaction
monitoring
genotype
Base Composition
Electrospray ionization
Viral Vaccines
Transcription
Chemical analysis
Influenza in Birds
Electrospray Ionization Mass Spectrometry
avian influenza

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Sampath, R., Russell, K. L., Massire, C., Eshoo, M. W., Harpin, V., Blyn, L. B., ... Ecker, D. J. (2007). Global surveillance of emerging influenza virus genotypes by mass spectrometry. PLoS One, 2(5), [e489]. https://doi.org/10.1371/journal.pone.0000489

Global surveillance of emerging influenza virus genotypes by mass spectrometry. / Sampath, Rangarajan; Russell, Kevin L.; Massire, Christian; Eshoo, Mark W.; Harpin, Vanessa; Blyn, Lawrence B.; Melton, Rachael; Ivy, Cristina; Pennella, Thuy; Li, Feng; Levene, Harold; Hall, Thomas A.; Libby, Brian; Fan, Nancy; Walcott, Demetrius J.; Ranken, Raymond; Pear, Michael; Schink, Amy; Gutierrez, Jose; Drader, Jared; Moore, David; Metzgar, David; Addington, Lynda; Rothman, Richard; Gaydos, Charlotte A; Yang, Samuel; St George, Kirsten; Fuschino, Meghan E.; Dean, Amy B.; Stallknecht, David E.; Goekjian, Ginger; Yingst, Samuel; Monteville, Marshall; Saad, Magdi D.; Whitehouse, Chris A.; Baldwin, Carson; Rudnick, Karl H.; Hofstadler, Steven A.; Lemon, Stanley M.; Ecker, David J.

In: PLoS One, Vol. 2, No. 5, e489, 30.05.2007.

Research output: Contribution to journalArticle

Sampath, R, Russell, KL, Massire, C, Eshoo, MW, Harpin, V, Blyn, LB, Melton, R, Ivy, C, Pennella, T, Li, F, Levene, H, Hall, TA, Libby, B, Fan, N, Walcott, DJ, Ranken, R, Pear, M, Schink, A, Gutierrez, J, Drader, J, Moore, D, Metzgar, D, Addington, L, Rothman, R, Gaydos, CA, Yang, S, St George, K, Fuschino, ME, Dean, AB, Stallknecht, DE, Goekjian, G, Yingst, S, Monteville, M, Saad, MD, Whitehouse, CA, Baldwin, C, Rudnick, KH, Hofstadler, SA, Lemon, SM & Ecker, DJ 2007, 'Global surveillance of emerging influenza virus genotypes by mass spectrometry', PLoS One, vol. 2, no. 5, e489. https://doi.org/10.1371/journal.pone.0000489
Sampath R, Russell KL, Massire C, Eshoo MW, Harpin V, Blyn LB et al. Global surveillance of emerging influenza virus genotypes by mass spectrometry. PLoS One. 2007 May 30;2(5). e489. https://doi.org/10.1371/journal.pone.0000489
Sampath, Rangarajan ; Russell, Kevin L. ; Massire, Christian ; Eshoo, Mark W. ; Harpin, Vanessa ; Blyn, Lawrence B. ; Melton, Rachael ; Ivy, Cristina ; Pennella, Thuy ; Li, Feng ; Levene, Harold ; Hall, Thomas A. ; Libby, Brian ; Fan, Nancy ; Walcott, Demetrius J. ; Ranken, Raymond ; Pear, Michael ; Schink, Amy ; Gutierrez, Jose ; Drader, Jared ; Moore, David ; Metzgar, David ; Addington, Lynda ; Rothman, Richard ; Gaydos, Charlotte A ; Yang, Samuel ; St George, Kirsten ; Fuschino, Meghan E. ; Dean, Amy B. ; Stallknecht, David E. ; Goekjian, Ginger ; Yingst, Samuel ; Monteville, Marshall ; Saad, Magdi D. ; Whitehouse, Chris A. ; Baldwin, Carson ; Rudnick, Karl H. ; Hofstadler, Steven A. ; Lemon, Stanley M. ; Ecker, David J. / Global surveillance of emerging influenza virus genotypes by mass spectrometry. In: PLoS One. 2007 ; Vol. 2, No. 5.
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AU - Sampath, Rangarajan

AU - Russell, Kevin L.

AU - Massire, Christian

AU - Eshoo, Mark W.

AU - Harpin, Vanessa

AU - Blyn, Lawrence B.

AU - Melton, Rachael

AU - Ivy, Cristina

AU - Pennella, Thuy

AU - Li, Feng

AU - Levene, Harold

AU - Hall, Thomas A.

AU - Libby, Brian

AU - Fan, Nancy

AU - Walcott, Demetrius J.

AU - Ranken, Raymond

AU - Pear, Michael

AU - Schink, Amy

AU - Gutierrez, Jose

AU - Drader, Jared

AU - Moore, David

AU - Metzgar, David

AU - Addington, Lynda

AU - Rothman, Richard

AU - Gaydos, Charlotte A

AU - Yang, Samuel

AU - St George, Kirsten

AU - Fuschino, Meghan E.

AU - Dean, Amy B.

AU - Stallknecht, David E.

AU - Goekjian, Ginger

AU - Yingst, Samuel

AU - Monteville, Marshall

AU - Saad, Magdi D.

AU - Whitehouse, Chris A.

AU - Baldwin, Carson

AU - Rudnick, Karl H.

AU - Hofstadler, Steven A.

AU - Lemon, Stanley M.

AU - Ecker, David J.

PY - 2007/5/30

Y1 - 2007/5/30

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