Global surveillance of emerging Influenza virus genotypes by mass spectrometry.
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 previo...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2007-05-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC1876795?pdf=render |
| _version_ | 1811309564219359232 |
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| author | 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 Drader David 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 |
| author_facet | 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 Drader David 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 |
| author_sort | Rangarajan Sampath |
| collection | DOAJ |
| description | 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.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.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. |
| first_indexed | 2024-04-13T09:44:08Z |
| format | Article |
| id | doaj.art-c99229be3506447dbf48c58321babbdc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T09:44:08Z |
| publishDate | 2007-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c99229be3506447dbf48c58321babbdc2022-12-22T02:51:50ZengPublic Library of Science (PLoS)PLoS ONE1932-62032007-05-0125e48910.1371/journal.pone.0000489Global surveillance of emerging Influenza virus genotypes by mass spectrometry.Rangarajan SampathKevin L RussellChristian MassireMark W EshooVanessa HarpinLawrence B BlynRachael MeltonCristina IvyThuy PennellaFeng LiHarold LeveneThomas A HallBrian LibbyNancy FanDemetrius J WalcottRaymond RankenMichael PearAmy SchinkJose GutierrezJared DraderDavid MooreDavid MetzgarLynda AddingtonRichard RothmanCharlotte A GaydosSamuel YangKirsten St GeorgeMeghan E FuschinoAmy B DeanDavid E StallknechtGinger GoekjianSamuel YingstMarshall MontevilleMagdi D SaadChris A WhitehouseCarson BaldwinKarl H RudnickSteven A HofstadlerStanley M LemonDavid J EckerEffective 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.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.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.http://europepmc.org/articles/PMC1876795?pdf=render |
| spellingShingle | 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 Drader David 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 Global surveillance of emerging Influenza virus genotypes by mass spectrometry. PLoS ONE |
| title | Global surveillance of emerging Influenza virus genotypes by mass spectrometry. |
| title_full | Global surveillance of emerging Influenza virus genotypes by mass spectrometry. |
| title_fullStr | Global surveillance of emerging Influenza virus genotypes by mass spectrometry. |
| title_full_unstemmed | Global surveillance of emerging Influenza virus genotypes by mass spectrometry. |
| title_short | Global surveillance of emerging Influenza virus genotypes by mass spectrometry. |
| title_sort | global surveillance of emerging influenza virus genotypes by mass spectrometry |
| url | http://europepmc.org/articles/PMC1876795?pdf=render |
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