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Volumn 8, Issue 7, 2013, Pages

Using High-Throughput Sequencing to Leverage Surveillance of Genetic Diversity and Oseltamivir Resistance: A Pilot Study during the 2009 Influenza A(H1N1) Pandemic

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; OSELTAMIVIR; VIRUS SIALIDASE;

EID: 84879753467     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067010     Document Type: Article
Times cited : (15)

References (50)
  • 1
    • 67650407532 scopus 로고    scopus 로고
    • Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans
    • Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, et al. (2009) Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325: 197-201.
    • (2009) Science , vol.325 , pp. 197-201
    • Garten, R.J.1    Davis, C.T.2    Russell, C.A.3    Shu, B.4    Lindstrom, S.5
  • 2
    • 84865307690 scopus 로고    scopus 로고
    • Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study
    • Dawood FS, Iuliano AD, Reed C, Meltzer MI, Shay DK, et al. (2012) Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study. Lancet Infect Dis 12: 687-695.
    • (2012) Lancet Infect Dis , vol.12 , pp. 687-695
    • Dawood, F.S.1    Iuliano, A.D.2    Reed, C.3    Meltzer, M.I.4    Shay, D.K.5
  • 4
    • 70349196002 scopus 로고    scopus 로고
    • RNA virus genomics: a world of possibilities
    • Holmes EC, (2009) RNA virus genomics: a world of possibilities. J Clin Invest 119: 2488-2495.
    • (2009) J Clin Invest , vol.119 , pp. 2488-2495
    • Holmes, E.C.1
  • 5
    • 50949106863 scopus 로고    scopus 로고
    • Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008
    • Sheu TG, Deyde VM, Okomo-Adhiambo M, Garten RJ, Xu X, et al. (2008) Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. Antimicrob Agents Chemother 52: 3284-3292.
    • (2008) Antimicrob Agents Chemother , vol.52 , pp. 3284-3292
    • Sheu, T.G.1    Deyde, V.M.2    Okomo-Adhiambo, M.3    Garten, R.J.4    Xu, X.5
  • 6
    • 62149120632 scopus 로고    scopus 로고
    • Infections with oseltamivir-resistant Influenza A(H1N1) virus in the United States
    • Dharan NJ, Gubareva LV, Meyer JJ, Okomo-Adhiambo M, McClinton RC, et al. (2009) Infections with oseltamivir-resistant Influenza A(H1N1) virus in the United States. JAMA 301: 1034-1041.
    • (2009) JAMA , vol.301 , pp. 1034-1041
    • Dharan, N.J.1    Gubareva, L.V.2    Meyer, J.J.3    Okomo-Adhiambo, M.4    McClinton, R.C.5
  • 7
    • 80052770280 scopus 로고    scopus 로고
    • Emerging oseltamivir resistance in seasonal and pandemic influenza A/H1N1
    • Renaud C, Kuypers J, Englund JA, (2011) Emerging oseltamivir resistance in seasonal and pandemic influenza A/H1N1. J Clin Virol 52: 70-78.
    • (2011) J Clin Virol , vol.52 , pp. 70-78
    • Renaud, C.1    Kuypers, J.2    Englund, J.A.3
  • 8
    • 79960267817 scopus 로고    scopus 로고
    • Increased detection in Australia and Singapore of a novel influenza AH1N1 2009 variant with reduced oseltamivir and zanamivir sensitivity due to a S247N neuraminidase mutation
    • Hurt AC, Lee RT, Leang SK, Cui L, Deng YM, et al. (2011) Increased detection in Australia and Singapore of a novel influenza AH1N1 2009 variant with reduced oseltamivir and zanamivir sensitivity due to a S247N neuraminidase mutation. Euro Surveill 16: 19884.
    • (2011) Euro Surveill , vol.16 , pp. 19884
    • Hurt, A.C.1    Lee, R.T.2    Leang, S.K.3    Cui, L.4    Deng, Y.M.5
  • 10
    • 48249156625 scopus 로고    scopus 로고
    • Enzymatic properties of the neuraminidase of seasonal H1N1 influenza viruses provide insights for the emergence of natural resistance to oseltamivir
    • Rameix-Welti MA, Enouf V, Cuvelier F, Jeannin P, van der Werf S, (2008) Enzymatic properties of the neuraminidase of seasonal H1N1 influenza viruses provide insights for the emergence of natural resistance to oseltamivir. PLoS Pathog 4: e1000103.
    • (2008) PLoS Pathog , vol.4
    • Rameix-Welti, M.A.1    Enouf, V.2    Cuvelier, F.3    Jeannin, P.4    van der Werf, S.5
  • 11
    • 77953262416 scopus 로고    scopus 로고
    • Permissive secondary mutations enable the evolution of influenza oseltamivir resistance
    • Bloom JD, Gong LI, Baltimore D, (2010) Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science 328: 1272-1275.
    • (2010) Science , vol.328 , pp. 1272-1275
    • Bloom, J.D.1    Gong, L.I.2    Baltimore, D.3
  • 12
    • 79952050801 scopus 로고    scopus 로고
    • Influenza A virus hemagglutinin antibody escape promotes neuraminidase antigenic variation and drug resistance
    • Hensley SE, Das SR, Gibbs JS, Bailey AL, Schmidt LM, et al. (2011) Influenza A virus hemagglutinin antibody escape promotes neuraminidase antigenic variation and drug resistance. PLoS One 6: e15190.
    • (2011) PLoS One , vol.6
    • Hensley, S.E.1    Das, S.R.2    Gibbs, J.S.3    Bailey, A.L.4    Schmidt, L.M.5
  • 13
    • 70349816881 scopus 로고    scopus 로고
    • How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count
    • Lipsitch M, Hayden FG, Cowling BJ, Leung GM, (2009) How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count. The Lancet 374: 1209-1211.
    • (2009) The Lancet , vol.374 , pp. 1209-1211
    • Lipsitch, M.1    Hayden, F.G.2    Cowling, B.J.3    Leung, G.M.4
  • 14
    • 79951808135 scopus 로고    scopus 로고
    • Next-generation sequencing as a tool to study microbial evolution
    • Brockhurst MA, Colegrave N, Rozen DE, (2011) Next-generation sequencing as a tool to study microbial evolution. Mol Ecol 20: 972-980.
    • (2011) Mol Ecol , vol.20 , pp. 972-980
    • Brockhurst, M.A.1    Colegrave, N.2    Rozen, D.E.3
  • 15
    • 84855295480 scopus 로고    scopus 로고
    • Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities
    • Suenaga H, (2012) Targeted metagenomics: a high-resolution metagenomics approach for specific gene clusters in complex microbial communities. Environ Microbiol 14: 13-22.
    • (2012) Environ Microbiol , vol.14 , pp. 13-22
    • Suenaga, H.1
  • 16
    • 64149083137 scopus 로고    scopus 로고
    • Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach
    • Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, et al. (2009) Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 4: e4219.
    • (2009) PLoS One , vol.4
    • Nakamura, S.1    Yang, C.S.2    Sakon, N.3    Ueda, M.4    Tougan, T.5
  • 17
    • 77956522256 scopus 로고    scopus 로고
    • Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer
    • Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, et al. (2010) Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer. PLoS One 5: e10256.
    • (2010) PLoS One , vol.5
    • Kuroda, M.1    Katano, H.2    Nakajima, N.3    Tobiume, M.4    Ainai, A.5
  • 18
    • 78149461455 scopus 로고    scopus 로고
    • A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America
    • Greninger AL, Chen EC, Sittler T, Scheinerman A, Roubinian N, et al. (2010) A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 5: e13381.
    • (2010) PLoS One , vol.5
    • Greninger, A.L.1    Chen, E.C.2    Sittler, T.3    Scheinerman, A.4    Roubinian, N.5
  • 19
    • 34547829263 scopus 로고    scopus 로고
    • DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
    • Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, et al. (2007) DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 35: e91.
    • (2007) Nucleic Acids Res , vol.35
    • Hoffmann, C.1    Minkah, N.2    Leipzig, J.3    Wang, G.4    Arens, M.Q.5
  • 20
    • 55249120981 scopus 로고    scopus 로고
    • Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations
    • Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, et al. (2008) Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. J Virol 82: 10747-10755.
    • (2008) J Virol , vol.82 , pp. 10747-10755
    • Mitsuya, Y.1    Varghese, V.2    Wang, C.3    Liu, T.F.4    Holmes, S.P.5
  • 21
    • 34547643929 scopus 로고    scopus 로고
    • Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance
    • Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW, (2007) Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res 17: 1195-1201.
    • (2007) Genome Res , vol.17 , pp. 1195-1201
    • Wang, C.1    Mitsuya, Y.2    Gharizadeh, B.3    Ronaghi, M.4    Shafer, R.W.5
  • 22
    • 33947525868 scopus 로고    scopus 로고
    • Detection of minor drug-resistant populations by parallel allele-specific sequencing
    • Cai F, Chen H, Hicks CB, Bartlett JA, Zhu J, et al. (2007) Detection of minor drug-resistant populations by parallel allele-specific sequencing. Nat Methods 4: 123-125.
    • (2007) Nat Methods , vol.4 , pp. 123-125
    • Cai, F.1    Chen, H.2    Hicks, C.B.3    Bartlett, J.A.4    Zhu, J.5
  • 23
    • 70349628591 scopus 로고    scopus 로고
    • The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies
    • Ramakrishnan MA, Tu ZJ, Singh S, Chockalingam AK, Gramer MR, et al. (2009) The feasibility of using high resolution genome sequencing of influenza A viruses to detect mixed infections and quasispecies. PLoS One 4: e7105.
    • (2009) PLoS One , vol.4
    • Ramakrishnan, M.A.1    Tu, Z.J.2    Singh, S.3    Chockalingam, A.K.4    Gramer, M.R.5
  • 24
    • 84894408096 scopus 로고    scopus 로고
    • Detection of haemagglutinin D222 polymorphisms in Influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing
    • Selleri M, Piralla A, Rozera G, Giombini E, Bartolini B, et al. (2012) Detection of haemagglutinin D222 polymorphisms in Influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing. Clin Microbiol Infect.
    • (2012) Clin Microbiol Infect
    • Selleri, M.1    Piralla, A.2    Rozera, G.3    Giombini, E.4    Bartolini, B.5
  • 25
    • 84867692130 scopus 로고    scopus 로고
    • Presence of Oseltamivir-Resistant Pandemic A/H1N1 Minor Variants Before Drug Therapy With Subsequent Selection and Transmission
    • Ghedin E, Holmes EC, Depasse JV, Pinilla LT, Fitch A, et al. (2012) Presence of Oseltamivir-Resistant Pandemic A/H1N1 Minor Variants Before Drug Therapy With Subsequent Selection and Transmission. J Infect Dis 206: 1504-1511.
    • (2012) J Infect Dis , vol.206 , pp. 1504-1511
    • Ghedin, E.1    Holmes, E.C.2    Depasse, J.V.3    Pinilla, L.T.4    Fitch, A.5
  • 26
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 27
    • 80054705708 scopus 로고    scopus 로고
    • Sentinel' mutations in standard population sequencing can predict the presence of HIV-1 reverse transcriptase major mutations detectable only by ultra-deep pyrosequencing
    • Alteri C, Santoro MM, Abbate I, Rozera G, Bruselles A, et al. (2011) 'Sentinel' mutations in standard population sequencing can predict the presence of HIV-1 reverse transcriptase major mutations detectable only by ultra-deep pyrosequencing. J Antimicrob Chemother 66: 2615-2623.
    • (2011) J Antimicrob Chemother , vol.66 , pp. 2615-2623
    • Alteri, C.1    Santoro, M.M.2    Abbate, I.3    Rozera, G.4    Bruselles, A.5
  • 29
    • 75549084216 scopus 로고    scopus 로고
    • Differentiation of two distinct clusters among currently circulating Influenza A(H1N1)v viruses
    • Fereidouni SR, Beer M, Vahlenkamp T, Starick E (2009) Differentiation of two distinct clusters among currently circulating Influenza A(H1N1)v viruses. Eurosurveillance, Volume 14, Issue 46.
    • (2009) Eurosurveillance , vol.14 , Issue.46
    • Fereidouni, S.R.1    Beer, M.2    Vahlenkamp, T.3    Starick, E.4
  • 30
    • 79955743374 scopus 로고    scopus 로고
    • Mutation analysis of 2009 pandemic Influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic
    • Morlighem JE, Aoki S, Kishima M, Hanami M, Ogawa C, et al. (2011) Mutation analysis of 2009 pandemic Influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. PLoS One 6: e18956.
    • (2011) PLoS One , vol.6
    • Morlighem, J.E.1    Aoki, S.2    Kishima, M.3    Hanami, M.4    Ogawa, C.5
  • 31
    • 78650978283 scopus 로고    scopus 로고
    • Comprehensive assessment of 2009 pandemic influenza A (H1N1) virus drug susceptibility in vitro
    • Gubareva LV, Trujillo AA, Okomo-Adhiambo M, Mishin VP, Deyde VM, et al. (2010) Comprehensive assessment of 2009 pandemic influenza A (H1N1) virus drug susceptibility in vitro. Antivir Ther 15: 1151-1159.
    • (2010) Antivir Ther , vol.15 , pp. 1151-1159
    • Gubareva, L.V.1    Trujillo, A.A.2    Okomo-Adhiambo, M.3    Mishin, V.P.4    Deyde, V.M.5
  • 33
    • 79958016930 scopus 로고    scopus 로고
    • Characterizing the epidemiology of the 2009 influenza A/H1N1 pandemic in Mexico
    • Chowell G, Echevarria-Zuno S, Viboud C, Simonsen L, Tamerius J, et al. (2011) Characterizing the epidemiology of the 2009 influenza A/H1N1 pandemic in Mexico. PLoS Med 8: e1000436.
    • (2011) PLoS Med , vol.8
    • Chowell, G.1    Echevarria-Zuno, S.2    Viboud, C.3    Simonsen, L.4    Tamerius, J.5
  • 35
    • 79960423085 scopus 로고    scopus 로고
    • Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community
    • Holmes EC, Ghedin E, Halpin RA, Stockwell TB, Zhang XQ, et al. (2011) Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community. J Virol 85: 6923-6929.
    • (2011) J Virol , vol.85 , pp. 6923-6929
    • Holmes, E.C.1    Ghedin, E.2    Halpin, R.A.3    Stockwell, T.B.4    Zhang, X.Q.5
  • 37
    • 84867060060 scopus 로고    scopus 로고
    • Read length versus Depth of Coverage for Viral Quasispecies Reconstruction
    • Zagordi O, Daumer M, Beisel C, Beerenwinkel N, (2012) Read length versus Depth of Coverage for Viral Quasispecies Reconstruction. PLoS One 7: e47046.
    • (2012) PLoS One , vol.7
    • Zagordi, O.1    Daumer, M.2    Beisel, C.3    Beerenwinkel, N.4
  • 38
    • 79955714221 scopus 로고    scopus 로고
    • A comprehensive deep sequencing strategy for full-length genomes of influenza A
    • Hoper D, Hoffmann B, Beer M, (2011) A comprehensive deep sequencing strategy for full-length genomes of influenza A. PLoS One. 6: e19075.
    • (2011) PLoS One , vol.6
    • Hoper, D.1    Hoffmann, B.2    Beer, M.3
  • 39
    • 79960044932 scopus 로고    scopus 로고
    • 96-plex molecular barcoding for the Illumina Genome Analyzer
    • Kozarewa I, Turner DJ, (2011) 96-plex molecular barcoding for the Illumina Genome Analyzer. Methods Mol Biol 733: 279-298.
    • (2011) Methods Mol Biol , vol.733 , pp. 279-298
    • Kozarewa, I.1    Turner, D.J.2
  • 40
    • 84856103017 scopus 로고    scopus 로고
    • Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis
    • Tu J, Ge Q, Wang S, Wang L, Sun B, et al. (2012) Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis. BMC Genomics 13: 43.
    • (2012) BMC Genomics , vol.13 , pp. 43
    • Tu, J.1    Ge, Q.2    Wang, S.3    Wang, L.4    Sun, B.5
  • 41
    • 67650047735 scopus 로고    scopus 로고
    • DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis
    • Erlich Y, Chang K, Gordon A, Ronen R, Navon O, et al. (2009) DNA Sudoku-harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res 19: 1243-1253.
    • (2009) Genome Res , vol.19 , pp. 1243-1253
    • Erlich, Y.1    Chang, K.2    Gordon, A.3    Ronen, R.4    Navon, O.5
  • 42
    • 77953218382 scopus 로고    scopus 로고
    • A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
    • Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, et al. (2010) A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol 11: R15.
    • (2010) Genome Biol , vol.11
    • Lennon, N.J.1    Lintner, R.E.2    Anderson, S.3    Alvarez, P.4    Barry, A.5
  • 43
    • 79955691833 scopus 로고    scopus 로고
    • Large scale library generation for high throughput sequencing
    • Borgstrom E, Lundin S, Lundeberg J, (2011) Large scale library generation for high throughput sequencing. PLoS One 6: e19119.
    • (2011) PLoS One , vol.6
    • Borgstrom, E.1    Lundin, S.2    Lundeberg, J.3
  • 44
    • 84859345581 scopus 로고    scopus 로고
    • Microfluidic amplification as a tool for massive parallel sequencing of the familial hypercholesterolemia genes
    • Hollants S, Redeker EJ, Matthijs G, (2012) Microfluidic amplification as a tool for massive parallel sequencing of the familial hypercholesterolemia genes. Clin Chem 58: 717-724.
    • (2012) Clin Chem , vol.58 , pp. 717-724
    • Hollants, S.1    Redeker, E.J.2    Matthijs, G.3
  • 45
    • 84860521943 scopus 로고    scopus 로고
    • Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance
    • Dudley DM, Chin EN, Bimber BN, Sanabani SS, Tarosso LF, et al. (2012) Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One 7: e36494.
    • (2012) PLoS One , vol.7
    • Dudley, D.M.1    Chin, E.N.2    Bimber, B.N.3    Sanabani, S.S.4    Tarosso, L.F.5
  • 46
    • 82255181690 scopus 로고    scopus 로고
    • Applications of next-generation sequencing technologies to diagnostic virology
    • Barzon L, Lavezzo E, Militello V, Toppo S, Palu G, (2011) Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12: 7861-7884.
    • (2011) Int J Mol Sci , vol.12 , pp. 7861-7884
    • Barzon, L.1    Lavezzo, E.2    Militello, V.3    Toppo, S.4    Palu, G.5
  • 47
    • 84861394598 scopus 로고    scopus 로고
    • Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets
    • Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, et al. (2012) Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Nature 486: 420-428.
    • (2012) Nature , vol.486 , pp. 420-428
    • Imai, M.1    Watanabe, T.2    Hatta, M.3    Das, S.C.4    Ozawa, M.5
  • 48
  • 49
    • 0029170835 scopus 로고
    • PCR-ligation-PCR mutagenesis: a protocol for creating gene fusions and mutations
    • Ali SA, Steinkasserer A, (1995) PCR-ligation-PCR mutagenesis: a protocol for creating gene fusions and mutations. Biotechniques 18: 746-750.
    • (1995) Biotechniques , vol.18 , pp. 746-750
    • Ali, S.A.1    Steinkasserer, A.2
  • 50
    • 79959438245 scopus 로고    scopus 로고
    • Systematic exploration of error sources in pyrosequencing flowgram data
    • Balzer S, Malde K, Jonassen I, (2011) Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics 27: i304-309.
    • (2011) Bioinformatics , vol.27
    • Balzer, S.1    Malde, K.2    Jonassen, I.3


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