Rapid quantification of single-nucleotide mutations in mixed influenza A viral populations using allele-specific mixture analysis

Journal of Virological Methods

Volumn 163, Issue 1, 2010, Pages 109-115

  Liu, Cindy M ^a,b   Driebe, Elizabeth M ^a   Schupp, James ^b   Kelley, Erin ^a   Nguyen, Jack T ^c   McSharry, James J ^d   Weng, Qingmei ^d   Engelthaler, David M ^a   Keim, Paul S ^a,b  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^b NORTHERN ARIZONA UNIVERSITY   (United States)

^c Adamas Pharmaceutical   (United States)

^d ORDWAY RESEARCH INSTITUTE   (United States)

Author keywords

Allele specific PCR; Antiviral resistance; Influenza resistance; Mixture analysis; Quantitative genotyping; Single nucleotide polymorphism (SNP) analysis

Indexed keywords

ALANINE; ASPARAGINE; COMPLEMENTARY DNA; HISTIDINE; LEUCINE; MATRIX PROTEIN; MATRIX PROTEIN 2; PHENYLALANINE; SERINE; SIALIDASE; THREONINE; TYROSINE; UNCLASSIFIED DRUG; VALINE;

ALLELE; ALLELE SPECIFIC MIXTURE ANALYSIS; ANALYTIC METHOD; ANALYTICAL ERROR; ANTIVIRAL RESISTANCE; ARTICLE; CONTROLLED STUDY; GENE MUTATION; GENOTYPE; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H2N2; INTERMETHOD COMPARISON; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; VIRUS MUTANT;

ALLELES; DRUG RESISTANCE, VIRAL; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN; POINT MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ORTHOMYXOVIRIDAE;

EID: 70649093850     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2009.09.007     Document Type: Article

References (35)

1. Abed Y., Baz M., and Boivin G. Impact of neuraminidase mutations conferring influenza resistance to neuraminidase inhibitors in the N1 and N2 genetic backgrounds. Antivir. Ther. 11 8 (2006) 971-976
2. Archambeault S., Flores N.J., Yoshimi A., Kratz C.P., Reising M., Fischer A., Noellke P., Locatelli F., Sedlacek P., Flotho C., Zecca M., Emanuel P.D., Castleberry R.P., Niemeyer C.M., Bader P., and Loh M.L. Development of an allele-specific minimal residual disease assay for patients with juvenile myelomonocytic leukemia. Blood 111 3 (2008) 1124-1127
3. Baz M., Abed Y., and Boivin G. Characterization of drug-resistant recombinant influenza A/H1N1 viruses selected in vitro with peramivir and zanamivir. Antiviral Res. 74 2 (2007) 159-162
4. Bright R.A., Shay D.K., Shu B., Cox N.J., and Klimov A.I. Adamantane resistance among influenza A viruses isolated early during the 2005-2006 influenza season in the United States. JAMA 295 8 (2006) 891-894
5. Bright R.A., Medina M.J., Xu X., Perez-Oronoz G., Wallis T.R., Davis X.M., Povinelli L., Cox N.J., and Klimov A.I. Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: a cause for concern. Lancet 366 9492 (2005) 1175-1181
6. Center for Disease Control, Influenza Weekly Report: Influenza Summary Update Week 11, 2008-2009 Season, http://www.cdc.gov/flu/weekly, world wide web, (accessed 04.02.09).
7. Cox N.J., and Klimov A.I. Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: a cause for concern. Lancet 366 9492 (2005) 1175-1181
8. Detsika M.G., Chandler B., Khoo S.H., Winstanley C., Cane P., Back D.J., and Owen A. Detection and quantification of minority HIV isolates harbouring the D30N mutation by real-time PCR amplification. J. Antimicrob. Chemother. 60 4 (2007) 881-884
9. Deyde V.M., Nguyen T., Bright R.A., Balish A., Shu B., Lindstrom S., Klimov A.I., and Gubareva L.V. Detection of molecular markers of antiviral resistance in influenza A (H5N1) viruses using a pyrosequencing method. Antimicrob. Agents Chemother. 53 3 (2009) 1039-1047
10. Dharan N.J., Gubareva L.V., Meyer J.J., Okomo-Adhiambo M., McClinton R.C., Marshall S.A., St George K., Epperson S., Brammer L., Klimov A.I., Bresee J.S., Fry A.M., and Oseltamivir-Resistance Working Group. Infections with oseltamivir-resistant influenza A(H1N1) virus in the United States. JAMA 301 10 (2009) 1034-1041
11. Duwe S., and Schweiger B. A new and rapid genotypic assay for the detection of neuraminidase inhibitor resistant influenza A viruses of subtype H1N1, H3N2, and H5N1. J. Virol. Methods 153 2 (2008) 134-141
12. Germer S., Holland M.J., and Higuchi R. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10 2 (2000) 258-266
13. Hirt C., Schüler F., and Dölken G. Minimal residual disease (MRD) in follicular lymphoma in the era of immunotherapy with rituximab. Semin. Cancer Biol. 13 3 (2003) 223-231
14. Hurt A.C., Holien J.K., Parker M., Kelso A., and Barr I.G. Zanamivir-resistant influenza viruses with a novel neuraminidase mutation. J Virol Methods 83 20 (2009) 10366-10373
15. Ives J.A., Carr J.A., Mendel D.B., Tai C.Y., Lambkin R., Kelly L., Oxford J.S., Hayden F.G., and Roberts N.A. The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. Antiviral Res. 55 2 (2002) 307-317
16. Kibbe W.A. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 35 July (2007) W43-W46 (web server issue)
17. Johnson J.A., Li J.F., Wei X., Lipscomb J., Irlbeck D., Craig C., Smith A., Bennett D.E., Monsour M., Sandstrom P., Lanier E.R., and Heneine W. Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy. PLoS Med. 5 7 (2008) e158
18. Kibbe W.A. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res. 35 (2007) W43-W46
19. Lackenby A., Hungnes O., Dudman S.G., Meijer A., Paget W.J., Hay A.J., and Zambon M.C. Emergence of resistance to oseltamivir among influenza A (H1N1) viruses in Europe. Euro Surveill. 13 5 (2008) pii: 8026
20. Lackenby A., Democratis J., Siqueira M.M., and Zambon M.C. Rapid quantitation of neuraminidase inhibitor drug resistance in influenza virus quasispecies. Antivir. Ther. 13 6 (2008) 809-820
21. Larder B.A., Kohli A., Kellam P., Kemp S.D., Kronick M., and Henfrey R.D. Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing. Nature 365 6447 (1993) 671-673
22. Lipsitch M., Cohen T., Murray M., and Levin B.R. Antiviral resistance and the control of pandemic influenza. PLoS Med. 4 1 (2007) e15
23. Louvel S., Battegay M., Vernazza P., Bregenzer T., Klimkait T., Hamy F., and Swiss HIV Cohort Study. Detection of drug-resistant HIV minorities in clinical specimens and therapy failure. HIV Med. 9 3 (2008) 133-141
24. Metzner K.J., Giulieri S.G., Knoepfel S.A., Rauch P., Burgisser P., Yerly S., Günthard H.F., and Cavassini M. Minority quasispecies of drug-resistant HIV-1 that lead to early therapy failure in treatment-naive and -adherent patients. Clin. Infect. Dis. 48 2 (2009) 239-247
25. Metzner K.J., Rauch P., Walter H., Boesecke C., Zöllner B., Jessen H., Schewe K., Fenske S., Gellermann H., and Stellbrink H.J. Detection of minor populations of drug-resistant HIV-1 in acute seroconverters. AIDS 19 16 (2005) 1819-1825
26. Monto A.S., McKimm-Breschkin J.L., Macken C., Hampson A.W., Hay A., Klimov A., Tashiro M., Webster R.G., Aymard M., Hayden F.G., and Zambon M. Detection of influenza viruses resistant to neuraminidase inhibitors in global surveillance during the first 3 years of their use. Antimicrob. Agents Chemother. 50 7 (2006) 2395-2402
27. Moscona A. Global transmission of oseltamivir-resistant influenza. N. Engl. J. Med. 360 10 (2009) 953-956
28. Moscona A. Neuraminidase inhibitors for influenza. N. Engl. J. Med. 353 13 (2005) 1363-1373
29. Ottone T., Ammatuna E., Lavorgna S., Noguera N.I., Buccisano F., Venditti A., Giannì L., Postorino M., Federici G., Amadori S., and Lo-Coco F. An allele-specific rt-PCR assay to detect type A mutation of the nucleophosmin-1 gene in acute myeloid leukemia. J. Mol. Diagn. 10 3 (2008) 212-216
30. Peuchant O., Thiébaut R., Capdepont S., Lavignolle-Aurillac V., Neau D., Morlat P., Dabis F., Fleury H., and Masquelier B. ANRS CO3 Aquitaine Cohort. Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy. AIDS 22 12 (2008) 1417-1423
31. Regoes R.R., and Bonhoeffer S. Emergence of drug-resistant influenza virus: population dynamical considerations. Science 312 5772 (2006) 389-391
32. Schnell J.R., and Chou J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451 7178 (2008) 591-595
33. Schwarz G., Bäumler S., Block A., Felsenstein F.G., and Wenzel G. Determination of detection and quantification limits for SNP allele frequency estimation in DNA pools using real time PCR. Nucleic Acids Res. 32 3 (2004) e24 (PubMed)
34. Sheu T.G., Deyde V.M., Okomo-Adhiambo M., Garten R.J., Xu X., Bright R.A., Butler E.N., Wallis T.R., Klimov A.I., and Gubareva L.V. Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. Antimicrob. Agents Chemother. 52 9 (2008) 3284-3292
35. Stanssens P., Zabeau M., Meersseman G., Remes G., Gansemans Y., Storm N., Hartmer R., Honisch C., Rodi C.P., Böcker S., and van den Boom D. High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res. 14 1 (2004) 126-133