A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments

Journal of Virological Methods

Volumn 139, Issue 2, 2007, Pages 181-188

  Carrasco, P ^a   Daros J A ^a   Agudelo Romero, P ^a   Elena, S F ^a  

^a Ciudad Politécnica de la Innovación   (Spain)

Author keywords

Fitness; Real time TaqMan PCR; Tobacco etch virus; Virus evolution

Indexed keywords

RNA POLYMERASE;

ARTICLE; GENOTYPE; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; POTYVIRUS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; RNA ANALYSIS; SENSITIVITY ANALYSIS; TOBACCO ETCH POTYVIRUS;

GENE AMPLIFICATION; GENES, VIRAL; POTYVIRUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; TOBACCO;

TOBACCO ETCH VIRUS;

EID: 33846092128     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2006.09.020     Document Type: Article

References (23)

1. Dietrich C., and Maiss E. Fluorescent labeling reveals spatial separation of potyvirus populations in mixed infected Nicotiana benthamiana plants. J. Gen. Virol. 84 (2003) 2871-2876
2. Dolja V.V., McBride H.J., and Carrington J.C. Tagging of plant potyvirus replication and movement by insertion of beta-glucuronidase into the viral polyprotein. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 10208-10212
3. Domingo E., Escarmís C., Baranowski E., Ruiz-Jarabo C.M., Carrillo E., Núñez J.I., and Sobrino F. Evolution of foot-and-mouth disease virus. Virus Res. 91 (2003) 47-63
4. Edgar R.C. MUSCLE. Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
5. Elena S.F., and Lenski R.E. Evolution experiments with microorganisms: the dyanamics and genetic bases of adaptation. Nat. Rev. Genet. 4 (2003) 457-469
6. Gachon C., Mingam A., and Charrier B. Real-time PCR: what relevance to plant studies?. J. Exp. Bot. 55 (2004) 1445-1454
7. Hartl D.L., and Clark A.G. Principles of Population Genetics (1989), Sinauer, Sunderland, MA
8. Holland J.J., de la Torre J.C., Clarke D.K., and Duarte E.A. Quantitation of relative fitness and great adaptability of clonal populations of RNA viruses. J. Virol. 65 (1991) 2960-2967
9. Jenner C.E., Wang X., Ponz F., and Walsh J.A. A fitness cost for Turnip mosaic virus to overcome host resistance. Virus Res. 86 (2002) 1-6
10. Lenhoff R.J., Luscombe C.A., and Summers J. Competition in vivo between a cytopathic variant and a wild-type duck hepatitis B virus. Virology 251 (1998) 85-95
11. López-Moya J.J., and García J.A. Construction of a stable and highly infectious intron-containing cDNA clone of plum pox potyvirus and its use to infect plants by particle bombardment. Virus Res. 68 (2000) 99-107
12. Lu J., and Kuritzkes D.R. A novel recombinant marker virus assay for comparing the relative fitness of HIV-1 reverse transcriptase variants. J. Acquir. Immune Defic. Syndr. 27 (2001) 7-13
13. Mackay I.M., Arden K.E., and Nitsche A. Real-time PCR in virology. Nucleic Acids Res. 30 (2002) 1292-1305
14. Novella I.S. Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution. Curr. Opin. Microbiol. 6 (2003) 399-405
15. O'Reilly E.K., and Kao C.C. Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure. Virology 252 (1998) 287-303
16. Poch O., Sauvaget I., Delarue M., and Tordo N. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J. 8 (1989) 3867-3874
17. Riechmann J.L., Laín S., and García J.A. Highlights and prospects of potyvirus molecular biology. J. Gen. Virol. 73 (1992) 1-16
18. Sánchez F., Martínez-Herrera D., Aguilar I., and Ponz F. Infectivity of turnip mosaic Potyvirus cDNA clones and transcripts on the systemic host Arabidopsis thaliana and local lesions hosts. Virus Res. 55 (1998) 207-219
19. van Maarseveen N.M., Huigen M.C.D.G., de Jong D., Smits A.M., Boucher C.A.B., and Nijhuis M. A novel real-time PCR assay to determine relative replication capacity for HIV-1 protease variants and/or reverse transcriptase variants. J. Virol. Methods 133 (2006) 185-194
20. Weber J., Rangel H.R., Chakraborty B., Tadele M., Martinez M.A., Martínez-Picado J., Marotta M.L., Mirza M., Ruiz L., Clotet B., Wrin T., Petropoulos C.J., and Quinones-Mateu M.E. A novel TaqMan real-time PCR assay to estimate ex vivo human immunodeficiency virus type 1 fitness in the era of multi-target (pol and env) antiretroviral therapy. J. Gen. Virol. 84 (2003) 2217-2228
21. Yuste E., Sánchez-Palomino S., Casado C., Domingo E., and López-Galíndez C. Drastic fitness loss in human immunodeficiency virus type 1 upon serial bottleneck events. J. Virol. 73 (1999) 2745-2751
22. Yuste E., López-Galíndez C., and Domingo E. Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1. J. Virol. 74 (2000) 9546-9552
23. Yuste E., Bordería A.V., Domingo E., and López-Galíndez C. Few mutations in the 5' leader region mediate fitness recovery of debilitated human immunodeficiency type 1 viruses. J. Virol. 79 (2005) 5421-5427