Dynamics of in vitro fitness recovery of HIV-1

Journal of Virology

Volumn 85, Issue 4, 2011, Pages 1861-1870

  Lorenzo Redondo, Ramón ^a   Bordería, Antonio V ^a,b   Lopez Galindez, Cecilio ^a  

^a INSTITUTO DE SALUD CARLOS III   (Spain)

^b INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN P17;

AMINO ACID SUBSTITUTION; ARTICLE; GENE MAPPING; GENE SEQUENCE; GENETIC HETEROGENEITY; HUMAN IMMUNODEFICIENCY VIRUS; IN VITRO STUDY; MICROBIAL POPULATION DYNAMICS; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; PHENOTYPE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; VIRUS DETECTION; VIRUS GENE; VIRUS MUTATION; VIRUS REPLICATION; VIRUS VIRULENCE;

EVOLUTION, MOLECULAR; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENOME, VIRAL; HIV ANTIGENS; HIV ENVELOPE PROTEIN GP120; HIV REVERSE TRANSCRIPTASE; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION; PHENOTYPE; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SERIAL PASSAGE;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 78951492483     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01254-10     Document Type: Article

References (42)

1. Borderia, A. V., et al. 2010. Initial fitness recovery of HIV-1 is associated with quasispecies heterogeneity and can occur without modifications in the consensus sequence. PLoS One 5:e10319.
2. Bukrinsky, M. I., et al. 1993. A nuclear localization signal within HIV-1 matrix protein that governs infection of non-dividing cells. Nature 365:666-669.
3. Chao, L. 1990. Fitness of RNA virus decreased by Muller's ratchet. Nature 348:454-455.
4. Clarke, D. K., et al. 1993. Genetic bottlenecks and population passages cause profound fitness differences in RNA viruses. J. Virol. 67:222-228.
5. Cornelissen, M., E. Hogervorst, F. Zorgdrager, S. Hartman, and J. Goudsmit. 1995. Maintenance of syncytium-inducing phenotype of HIV type 1 is associated with positively charged residues in the HIV type 1 gp120 V2 domain without fixed positions, elongation, or relocated N-linked glycosylation sites. AIDS Res. Hum. Retroviruses 11:1169-1175.
6. Derdeyn, C. A., et al. 2004. Envelope-constrained neutralization- sensitive HIV-1 after heterosexual transmission. Science 303:2019-2022.
7. Domingo, E., C. Escarmis, L. Menendez-Arias, and J. J. Holland. 1999. Viral quasispecies and fitness variations, p. 141-161. In E. Domingo, R. Webster, and J. Holland (ed.), Origin and evolution of viruses. Academic Press, San Diego, CA.
8. Domingo, E., et al. 1985. The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance - a review. Gene 40:1-8.
9. Domingo, E., C. R. Parrish, and J. J. Holland (ed.). 2008. Origin and evolution of viruses, 2nd ed. Elsevier, London, United Kingdom.
10. Eigen, M. 1971. Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465-523.
11. Elena, S. F., et al. 1996. Evolution of fitness in experimental populations of vesicular stomatitis virus. Genetics 142:673-679.
12. Fischer, W., et al. 2007. Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nat. Med. 13:100-106.
13. Ganeshan, S., R. Dickover, B. T. M. Korber, Y. J. Bryson, and S. M. Wolinsky. 1997. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virol. 71:663-677.
14. Gaschen, B., et al. 2002. Diversity considerations in HIV-1 vaccine selection. Science 296:2354-2360.
15. Gatanaga, H., et al. 2002. Amino acid substitutions in Gag protein at non-cleavage sites are indispensable for the development of a high multitude of HIV-1 resistance against protease inhibitors. J. Biol. Chem. 277:5952-5961.
16. Harada, S., Y. Koyanagi, and N. Yamamoto. 1985. Infection of HTLV-III/LAV in HTLV-I-carrying cells MT-2 and MT-4 and application in a plaque assay. Science 229:563-566.
17. Holland, J. J., J. C. de la Torre, D. K. Clarke, and E. Duarte. 1991. Quantitation of relative fitness and great adaptability of clonal populations of RNA viruses. J. Virol. 65:2960-2967.
18. Huson, D. H., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
19. Jerzak, G. V., K. Bernard, L. D. Kramer, P. Y. Shi, and G. D. Ebel. 2007. The West Nile virus mutant spectrum is host-dependant and a determinant of mortality in mice. Virology 360:469-476.
20. Kuiken, C., et al. 2009. HIV sequence compendium 2009. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM.
21. Lassen, K. G., et al. 2009. Elite suppressor-derived HIV-1 envelope glycoproteins exhibit reduced entry efficiency and kinetics. PLoS Pathog. 5:e1000377.
22. Najera, I., et al. 1995. pol gene quasispecies of human immunodeficiency virus: mutations associated with drug resistance in virus from patients undergoing no drug therapy. J. Virol. 69:23-31.
23. Najera, I., et al. 1994. Natural occurrence of drug resistance mutations in the reverse transcriptase of human immunodeficiency virus type 1 isolates. AIDS Res. Hum. Retroviruses 10:1479-1488.
24. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
25. Novella, I. S. 2003. Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution. Curr. Opin. Microbiol. 6:399-405.
26. Novella, I. S., et al. 1995. Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells. J. Virol. 69:6805-6809.
27. Novella, I. S., et al. 1995. Exponential increases of RNA virus fitness during large population transmissions. Proc. Nat. Acad. Sci. U. S. A. 92:5841-5844.
28. Posada, D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25:1253-1256.
29. Salazar-Gonzalez, J. F., et al. 2009. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206:1273-1289.
30. Sanchez-Palomino, S., et al. 1993. Dilute passage promotes expression of genetic and phenotypic variants of human immunodeficiency virus type 1 in cell culture. J. Virol. 67:2938-2943.
31. Sauder, C. J., et al. 2006. Changes in mumps virus neurovirulence phenotype associated with quasispecies heterogeneity. Virology 350:48-57.
32. Shankarappa, R., et al. 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73:10489-10502.
33. Swofford, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (* and other methods) version 4.0 beta. Sinauer, Sunderland, MA.
34. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
35. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
36. Troyer, R. M., et al. 2005. Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. J. Virol. 79:9006-9018.
37. Vignuzzi, M., J. K. Stone, J. J. Arnold, C. E. Cameron, and R. Andino. 2006. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439:344-348.
38. Vignuzzi, M., E. Wendt, and R. Andino. 2008. Engineering attenuated virus vaccines by controlling replication fidelity. Nat. Med. 14:154-161.
39. Wolinsky, S. M., et al. 1996. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272:537-542.
40. Yuste, E., A. V. Borderia, E. Domingo, and C. Lopez-Galindez. 2005. Few mutations in the 5′ leader region mediate fitness recovery of debilitated human immunodeficiency type 1 viruses. J. Virol. 79:5421-5427.
41. Yuste, E., C. Lopez-Galindez, and E. Domingo. 2000. Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1. J. Virol. 74:9546-9552.
42. Yuste, E., S. Sanchez-Palomino, C. Casado, E. Domingo, and C. Lopez- Galindez. 1999. Drastic fitness loss in human immunodeficiency virus type 1 upon serial bottleneck events. J. Virol. 73:2745-2751.