Patterns of intra- and interhost nonsynonymous variation reveal strong purifying selection in dengue virus

Journal of Virology

Volumn 77, Issue 20, 2003, Pages 11296-11298

  Holmes, Edward C ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARBOVIRUS; ARTICLE; DENGUE VIRUS; EVOLUTION; GENETIC VARIABILITY; MOSQUITO; MUTATION; PARASITE VECTOR; PHYLOGENY; PRIORITY JOURNAL;

DENGUE VIRUS; MUTATION; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 0141565071     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.77.20.11296-11298.2003     Document Type: Article

References (23)

1. Clinis, M. J., W. Kang, and S. C. Weaver. 1996. Genetic conservation of Highlands J viruses. Virology 218:343-351.
2. Cooper, L. A., and T. W. Scott. 2001. Differential evolution of eastern equine encephalitis virus populations in response to host cell type. Genetics 157:1403-1412.
3. Craig, S., H. M. Thu, K. Lowry, X.-F. Wang, E. C. Holmes, and J. Aaskov. 2003. Diverse dengue type 2 virus populations contain recombinant and both parental viruses in a single mosquito host, J. Virol. 77:4463-4467.
4. Eyre-Walker, A. C. 1999. Evidence of selection on silent site base composition in mammals: potential implications for the evolution of isochores and junk DNA. Genetics 152:675-683.
5. Fay, J. C., G. J. Wyckoff, and C.-I. Wu. 2001. Positive and negative selection on the human genome. Genetics 158:1227-1234.
6. Jenkins, G. M., and E. C. Holmes. 2003. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92:1-7.
7. Jenkins, G. M., A. Rambaut, O. G. Pybus, and E. C. Holmes. 2002. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54:152-161.
8. Novella, I. S., C. L. Hershey, C. Escarmis, E. Domingo, and J. J. Holland. 1999. Lack of evolutionary stasis during alternating replication of an arbovirus in insect and mammalian cells. J. Mol. Biol. 287:459-465.
9. Scott, T. W., S. C. Weaver, and V. L. Mallampalli. 1994. Evolution of mosquito-borne viruses, p. 293-324. In S. S. Morse (ed.), Evolutionary biology of viruses. Raven Press, New York, N.Y.
10. Simmonds, P., and D. B. Smith. 1999. Structural constraints on RNA virus evolution. J. Virol. 73:5787-5794.
11. Strauss, J. H., and E. G. Strauss. 1994. The alphaviruses: gene expression, replication, and evolution. Microbiol. Rev. 58:491-562.
12. Twiddy, S. S., J. F. Farrar, N. V. Chau, B. Wills, E. A. Gould, T. Gritsun, G. Lloyd, and E. C. Holmes. 2002. Phylogenetic relationships and differential selection pressures among genotypes of dengue-2 virus. Virology 298:63-72.
13. Twiddy, S. S., C. H. Woelk, and E. C. Holmes. 2002. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J. Gen. Virol. 83:1679-1689.
14. Uzcategui, N. Y., D. Camacho, G. Comach, E. C. Holmes, and E. A. Gould. 2001. The molecular epidemiology of dengue-2 virus in Venezuela: evidence for in situ viral evolution and recombination. J. Gen. Virol. 82:2945-2953.
15. Uzcategui, N. Y., G. Comach, D. Camacho, M. Salcedo, M. Cabello deq Uintana, M. Jimenez, G. Sierra, R. Cuello de Uzcategui, W. S. James, S. Turner, E. C. Holmes, and E. A. Gould. 2003. The molecular epidemiology of dengue-3 virus in Venezuela. J. Gen. Virol. 84:1569-1575.
16. Wang, W.-K., T.-L. Sung, C.-N. Lee, T.-Y. Lin, and C.-C. King. 2002. Sequence diversity of the capsid gene and the nonstructural gene NS2B of dengue-3 virus in vivo. Virology 303:181-191.
17. Wang, W.-K., S.-R. Lin, C.-M. Lee, C.-C. King, and S.-C. Chang. 2002. Dengue type 3 virus in plasma is a population of closely related genomes: quasispecies. J. Virol. 76:4662-4665.
18. Weaver, S. C., A. C. Brault, W. Kang, and J. J. Holland. 1999. Genetic and fitness changes accompanying adaptation of an arbovirus to vertebrate and invertebrate cells. J. Virol. 73:4316-4326.
19. Weaver, S. C., R. Rico-Hesse, and T. W. Scott. 1992. Genetic diversification and slow rates of evolution in New World alphaviruses. Curr. Top. Microbiol. Immunol. 176:99-117.
20. Wittke, V., T. E. Robb, H. M. Thu, S. Nimmannitya, S. Kalayanrooj, D. W. Vaughn, T. P. Endy, E. C. Holmes, and J. G. Aaskov. 2002. Extinction and rapid emergence of strains of dengue 3 virus during an interepidemic period. Virology 301:148-156.
21. Woelk, C. H., and E. C. Holmes. 2002. Reduced positive selection in vector-borne RNA viruses. Mol. Biol. Evol. 19:2333-2336.
22. Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
23. Yang, Z., R. Nielsen, N. Goldman, and A. M. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.