The HIV positive selection mutation database

Nucleic Acids Research

Volumn 35, Issue SUPPL. 1, 2007, Pages

  Pan, Calvin ^a   Kim, Joseph ^a   Chen, Lamei ^a   Wang, Qi ^a   Lee, Christopher ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; PROTEINASE; RNA DIRECTED DNA POLYMERASE;

ARTICLE; BIOINFORMATICS; DATA BASE; DRUG EFFECT; DRUG TARGETING; FACTUAL DATABASE; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; GENETIC SELECTION; HUMAN IMMUNODEFICIENCY VIRUS; NONHUMAN; PRIORITY JOURNAL; STANFORD HIV DATABASE; VALIDATION PROCESS; VIRUS MUTATION;

ACQUIRED IMMUNODEFICIENCY SYNDROME; CODON; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; DRUG RESISTANCE, VIRAL; HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV-1; HIV-1 REVERSE TRANSCRIPTASE; HUMANS; INTERNET; MUTATION; REVERSE TRANSCRIPTASE INHIBITORS; SELECTION (GENETICS); USER-COMPUTER INTERFACE;

EID: 33846054821     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl855     Document Type: Article

References (24)

1. Dybul,M., Fauci,A.S., Bartlett,J.G., Kaplan,J.E., Pau,A.K. and Panel on Clinical Practices for Treatment of HIV. (2002) Guidelines for using antiretroviral agents among HIV-infected adults and adolescents. Ann. Intern. Med., 137, 381-433.
2. Richman,D.D., Havlir,D., Corbeil,J., Looney,D., Ignacio,C., Spector,S.A., Sullivan,J., Cheeseman,S., Barringer,K., Pauletti,D. et al. (1994) Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy. J. Virol., 68, 1660-1666.
3. Wei,X., Ghosh,S.K., Taylor,M.E., Johnson,V.A., Emini,E.A., Deutsch,P., Lifson,J.D., Bonhoeffer,S., Nowak,M.A., Hahn,B.H. et al. (1995) Viral dynamics in human immunodeficiency virus type 1 infection. Nature, 373, 117-122.
4. Mansky,L.M. and Temin,H.M. (1995) Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol., 69, 5087-5094.
5. Korber,B., Theiler,J. and Wolinsky,S. (1998) Limitations of a molecular clock applied to considerations of the origin of HIV-1. Science, 280, 1868-1871.
6. Ho,D.D., Neumann,A.U., Perelson,A.S., Chen,W., Leonard,J.M. and Markowitz,M. (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373, 123-126.
7. Perelson,A.S., Neumann,A.U., Markowitz,M., Leonard,J.M. and Ho,D.D. (1996) HIV-1 dynamics in vivo: Virion clearance rate, infected cell life-span and viral generation time. Science, 271, 1582-1586.
8. Coffin,J.M. (1995) HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy. Science, 267, 483-489.
9. Kuhmann,S.E., Pugach,P., Kunstman,K.J., Taylor,J., Stanfield,R.L., Snyder,A., Strizki,J.M., Riley,J., Baroudy,B.M., Wilson,I.A. et al. (2004) Genetic and phenotypic analyses of human immunodeficiency virus type 1 escape from a small-molecule CCR5 inhibitor. J. Virol., 78, 2790-2807.
10. Bonhoeffer,S., Chappey,C., Parkin,N.T., Whitcomb,J.M. and Petropoulos,C.J. (2004) Evidence for positive epistasis in HIV-1. Science, 306, 1547-1550.
11. Wu,T.D., Schiffer,C.A., Gonzales,M.J., Taylor,J., Kantor,R., Chou,S., Israelski,D., Zolopa,A.R., Fessel,W.J. and Shafer,R.W. (2003) Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J. Virol., 77, 4836-4847.
12. Chen,L., Perlina,A. and Lee,C.J. (2004) Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. J. Virol., 78, 3722-3732.
13. Nei,M. and Gojobori,J. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3, 418-426.
14. Li,W.H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol., 36, 96-99.
15. Felsenstein,J. (1989) PHYLIP - phylogeny inference package (version 3.2). Cladistics, 5, 164-166.
16. Grassly,N.C., Harvey,P.H. and Holmes,E.C. (1999) Population dynamics of HIV-1 inferred from gene sequences. Genetics, 151, 427-438.
17. Anderson,J.P., Rodrigo,A.G., Learn,G.H., Wang,Y., Weinstock,H., Kalish,M.L., Robbins,K.E., Hood,L. and Mullins,J.I. (2001) Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. J. Mol. Evol., 53, 55-62.
18. Chen,L. and Lee,C. (2006) Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples. Biol. Direct., 1, 14.
19. Rhee,S.Y., Gonzales,M.J, Kantor,R., Betts,B.J, Ravela,J. and Shafer,R.W. (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res., 31, 298-303.
20. Loeb,D.D., Hutchison,C.A.,3rd, Edgell,M.H., Farmerie,W.G. and Swanstrom,R. (1989) Mutational analysis of human immunodeficiency virus type 1 protease suggests functional homology with aspartic proteinases. J. Virol., 63, 111-121.
21. Para,M.F., Glidden,D.V., Coombs,R.W., Collier,A.C., Condra,J.H., Craig,C., Bassett,R., Leavitt,R., Snyder,S., McAuliffe,V. et al. (2000) Baseline human immunodeficiency virus type 1 phenotype, genotype, and RNA response after switching from long-term hard-capsule saquinavir to indinavir or soft-gel-capsule saquinavir in AIDS clinical trials group protocol 333. J. Infect. Dis., 182, 733-743.
22. Rhee,S.Y., Gonzales,M.J., Kantor,R., Betts,B.J., Ravela,J. and Shafer,R.W. (2003) Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res., 31, 298-303.
23. Kuiken,C., Korber,B. and Shafer,R.W. (2003) HIV sequence databases. AIDS Rev., 5, 52-61.
24. Johnson,W.E. and Desrosiers,R.C. (2002) Viral persistance: HIV's strategies of immune system evasion. Annu. Rev. Med., 53, 499-518.