Molecular Biology and Evolution, Vol 12, 803-813, Copyright © 1995 by Society for Molecular Biology and Evolution
SA Seibert, CY Howell, MK Hughes and AL Hughes
Natural selection on polymorphic protein-coding loci of human
immunodeficiency virus-1 (HIV-1), the more geographically widespread of the
two viruses causing human acquired immune deficiency syndrome (AIDS), was
studied by estimating the rates of nucleotide substitution per site in
comparisons among alleles classified in families of related alleles on the
basis of a phylogenetic analysis. In the case of gag, pol, and gp41, the
rate of synonymous substitution generally exceeded that of nonsynonymous
substitution, indicating that these genes are subject to purifying
selection. However, in the case of several of the variable (V) regions of
the gp120 gene, especially V2 and V3, comparisons within and between
families often showed a significantly higher rate of nonsynonymous than of
synonymous nucleotide substitution. This pattern of nucleotide substitution
indicates that positive Darwinian selection has acted to diversify these
regions at the amino acid level. The V regions have been identified as
probable epitopes for antibody recognition; therefore, avoidance of such
recognition seems likely to be the basis for positive selection on these
regions. By contrast, regions of HIV-1 proteins identified as epitopes for
T cell recognition show no evidence of positive selection and are often
highly conserved at the amino acid level. These results suggest that
selection favoring avoidance of T cell recognition has not been a major
factor in the history of HIV-1 and thus that avoidance of T cell
recognition is not likely to be a major factor in the pathogenesis of AIDS.
ORIGINAL ARTICLE
Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1)
Department of Biology, Pennsylvania State University, University Park 16802, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. A. A. Travers, D. C. Tully, G. P. McCormack, and M. A. Fares A Study of the Coevolutionary Patterns Operating within the env Gene of the HIV-1 Group M Subtypes Mol. Biol. Evol., December 1, 2007; 24(12): 2787 - 2801. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. McCauley, S. de Groot, T. Mailund, and J. Hein Annotation of selection strengths in viral genomes Bioinformatics, November 15, 2007; 23(22): 2978 - 2986. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. de Groot, T. Mailund, and J. Hein Comparative annotation of viral genomes with non-conserved gene structure Bioinformatics, May 1, 2007; 23(9): 1080 - 1089. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A.-C. Jouvencel, D. Neau, M. Faure, M. Neau, C. Martinaud, E. Legrand, P. Trimoulet, I. Garrigue, B. Le Bail, P. Bioulac-Sage, et al. Plasma and liver hepatitis C virus variability in patients coinfected with human immunodeficiency virus. J. Clin. Microbiol., May 1, 2006; 44(5): 1877 - 1880. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Ceccherini-Silberstein, F. Gago, M. Santoro, C. Gori, V. Svicher, F. Rodriguez-Barrios, R. d'Arrigo, M. Ciccozzi, A. Bertoli, A. d. Monforte, et al. High Sequence Conservation of Human Immunodeficiency Virus Type 1 Reverse Transcriptase under Drug Pressure despite the Continuous Appearance of Mutations J. Virol., August 15, 2005; 79(16): 10718 - 10729. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Piontkivska and A. L. Hughes Between-Host Evolution of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1: an Approach Based on Phylogenetically Independent Comparisons J. Virol., November 1, 2004; 78(21): 11758 - 11765. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. R. Templeton, R. A. Reichert, A. E. Weisstein, X.-F. Yu, and R. B. Markham Selection in Context: Patterns of Natural Selection in the Glycoprotein 120 Region of Human Immunodeficiency Virus 1 Within Infected Individuals Genetics, August 1, 2004; 167(4): 1547 - 1561. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Chen, A. Perlina, and C. J. Lee 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., April 1, 2004; 78(7): 3722 - 3732. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Shriner, R. Shankarappa, M. A. Jensen, D. C. Nickle, J. E. Mittler, J. B. Margolick, and J. I. Mullins Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1 env Evolution During Chronic Infection Genetics, March 1, 2004; 166(3): 1155 - 1164. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Costa-Mattioli, A. D. Napoli, V. Ferre, S. Billaudel, R. Perez-Bercoff, and J. Cristina Genetic variability of hepatitis A virus J. Gen. Virol., December 1, 2003; 84(12): 3191 - 3201. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Biek, A. G. Rodrigo, D. Holley, A. Drummond, C. R. Anderson Jr., H. A. Ross, and M. Poss Epidemiology, Genetic Diversity, and Evolution of Endemic Feline Immunodeficiency Virus in a Population of Wild Cougars J. Virol., September 1, 2003; 77(17): 9578 - 9589. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Kitrinos, N. G. Hoffman, J. A. E. Nelson, and R. Swanstrom Turnover of env Variable Region 1 and 2 Genotypes in Subjects with Late-Stage Human Immunodeficiency Virus Type 1 Infection J. Virol., June 15, 2003; 77(12): 6811 - 6822. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 O. O. Yang, P. T. N. Sarkis, A. Ali, J. D. Harlow, C. Brander, S. A. Kalams, and B. D. Walker Determinants of HIV-1 Mutational Escape From Cytotoxic T Lymphocytes J. Exp. Med., May 19, 2003; 197(10): 1365 - 1375. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Alvarez, H. M. Lwamba, D. R. Kapczynski, M. K. Njenga, and B. S. Seal Nucleotide and Predicted Amino Acid Sequence-Based Analysis of the Avian Metapneumovirus Type C Cell Attachment Glycoprotein Gene: Phylogenetic Analysis and Molecular Epidemiology of U.S. Pneumoviruses J. Clin. Microbiol., April 1, 2003; 41(4): 1730 - 1735. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Babik and M. Holodniy Impact of Highly Active Antiretroviral Therapy and Immunologic Status on Hepatitis C Virus Quasispecies Diversity in Human Immunodeficiency Virus/Hepatitis C Virus-Coinfected Patients J. Virol., February 1, 2003; 77(3): 1940 - 1950. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. L. V. Skjot, I. Brock, S. M. Arend, M. E. Munk, M. Theisen, T. H. M. Ottenhoff, and P. Andersen Epitope Mapping of the Immunodominant Antigen TB10.4 and the Two Homologous Proteins TB10.3 and TB12.9, Which Constitute a Subfamily of the esat-6 Gene Family Infect. Immun., October 1, 2002; 70(10): 5446 - 5453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Novitsky, H. Cao, N. Rybak, P. Gilbert, M. F. McLane, S. Gaolekwe, T. Peter, I. Thior, T. Ndung'u, R. Marlink, et al. Magnitude and Frequency of Cytotoxic T-Lymphocyte Responses: Identification of Immunodominant Regions of Human Immunodeficiency Virus Type 1 Subtype C J. Virol., September 11, 2002; 76(20): 10155 - 10168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Costa-Mattioli, J. Cristina, H. Romero, R. Perez-Bercof, D. Casane, R. Colina, L. Garcia, I. Vega, G. Glikman, V. Romanowsky, et al. Molecular Evolution of Hepatitis A Virus: a New Classification Based on the Complete VP1 Protein J. Virol., August 12, 2002; 76(18): 9516 - 9525. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. M. Rouzine, A. Rodrigo, and J. M. Coffin Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology Microbiol. Mol. Biol. Rev., March 1, 2001; 65(1): 151 - 185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. T. Haydon, A. D. Bastos, N. J. Knowles, and A. R. Samuel Evidence for Positive Selection in Foot-and-Mouth Disease Virus Capsid Genes From Field Isolates Genetics, January 1, 2001; 157(1): 7 - 15. [Abstract] [Full Text]
|
|
|
|
|
|
K. Misawa and F. Tajima A Simple Method for Classifying Genes and a Bootstrap Test for Classifications Mol. Biol. Evol., December 1, 2000; 17(12): 1879 - 1884. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Yamaguchi-Kabata and T. Gojobori Reevaluation of Amino Acid Variability of the Human Immunodeficiency Virus Type 1 gp120 Envelope Glycoprotein and Prediction of New Discontinuous Epitopes J. Virol., May 1, 2000; 74(9): 4335 - 4350. [Abstract] [Full Text]
|
|
|
|
|
|
Z. Yang, R. Nielsen, N. Goldman, and A.-M. K. Pedersen Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites Genetics, May 1, 2000; 155(1): 431 - 449. [Abstract] [Full Text]
|
|
|
|
|
|
T. Shiino, K. Kato, N. Kodaka, T. Miyakuni, Y. Takebe, and H. Sato A Group of V3 Sequences from Human Immunodeficiency Virus Type 1 Subtype E Non-Syncytium-Inducing, CCR5-Using Variants Are Resistant to Positive Selection Pressure J. Virol., February 1, 2000; 74(3): 1069 - 1078. [Abstract] [Full Text]
|
|
|
|
|
|
H. Sato, T. Shiino, N. Kodaka, K. Taniguchi, Y. Tomita, K. Kato, T. Miyakuni, and Y. Takebe Evolution and Biological Characterization of Human Immunodeficiency Virus Type 1 Subtype E gp120 V3 Sequences following Horizontal and Vertical Virus Transmission in a Single Family J. Virol., May 1, 1999; 73(5): 3551 - 3559. [Abstract] [Full Text]
|
|
|
|
 |
|
 A. Tanuri, A. C. P. Vicente, K. Otsuki, C. A. Ramos, O. C. Ferreira Jr., M. Schechter, L. M. Janini, D. Pieniazek, and M. A. Rayfield Genetic Variation and Susceptibilities to Protease Inhibitors among Subtype B and F Isolates in Brazil Antimicrob. Agents Chemother., February 1, 1999; 43(2): 253 - 258. [Abstract] [Full Text]
|
|
|
|
|
|
I.-N. Wang, D. E. Dykhuizen, W. Qiu, J. J. Dunn, E. M. Bosler, and B. J. Luft Genetic Diversity of ospC in a Local Population of Borrelia burgdorferi sensu stricto Genetics, January 1, 1999; 151(1): 15 - 30. [Abstract] [Full Text]
|
|
|
|
|
|
C. Apetrei, D. Descamps, G. Collin, I. Loussert-Ajaka, F. Damond, M. Duca, F. Simon, and F. Brun-Vezinet Human Immunodeficiency Virus Type 1 Subtype F Reverse Transcriptase Sequence and Drug Susceptibility J. Virol., May 1, 1998; 72(5): 3534 - 3538. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Escalante, A. A. Lal, and F. J. Ayala Genetic Polymorphism and Natural Selection in the Malaria Parasite Plasmodium falciparum Genetics, May 1, 1998; 149(1): 189 - 202. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. E. Stockbauer, D. Grigsby, X. Pan, Y.-X. Fu, L. M. P. Mejia, A. Cravioto, and J. M. Musser Hypervariability generated by natural selection in an extracellular complement-inhibiting protein of serotype M1 strains of group A Streptococcus PNAS, March 17, 1998; 95(6): 3128 - 3133. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. B. van't Wout, L. J. Ran, C. L. Kuiken, N. A. Kootstra, S. T. Pals, and H. Schuitemaker Analysis of the Temporal Relationship between Human Immunodeficiency Virus Type 1 Quasispecies in Sequential Blood Samples and Various Organs Obtained at Autopsy J. Virol., January 1, 1998; 72(1): 488 - 496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Price, P. J. R. Goulder, P. Klenerman, A. K. Sewell, P. J. Easterbrook, M. Troop, C. R. M. Bangham, and R. E. Phillips Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection PNAS, March 4, 1997; 94(5): 1890 - 1895. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Yamaguchi and T. Gojobori Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts PNAS, February 18, 1997; 94(4): 1264 - 1269. [Abstract] [Full Text] [PDF]
|
|