Evolution of the human immunodeficiency virus type 1 subtype-specific V3 domain is confined to a sequence space with a fixed distance to the subtype consensus

被引:32
作者
Lukashov, VV [1 ]
Goudsmit, J [1 ]
机构
[1] UNIV AMSTERDAM,ACAD MED CTR,DEPT HUMAN RETROVIROL,NL-1105 AZ AMSTERDAM,NETHERLANDS
关键词
D O I
10.1128/JVI.71.9.6332-6338.1997
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Human immunodeficiency virus type 1 (HIV-1) strains can be separated into genetic subtypes based on phylogenetic analysis of the envelope gene, Once it had been shown that population-wide intrasubtype genetic variation of HIV-1 strains increases in the course of the AIDS epidemic, it remained uncertain whether HIV-1 subtypes are phenotypic entities spreading as distinct virus populations, To examine this, we applied Eigen's concepts of sequence geometry and fitness topography to the analysis of intrasubtype evolution of the gp120 V3 domain of HIV-1 subtypes A, B, C, and D in the course of the global AIDS epidemic, We observed that despite the high evolution rate of HIV-1, the nonsynonymous distances to the subtype consensus of sequences obtained early in the epidemic are similar to those obtained more than 10 gears later, in contrast to the synonymous distances, which increased steadily over time, For HIV-1 subtype B, we observed that the evolution rate of the individual sequences is independent of their distance from the subtype B consensus, but for the individual sequences most distant from the consensus evolution away from the consensus is constrained, As a result, individual HIV-1 genomes fluctuate within a sequence space with fixed distance to the subtype consensus, Our findings suggest that the evolution of the V3 domain of HIV-1 subtypes A, B, C, and D is confined to an area in sequence space within a fixed distance to the consensus of a respective subtype. This in turn indicates that each HIV-1 subtype is a distinct viral quasispecies that is well adapted to the present environment, able to maintain its identity in the V3 region over time, and unlikely to merge during progression of the AIDS epidemic.
引用
收藏
页码:6332 / 6338
页数:7
相关论文
共 38 条
  • [1] Human immunodeficiency virus type 1 subtypes defined by env show high frequency of recombinant gag genes
    Cornelissen, M
    Kampinga, G
    Zorgdrager, F
    Goudsmit, J
    [J]. JOURNAL OF VIROLOGY, 1996, 70 (11) : 8209 - 8212
  • [2] SYNCYTIUM-INDUCING AND NON-SYNCYTIUM-INDUCING CAPACITY OF HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 SUBTYPES OTHER THAN B - PHENOTYPIC AND GENOTYPIC CHARACTERISTICS
    DEWOLF, F
    HOGERVORST, E
    GOUDSMIT, J
    FENYO, EM
    RUBSAMENWAIGMANN, H
    HOLMES, H
    GALVAOCASTRO, B
    KARITA, E
    WASI, C
    SEMPALA, SDK
    BAAN, E
    ZORGDRAGER, F
    LUKASHOV, V
    OSMANOV, S
    KUIKEN, C
    CORNELISSEN, M
    BELSEY, EM
    HEYWARD, W
    ESPARZA, J
    VANDEPERRE, P
    SEMPALA, S
    TUGUME, B
    BIRYAHWAHO, B
    VONBRIESEN, H
    ESSER, R
    GREZ, M
    NEWBERRY, A
    RANJBAR, S
    TOMLINSON, P
    BRADAC, J
    MCCUTCHAN, F
    LOUWAGIE, J
    HEGERICH, P
    LOPEZGALINDEZ, C
    OLIVARES, I
    DOPAZO, J
    MULLINS, JI
    DELWART, EL
    BACHMANN, HM
    HAHN, BH
    GAO, F
    YUE, L
    SARAGOSTI, S
    SCHOCHETMAN, G
    KALISH, M
    LUO, CC
    GEORGE, R
    PAU, CP
    WEBER, J
    CHEINGSONGPOPOV, R
    [J]. AIDS RESEARCH AND HUMAN RETROVIRUSES, 1994, 10 (11) : 1387 - 1400
  • [3] DIETRICH U, 1992, J ACQ IMMUN DEF SYND, V7, P23
  • [4] STATISTICAL GEOMETRY IN SEQUENCE SPACE - A METHOD OF QUANTITATIVE COMPARATIVE SEQUENCE-ANALYSIS
    EIGEN, M
    WINKLEROSWATITSCH, R
    DRESS, A
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (16) : 5913 - 5917
  • [5] SELFORGANIZATION OF MATTER AND EVOLUTION OF BIOLOGICAL MACROMOLECULES
    EIGEN, M
    [J]. NATURWISSENSCHAFTEN, 1971, 58 (10) : 465 - +
  • [6] MOLECULAR QUASI-SPECIES
    EIGEN, M
    MCCASKILL, J
    SCHUSTER, P
    [J]. JOURNAL OF PHYSICAL CHEMISTRY, 1988, 92 (24) : 6881 - 6891
  • [8] AN IMPROVED METHOD FOR DETERMINING CODON VARIABILITY IN A GENE AND ITS APPLICATION TO RATE OF FIXATION OF MUTATIONS IN EVOLUTION
    FITCH, WM
    MARKOWITZ, E
    [J]. BIOCHEMICAL GENETICS, 1970, 4 (05) : 579 - +
  • [9] PHENOTYPE-ASSOCIATED ENV GENE VARIATION AMONG 8 RELATED HUMAN-IMMUNODEFICIENCY-VIRUS TYPE-1 CLONES - EVIDENCE FOR INVIVO RECOMBINATION AND DETERMINANTS OF CYTOTROPISM OUTSIDE THE V3-DOMAIN
    GROENINK, M
    ANDEWEG, AC
    FOUCHIER, RAM
    BROERSEN, S
    VANDERJAGT, RCM
    SCHUITEMAKER, H
    DEGOEDE, REY
    BOSCH, ML
    HUISMAN, HG
    TERSMETTE, M
    [J]. JOURNAL OF VIROLOGY, 1992, 66 (10) : 6175 - 6180
  • [10] GENETIC-VARIATION IN HTLV-III/LAV OVER TIME IN PATIENTS WITH AIDS OR AT RISK FOR AIDS
    HAHN, BH
    SHAW, GM
    TAYLOR, ME
    REDFIELD, RR
    MARKHAM, PD
    SALAHUDDIN, SZ
    WONGSTAAL, F
    GALLO, RC
    PARKS, ES
    PARKS, WP
    [J]. SCIENCE, 1986, 232 (4757) : 1548 - 1553