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Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection

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Shankarappa, Raj, Margolick, Joseph B., Gange, Stephen J., Rodrigo, Allen G., Upchurch, David, Farzadegan, Homayoon, Gupta, Phalguni, Rinaldo, Charles R., Learn, Gerald H., He, Xi, Huang, Xiao-Li, Mullins, James I.·1999·Journal of Virology

DOI 10.1128/jvi.73.12.10489-10502.1999PMC PMC113104

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Abstract

To understand the high variability of the asymptomatic interval between primary human immunodeficiency virus type 1 (HIV-1) infection and the development of AIDS, we studied the evolution of the C2-V5 region of the HIV-1 env gene and of T-cell subsets in nine men with a moderate or slow rate of disease progression. They were monitored from the time of seroconversion for a period of 6 to 12 years until the development of advanced disease in seven men. Based on the analysis of viral divergence from the founder strain, viral population diversity within sequential time points, and the outgrowth of viruses capable of utilizing the CXCR4 receptor (X4 viruses), the existence of three distinct phases within the asymptomatic interval is suggested: an early phase of variable duration during which linear increases (∼1% per year) in both divergence and diversity were observed; an intermediate phase lasting an average of 1.8 years, characterized by a continued increase in divergence but with stabilization or decline in diversity; and a late phase characterized by a slowdown or stabilization of divergence and continued stability or decline in diversity. X4 variants emerged around the time of the early- to intermediate-phase transition and then achieved peak representation and began a decline around the transition between the intermediate and late phases. The late-phase transition was also associated with failure of T-cell homeostasis (defined by a downward inflection in CD3+T cells) and decline of CD4+T cells to ≤200 cells/μl. The strength of these temporal associations between viral divergence and diversity, viral coreceptor specificity, and T-cell homeostasis and subset composition supports the concept that the phases described represent a consistent pattern of viral evolution during the course of HIV-1 infection in moderate progressors. Recognition of this pattern may help explain previous conflicting data on the relationship between viral evolution and disease progression and may provide a useful framework for evaluating immune damage and recovery in untreated and treated HIV-1 infections.

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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
1993 Revised Classification System for HIV Infection and Expanded Surveillance Case Definition for AIDS Among Adolescents and Adults
Castro, K. G., Ward, J., Slutsker, L., Buehler, J. W., Jaffe, H. W., Berkelman, R. L., & Curran, J. W. (1993) · Clinical Infectious Diseases · doi:10.1093/clinids/17.4.802 · Cited by 4,347
Prognosis in HIV-1 Infection Predicted by the Quantity of Virus in Plasma
Mellors, J. W., Rinaldo, C. R., Gupta, P., White, R. M., Todd, J. A., & Kingsley, L. (1996) · Science · doi:10.1126/science.272.5265.1167 · Cited by 2,658
Self-citation
Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome
Koup, R. A., Safrit, J. T., Cao, Y., Andrews, C. A., McLeod, G. X., Borkowsky, W., Farthing, C., & Ho, D. D. (1994) · Journal of Virology · doi:10.1128/jvi.68.7.4650-4655.1994 · Cited by 2,494
Multiple Regression and Correlation Extensions of the Mantel Test of Matrix Correspondence
Smouse, P. E., Long, J. C., & Sokal, R. R. (1986) · Systematic Zoology · doi:10.2307/2413122 · Cited by 2,163
Plasma Viral Load and CD4+ Lymphocytes as Prognostic Markers of HIV-1 Infection
Mellors, J. W., Munoz, A., Giorgi, J. V., Margolick, J. B., Tassoni, C. J., Gupta, P., Kingsley, L. A., Todd, J. A., Saah, A. J., Detels, R., et al. (1997) · Annals of Internal Medicine · doi:10.7326/0003-4819-126-12-199706150-00003 · Cited by 2,063
Self-citation
The lymphocyte chemoattractant SDF-1 is a ligand for LESTR/fusin and blocks HIV-1 entry
Bleul, C. C., Farzan, M., Choe, H., Parolin, C., Clark‐Lewis, I., Sodroski, J., & Springer, T. A. (1996) · Nature · doi:10.1038/382829a0 · Cited by 1,953
Decay characteristics of HIV-1-infected compartments during combination therapy
Perelson, A. S., Essunger, P., Cao, Y., Vesanen, M., Hurley, A., Saksela, K., Markowitz, M. H., & Ho, D. D. (1997) · Nature · doi:10.1038/387188a0 · Cited by 1,861
Positive Effects of Combined Antiretroviral Therapy on CD4 + T Cell Homeostasis and Function in Advanced HIV Disease
Autran, B., Carcelain, G., Li, T., Blanc, C., Mathez, D., Tubiana, R., Katlama, C., Debré, P., & Leibowitch, J. (1997) · Science · doi:10.1126/science.277.5322.112 · Cited by 1,786

Show all 84 references

Research works printed but not linked: 3

Kuiken C. L. Korber B. Epidemiological significance of intra- and inter-person variation of HIV-1.AIDS 8 1994 S73 S83
Mantel N. The detection of disease clustering and a generalized regression approach.Cancer Res. 27 1967 209 220
Pelletier E. Wain-Hobson S. AIDS is not caused by the extreme genetic variability of HIV.J. NIH Res. 8 1996 45 48

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Authors: Shankarappa, R., Margolick, J. B., Gange, S. J., Rodrigo, A. G., Upchurch, D., Farzadegan, H., Gupta, P., Rinaldo, C. R., Learn, G. H., He, X., Huang, X.-L., & Mullins, J. I.
Affiliations: University of Washington (US)
Departments of Molecular Microbiology and Immunology2 and of
Johns Hopkins University (US)
University of Pittsburgh (US)
ORCID: Margolick, Joseph B.
Gange, Stephen J.
Rodrigo, Allen G.
Gupta, Phalguni
Rinaldo, Charles R.
Learn, Gerald H.
He, Xi
Mullins, James I.
Venue: Journal of Virology
Publisher: American Society for Microbiology
Published: 1999-12
Volume: 73
Issue: 12
Pages: 10489-10502
ISSN: 0022-538X (ISSN-L)
1098-5514
DOI: 10.1128/jvi.73.12.10489-10502.1999
PMC: PMC113104
OpenAlex: W2126515754
Cited by: 926
References: 84
Citations by year: 2026: 7 · 2025: 12 · 2024: 14 · 2023: 19 · 2022: 16 · 2021: 13 · 2020: 22 · 2019: 33 · 2018: 24 · 2017: 33 · 2016: 31 · 2015: 35 · 2014: 36 · 2013: 50 · 2012: 57
FWCI: 7.58
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Journal of Virology (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health (5r01ai034783-05, 5r01ai032885-06)
National Institute of Allergy and Infectious Diseases (AI-34783, AI37984, U01AI035040, U01AI037984, U01AI035041, AI-32885, U01AI035039, U01AI035042, P30AI027757)
Topics: Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
Keywords: HIV-1, viral evolution, disease progression, asymptomatic HIV infection, HIV-1 env gene, viral divergence, viral population diversity, CXCR4, T cell homeostasis, CD4+ T cells, CD3+ T cells
MeSH terms: Base Sequence, DNA, Viral, Humans, Male, Molecular Sequence Data, Prospective Studies, HIV-1, HIV Infections, Gene Products, env, Disease Progression, Evolution, Molecular

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Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection

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