Cited by 926HIV Research and TreatmentEvolution and Genetic DynamicsHIV/AIDS drug development and treatment

The DOI matches its Crossref record; 84 of the 84 references it cites were found in a registry or an index.

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

Open access

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

Open this paper in CoChat — free account Open PDF

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.

Integrity signals

Registry

Crossref · 10.1128/jvi.73.12.10489-10502.1999

Cites

84 of 84 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

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

Sorted by citations

Items 701–800 of 920

Limited Evolution of Human Immunodeficiency Virus Type 1 in the Thymus of a Perinatally Infected Child
Scinicariello, F., Kourtis, A. P., Nesheim, S. R., Abramowsky, C. R., & Lee, F. K. (2010) · Clinical Infectious Diseases · doi:10.1086/650453 · Cited by 5
Longitudinal Ultradeep Characterization of HIV Type 1 R5 and X4 Subpopulations in Patients Followed from Primary Infection to Coreceptor Switch
Hedskog, C., Brodin, J., Heddini, A., Bratt, G., Albert, J., & Mild, M. (2013) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2012.0349 · Cited by 5
Spouse-to-Spouse Transmission and Evolution of Hypervariable Region 1 and 5’ Untranslated Region of Hepatitis C Virus Analyzed by Next-Generation Sequencing
Cortés, K. C., Zagordi, O., Jabłońska, J., Pawełczyk, A., Kubisa, N., Perlejewski, K., Bukowska‐Ośko, I., Płoski, R., Radkowski, M., & Laskus, T. (2016) · PLoS ONE · doi:10.1371/journal.pone.0150311 · Cited by 5
Pairwise diversity and tMRCA as potential markers for HIV infection recency
Moyo, S. M., Wilkinson, E., Vandormael, A. M., Wang, R., Weng, J. F., Kotokwe, K. P., Gaseitsiwe, S., Musonda, R. M., Makhema, J. M., Essex, M., et al. (2017) · Medicine · doi:10.1097/md.0000000000006041 · Cited by 5
Sequence Accuracy in Primary Databases: A Case Study on HIV-1B
Balaji, S., Ramachandran, A., Nandy, K., & Shapshak, P. (2017) · Springer eBooks · doi:10.1007/978-1-4939-7290-6_32 · Cited by 5
Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns
Dickey, A. M., Smith, T. P. L., Clawson, M. L., Heaton, M. P., & Workman, A. M. (2020) · F1000Research · doi:10.12688/f1000research.27898.1 · Cited by 5
Reappearance of an 11-year-old sequence in an HIV-1 infected patient during treatment interruption
Madsen, T. V., Gerstoft, J., Nielsen, C., & Jørgensen, L. B. (2008) · Scandinavian Journal of Infectious Diseases · doi:10.1080/00365540701558706 · Cited by 5
CCR2b-64I Allelic Polymorphisms in Advanced HIV-Infected Koreans Accelerate Disease Progression
Choi, B., Choi, J., Kim, S. S., Kee, M., & Lee, J.-S. (2007) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2006.0133 · Cited by 5
Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1
Williams, S. G., Madan, R., Norris, M. G. S., Archer, J. P., Mizuguchi, K., Robertson, D. L., & Lovell, S. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.037 · Cited by 5
Reconstructing Ancestor-Descendant Lineages from Serially-Sampled Data: A Comparison Study
Buendia, P., Collins, T. M., & Narasimhan, G. (2006) · Lecture notes in computer science · doi:10.1007/11758525_108 · Cited by 5
Characterization of the gp120 of Circulating HIV Type 1 in a Group of Infected Chinese Blood/Plasma Donors with Asymptomatic and Symptomatic Stages of the Disease
Chen, Y., Craigo, J. K., Ding, M., Guo, Y., Shen, S., Zhou, Y., Wu, H., & Gupta, P. (2006) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2006.22.1167 · Cited by 5
Self-citation
Immunodeficiency in HIV-1 Infection
Sedaghat, A. R., & Siliciano, R. F. (2004) · Elsevier eBooks · doi:10.1016/b978-012764051-8/50013-5 · Cited by 5
HIV infection of the central nervous system
Anthony, I., Peter Simmonds, K., & Bell, J. E. (2008) · Cambridge University Press eBooks · doi:10.1017/cbo9780511541728.013 · Cited by 5
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model
Mai, U., Charvel, E., & Mirarab, S. (2024) · Systematic Biology · doi:10.1093/sysbio/syae034 · Cited by 5
HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data
Golubchik, T., Abeler‐Dörner, L., Hall, M., Wymant, C., Bonsall, D., MacIntyre-Cockett, G., Thomson, L., Baeten, J. M., Celum, C., Galiwango, R. M., et al. (2025) · BMC Bioinformatics · doi:10.1186/s12859-025-06189-y · Cited by 4
A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints
Kuzmin, K., Schmidt, H., Kang, M. K., Snir, S., Raphael, B. J., & Skums, P. (2025) · Nature Communications · doi:10.1038/s41467-025-63411-4 · Cited by 4
A time lag insensitive approach for estimating HIV-1 transmission direction
Yang, J., Ge, M., & Pan, X. (2012) · AIDS · doi:10.1097/qad.0b013e3283536b89 · Cited by 4
Identifying HLA-Associated Polymorphisms in HIV-1
Brumme, Z. L., Poon, A. F. Y., Carlson, J. M., & Walker, B. D. (2010) · Cited by 4
The Mutable Vaccine for Mutable Viruses
Cascalho, M., Balin, S. J., & Platt, J. L. (2017) · Immunotherapy · doi:10.2217/imt-2017-0030 · Cited by 4
Deep-Sequencing Analysis of the Dynamics of HIV-1 Quasiespecies in Naive Patients during a Short Exposure to Maraviroc
Cascajero, A., Rastrojo, A., Díez‐Fuertes, F., Hernández‐Novoa, B., Aguado, B., Moreno, S., Alcamı́, J., & Pérez‐Olmeda, M. (2018) · Journal of Virology · doi:10.1128/jvi.00390-18 · Cited by 4
Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years
Cho, Y.-K., Kim, J., & Foley, B. T. (2021) · Viruses · doi:10.3390/v13050806 · Cited by 4
RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection
Lewitus, É., Sanders‐Buell, E., Bose, M., O’Sullivan, A. M., Poltavee, K., Li, Y., Bai, H., Mdluli, T., Donofrio, G. C., Slike, B. M., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab057 · Cited by 4
Self-citation
Identification of HIV Rapid Mutations Using Differences in Nucleotide Distribution over Time
Sun, N., Yang, J., & Yau, S. S. ‐. (2022) · Genes · doi:10.3390/genes13020170 · Cited by 4
Identifying and Visualizing Space-Time Clusters of Vector-Borne Diseases
Desjardins, M. R., Hohl, A., Delmelle, E. M., & Casas, I. (2022) · Springer eBooks · doi:10.1007/978-3-030-71377-5_11 · Cited by 4
A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients
Fili, M., Hu, G., Han, C., Kort, A. J., Trettin, J., & Haim, H. (2023) · Algorithms for Molecular Biology · doi:10.1186/s13015-023-00228-0 · Cited by 4
Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
Goode, M., & Rodrigo, A. G. (2004) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0608s05 · Cited by 4
Self-citation
Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains
Buendia, P., & Narasimhan, G. (2009) · BMC Systems Biology · doi:10.1186/1752-0509-3-62 · Cited by 4
Antiretroviral therapy for HIV-1 vaccine efficacy trial participants who seroconvert
Kim, H. N., Tabet, S. R., Corey, L., & Celum, C. (2005) · Vaccine · doi:10.1016/j.vaccine.2005.05.049 · Cited by 4
Evolutionary gamut of in vivo Gag substitutions during early HIV-1 subtype C infection
Novitsky, V., Wang, R., Baca, J., Margolin, L., McLane, M. F., Moyo, S. M., van Widenfelt, E., Makhema, J. M., & Essex, M. (2011) · Virology · doi:10.1016/j.virol.2011.09.020 · Cited by 4
Amino Acid Covariation in a Functionally Important Human Immunodeficiency Virus Type 1 Protein Region Is Associated With Population Subdivision
da Silva, J. (2009) · Genetics · doi:10.1534/genetics.108.099853 · Cited by 4
Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression
Norström, M. M., Véras, N. M. C., Huang, W., Proper, M. C. F., Cook, J. W., Hartogensis, W., Hecht, F. M., Karlsoon, A. C., & Salemi, M. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003830 · Cited by 4
Discovery and Development of Maraviroc, a CCR5 Antagonist for the Treatment of HIV Infection
Dorr, P. K., Stammen, B., & van der Ryst, E. (2012) · Wiley eBooks · doi:10.1002/9781118219683.ch9 · Cited by 4
The genetic interaction between HIV and the antibody repertoirePreprint
Strauli, N. B., Fryer, E., Pham, O., Abdel‐Mohsen, M., Facente, S. N., Pilcher, C. D., Pennings, P. S., Pillai, S. K., & Hernandez, R. D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/646968 · Cited by 4
High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settingsPreprint
Berry, I. M., Treangen, T. J., Fung, C., Tai, S., Pollett, S., Hong, F. H., Li, T., Pireku, P. K., Thommana, A., German, J. R., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.01.450528 · Cited by 4
Capsid-dependent lentiviral restrictions
Twentyman, J., Emerman, M., & OhAinle, M. (2024) · Journal of Virology · doi:10.1128/jvi.00308-24 · Cited by 4
Long-term antiretroviral therapy mitigates mortality and morbidity independent of HIV tropism: 18 years follow-up in a women's cohort
Weiser, B., Shi, B., Kemal, K. S., Burger, H., MINKOFF, H. L., Shi, Q., Gao, W., Robison, E., Holman, S., Schroeder, T., et al. (2022) · AIDS · doi:10.1097/qad.0000000000003337 · Cited by 3
Inferring Human Immunodeficiency Virus 1 Proviral Integration Dates With Bayesian Inference
Jones, B. R., & Joy, J. B. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad156 · Cited by 3
Using viral sequence diversity to estimate time of HIV infection in infants
Russell, M. L., Fish, C. S., Drescher, S. M., Cassidy, N. A. J., Chanana, P., Benki-Nugent, S. F., Slyker, J. A., Mbori‐Ngacha, D., Bosire, R. K., Richardson, B. A., et al. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011861 · Cited by 3
Maraviroc in Antiretroviral-Naïve HIV-1 Patients
Ghebremedhin, B. (2012) · Infectious Diseases Research and Treatment · doi:10.4137/idrt.s7597 · Cited by 3
Biological properties of HIV-1 subtype B' isolates from infected Chinese blood donors at different disease stages
Chen, Y., Shen, C., Wu, H., Caruso, L., Ratner, D. M., Rodriguez, M. A., Chen, X., & Gupta, P. (2008) · Virology · doi:10.1016/j.virol.2008.10.050 · Cited by 3
Self-citation
Relaxation of Adaptive Evolution during the HIV-1 Infection Owing to Reduction of CD4+ T Cell Counts
Leal, E. D. S., Casseb, J., Hendry, M. T., Busch, M. P., & Diaz, R. S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039776 · Cited by 3
Long-term evolution of transmitted CXCR4-using HIV-1 under effective antiretroviral therapy
Raymond, S., Jeanne, N., Nicot, F., Lefèbvre, C., Carcenac, R., Minier, L., Chiabrando, J., Cazabat, M., Delobel, P., & Izopet, J. (2019) · AIDS · doi:10.1097/qad.0000000000002295 · Cited by 3
Variations in Env at amino acids 328 and 330 affect HIV-1 replicative fitness and entry inhibitor sensitivity
Wang, H., Yang, L., Li, Y., Li, B., Zhu, X., Yan, D., Li, M., Wu, W., Sun, M., & Yang, R. (2021) · Virus Research · doi:10.1016/j.virusres.2021.198424 · Cited by 3
SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells
Sambaturu, N., Fray, E. J., Hariharan, V., Wu, F., Zitzmann, C., Simonetti, F. R., Barouch, D. H., Siliciano, J. D., Siliciano, R. F., Ribeiro, R. M., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115663 · Cited by 3
Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing
Hora, B., Gulzar, N., Chen, Y., Karagiannis, K., Cai, F., Su, C., Smith, K., Simonyan, V. V., Shah, S. A., Ahmed, M., et al. (2020) · mSphere · doi:10.1128/msphere.00551-20 · Cited by 3
Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host
Magalis, B. R., Autissier, P., Williams, K. C., Chen, X., Browne, C. J., & Salemi, M. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.709962 · Cited by 3
Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana
Bhebhe, L. N., Moyo, S. M., Gaseitsiwe, S., Pretorius-Holme, M., Yankinda, E. K., Manyake, K., Kgathi, C., Mmalane, M. O., Lebelonyane, R., Gaolathe, T., et al. (2022) · BMC Infectious Diseases · doi:10.1186/s12879-022-07698-4 · Cited by 3
Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Subtype C Env gp120 Sequences Among Four Drug-Naive Families Following Subsequent Heterosexual and Vertical Transmissions
Duri, K., Gumbo, F. Z., Kristiansen, K., Mapingure, M. P., Munjoma, M. W., Chirenje, M. Z., Rusakaniko, S., Stray‐Pedersen, B., & Müller, F. (2011) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2011.0217 · Cited by 3
Genotypic Characterization of HIV Type 1 in Jamaica
Roye, M. E., Amarakoon, I. I., Hamilton, C.-L. C., Eyzaguirre, L. M., Figueroa, P., & Carr, J. K. (2010) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2010.0106 · Cited by 3
Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection
Ndolo, T., Syvanen, M., Ellison, T. J., & Dandekar, S. (2005) · Virology · doi:10.1016/j.virol.2005.08.013 · Cited by 3
Similar HIV‐1 evolution and immunological responses at 10 years despite several therapeutic strategies and host HLA Types
Arnedo, M., Plana, M., Más, A., Guilà, M., Gil, C., Castro, P., García, F., Domingo, E., Gatell, J. M., & Pumarola, T. (2004) · Journal of Medical Virology · doi:10.1002/jmv.20117 · Cited by 3
Modelling the impact of acute infection dynamics on the accumulation of HIV-1 mutations
Shiri, T., & Welte, A. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2011.03.011 · Cited by 3
Emergence, dominance, and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection
Meehan, C. J., Hedge, J., Robertson, D. L., McCormack, G. P., & Travers, S. A. A. (2010) · Journal of Medical Virology · doi:10.1002/jmv.21922 · Cited by 3
High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia
Nedellec, R., Herbeck, J. T., Hunt, P. W., Deeks, S. G., Mullins, J. I., Anton, E. D., Reeves, J. D., & Mosier, D. E. (2016) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2016.0153 · Cited by 3
Self-citation
Differentiating founder and chronic HIV envelope sequences
Murray, J. M., Maher, S. J., Mota, T. M., Suzuki, K., Kelleher, A. D., & Purcell, D. F. J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0171572 · Cited by 3
Association of HIV diversity and virologic outcomes in early antiretroviral treatment: HPTN 052
Palumbo, P. J., Wilson, E., Piwowar‐Manning, E., McCauley, M., Gamble, T., Kumwenda, J., Makhema, J. M., Kumarasamy, N., Chariyalertsak, S., Hakim, J. G., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0177281 · Cited by 3
The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats
Hayward, J. J., & Rodrigo, A. G. (2010) · Archives of Virology · doi:10.1007/s00705-010-0598-z · Cited by 3
Self-citation
Genetic analyses of HIV env associated with uveitis in antiretroviral-naive individuals
Williams-Wietzikoski, C. A., So, I. D., Bull, M. E., Samleerat, T., Pathanapitoon, K., Kunavisarut, P., Kongyai, N., Ngo‐Giang‐Huong, N., Frenkel, L. M., & Sirirungsi, W. (2017) · AIDS · doi:10.1097/qad.0000000000001550 · Cited by 3
Phylogenetic Analyses Comparing HIV Sequences from Plasma at Virologic Failure to Cervix Versus Blood Sequences from Antecedent Antiretroviral Therapy Suppression
Bull, M. E., McKernan, J. L., Styrchak, S. M., Kraft, K., Hitti, J. E., Cohn, S. E., Tapia, K. A., Deng, W., Holte, S., Mullins, J. I., et al. (2019) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2018.0211 · Cited by 3
Self-citation
Core set approach to reduce uncertainty of gene trees
Okabayashi, T., Kitazoe, Y., Kishino, H., Watabe, T., Nakajima, N., Okuhara, Y., O’Loughlin, S. M., & Walton, C. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-41 · Cited by 3
An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics
Munshaw, S., & Kepler, T. B. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn066 · Cited by 3
CD4+ T cell targeting of human immunodeficiency virus type 1 (HIV-1) peptide sequences present in vivo during chronic, progressive HIV-1 disease
Boritz, E., Rapaport, E. L., Campbell, T., Koeppe, J. R., & Wilson, C. C. (2006) · Virology · doi:10.1016/j.virol.2006.10.040 · Cited by 3
Migration coupled with recombination explains disparate HIV-1 anatomical compartmentalization signalsPreprint
Sarkar, S., Romero-Severson, E. O., & Leitner, T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.22.537949 · Cited by 3
Single genome amplification and molecular cloning of HIV-1 populations in acute HIV-1 infection: implications for studies on HIV-1 diversity and evolutionary rate
Hsieh, A. Y. Y., Hassan, A. S., Nazziwa, J., Lindquist, L., Karlson, S., Hare, J., Kamali, A., Karita, E., Kilembe, W., Price, M. A., et al. (2025) · Virus Evolution · doi:10.1093/ve/veaf099 · Cited by 2
Retroviruses and Cell Fusions: Overview
Kjeldbjerg, A. L., Bahrami, S., & Pedersen, F. S. (2010) · Springer eBooks · doi:10.1007/978-90-481-9772-9_2 · Cited by 2
Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution
Hool, A., Leventhal, G. E., & Bonhoeffer, S. (2014) · Epidemics · doi:10.1016/j.epidem.2014.01.002 · Cited by 2
Development and Validation of a Genotypic Assay to Quantify CXCR4- and CCR5-Tropic Human Immunodeficiency Virus Type-1 (HIV-1) Populations and a Comparison to Trofile®
Ko, D. L., McLaughlin, S., Deng, W., Mullins, J. I., Dragavon, J., Harb, S., Coombs, R. W., & Frenkel, L. M. (2024) · Viruses · doi:10.3390/v16040510 · Cited by 2
Self-citation
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies
Castro, L. A., Leitner, T., & Romero-Severson, E. O. (2023) · Virus Evolution · doi:10.1093/ve/vead032 · Cited by 2
Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs
Goldberg, E. E., Lundgren, E. J., Romero-Severson, E. O., & Leitner, T. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad282 · Cited by 2
HIV-1 diversity in viral reservoirs obtained from circulating T-cell subsets during early ART and beyond
Zhang, Y., Otte, F., Stoeckle, M. P., Thielen, A., Däumer, M., Kaiser, R., Kusejko, K., Metzner, K. J., Klimkait, T., & Study, A. T. S. H. C. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012526 · Cited by 2
A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1
Reisman, S., Hatzopoulos, T., Läufer, K., Thiruvathukal, G. K., & Putonti, C. (2016) · Evolutionary Bioinformatics · doi:10.4137/ebo.s32757 · Cited by 2
Characterization of human immunodeficiency virus type 1 CRF01_AE env genes derived from recently infected Thai individuals
Chaitaveep, N., Utachee, P., Nakamura, S., Chuenchitra, T., Ekpo, P., Takeda, N., Pattanapanyasat, K., & Kameoka, M. (2013) · Microbes and Infection · doi:10.1016/j.micinf.2013.10.015 · Cited by 2
Inferring viral population structures using heteroduplex mobility and DNA sequence analyses
Shankarappa, R., & Mullins, J. I. (2013) · Journal of Virological Methods · doi:10.1016/j.jviromet.2013.08.012 · Cited by 2
Self-citation
Homogenous HIV-1 subtype B quasispecies in Brazilian men and women recently infected via heterosexual transmission
Gouveia, N. L., Camargo, M., Caseiro, M. M., Janini, L. M., Sucupira, M. C. A., & Diaz, R. S. (2014) · Virus Genes · doi:10.1007/s11262-014-1048-x · Cited by 2
Development of a Novel Codon-Specific Polymerase Chain Reaction for the Detection of CXCR4-Utilizing HIV Type 1 Subtype B
McLaughlin, S., Swenson, L. C., Hu, S., Hughes, P., Harrigan, P. R., Coombs, R. W., & Frenkel, L. M. (2013) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2012.0024 · Cited by 2
Nucleotide and amino acid mutations in human immunodeficiency virus corresponding to CD4+ decline
Hill, M. D., & Hernandez, W. (2005) · Archives of Virology · doi:10.1007/s00705-005-0693-8 · Cited by 2
Broad Neutralization as a Byproduct of Antibody Maturation during HIV-1 Infection: a Personal Perspective
Gao, F. (2016) · DOAJ (DOAJ: Directory of Open Access Journals) · doi:10.11979/idtm.201602004 · Cited by 2
Molecular mechanisms of HIV-1 genetic diversity
Сосин, Д. В., & Tchurikov, N. A. (2017) · Molecular Biology · doi:10.1134/s0026893317030153 · Cited by 3
HIV vaccines: Lessons from basic research, clinical trials, and public policy
Saiz, A., & Farenhem, K. L. (2023) · MIT Science Policy Review · doi:10.38105/spr.0cg04tczoe · Cited by 2
Exploring and Predicting the Drivers of Ongoing HIV-1 Transmission in Guangyuan, Sichuan
Zhang, Y., Jiang, H., Xiang, W., Zhu, J., Hou, X., Liang, S., Yuan, D., Zhou, C., & Su, L. (2023) · Infection and Drug Resistance · doi:10.2147/idr.s421763 · Cited by 2
Evolution of HIV-1 from the viewpoint of information theory
Sato, K., & Ohya, M. (2010) · International Symposium on Applied Sciences in Biomedical and Communication Technologies · doi:10.1109/isabel.2010.5702806 · Cited by 2
Antigenic Stimulation Specifically Reactivates the Replication of Archived Simian Immunodeficiency Virus Genomes in Chronically Infected Macaques
Renoux, C., Wain–Hobson, S., Hurtrel, B., & Cheynier, R. (2005) · Journal of Virology · doi:10.1128/jvi.79.17.11231-11238.2005 · Cited by 2
Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts
Magalis, B. R., Pond, S. L. K., Summers, M. F., & Salemi, M. (2018) · Virus Evolution · doi:10.1093/ve/vey018 · Cited by 2
Differential utilization of CD4+ by transmitted/founder and chronic envelope glycoproteins in a MSM HIV-1 subtype B transmission cluster
Bouvin-Pley, M., Leoz, M., Roch, E., Moreau, A., Migraine, J., Bellini, N., Blake, O., Mammano, F., Braibant, M., Plantier, J., et al. (2020) · AIDS · doi:10.1097/qad.0000000000002690 · Cited by 2
Discovery and Development of Maraviroc and PF‐232798: CCR5 Antagonists for the Treatment of HIV‐1 Infection
Dorr, P. K., & Stupple, P. A. (2011) · Wiley eBooks · doi:10.1002/9780470929353.ch9 · Cited by 2
The Code Structure of HIV-1
Sato, K., Fushimi, N., & Ohya, M. (2007) · Open Systems & Information Dynamics · doi:10.1007/s11080-007-9053-3 · Cited by 2
Re: Follow-up Study of Intrahost HIV Type 2 Variability Reveals Discontinuous Evolution of C2V3 Sequences
Gottlieb, G. S., & Mullins, J. I. (2001) · AIDS Research and Human Retroviruses · doi:10.1089/08892220152644278 · Cited by 2
Self-citation
Real-time PCR Quantitation of Subtype C HIV DNA in a Zambian Discordant Couple Cohort
Johnson, R. W., Li, B., Sunay, S., Moore, R. H., Mulenga, J., Hunter, E., Allen, S. A., Blackwell, J. L., & Derdeyn, C. A. (2006) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2006.22.438 · Cited by 2
Molecular Mechanism of HIV-1 Infection: Role of Viral and Host Determinants
Sundaravaradan, V. (2006) · UA Campus Repository (The University of Arizona) · Cited by 2
A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferationPreprint
Reeves, D. B., Duke, E. R., Wagner, T. A., Palmer, S., Spivak, A. M., & Schiffer, J. T. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/146977 · Cited by 2
MinPD: distance-based phylogenic anlysis and recombination detection of serially-sampled HIV quasispecies
Buendia, P., & Narasimhan, G. (2004) · IEEE Computational Systems Bioinformatics Conference (CSB) · doi:10.1109/csb.2004.1332423 · Cited by 2
Human Immunodeficiency Virus
Guatelli, J., Siliciano, R. F., Kuritzkes, D. R., & Richman, D. D. (2009) · Wiley eBooks · doi:10.1128/9781555815981.ch33 · Cited by 2
Duration of antiretroviral therapy impacts the degree of residual SIV infection in the gut in long‐term non‐progressing Chinese rhesus macaques
Solis‐Leal, A., May, A., Mohan, M., Dufour, J., & Ling, B. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28185 · Cited by 1
wavess: An R package for simulation of adaptive within-host virus sequence evolution
Sambaturu, N., Lapp, Z., Tria, F. D. K., Romero-Severson, E. O., Molina-Parı́s, C., & Leitner, T. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013437 · Cited by 1
Immune responses may make HIV-1 therapeutic interfering particles less effective
Dodd, G. K., & de Boer, R. J. (2025) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2025.112317 · Cited by 1
A Framework Including Recombination for Analyzing the Dynamics of Within-Host HIV Genetic Diversity
Sargsyan, O. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087655 · Cited by 1
Intrahost and Interhost Variability of the HIV Type 1 nef Gene in Brazilian Children
Cavalieri, E., Florido, C., Leal, E. D. S., Machado, D. M., Camargo, M., Diaz, R. S., & Janini, L. M. (2009) · AIDS Research and Human Retroviruses · doi:10.1089/aid.2009.0061 · Cited by 1
Analysis of a stochastic predator–prey model with applications to intrahost HIV genetic diversity
Leviyang, S. (2011) · Journal of Mathematical Biology · doi:10.1007/s00285-011-0497-2 · Cited by 1
Modelagem matemática da evolução do fenótipo indutor de sincício na infecção HIV-1/AIDS
Joly, M., & Pinto, J. M. (2010) · Revista Brasileira de Epidemiologia · doi:10.1590/s1415-790x2010000200003 · Cited by 1
Tracing the origin and dynamics of the HIV-1 epidemic in Serbia
Šiljić, M., Salemović, D., Jevtović, D., Pešić-Pavlović, I., Žerjav, S., Nikolic, V., Ranin, J. T., & Stanojević, M. (2014) · Archives of Biological Sciences · doi:10.2298/abs1402507s · Cited by 1

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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks