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Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection
Open accessAbstract
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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If many calibration dates are available, it becomes possible to test the constancy of rates across the viral phylogeny.
“If many calibration dates are available - for example, if a series of samples from a single infected patient 62 or a collection of archived samples 63 is available - it becomes possible to test the constancy of rates across the viral phylogeny.”
From The modern molecular clock (2003) · cites this paper as [62]
Citations
Cites
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
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-citationKoup, 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-citationThe 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
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
Kaslow, R. A., Ostrow, D. G., Detels, R., Phair, J., Polk, B. F., & Rinaldo, C. R. (1987) · American Journal of Epidemiology · doi:10.1093/aje/126.2.310 · Cited by 1,195
Self-citationMEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
Kumar, S., Tamura, K., & Nei, M. (1994) · Computer applications in the biosciences · doi:10.1093/bioinformatics/10.2.189 · Cited by 1,166
The HIV coreceptors CXCR4 and CCR5 are differentially expressed and regulated on human T lymphocytes
Bleul, C. C., Wu, L., Hoxie, J. A., Springer, T. A., & Mackay, C. R. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.5.1925 · Cited by 1,134
Recent Advances in the Polymerase Chain Reaction
Erlich, H. A., Gelfand, D. H., & Sninsky, J. J. (1991) · Science · doi:10.1126/science.2047872 · Cited by 1,080
Carr, A., Samaras, K., Chisholm, D. J., & Cooper, D. A. (1998) · The Lancet · doi:10.1016/s0140-6736(98)03391-1 · Cited by 1,065
Pathogenesis of human immunodeficiency virus infection
Levy, J. A. (1993) · Microbiological Reviews · doi:10.1128/mr.57.1.183-289.1993 · Cited by 1,046
Schuitemaker, H., KOOT, M., Kootstra, N. A., Dercksen, M. W., de Goede, R. E. Y., van Steenwijk, R. P., Lange, J. M. A., Schattenkerk, J. K. M. E., Miedema, F. F., & Tersmette, M. (1992) · Journal of Virology · doi:10.1128/jvi.66.3.1354-1360.1992 · Cited by 1,031
Quantitation of HIV-1 RNA in Plasma Predicts Outcome after Seroconversion
Mellors, J. W., Kingsley, L. A., Rinaldo, C. R., Todd, J. A., Hoo, B. S., Kokka, R. P., & Gupta, P. (1995) · Annals of Internal Medicine · doi:10.7326/0003-4819-122-8-199504150-00003 · Cited by 904
Self-citationA new classification for HIV-1
Berger, E. A., Doms, R. W., Fenyö, E. M., Korber, B., Littman, D. R., Moore, J. P., Sattentau, Q. J., Schuitemaker, H., Sodroski, J., & Weiss, R. A. (1998) · Nature · doi:10.1038/34571 · Cited by 825
In vivo fate of HIV-1-infected T cells: Quantitative analysis of the transition to stable latency
Chun, T., Finzi, D., Margolick, J. B., Chadwick, K. R., Schwartz, D. H., & Siliciano, R. F. (1995) · Nature Medicine · doi:10.1038/nm1295-1284 · Cited by 787
Self-citationKOOT, M., Keet, I. P. M., Vos, A. H. V., de Goede, R. E. Y., Roos, M. T. L., Coutinho, R. A., Miedema, F. F., Schellekens, P. T. A., & Tersmette, M. (1993) · Annals of Internal Medicine · doi:10.7326/0003-4819-118-9-199305010-00004 · Cited by 785
Direct Observation of Vortex Dynamics in Superconducting Films with Regular Arrays of Defects
Harada, K., Kamimura, O., Kasai, H., Matsuda, T., Tonomura, A., & Moshchalkov, V. V. (1996) · Science · doi:10.1126/science.274.5290.1167 · Cited by 778
Fouchier, R. A. M., Groenink, M., Kootstra, N. A., Tersmette, M., Huisman, H. G., Miedema, F. F., & Schuitemaker, H. (1992) · Journal of Virology · doi:10.1128/jvi.66.5.3183-3187.1992 · Cited by 767
Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes
Delwart, E., Shpaer, E. G., Louwagie, J., McCutchan, F. E., Grez, M., Rübsamen‐Waigmann, H., & Mullins, J. I. (1993) · Science · doi:10.1126/science.8235655 · Cited by 756
Self-citationThe Reservoir for HIV-1 in Human Peripheral Blood Is a T Cell That Maintains Expression of CD4
Schnittman, S., Psallidopoulos, M. C., Lane, H. C., Thompson, L., Baseler, M., Massari, F. E., Fox, C. H., Salzman, N. P., & Fauci, A. S. (1989) · Science · doi:10.1126/science.2665081 · Cited by 714
Genetic Restriction of AIDS Pathogenesis by an SDF-1 Chemokine Gene Variant
Winkler, C. A., Modi, W. S., Smith, M. W., Nelson, G. W., Wu, X., Carrington, M. N., Dean, M. C., Honjo, T., Tashiro, K., Yabe, D., et al. (1998) · Science · doi:10.1126/science.279.5349.389 · Cited by 707
Tersmette, M., Gruters, R. A., de Wolf, F., de Goede, R. E. Y., Lange, J. M. A., Schellekens, P. T. A., Goudsmit, J., Huisman, H. G., & Miedema, F. F. (1989) · Journal of Virology · doi:10.1128/jvi.63.5.2118-2125.1989 · Cited by 636
Björndal, Å. S., Deng, H., Jansson, M., Fiore, J. R., Colognesi, C., Karlsson, A., Albert, J., Scarlatti, G., Littman, D. R., & Fenyö, E. M. (1997) · Journal of Virology · doi:10.1128/jvi.71.10.7478-7487.1997 · Cited by 608
(1993) · Archives of Dermatology · doi:10.1001/archderm.1993.01680240023002 · Cited by 569
Adaptive Evolution of Human Immunodeficiency Virus-Type 1 During the Natural Course of Infection
Wolinsky, S. M., Korber, B., Neumann, A. U., Daniels, M., Kunstman, K., Whetsell, A., Furtado, M. R., Cao, Y., Ho, D. D., Safrit, J. T., et al. (1996) · Science · doi:10.1126/science.272.5261.537 · Cited by 566
Viral Load and Disease Progression in Infants Infected with Human Immunodeficiency Virus Type 1
Shearer, W. T., Quinn, T. C., LaRussa, P. S., Lew, J., MOFENSON, L. M., Almy, S., RICH, K. C., Handelsman, E. L., Díaz, C., Pagano, M., et al. (1997) · New England Journal of Medicine · doi:10.1056/nejm199705083361901 · Cited by 538
Antigenic Diversity Thresholds and the Development of AIDS
Nowak, M. A., Anderson, R. M., McLean, A. R., Wolfs, T. F. W., Goudsmit, J., & May, R. M. (1991) · Science · doi:10.1126/science.1683006 · Cited by 518
Severe premature coronary artery disease with protease inhibitors
Henry, K., Melroe, H., Huebsch, J. A., Hermundson, J., Levine, C., Swensen, L., & Daley, J. (1998) · The Lancet · doi:10.1016/s0140-6736(05)79053-x · Cited by 509
de Jong, J. J., de Ronde, A., Keulen, W., Tersmette, M., & Goudsmit, J. (1992) · Journal of Virology · doi:10.1128/jvi.66.11.6777-6780.1992 · Cited by 500
Toward an Understanding of the Correlates of Protective Immunity to HIV Infection
Haynes, B. F., Pantaleo, G., & Fauci, A. S. (1996) · Science · doi:10.1126/science.271.5247.324 · Cited by 418
Folks, T. M., Powell, D., Lightfoote, M. M., Koenig, S., Fauci, A. S., Benn, S., Rabson, A. B., Daugherty, D. F., Gendelman, H. E., & HOGGAN, M. D. (1986) · The Journal of Experimental Medicine · doi:10.1084/jem.164.1.280 · Cited by 416
Richman, D. D., & Bozzette, S. A. (1994) · The Journal of Infectious Diseases · doi:10.1093/infdis/169.5.968 · Cited by 406
Herbein, G., Mahlknecht, U., Batliwalla, F., Gregersen, P. K., Pappas, T. C., Butler, J., O’Brien, W. A., & Verdin, E. M. (1998) · Nature · doi:10.1038/26026 · Cited by 400
Goodenow, M. M., Huet, T., Saurin, W., Kwok, S., Sninsky, J. J., & Wain–Hobson, S. (1989) · PubMed · Cited by 344
HIV entry and tropism: the chemokine receptor connection.
Ea, B. (1997) · PubMed · Cited by 317
Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays
Delwart, E., Sheppard, H. W., Walker, B. D., Goudsmit, J., & Mullins, J. I. (1994) · Journal of Virology · doi:10.1128/jvi.68.10.6672-6683.1994 · Cited by 295
Self-citationHigh prevalence of thymic tissue in adults with human immunodeficiency virus-1 infection.
McCune, J. M., Loftus, R., Schmidt, D. K., Carroll, P. R., Webster, D., Swor-Yim, L. B., Francis, I. R., Gross, B. H., & Grant, R. M. (1998) · Journal of Clinical Investigation · doi:10.1172/jci2834 · Cited by 250
Failure of T-cell homeostasis preceding AIDS in HIV-1 infection
Margolick, J. B., Muñoz, A., Donnenberg, A. D., Park, L. P., Galai, N., Giorgi, J. V., O’Gorman, M. R. G., & Ferbas, J. (1995) · Nature Medicine · doi:10.1038/nm0795-674 · Cited by 233
Self-citationGiorgi, J. V., Cheng, H.-L., Margolick, J. B., Bauer, K. D., Ferbas, J., Waxdal, M. J., Schmid, I., Hultin, L. E., Jackson, A. L., Park, L., et al. (1990) · Clinical Immunology and Immunopathology · doi:10.1016/0090-1229(90)90096-9 · Cited by 232
Self-citationRelationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease.
McNearney, T. A., Horníčková, Z., Markham, R. B., Birdwell, A., Arens, M. Q., Saah, A. J., & Ratner, L. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.21.10247 · Cited by 224
Spina, C. A., Prince, H. E., & Richman, D. D. (1997) · Journal of Clinical Investigation · doi:10.1172/jci119342 · Cited by 185
Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS
Delwart, E., Pan, H., Sheppard, H. W., Wolpert, D. H., Neumann, A. U., Korber, B., & Mullins, J. I. (1997) · Journal of Virology · doi:10.1128/jvi.71.10.7498-7508.1997 · Cited by 175
Self-citationJurriaans, S., van Gemen, B., Weverling, G. J., Strup, D. V., Nara, P. L., Coutinho, R. A., KOOT, M., Schuitemaker, H., & Goudsmit, J. (1994) · Virology · doi:10.1006/viro.1994.1526 · Cited by 173
HIV Quasispecies and Resampling
Liu, S., Rodrigo, A. G., Shankarappa, R., Learn, G. H., Hsu, L., Davidov, O., Zhao, L. P., & Mullins, J. I. (1996) · Science · doi:10.1126/science.273.5274.415 · Cited by 169
Self-citationde Wolf, F., Hogervorst, E. J. M., Goudsmit, J., Fenyö, E.-M., Rübsamen‐Waigmann, H., Holmes, H. C., Galvão‐Castro, B., Karita, E., Wasi, C., Sempala, S. D. K., et al. (1994) · AIDS Research and Human Retroviruses · doi:10.1089/aid.1994.10.1387 · Cited by 165
Ganeshan, S., Dickover, R. E., Korber, B., Bryson, Y. J., & Wolinsky, S. M. (1997) · Journal of Virology · doi:10.1128/jvi.71.1.663-677.1997 · Cited by 163
Lukashov, V. V., KUIKEN, C. L., & Goudsmit, J. (1995) · Journal of Virology · doi:10.1128/jvi.69.11.6911-6916.1995 · Cited by 160
Psallidopoulos, M. C., Schnittman, S., Thompson, L., Baseler, M., Fauci, A. S., Lane, H. C., & Salzman, N. P. (1989) · Journal of Virology · doi:10.1128/jvi.63.11.4626-4631.1989 · Cited by 153
Wolfs, T. F. W., de Jong, J. J., van den Berg, H., Tijnagel, J. M. G. H., Krone, W., & Goudsmit, J. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.24.9938 · Cited by 141
Poss, M. L., Rodrigo, A. G., Gosink, J. J., Learn, G. H., Panteleeff, D., Martin, H., Bwayo, J. J., Kreiss, J. K., & Overbaugh, J. M. (1998) · Journal of Virology · doi:10.1128/jvi.72.10.8240-8251.1998 · Cited by 140
Self-citationQuantitation of Target Molecules from Polymerase Chain Reaction-Based Limiting Dilution Assays
Rodrigo, A. G., Goracke, P. C., ROWHANIAN, K., & Mullins, J. I. (1997) · AIDS Research and Human Retroviruses · doi:10.1089/aid.1997.13.737 · Cited by 136
Self-citationLiu, S., Schacker, T. W., Musey, L. K., Shriner, D., McElrath, M. J., Corey, L., & Mullins, J. I. (1997) · Journal of Virology · doi:10.1128/jvi.71.6.4284-4295.1997 · Cited by 134
Self-citationPeeters, M., Vincent, R., Perret, J., Lasky, M., Patrel, D., Liégeois, F., Courgnaud, V., Seng, R., Matton, T., Molinier, S., et al. (1999) · Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology · doi:10.1097/00042560-199902010-00002 · Cited by 127
Leitner, T., Kumar, S., & Albert, J. (1997) · Journal of Virology · doi:10.1128/jvi.71.6.4761-4770.1997 · Cited by 125
Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline
Markham, R. B., Wang, W.-C., Weisstein, A. E., Wang, Z., Muñoz, Á., Templeton, A. R., Margolick, J. B., Vlahov, D., Quinn, T. C., Farzadegan, H., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.21.12568 · Cited by 116
Self-citationCXCR4 and CCR5 Expression Delineates Targets for HIV-1 Disruption of T Cell Differentiation
Berkowitz, R. D., Beckerman, K., Schall, T. J., & McCune, J. M. (1998) · The Journal of Immunology · doi:10.4049/jimmunol.161.7.3702 · Cited by 110
Berkowitz, R. D., Alexander, S. A., Bare, C., Linquist-Stepps, V. D., Bogan, M., Moreno, M. E., Gibson, L., Wieder, E., Kosek, J. C., Stoddart, C. A., et al. (1998) · Journal of Virology · doi:10.1128/jvi.72.12.10108-10117.1998 · Cited by 106
Kaneshima, H., Su, L., Bonyhadi, M. L., Connor, R. I., Ho, D. D., & McCune, J. M. (1994) · Journal of Virology · doi:10.1128/jvi.68.12.8188-8192.1994 · Cited by 103
Schenker, E. L., Hultin, L. E., Bauer, K. D., Ferbas, J., Margolick, J. B., & Giorgi, J. V. (1993) · Cytometry · doi:10.1002/cyto.990140311 · Cited by 98
Self-citationLifson, A. R., Hilton, J. F., Westenhouse, J. L., Canchola, A. J., Samuel, M. C., Katz, M. H., Buchbinder, S., Hessol, N. A., Osmond, D. H., Shiboski, S. C., et al. (1994) · AIDS · doi:10.1097/00002030-199401000-00011 · Cited by 98
Shankarappa, R., Gupta, P., Learn, G. H., Rodrigo, A. G., Rinaldo, C. R., Gorry, M. C., Mullins, J. I., Nara, P. L., & Ehrlich, G. D. (1998) · Virology · doi:10.1006/viro.1997.8996 · Cited by 87
Self-citationThe incubation period of AIDS.
Muñoz, Á., Sabin, C. A., & Phillips, A. N. (1997) · PubMed · Cited by 83
Shioda, T., Oka, S., Xin, X., Liu, H., Harukuni, R., Kurotani, A., Fukushima, M., Hasan, M. K., Shiino, T., Takebe, Y., et al. (1997) · Journal of Virology · doi:10.1128/jvi.71.7.4871-4881.1997 · Cited by 80
Matrix correlation tests support a single origin for modern humans
Waddle, D. M. (1994) · Nature · doi:10.1038/368452a0 · Cited by 78
Japour, A. J., Fiscus, S. A., Arduino, J. M., Mayers, D. L., Reichelderfer, P. S., & Kuritzkes, D. R. (1994) · Journal of Clinical Microbiology · doi:10.1128/jcm.32.9.2291-2294.1994 · Cited by 77
Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo
Zhang, L., Diaz, R. S., Ho, D. D., Mosley, J. W., Busch, M. P., & Mayer, A. J. (1997) · Journal of Virology · doi:10.1128/jvi.71.3.2555-2561.1997 · Cited by 76
Nelson, J. A., Fiscus, S. A., & Swanstrom, R. I. (1997) · Journal of Virology · doi:10.1128/jvi.71.11.8750-8758.1997 · Cited by 66
Strunnikova, N., Ray, S. C., Livingston, R. A., Rubalcaba, E., & Viscidi, R. P. (1995) · Journal of Virology · doi:10.1128/jvi.69.12.7548-7558.1995 · Cited by 63
Rapid Molecular Epidemiology of Human Immunodeficiency Virus Transmission
Delwart, E., Busch, M. P., Kalish, M. L., Mosley, J. W., & Mullins, J. I. (1995) · AIDS Research and Human Retroviruses · doi:10.1089/aid.1995.11.1081 · Cited by 56
Self-citationMcDonald, R. A., Mayers, D., Chung, R. C. Y., Wagner, K., Ratto‐Kim, S., Birx, D. L., & Michael, N. L. (1997) · Journal of Virology · doi:10.1128/jvi.71.3.1871-1879.1997 · Cited by 49
Salvatori, F., Masiero, S., Giaquinto, C., Wade, C. M., Brown, A., Chieco‐Bianchi, L., & Rossi, A. D. (1997) · Journal of Virology · doi:10.1128/jvi.71.6.4694-4706.1997 · Cited by 45
Bagnarelli, P., Mazzola, F., Menzo, S., Montroni, M., Butini, L., & Clementi, M. (1999) · Journal of Virology · doi:10.1128/jvi.73.5.3764-3777.1999 · Cited by 38
Primary Subtype C HIV-1 Infection in Harare, Zimbabwe
Tien, P. C., Chiu, T., Latif, A., Ray, S. C., Batra, M., Contag, C. H., Zejena, L., Mbizvo, M., Delwart, E., Mullins, J. I., et al. (1999) · Journal of Acquired Immune Deficiency Syndromes & Human Retrovirology · doi:10.1097/00042560-199902010-00006 · Cited by 33
Self-citationIda, S., Gatanaga, H., Shioda, T., Nagai, Y., Kobayashi, N., SHIMADA, K., Kimura, S., Iwamoto, A., & Oka, S. (1997) · AIDS Research and Human Retroviruses · doi:10.1089/aid.1997.13.1597 · Cited by 30
Gange, S. J., Muñoz, Á., Chmiel, J. S., Donnenberg, A. D., Kirstein, L. M., Detels, R., & Margolick, J. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.18.10848 · Cited by 28
Self-citationRinaldo, C. R., Gupta, P., HUANG, X.-L., FAN, Z., Mullins, J. I., Gange, S. J., Farzadegan, H., Shankarappa, R., Muñoz, Á., & Margolick, J. B. (1998) · AIDS Research and Human Retroviruses · doi:10.1089/aid.1998.14.1423 · Cited by 24
Self-citationDalapicolla, J., do Prado, J. R., Percequillo, A. R., & Knowles, L. L. (2021) · Journal of Biogeography · doi:10.1111/jbi.14281 · Cited by 13
Flagged first, then by citations
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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Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., MUMFORD, J. A., & Holmes, E. C. (2004) · Science · doi:10.1126/science.1090727 · Cited by 1,370
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Domingo, E., Sheldon, J., & Perales, C. (2012) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.05023-11 · Cited by 1,009
Antiretroviral Treatment for Adult HIV Infection in 2002
Yéni, P., Hammer, S. M., Carpenter, C. C. J., Cooper, D. A., Fischl, M. A., Gatell, J. M., Gazzard, B., Hirsch, M., Jacobsen, D. M., Katzenstein, D. A., et al. (2002) · JAMA · doi:10.1001/jama.288.2.222 · Cited by 710
Binley, J. Μ., Wrin, T., Korber, B., Zwick, M. B., Wang, M., Chappey, C., Stiegler, G. M., Kunert, R., Zolla‐Pazner, S., Katinger, H. W. D., et al. (2004) · Journal of Virology · doi:10.1128/jvi.78.23.13232-13252.2004 · Cited by 701
Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics
Minin, V. N., Bloomquist, E. W., & Suchard, M. A. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn090 · Cited by 695
Deeks, S. G., Overbaugh, J. M., Phillips, A. N., & Buchbinder, S. P. (2015) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2015.35 · Cited by 718
The Challenge of Viral Reservoirs in HIV-1 Infection
Blankson, J. N., Persaud, D., & Siliciano, R. F. (2002) · Annual Review of Medicine · doi:10.1146/annurev.med.53.082901.104024 · Cited by 649
Bromham, L., & Penny, D. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1020 · Cited by 615
Evolutionary analysis of the dynamics of viral infectious disease
Pybus, O. G., & Rambaut, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2583 · Cited by 634
Salazar-Gonzalez, J. F., Bailes, E., Pham, K. T., Salazar, M. G., Guffey, M. B., Keele, B. F., Derdeyn, C. A., FARMER, P. K., Hunter, E., Allen, S., et al. (2008) · Journal of Virology · doi:10.1128/jvi.02660-07 · Cited by 587
The causes and consequences of HIV evolution
Rambaut, A., Posada, D., Crandall, K. A., & Holmes, E. C. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1246 · Cited by 563
Evolutionary and immunological implications of contemporary HIV-1 variation
Korber, B., Gaschen, B. K., Yusim, K., Thakallapally, R., Keşmir, C., & Detours, V. (2001) · British Medical Bulletin · doi:10.1093/bmb/58.1.19 · Cited by 534
Palmer, S., Kearney, M., Maldarelli, F., Halvas, E. K., Bixby, C. J., Bazmi, H., Rock, D., Falloon, J., Davey, R. T., Dewar, R. L., et al. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.1.406-413.2005 · Cited by 506
Moore, J. P., Kitchen, S. G., Pugach, P., & Zack, J. A. (2004) · AIDS Research and Human Retroviruses · doi:10.1089/088922204322749567 · Cited by 492
Corti, D., Langedijk, J. P. M., Hinz, A., Seaman, M. S., Zatta, F., Fernandez-Rodriguez, B. M., Silacci, C., Pinna, D., Jarrossay, D., Balla-Jhagjhoorsingh, S. S., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008805 · Cited by 427
Jensen, M. A., Li, F.-S., Wout, A. B. V. ’., Nickle, D. C., Shriner, D., He, H.-X., McLaughlin, S., Shankarappa, R., Margolick, J. B., & Mullins, J. I. (2003) · Journal of Virology · doi:10.1128/jvi.77.24.13376-13388.2003 · Cited by 425
Self-citationBailey, J. R., Sedaghat, A. R., Kieffer, T. L., Brennan, T. P., Lee, P. K., Wind‐Rotolo, M., Haggerty, C. M., Kamireddi, A. R., Liu‐Chittenden, Y., Lee, J., et al. (2006) · Journal of Virology · doi:10.1128/jvi.00591-06 · Cited by 425
Fast Dating Using Least-Squares Criteria and Algorithms
To, T., Jung, M., Lycett, S., & Gascuel, O. (2015) · Systematic Biology · doi:10.1093/sysbio/syv068 · Cited by 438
Measurably evolving populations
Drummond, A. J., Pybus, O. G., Rambaut, A., Forsberg, R., & Rodrigo, A. G. (2003) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(03)00216-7 · Cited by 413
Self-citationThe population genetics and evolutionary epidemiology of RNA viruses
Moyá, A., Holmes, E. C., & Gónzález‐Candelas, F. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro863 · Cited by 402
Altfeld, M. A., Rosenberg, E. S., Shankarappa, R., Mukherjee, J. S., Hecht, F. M., Eldridge, R. L., Addo, M. M., Poon, S. H. T., Phillips, M. N., Robbins, G. K., et al. (2001) · The Journal of Experimental Medicine · doi:10.1084/jem.193.2.169 · Cited by 383
Self-citationHosmane, N. N., Kwon, K. J., Bruner, K. M., Capoferri, A. A., Beg, S. A., Rosenbloom, D. I. S., Keele, B. F., Ho, Y., Siliciano, J. D., & Siliciano, R. F. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20170193 · Cited by 386
Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
Gavryushkina, A. “., Welch, D., Stadler, T., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003919 · Cited by 372
Frost, S. D. W., Wrin, T., Smith, D. M., Pond, S. L. K., Liu, Y., Paxinos, E. E., Chappey, C., Galovich, J., Beauchaine, J., Petropoulos, C. J., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504658102 · Cited by 351
Westby, M., Smith‐Burchnell, C., Mori, J., Lewis, M., Mosley, M., Stockdale, M., Dorr, P. K., Ciaramella, G., & Perros, M. (2006) · Journal of Virology · doi:10.1128/jvi.02006-06 · Cited by 348
Westby, M., Lewis, M., Whitcomb, J. M., Youle, M. S., Pozniak, A., James, I., Jenkins, T. M., Perros, M., & van der Ryst, E. (2006) · Journal of Virology · doi:10.1128/jvi.80.10.4909-4920.2006 · Cited by 333
Early and nonreversible decrease of CD161++/MAIT cells in HIV infection
Cosgrove, C., Ussher, J. E., Rauch, A., Gärtner, K., Kurioka, A., Hühn, M. H., Adelmann, K., Kang, Y.-H., Fergusson, J. R., Peter Simmonds, K., et al. (2012) · Blood · doi:10.1182/blood-2012-06-436436 · Cited by 318
Keele, B. F., Li, H., Learn, G. H., Hraber, P., Giorgi, E. E., Grayson, T. B., Sun, C., Chen, Y., Yeh, W. W., Letvin, N. L., et al. (2009) · The Journal of Experimental Medicine · doi:10.1084/jem.20082831 · Cited by 307
Self-citationNeutralism and selectionism: a network-based reconciliation
Wagner, A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2473 · Cited by 307
Zhu, T., Muthui, D., Holte, S., Nickle, D. C., Feng, F., Brodie, S. J., Hwangbo, Y., Mullins, J. I., & Corey, L. (2002) · Journal of Virology · doi:10.1128/jvi.76.2.707-716.2002 · Cited by 317
Self-citationEvolutionary principles and their practical application
Hendry, A. P., Kinnison, M. T., Heino, M., Day, T., Smith, T. B., Fitt, G. P., Bergstrom, C. T., Oakeshott, J. G., Jørgensen, P. S., Zalucki, M. P., et al. (2011) · Evolutionary Applications · doi:10.1111/j.1752-4571.2010.00165.x · Cited by 309
HIV rebounds from latently infected cells, rather than from continuing low-level replication
Joos, B., Fischer, M., Kuster, H., Pillai, S. K., Wong, J. K., Böni, J., Hirschel, B. J., Weber, R. K., Trkola, A., Günthard, H. F., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804192105 · Cited by 291
Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication
Abram, M. E., Ferris, A. L., Shao, W., Alvord, W. G., & Hughes, S. H. (2010) · Journal of Virology · doi:10.1128/jvi.00915-10 · Cited by 283
Long-Term Transmission of Defective RNA Viruses in Humans and Aedes Mosquitoes
Aaskov, J., Buzacott, K., Thu, H. M., Lowry, K., & Holmes, E. C. (2006) · Science · doi:10.1126/science.1115030 · Cited by 260
Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection
Bull, R. A., Luciani, F., McElroy, K., Gaudieri, S., Pham, S. T., Chopra, A., Cameron, B., Maher, L., Dore, G. J., White, P. A., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002243 · Cited by 265
Cell surface receptors, virus entry and tropism of primate lentiviruses
Clapham, P. R., & McKnight, Á. (2002) · Journal of General Virology · doi:10.1099/0022-1317-83-8-1809 · Cited by 255
Yusim, K., Keşmir, C., Gaschen, B. K., Addo, M. M., Altfeld, M. A., Brunak, S., Chigaev, A., Detours, V., & Korber, B. (2002) · Journal of Virology · doi:10.1128/jvi.76.17.8757-8768.2002 · Cited by 246
Population genomics of intrapatient HIV-1 evolution
Zanini, F., Brodin, J., Thebo, L., Lanz, C., Bratt, G., Albert, J., & Neher, R. A. (2015) · eLife · doi:10.7554/elife.11282 · Cited by 239
HIV and the chemokine system: 10 years later
Lusso, P. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600947 · Cited by 234
Viral Population Estimation Using Pyrosequencing
Eriksson, N., Pachter, L. S., Mitsuya, Y., Rhee, S., Wang, C., Gharizadeh, B., Ronaghi, M., Shafer, R. W., & Beerenwinkel, N. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000074 · Cited by 224
HIV evolutionary dynamics within and among hosts.
Lemey, P., Rambaut, A., & Pybus, O. G. (2006) · PubMed · Cited by 222
Reviews Of Anti‐infective Agents: Maraviroc: The First of a New Class of Antiretroviral Agents
MacArthur, R. D., & Novak, R. M. (2008) · Clinical Infectious Diseases · doi:10.1086/589289 · Cited by 207
Malim, M. H., & Emerman, M. (2001) · Cell · doi:10.1016/s0092-8674(01)00234-3 · Cited by 201
Gao, F., Weaver, E. A., Lu, Z., Li, Y., Liao, H., Ma, B., Alam, S. M., Scearce, R. M., Sutherland, L. L., Yu, J.-S., et al. (2004) · Journal of Virology · doi:10.1128/jvi.79.2.1154-1163.2005 · Cited by 200
Kieffer, T. L., Finucane, M. M., Nettles, R. E., Quinn, T. C., Broman, K. W., Ray, S. C., Persaud, D., & Siliciano, R. F. (2004) · The Journal of Infectious Diseases · doi:10.1086/382488 · Cited by 202
The HIV coreceptor switch: a population dynamical perspective
Regoes, R. R., & Bonhoeffer, S. (2005) · Trends in Microbiology · doi:10.1016/j.tim.2005.04.005 · Cited by 198
Troyer, R. M., Collins, K. R., Abraha, A., Fraundorf, E., Moore, D. M., Krizan, R. W., Toossi, Z., Colebunders, R., Jensen, M. A., Mullins, J. I., et al. (2005) · Journal of Virology · doi:10.1128/jvi.79.14.9006-9018.2005 · Cited by 198
Self-citationDIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites
Deng, W., Maust, B. S., Nickle, D. C., Learn, G. H., Liu, Y., Heath, L., Pond, S. L. K., & Mullins, J. I. (2010) · BioTechniques · doi:10.2144/000113370 · Cited by 197
Self-citationAbrahams, M.-R., Joseph, S. B., Garrett, N., Tyers, L., Moeser, M., Archin, N., Council, O. D., Matten, D., Zhou, S., Doolabh, D., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aaw5589 · Cited by 196
Kuhmann, S. E., Pugach, P., Kunstman, K., Taylor, J., Stanfield, R. L., Snyder, A., Strizki, J., Riley, J., Baroudy, B. M., Wilson, I. A., et al. (2004) · Journal of Virology · doi:10.1128/jvi.78.6.2790-2807.2004 · Cited by 194
HIV-1 Group M Conserved Elements Vaccine
Rolland, M., Nickle, D. C., & Mullins, J. I. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030157 · Cited by 189
Self-citationThe phylogeography of human viruses
Holmes, E. C. (2003) · Molecular Ecology · doi:10.1046/j.1365-294x.2003.02051.x · Cited by 188
Antiretroviral dynamics determines HIV evolution and predicts therapy outcome
Rosenbloom, D. I. S., Hill, A. L., Rabi, S. A., Siliciano, R. F., & Nowak, M. A. (2012) · Nature Medicine · doi:10.1038/nm.2892 · Cited by 188
Is HIV-1 evolving to a less virulent form in humans?
Ariën, K. K., Vanham, G., & Arts, E. J. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1594 · Cited by 188
Frost, S. D. W., Liu, Y., Pond, S. L. K., Chappey, C., Wrin, T., Petropoulos, C. J., Little, S. J., & Richman, D. D. (2005) · Journal of Virology · doi:10.1128/jvi.79.10.6523-6527.2005 · Cited by 184
Modeling the site-specific variation of selection patterns along lineages
Guindon, S., Rodrigo, A. G., Dyer, K. A., & Huelsenbeck, J. P. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402177101 · Cited by 187
Self-citationDeterminants of HIV-1 broadly neutralizing antibody induction
Rusert, P., Kouyos, R. D., Kadelka, C., Ebner, H., Schanz, M. M., Huber, M., Braun, D. L., Hozé, N., Scherrer, A., Magnus, C., et al. (2016) · Nature Medicine · doi:10.1038/nm.4187 · Cited by 175
Rouzine, I. M., Rodrigo, A., & Coffin, J. M. (2001) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.65.1.151-185.2001 · Cited by 173
Self-citationLemey, P., Pond, S. L. K., Drummond, A. J., Pybus, O. G., Shapiro, B., Barroso, H., Taveira, N., & Rambaut, A. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030029 · Cited by 174
Bailey, J. R., Lassen, K. G., Yang, H., Quinn, T. C., Ray, S. C., Blankson, J. N., & Siliciano, R. F. (2006) · Journal of Virology · doi:10.1128/jvi.80.10.4758-4770.2006 · Cited by 172
Modeling sequence evolution in acute HIV-1 infection
Lee, H. Y., Giorgi, E. E., Keele, B. F., Gaschen, B. K., Athreya, G. S., Salazar-Gonzalez, J. F., Pham, K. T., Goepfert, P., Kilby, J. M., Saag, M. S., et al. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.07.038 · Cited by 171
Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected Individuals
Kearney, M. F., Maldarelli, F. M., Shao, W., Margolick, J. B., Daar, E. S., Mellors, J. W., Rao, V. B., Coffin, J. M., & Palmer, S. (2008) · Journal of Virology · doi:10.1128/jvi.01960-08 · Cited by 170
Self-citationOutwitting Evolution: Fighting Drug-Resistant TB, Malaria, and HIV
Goldberg, D. E., Siliciano, R. F., & Jacobs, W. R. (2012) · Cell · doi:10.1016/j.cell.2012.02.021 · Cited by 168
Hoffman, N. G., Seillier‐Moiseiwitsch, F., Ahn, J. A. O. K., Walker, J. M., & Swanstrom, R. I. (2002) · Journal of Virology · doi:10.1128/jvi.76.8.3852-3864.2002 · Cited by 168
Recombination Rate and Selection Strength in HIV Intra-patient Evolution
Neher, R. A., & Leitner, T. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000660 · Cited by 168
Inference of Viral Evolutionary Rates from Molecular Sequences
DRUMMON, A., Pybus, O. G., & Rambaut, A. (2003) · Advances in Parasitology/Advances in parasitology · doi:10.1016/s0065-308x(03)54008-8 · Cited by 170
Potential impact of recombination on sitewise approaches for detecting positive natural selection
Shriner, D., Nickle, D. C., Jensen, M. A., & Mullins, J. I. (2003) · Genetics Research · doi:10.1017/s0016672303006128 · Cited by 167
Self-citationFast, accurate and simulation-free stochastic mapping
Minin, V. N., & Suchard, M. A. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2008.0176 · Cited by 165
Latency in Human Immunodeficiency Virus Type 1 Infection: No Easy Answers
Persaud, D., Zhou, Y., Siliciano, J. D., & Siliciano, R. F. (2003) · Journal of Virology · doi:10.1128/jvi.77.3.1659-1665.2003 · Cited by 168
De Scheerder, M.-A., Vrancken, B., Dellicour, S., Schlub, T., Lee, E., Shao, W., Rutsaert, S., Verhofstede, C., Kerre, T., Malfait, T., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.003 · Cited by 165
Molecular basis of human immunodeficiency virus drug resistance: An update
Menéndez‐Arias, L. (2009) · Antiviral Research · doi:10.1016/j.antiviral.2009.07.006 · Cited by 163
Ultra-deep sequencing for the analysis of viral populations
Beerenwinkel, N., & Zagordi, O. (2011) · Current Opinion in Virology · doi:10.1016/j.coviro.2011.07.008 · Cited by 162
Predicting HIV Coreceptor Usage on the Basis of Genetic and Clinical Covariates
Sing, T., Low, A., Beerenwinkel, N., Sander, O., Cheung, P. K., Domingues, F. S., Büch, J., Däumer, M., Kaiser, R., Lengauer, T., et al. (2007) · Antiviral Therapy · doi:10.1177/135965350701200709 · Cited by 161
Pastore, C., Nedellec, R., Ramos, A. G., Pontow, S. E., Ratner, L., & Mosier, D. E. (2005) · Journal of Virology · doi:10.1128/jvi.80.2.750-758.2006 · Cited by 157
Estimation of 2Nes From Temporal Allele Frequency Data
Bollback, J. P., York, A., & Nielsen, R. (2008) · Genetics · doi:10.1534/genetics.107.085019 · Cited by 156
Immune control of HIV: the obstacles of HLA and viral diversity
Walker, B. D., & Korber, B. (2001) · Nature Immunology · doi:10.1038/88656 · Cited by 155
Murray, A. J., Kwon, K. J., Färber, D. L., & Siliciano, R. F. (2016) · The Journal of Immunology · doi:10.4049/jimmunol.1600343 · Cited by 160
The origin of genetic diversity in HIV-1
Smyth, R. P., Davenport, M. P., & Mak, J. (2012) · Virus Research · doi:10.1016/j.virusres.2012.06.015 · Cited by 166
Shriner, D., Rodrigo, A. G., Nickle, D. C., & Mullins, J. I. (2004) · Genetics · doi:10.1534/genetics.103.023382 · Cited by 155
Self-citationHierarchical Phylogenetic Models for Analyzing Multipartite Sequence Data
Suchard, M. A., Ramirez, C. M., Sinsheimer, J. S., & Weiss, R. E. (2003) · Systematic Biology · doi:10.1080/10635150390238879 · Cited by 152
Inferences from tip‐calibrated phylogenies: a review and a practical guide
Rieux, A., & Balloux, F. (2016) · Molecular Ecology · doi:10.1111/mec.13586 · Cited by 155
Bures, R., Gaitan, A., Zhu, T., Graziosi, C., McGrath, K. M., Tartaglia, J., Caudrelier, P., Habib, R. E., Klein, M. C. A., Lazzarin, A., et al. (2000) · AIDS Research and Human Retroviruses · doi:10.1089/088922200750054756 · Cited by 147
HIV Pathogenesis: Dynamics and Genetics of Viral Populations and Infected CellsPreprint
Coffin, J. M., & Swanstrom, R. (2013) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a012526 · Cited by 160
Posada, D., & Crandall, K. A. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003890 · Cited by 145
Cecilia, D., Kulkarni, S., Tripathy, S. P., Gangakhedkar, R., Paranjape, R., & Gadkari, D. A. (2000) · Virology · doi:10.1006/viro.2000.0297 · Cited by 143
Altfeld, M. A., Addo, M. M., Shankarappa, R., Lee, P. K., Allen, T. M., Yu, X. G., Rathod, A., Harlow, J., O’Sullivan, K., Johnston, M. N., et al. (2003) · Journal of Virology · doi:10.1128/jvi.77.13.7330-7340.2003 · Cited by 143
Self-citationChronic HIV-1 Infection Frequently Fails to Protect against Superinfection
Piantadosi, A. L., Chohan, B. H., Chohan, V., McClelland, R. S., & Overbaugh, J. M. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030177 · Cited by 140
A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferation
Reeves, D. B., Duke, E. R., Wagner, T. A., Palmer, S., Spivak, A. M., & Schiffer, J. T. (2018) · Nature Communications · doi:10.1038/s41467-018-06843-5 · Cited by 143
Within-host and between-host evolutionary rates across the HIV-1 genome
Alizon, S., & Fraser, C. (2013) · Retrovirology · doi:10.1186/1742-4690-10-49 · Cited by 141
Kouyos, R. D., von Wyl, V., Yerly, S., Böni, J., Rieder, P., Joos, B., Taffé, P., Shah, C., Bürgisser, P., Klimkait, T., et al. (2011) · Clinical Infectious Diseases · doi:10.1093/cid/ciq164 · Cited by 138
Adaptation in the env Gene of HIV-1 and Evolutionary Theories of Disease Progression
Williamson, S. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg144 · Cited by 138
HIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion
Maldarelli, F. M., Kearney, M. F., Palmer, S., Stephens, R. M., Mican, J. M., Polis, M. A., Davey, R. T., Kovacs, J. A., Shao, W., Rock-Kress, D., et al. (2013) · Journal of Virology · doi:10.1128/jvi.01225-12 · Cited by 130
Control of HIV-1 in Elite Suppressors despite Ongoing Replication and Evolution in Plasma Virus
O’Connell, K. A., Brennan, T. P., Bailey, J. R., Ray, S. C., Siliciano, R. F., & Blankson, J. N. (2010) · Journal of Virology · doi:10.1128/jvi.00548-10 · Cited by 129
Gnanakaran, S., Tanmoy Bhattacharya, A., Daniels, M., Keele, B. F., Hraber, P., Lapedes, A. S., Shen, T., Gaschen, B. K., Krishnamoorthy, M., Li, H.-H., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002209 · Cited by 128
Ruff, C. T., Ray, S. C., Kwon, P., Zinn, R. L., Pendleton, A. R., Hutton, N., Ashworth, R. G., Gange, S. J., Quinn, T. C., Siliciano, R. F., et al. (2002) · Journal of Virology · doi:10.1128/jvi.76.18.9481-9492.2002 · Cited by 129
Self-citationThe effect of genetic structure on molecular dating and tests for temporal signal
Murray, G. G. R., Wang, F., Harrison, E. M., Paterson, G. K., Mather, A. E., Harris, S. R., Holmes, M. A., Rambaut, A., & Welch, J. J. (2015) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12466 · Cited by 126
Carlson, J. M., Brumme, Z. L., Rousseau, C. M., Brumme, C. J., Matthews, P. C., Kadie, C. M., Mullins, J. I., Walker, B. D., Harrigan, P. R., Goulder, P., et al. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000225 · Cited by 126
Self-citation
Metadata
- 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)
- <!--label omitted: 2-->Departments of Molecular Microbiology and Immunology2 and of
- Johns Hopkins University (US)
- University of Pittsburgh (US)
- ORCID
- 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
- 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
- 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 ›
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