TY - JOUR AU - Salazar-Gonzalez, J. F. AU - Bailes, E. AU - Pham, K. T. AU - Salazar, M. G. AU - Guffey, M. B. AU - Keele, B. F. AU - Derdeyn, C. A. AU - Farmer, P. AU - Hunter, E. AU - Allen, S. PY - 2008 DA - 2008// TI - Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single Genome Amplification and Sequencing JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.02660-07 DO - 10.1128/JVI.02660-07 ID - Salazar-Gonzalez2008 ER - TY - JOUR AU - Keele, B. F. AU - Salazar-Gonzalez, J. F. AU - Pham, K. T. AU - Salazar, M. G. AU - Sun, C. AU - Grayson, T. AU - Decker, J. M. AU - Wei, X. AU - Wang, S. AU - Goepfert, P. A. PY - 2008 DA - 2008// TI - Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 Infection JO - Proc Natl Acad Sci USA VL - 105 UR - https://doi.org/10.1073/pnas.0802203105 DO - 10.1073/pnas.0802203105 ID - Keele2008 ER - TY - JOUR AU - Gottlieb, G. S. AU - Heath, L. AU - Nickle, D. C. AU - Wong, K. G. AU - Leach, S. E. AU - Jacobs, B. AU - Gezahegne, S. AU - van 't Wout, A. B. AU - Jacobson, L. P. AU - Margolick, J. B. AU - Mullins, J. I. PY - 2008 DA - 2008// TI - HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study JO - J Infect Dis VL - 197 UR - https://doi.org/10.1086/529206 DO - 10.1086/529206 ID - Gottlieb2008 ER - TY - JOUR AU - Kuyl, A. C. v. a. n. d. e. r. AU - Cornelissen, M. PY - 2007 DA - 2007// TI - Identifying HIV-1 dual infections JO - Retrovirology VL - 4 UR - https://doi.org/10.1186/1742-4690-4-67 DO - 10.1186/1742-4690-4-67 ID - Kuyl2007 ER - TY - JOUR AU - Gottlieb, G. S. AU - Nickle, D. C. AU - Jensen, M. A. AU - Wong, K. G. AU - Grobler, J. AU - Li, F. AU - Liu, S. L. AU - Rademeyer, C. AU - Learn, G. H. AU - Karim, S. S. PY - 2004 DA - 2004// TI - Dual HIV-1 infection associated with rapid disease progression JO - Lancet VL - 363 UR - https://doi.org/10.1016/S0140-6736(04)15596-7 DO - 10.1016/S0140-6736(04)15596-7 ID - Gottlieb2004 ER - TY - JOUR AU - Gottlieb, G. S. AU - Nickle, D. C. AU - Jensen, M. A. AU - Wong, K. G. AU - Kaslow, R. A. AU - Shepherd, J. C. AU - Margolick, J. B. AU - Mullins, J. I. PY - 2007 DA - 2007// TI - HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report JO - Clin Infect Dis VL - 45 UR - https://doi.org/10.1086/520024 DO - 10.1086/520024 ID - Gottlieb2007 ER - TY - JOUR AU - Costa, L. J. AU - Mayer, A. J. AU - Busch, M. P. AU - Diaz, R. S. PY - 2004 DA - 2004// TI - Evidence for Selection of more Adapted Human Immunodeficiency Virus Type 1 Recombinant Strains in a Dually Infected Transfusion Recipient JO - Virus Genes VL - 28 UR - https://doi.org/10.1023/B:VIRU.0000025773.12621.a8 DO - 10.1023/B:VIRU.0000025773.12621.a8 ID - Costa2004 ER - TY - JOUR AU - Haigwood, N. L. PY - 2004 DA - 2004// TI - Predictive value of primate models for AIDS JO - AIDS Rev VL - 6 ID - Haigwood2004 ER - TY - JOUR AU - Hu, S. L. PY - 2005 DA - 2005// TI - Non-human primate models for AIDS vaccine research JO - Curr Drug Targets Infect Disord VL - 5 UR - https://doi.org/10.2174/1568005054201508 DO - 10.2174/1568005054201508 ID - Hu2005 ER - TY - JOUR AU - Lackner, A. A. AU - Veazey, R. S. PY - 2007 DA - 2007// TI - Current concepts in AIDS pathogenesis: insights from the SIV/macaque model JO - Annu Rev Med VL - 58 UR - https://doi.org/10.1146/annurev.med.58.082405.094316 DO - 10.1146/annurev.med.58.082405.094316 ID - Lackner2007 ER - TY - JOUR AU - Staprans, S. I. AU - Dailey, P. J. AU - Rosenthal, A. AU - Horton, C. AU - Grant, R. M. AU - Lerche, N. AU - Feinberg, M. B. PY - 1999 DA - 1999// TI - Simian immunodeficiency virus disease course is predicted by the extent of virus replication during primary infection JO - J Virol VL - 73 ID - Staprans1999 ER - TY - JOUR AU - Mellors, J. W. AU - Kingsley, L. A. AU - Rinaldo, C. R. AU - Todd, J. A. AU - Hoo, B. S. AU - Kokka, R. P. AU - Gupta, P. PY - 1995 DA - 1995// TI - Quantitation of HIV-1 RNA in plasma predicts outcome after seroconversion JO - Ann Intern Med VL - 122 UR - https://doi.org/10.7326/0003-4819-122-8-199504150-00003 DO - 10.7326/0003-4819-122-8-199504150-00003 ID - Mellors1995 ER - TY - JOUR AU - Mellors, J. W. AU - Rinaldo, C. R. AU - Gupta, P. AU - White, R. M. AU - Todd, J. A. AU - Kingsley, L. A. PY - 1996 DA - 1996// TI - Prognosis in HIV-1 infection predicted by the quantity of virus in plasma JO - Science VL - 272 UR - https://doi.org/10.1126/science.272.5265.1167 DO - 10.1126/science.272.5265.1167 ID - Mellors1996 ER - TY - JOUR AU - Centlivre, M. AU - Sala, M. AU - Wain-Hobson, S. AU - Berkhout, B. PY - 2007 DA - 2007// TI - In HIV-1 pathogenesis the die is cast during primary infection JO - Aids VL - 21 UR - https://doi.org/10.1097/QAD.0b013e3280117f7f DO - 10.1097/QAD.0b013e3280117f7f ID - Centlivre2007 ER - TY - JOUR AU - Overbaugh, J. AU - Bangham, C. R. PY - 2001 DA - 2001// TI - Selection forces and constraints on retroviral sequence variation JO - Science VL - 292 UR - https://doi.org/10.1126/science.1059128 DO - 10.1126/science.1059128 ID - Overbaugh2001 ER - TY - JOUR AU - Rybarczyk, B. J. AU - Montefiori, D. AU - Johnson, P. R. AU - West, A. AU - Johnston, R. E. AU - Swanstrom, R. PY - 2004 DA - 2004// TI - Correlation between env V1/V2 region diversification and neutralizing antibodies during primary infection by simian immunodeficiency virus sm in rhesus macaques JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.7.3561-3571.2004 DO - 10.1128/JVI.78.7.3561-3571.2004 ID - Rybarczyk2004 ER - TY - JOUR AU - Allen, T. M. AU - O'Connor, D. H. AU - Jing, P. AU - Dzuris, J. L. AU - Mothe, B. R. AU - Vogel, T. U. AU - Dunphy, E. AU - Liebl, M. E. AU - Emerson, C. AU - Wilson, N. PY - 2000 DA - 2000// TI - Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia JO - Nature VL - 407 UR - https://doi.org/10.1038/35036559 DO - 10.1038/35036559 ID - Allen2000 ER - TY - JOUR AU - O'Connor, D. H. AU - Allen, T. M. AU - Vogel, T. U. AU - Jing, P. AU - DeSouza, I. P. AU - Dodds, E. AU - Dunphy, E. J. AU - Melsaether, C. AU - Mothe, B. AU - Yamamoto, H. PY - 2002 DA - 2002// TI - Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection JO - Nat Med VL - 8 UR - https://doi.org/10.1038/nm0502-493 DO - 10.1038/nm0502-493 ID - O'Connor2002 ER - TY - JOUR AU - Lichterfeld, M. AU - Yu, X. G. AU - Cohen, D. AU - Addo, M. M. AU - Malenfant, J. AU - Perkins, B. AU - Pae, E. AU - Johnston, M. N. AU - Strick, D. AU - Allen, T. M. PY - 2004 DA - 2004// TI - HIV-1 Nef is preferentially recognized by CD8 T cells in primary HIV-1 infection despite a relatively high degree of genetic diversity JO - AIDS VL - 18 UR - https://doi.org/10.1097/01.aids.0000131329.51633.a3 DO - 10.1097/01.aids.0000131329.51633.a3 ID - Lichterfeld2004 ER - TY - JOUR AU - Ueno, T. AU - Motozono, C. AU - Dohki, S. AU - Mwimanzi, P. AU - Rauch, S. AU - Fackler, O. T. AU - Oka, S. AU - Takiguchi, M. PY - 2008 DA - 2008// TI - CTL-mediated selective pressure influences dynamic evolution and pathogenic functions of HIV-1 Nef JO - J Immunol VL - 180 UR - https://doi.org/10.4049/jimmunol.180.2.1107 DO - 10.4049/jimmunol.180.2.1107 ID - Ueno2008 ER - TY - JOUR AU - Huang, K. J. AU - Wooley, D. P. PY - 2005 DA - 2005// TI - A new cell-based assay for measuring the forward mutation rate of HIV-1 JO - J Virol Methods VL - 124 UR - https://doi.org/10.1016/j.jviromet.2004.11.010 DO - 10.1016/j.jviromet.2004.11.010 ID - Huang2005 ER - TY - JOUR AU - Kirchhoff, F. AU - Easterbrook, P. J. AU - Douglas, N. AU - Troop, M. AU - Greenough, T. C. AU - Weber, J. AU - Carl, S. AU - Sullivan, J. L. AU - Daniels, R. S. PY - 1999 DA - 1999// TI - Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease JO - J Virol VL - 73 ID - Kirchhoff1999 ER - TY - JOUR AU - Palmer, S. AU - Kearney, M. AU - Maldarelli, F. AU - Halvas, E. K. AU - Bixby, C. J. AU - Bazmi, H. AU - Rock, D. AU - Falloon, J. AU - Davey, R. T. AU - Dewar, R. L. PY - 2005 DA - 2005// TI - Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis JO - J Clin Microbiol VL - 43 UR - https://doi.org/10.1128/JCM.43.1.406-413.2005 DO - 10.1128/JCM.43.1.406-413.2005 ID - Palmer2005 ER - TY - JOUR AU - Shriner, D. AU - Rodrigo, A. G. AU - Nickle, D. C. AU - Mullins, J. I. PY - 2004 DA - 2004// TI - Pervasive genomic recombination of HIV-1 in vivo JO - Genetics VL - 167 UR - https://doi.org/10.1534/genetics.103.023382 DO - 10.1534/genetics.103.023382 ID - Shriner2004 ER - TY - JOUR AU - Harris, R. S. AU - Liddament, M. T. PY - 2004 DA - 2004// TI - Retroviral restriction by APOBEC proteins JO - Nat Rev Immunol VL - 4 UR - https://doi.org/10.1038/nri1489 DO - 10.1038/nri1489 ID - Harris2004 ER - TY - JOUR AU - Simon, V. AU - Zennou, V. AU - Murray, D. AU - Huang, Y. AU - Ho, D. D. AU - Bieniasz, P. D. PY - 2005 DA - 2005// TI - Natural variation in Vif: differential impact on APOBEC3G/3F and a potential role in HIV-1 diversification JO - PLoS Pathog VL - 1 UR - https://doi.org/10.1371/journal.ppat.0010006 DO - 10.1371/journal.ppat.0010006 ID - Simon2005 ER - TY - JOUR AU - Bourara, K. AU - Liegler, T. J. AU - Grant, R. M. PY - 2007 DA - 2007// TI - Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1 JO - PLoS Pathog VL - 3 UR - https://doi.org/10.1371/journal.ppat.0030153 DO - 10.1371/journal.ppat.0030153 ID - Bourara2007 ER - TY - JOUR AU - Slatkin, M. AU - Hudson, R. R. PY - 1991 DA - 1991// TI - Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations JO - Genetics VL - 129 ID - Slatkin1991 ER - TY - JOUR AU - Smith, J. M. AU - Haigh, J. PY - 1974 DA - 1974// TI - The hitch-hiking effect of a favourable gene JO - Genet Res VL - 23 UR - https://doi.org/10.1017/S0016672300014634 DO - 10.1017/S0016672300014634 ID - Smith1974 ER - TY - JOUR AU - Charlesworth, D. AU - Morgan, M. T. AU - Charlesworth, B. PY - 1992 DA - 1992// TI - The effect of linkage and population size on inbreeding depression due to mutational load JO - Genet Res VL - 59 UR - https://doi.org/10.1017/S0016672300030160 DO - 10.1017/S0016672300030160 ID - Charlesworth1992 ER - TY - JOUR AU - Miller, M. D. AU - Warmerdam, M. T. AU - Gaston, I. AU - Greene, W. C. AU - Feinberg, M. B. PY - 1994 DA - 1994// TI - The human immunodeficiency virus-1 nef gene product: a positive factor for viral infection and replication in primary lymphocytes and macrophages JO - J Exp Med VL - 179 UR - https://doi.org/10.1084/jem.179.1.101 DO - 10.1084/jem.179.1.101 ID - Miller1994 ER - TY - JOUR AU - Sinclair, E. AU - Barbosa, P. AU - Feinberg, M. B. PY - 1997 DA - 1997// TI - The nef gene products of both simian and human immunodeficiency viruses enhance virus infectivity and are functionally interchangeable JO - J Virol VL - 71 ID - Sinclair1997 ER - TY - JOUR AU - Arien, K. K. AU - Verhasselt, B. PY - 2008 DA - 2008// TI - HIV Nef: role in pathogenesis and viral fitness JO - Curr HIV Res VL - 6 UR - https://doi.org/10.2174/157016208784325001 DO - 10.2174/157016208784325001 ID - Arien2008 ER - TY - BOOK AU - Wakeley, J. PY - 2008 DA - 2008// TI - Coalescent Theory: An Introduction ID - Wakeley2008 ER - TY - JOUR AU - Brown, A. J. PY - 1997 DA - 1997// TI - Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.5.1862 DO - 10.1073/pnas.94.5.1862 ID - Brown1997 ER - TY - JOUR AU - Achaz, G. AU - Palmer, S. AU - Kearney, M. AU - Maldarelli, F. AU - Mellors, J. W. AU - Coffin, J. M. AU - Wakeley, J. PY - 2004 DA - 2004// TI - A robust measure of HIV-1 population turnover within chronically infected individuals JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh196 DO - 10.1093/molbev/msh196 ID - Achaz2004 ER - TY - JOUR AU - Shriner, D. AU - Liu, Y. AU - Nickle, D. C. AU - Mullins, J. I. PY - 2006 DA - 2006// TI - Evolution of intrahost HIV-1 genetic diversity during chronic infection JO - Evolution VL - 60 ID - Shriner2006 ER - TY - JOUR AU - Rouzine, I. M. AU - Coffin, J. M. PY - 1999 DA - 1999// TI - Linkage disequilibrium test implies a large effective population number for HIV in vivo JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.19.10758 DO - 10.1073/pnas.96.19.10758 ID - Rouzine1999 ER - TY - JOUR AU - Ronaghi, M. AU - Uhlen, M. AU - Nyren, P. PY - 1998 DA - 1998// TI - A sequencing method based on real-time pyrophosphate JO - Science VL - 281 UR - https://doi.org/10.1126/science.281.5375.363 DO - 10.1126/science.281.5375.363 ID - Ronaghi1998 ER - TY - JOUR AU - Kestler, H. AU - Kodama, T. AU - Ringler, D. AU - Marthas, M. AU - Pedersen, N. AU - Lackner, A. AU - Regier, D. AU - Sehgal, P. AU - Daniel, M. AU - King, N. PY - 1990 DA - 1990// TI - Induction of AIDS in rhesus monkeys by molecularly cloned simian immunodeficiency virus JO - Science VL - 248 UR - https://doi.org/10.1126/science.2160735 DO - 10.1126/science.2160735 ID - Kestler1990 ER - TY - JOUR AU - Stafford, M. A. AU - Corey, L. AU - Cao, Y. AU - Daar, E. S. AU - Ho, D. D. AU - Perelson, A. S. PY - 2000 DA - 2000// TI - Modeling plasma virus concentration during primary HIV infection JO - J Theor Biol VL - 203 UR - https://doi.org/10.1006/jtbi.2000.1076 DO - 10.1006/jtbi.2000.1076 ID - Stafford2000 ER - TY - JOUR AU - Mattapallil, J. J. AU - Douek, D. C. AU - Hill, B. AU - Nishimura, Y. AU - Martin, M. AU - Roederer, M. PY - 2005 DA - 2005// TI - Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection JO - Nature VL - 434 UR - https://doi.org/10.1038/nature03501 DO - 10.1038/nature03501 ID - Mattapallil2005 ER - TY - JOUR AU - Nowak, M. A. AU - Lloyd, A. L. AU - Vasquez, G. M. AU - Wiltrout, T. A. AU - Wahl, L. M. AU - Bischofberger, N. AU - Williams, J. AU - Kinter, A. AU - Fauci, A. S. AU - Hirsch, V. M. AU - Lifson, J. D. PY - 1997 DA - 1997// TI - Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection JO - J Virol VL - 71 ID - Nowak1997 ER - TY - JOUR AU - Perelson, A. S. AU - Neumann, A. U. AU - Markowitz, M. AU - Leonard, J. M. AU - Ho, D. D. PY - 1996 DA - 1996// TI - HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time JO - Science VL - 271 UR - https://doi.org/10.1126/science.271.5255.1582 DO - 10.1126/science.271.5255.1582 ID - Perelson1996 ER - TY - JOUR AU - Markowitz, M. AU - Louie, M. AU - Hurley, A. AU - Sun, E. AU - Di Mascio, M. AU - Perelson, A. S. AU - Ho, D. D. PY - 2003 DA - 2003// TI - A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo JO - J Virol VL - 77 UR - https://doi.org/10.1128/JVI.77.8.5037-5038.2003 DO - 10.1128/JVI.77.8.5037-5038.2003 ID - Markowitz2003 ER - TY - JOUR AU - Mansky, L. M. AU - Temin, H. M. PY - 1995 DA - 1995// TI - Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase JO - J Virol VL - 69 ID - Mansky1995 ER -