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 - Shankarappa, R. AU - Margolick, J. B. AU - Gange, S. J. AU - Rodrigo, A. G. AU - Upchurch, D. AU - Farzadegan, H. AU - Gupta, P. AU - Rinaldo, C. R. AU - Learn, G. H. AU - He, X. AU - Huang, X. L. AU - Mullins, J. I. PY - 1999 DA - 1999// TI - Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection JO - J Virol VL - 73 ID - Shankarappa1999 ER - TY - JOUR AU - Burns, D. P. AU - Desrosiers, R. C. PY - 1991 DA - 1991// TI - Selection of genetic variants of simian immunodeficiency virus in persistently infected rhesus monkeys JO - J Virol VL - 65 ID - Burns1991 ER - TY - JOUR AU - Johnson, P. R. AU - Hamm, T. E. AU - Goldstein, S. AU - Kitov, S. AU - Hirsch, V. M. PY - 1991 DA - 1991// TI - The genetic fate of molecularly cloned simian immunodeficiency virus in experimentally infected macaques JO - Virology VL - 185 UR - https://doi.org/10.1016/0042-6822(91)90769-8 DO - 10.1016/0042-6822(91)90769-8 ID - Johnson1991 ER - TY - JOUR AU - Overbaugh, J. AU - Rudensey, L. M. AU - Papenhausen, M. D. AU - Benveniste, R. E. AU - Morton, W. R. PY - 1991 DA - 1991// TI - Variation in simian immunodeficiency virus env is confined to V1 and V4 during progression to simian AIDS JO - J Virol VL - 65 ID - Overbaugh1991 ER - TY - JOUR AU - Chackerian, B. AU - Rudensey, L. AU - Overbaugh, J. PY - 1997 DA - 1997// TI - Specific N-linked and O-linked glycosylation additions in the envelope V1 domain of SIV variants that evolve in the host alter neutralizing antibody recognition JO - J Virol VL - 71 ID - Chackerian1997 ER - TY - JOUR AU - Rudensey, L. M. AU - Kimata, J. T. AU - Long, E. M. AU - Chackerian, B. AU - Overbaugh, J. PY - 1998 DA - 1998// TI - Changes in the extracellular envelope glycoprotein of variants that evolve during the course of simian immunodeficiency virus SIVMne infection affect neutralizing antibody recognition, syncytium formation, and macrophage tropism but not replication, cytopathicity, or CCR-5 coreceptor recognition JO - J Virol VL - 72 ID - Rudensey1998 ER - TY - JOUR AU - Overbaugh, J. AU - Rudensey, L. M. PY - 1992 DA - 1992// TI - Alterations in potential sites for glycosylation predominate during evolution of the simian immunodeficiency virus envelope gene in macaques JO - J Virol VL - 66 ID - Overbaugh1992 ER - TY - JOUR AU - Wyatt, R. AU - Sodroski, J. PY - 1998 DA - 1998// TI - The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens JO - Science VL - 280 UR - https://doi.org/10.1126/science.280.5371.1884 DO - 10.1126/science.280.5371.1884 ID - Wyatt1998 ER - TY - JOUR AU - Blay, W. M. AU - Gnanakaran, S. AU - Foley, B. AU - Doria-Rose, N. A. AU - Korber, B. T. AU - Haigwood, N. L. PY - 2006 DA - 2006// TI - Consistent patterns of change during the divergence of human immunodeficiency virus type 1 envelope from that of the inoculated virus in simian/human immunodeficiency virus-infected macaques JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.80.2.999-1014.2006 DO - 10.1128/JVI.80.2.999-1014.2006 ID - Blay2006 ER - TY - JOUR AU - Cheng-Mayer, C. AU - Brown, A. AU - Harouse, J. AU - Luciw, P. A. AU - Mayer, A. J. PY - 1999 DA - 1999// TI - Selection for neutralization resistance of the simian/human immunodeficiency virus SHIVSF33A variant in vivo by virtue of sequence changes in the extracellular envelope glycoprotein that modify N-linked glycosylation JO - J Virol VL - 73 ID - Cheng-Mayer1999 ER - TY - JOUR AU - Narayan, S. V. AU - Mukherjee, S. AU - Jia, F. AU - Li, Z. AU - Wang, C. AU - Foresman, L. AU - McCormick-Davis, C. AU - Stephens, E. B. AU - Joag, S. V. AU - Narayan, O. PY - 1999 DA - 1999// TI - Characterization of a neutralization-escape variant of SHIVKU-1, a virus that causes acquired immune deficiency syndrome in pig-tailed macaques JO - Virology VL - 256 UR - https://doi.org/10.1006/viro.1999.9605 DO - 10.1006/viro.1999.9605 ID - Narayan1999 ER - TY - JOUR AU - Sagar, M. AU - Wu, X. AU - Lee, S. AU - Overbaugh, J. PY - 2006 DA - 2006// TI - Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.00141-06 DO - 10.1128/JVI.00141-06 ID - Sagar2006 ER - TY - JOUR AU - Wei, X. AU - Decker, J. M. AU - Wang, S. AU - Hui, H. AU - Kappes, J. C. AU - Wu, X. AU - Salazar-Gonzalez, J. F. AU - Salazar, M. G. AU - Kilby, J. M. AU - Saag, M. S. AU - Komarova, N. L. AU - Nowak, M. A. AU - Hahn, B. H. AU - Kwong, P. D. AU - Shaw, G. M. PY - 2003 DA - 2003// TI - Antibody neutralization and escape by HIV-1 JO - Nature VL - 422 UR - https://doi.org/10.1038/nature01470 DO - 10.1038/nature01470 ID - Wei2003 ER - TY - JOUR AU - Mozaffarian, A. AU - Overbaugh, J. PY - 1998 DA - 1998// TI - A lymph-node derived cytopathic simian immunodeficieny virus Mne variant replicates in nonstimulated peripheral blood mononuclear cells JO - J Virol VL - 72 ID - Mozaffarian1998 ER - TY - JOUR AU - Kimata, J. T. AU - Overbaugh, J. PY - 1997 DA - 1997// TI - The cytopathicity of a simian immunodeficiency virus Mne variant is determined by mutation in Gag and Env JO - J Virol VL - 71 ID - Kimata1997 ER - TY - JOUR AU - Kimata, J. T. AU - Kuller, L. AU - Anderson, D. B. AU - Dailey, P. AU - Overbaugh, J. PY - 1999 DA - 1999// TI - Emerging cytopathic and antigenic simian immunodeficiency virus variants influence AIDS progression. JO - Nat Med VL - 5 UR - https://doi.org/10.1038/8414 DO - 10.1038/8414 ID - Kimata1999 ER - TY - JOUR AU - Forthal, D. N. AU - Landucci, G. AU - Daar, E. S. PY - 2001 DA - 2001// TI - Antibody from patients with acute human immunodeficiency virus (HIV) infection inhibits primary strains of HIV type 1 in the presence of natural-killer effector cells JO - J Virol VL - 75 UR - https://doi.org/10.1128/JVI.75.15.6953-6961.2001 DO - 10.1128/JVI.75.15.6953-6961.2001 ID - Forthal2001 ER - TY - JOUR AU - Herbeck, J. T. AU - Nickle, D. C. AU - Learn, G. H. AU - Gottlieb, G. S. AU - Curlin, M. E. AU - Heath, L. AU - Mullins, J. I. PY - 2006 DA - 2006// TI - Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.80.4.1637-1644.2006 DO - 10.1128/JVI.80.4.1637-1644.2006 ID - Herbeck2006 ER - TY - CHAP AU - Korber, B. ED - Rodrigo, A. G. G. H. L. PY - 2000 DA - 2000// TI - HIV signature and sequence variation analysis BT - Computational Analysis of HIV Molecular Sequences PB - Dordrecht, Netherlands , Kluwer Academic Publishers CY - Netherlands ID - Korber2000 ER - TY - JOUR AU - Wei, X. AU - Decker, J. M. AU - Liu, H. AU - Zhang, Z. AU - Arani, R. B. AU - Kilby, J. M. AU - Saag, M. S. AU - Wu, X. AU - Shaw, G. M. AU - Kappes, J. C. PY - 2002 DA - 2002// TI - Emergence of resistant human immunodeficiency virus type 1 in patients receiving fusion inhibitor (T-20) monotherapy JO - Antimicrob Agents Chemother VL - 46 UR - https://doi.org/10.1128/AAC.46.6.1896-1905.2002 DO - 10.1128/AAC.46.6.1896-1905.2002 ID - Wei2002 ER - TY - JOUR AU - Kuwata, T. AU - Byrum, R. AU - Whitted, S. AU - Goeken, R. AU - Buckler-White, A. AU - Plishka, R. AU - Iyengar, R. AU - Hirsch, V. M. PY - 2007 DA - 2007// TI - A rapid progressor-specific variant clone of simian immunodeficiency virus replicates efficiently in vivo only in the absence of immune responses JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.00614-07 DO - 10.1128/JVI.00614-07 ID - Kuwata2007 ER - TY - JOUR AU - Kuwata, T. AU - Dehghani, H. AU - Brown, C. R. AU - Plishka, R. AU - Buckler-White, A. AU - Igarashi, T. AU - Mattapallil, J. AU - Roederer, M. AU - Hirsch, V. M. PY - 2006 DA - 2006// TI - Infectious molecular clones from a simian immunodeficiency virus-infected rapid-progressor (RP) macaque: evidence of differential selection of RP-specific envelope mutations in vitro and in vivo JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.80.3.1463-1475.2006 DO - 10.1128/JVI.80.3.1463-1475.2006 ID - Kuwata2006 ER - TY - JOUR AU - Li, B. AU - Gladden, A. D. AU - Altfeld, M. AU - Kaldor, J. M. AU - Cooper, D. A. AU - Kelleher, A. D. AU - Allen, T. M. PY - 2007 DA - 2007// TI - Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.01231-06 DO - 10.1128/JVI.01231-06 ID - Li2007 ER - TY - JOUR AU - Pohlmann, S. AU - Davis, C. AU - Meister, S. AU - Leslie, G. J. AU - Otto, C. AU - Reeves, J. D. AU - Puffer, B. A. AU - Papkalla, A. AU - Krumbiegel, M. AU - Marzi, A. AU - Lorenz, S. AU - Munch, J. AU - Doms, R. W. AU - Kirchhoff, F. PY - 2004 DA - 2004// TI - Amino acid 324 in the simian immunodeficiency virus SIVmac V3 loop can confer CD4 independence and modulate the interaction with CCR5 and alternative coreceptors JO - J Virol VL - 78 UR - https://doi.org/10.1128/JVI.78.7.3223-3232.2004 DO - 10.1128/JVI.78.7.3223-3232.2004 ID - Pohlmann2004 ER - TY - JOUR AU - Deeks, S. G. AU - Schweighardt, B. AU - Wrin, T. AU - Galovich, J. AU - Hoh, R. AU - Sinclair, E. AU - Hunt, P. AU - McCune, J. M. AU - Martin, J. N. AU - Petropoulos, C. J. AU - Hecht, F. M. PY - 2006 DA - 2006// TI - Neutralizing antibody responses against autologous and heterologous viruses in acute versus chronic human immunodeficiency virus (HIV) infection: evidence for a constraint on the ability of HIV to completely evade neutralizing antibody responses JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.00093-06 DO - 10.1128/JVI.00093-06 ID - Deeks2006 ER - TY - JOUR AU - Verity, E. E. AU - Zotos, D. AU - Wilson, K. AU - Chatfield, C. AU - Lawson, V. A. AU - Dwyer, D. E. AU - Cunningham, A. AU - Learmont, J. AU - Dyer, W. AU - Sullivan, J. AU - Churchill, M. AU - Wesselingh, S. L. AU - Gabuzda, D. AU - Gorry, P. R. AU - McPhee, D. A. PY - 2007 DA - 2007// TI - Viral phenotypes and antibody responses in long-term survivors infected with attenuated human immunodeficiency virus type 1 containing deletions in the nef and long terminal repeat regions JO - J Virol VL - 81 UR - https://doi.org/10.1128/JVI.00650-07 DO - 10.1128/JVI.00650-07 ID - Verity2007 ER - TY - JOUR AU - Frost, S. D. AU - Wrin, T. AU - Smith, D. M. AU - Kosakovsky Pond, S. L. AU - Liu, Y. AU - Paxinos, E. AU - Chappey, C. AU - Galovich, J. AU - Beauchaine, J. AU - Petropoulos, C. J. AU - Little, S. J. AU - Richman, D. D. PY - 2005 DA - 2005// TI - Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0504658102 DO - 10.1073/pnas.0504658102 ID - Frost2005 ER - TY - JOUR AU - Hessell, A. J. AU - Hangartner, L. AU - Hunter, M. AU - Havenith, C. E. AU - Beurskens, F. J. AU - Bakker, J. M. AU - Lanigan, C. M. AU - Landucci, G. AU - Forthal, D. N. AU - Parren, P. W. AU - Marx, P. A. AU - Burton, D. R. PY - 2007 DA - 2007// TI - Fc receptor but not complement binding is important in antibody protection against HIV JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06106 DO - 10.1038/nature06106 ID - Hessell2007 ER - TY - JOUR AU - Williams, D. AU - Overbaugh, J. PY - 2004 DA - 2004// TI - A real-time PCR-based method to independently sample single simian immunodeficiency virus genomes from macaques with a range of viral loads JO - J Med Primatol VL - 33 UR - https://doi.org/10.1111/j.1600-0684.2004.00073.x DO - 10.1111/j.1600-0684.2004.00073.x ID - Williams2004 ER - TY - JOUR AU - Thompson, J. D. AU - Gibson, T. J. AU - Plewniak, F. AU - Jeanmougin, F. AU - Higgins, D. G. PY - 1997 DA - 1997// TI - The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.24.4876 DO - 10.1093/nar/25.24.4876 ID - Thompson1997 ER - TY - CHAP AU - Maddison, D. R. AU - Maddison, W. P. PY - 2005 DA - 2005// BT - Macclade 4: Analysis of Phylogeny and Character Evolution PB - Sunderland, MA , Sinauer CY - MA ID - Maddison2005 ER - TY - CHAP AU - Swofford, D. PY - 1991 DA - 1991// BT - PAUP: phylogenetic analysis using parsimony PB - Champaign CY - Illinois Natural History Survey ID - Swofford1991 ER - TY - JOUR AU - Forthal, D. N. AU - Landucci, G. AU - Cole, K. S. AU - Marthas, M. AU - Becerra, J. C. AU - Van Rompay, K. PY - 2006 DA - 2006// TI - Rhesus macaque polyclonal and monoclonal antibodies inhibit simian immunodeficiency virus in the presence of human or autologous rhesus effector cells JO - J Virol VL - 80 UR - https://doi.org/10.1128/JVI.02746-05 DO - 10.1128/JVI.02746-05 ID - Forthal2006 ER - TY - STD TI - Stata Statistical Software: Release 9 9th edition. College Station, TX , StataCorp; 2005. ID - ref35 ER -