Table of Contents Author Guidelines Submit a Manuscript
Advances in Virology
Volume 2012 (2012), Article ID 508967, 16 pages
http://dx.doi.org/10.1155/2012/508967
Review Article

Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response

1Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada R3E 0J9
2National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada R3E 3R2

Received 9 December 2011; Revised 26 February 2012; Accepted 11 March 2012

Academic Editor: Nicola Coppola

Copyright © 2012 Raghavan Sampathkumar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. J. O'Brien and J. J. Goedert, “HIV causes AIDS: Koch's postulates fulfilled,” Current Opinion in Immunology, vol. 8, no. 5, pp. 613–618, 1996. View at Publisher · View at Google Scholar · View at Scopus
  2. UNAIDS, “World AIDS day report 2011,” Joint United Nations Programme on HIV/AIDS (UNAIDS), 2011.
  3. R. Marlink, R. Kanki, I. Thior et al., “Reduced rate of disease development after HIV-2 infection as compared to HIV-1,” Science, vol. 265, no. 5178, pp. 1587–1590, 1994. View at Google Scholar · View at Scopus
  4. L. Buonaguro, M. L. Tornesello, and F. M. Buonaguro, “Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications,” Journal of Virology, vol. 81, no. 19, pp. 10209–10219, 2007. View at Publisher · View at Google Scholar · View at Scopus
  5. P. M. Sharp and B. H. Hahn, “Origins of HIV and the AIDS Pandemic,” Cold Spring Harbor Perspectives in Medicine, vol. 1, no. 1, Article ID a006841, 2011. View at Google Scholar
  6. E. Hooper, B. Korber, T. Bhattacharya et al., “Search for the origin of HIV and AIDS,” Science, vol. 289, no. 5482, pp. 1140–1141, 2000. View at Publisher · View at Google Scholar · View at Scopus
  7. F. Simon, P. Mauclere, P. Roques et al., “Identification of a new human immunodeficiency virus type 1 distinct from group M and group O,” Nature Medicine, vol. 4, no. 9, pp. 1032–1037, 1998. View at Google Scholar
  8. D. M. Tebit and E. J. Arts, “Tracking a century of global expansion and evolution of HIV to drive understanding and to combat disease,” The Lancet Infectious Diseases, vol. 11, no. 1, pp. 45–56, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. J. C. Plantier, M. Leoz, J. E. Dickerson et al., “A new human immunodeficiency virus derived from gorillas,” Nature Medicine, vol. 15, no. 8, pp. 871–872, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. A. Vallari, V. Holzmayer, B. Harris et al., “Confirmation of putative HIV-1 group P in Cameroon,” Journal of Virology, vol. 85, no. 3, pp. 1403–1407, 2011. View at Google Scholar
  11. B. Korber, M. Muldoon, J. Theiler et al., “Timing the ancestor of the HIV-1 pandemic strains,” Science, vol. 288, no. 5472, pp. 1789–1796, 2000. View at Publisher · View at Google Scholar · View at Scopus
  12. P. Lemey, O. G. Pybus, A. Rambaut et al., “The molecular population genetics of HIV-1 group O,” Genetics, vol. 167, no. 3, pp. 1059–1068, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. J. O. Wertheim and M. Worobey, “Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2,” PLoS Computational Biology, vol. 5, no. 5, Article ID e1000377, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. “HIV Databases,” February 2012, http://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html.
  15. P. J. Kanki, D. J. Hamel, J. L. Sankale et al., “Human immunodeficiency virus type 1 subtypes differ in disease progression,” Journal of Infectious Diseases, vol. 179, no. 1, pp. 68–73, 1999. View at Google Scholar
  16. B. G. Brenner, “Resistance and viral subtypes: how important are the differences and why do they occur?” Current Opinion in HIV and AIDS, vol. 2, no. 2, pp. 94–102, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. A. Vasan, B. Renjifo, E. Hertzmark et al., “Different rates of disease progression of HIV type 1 infection in Tanzania based on infecting subtype,” Clinical Infectious Diseases, vol. 42, no. 6, pp. 843–852, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. A. Abraha, I. L. Nankya, R. Gibson et al., “CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic,” Journal of Virology, vol. 83, no. 11, pp. 5592–5602, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. J. E. Cummins Jr., W. J. Bunn, S. D. Hall, H. H. Donze, J. Mestecky, and S. Jackson, “In Vitro exposure to highly cytopathic HIV-1 X4 strains increases expression of mucosa-associated integrins on CD4+ T Cells,” Virology, vol. 280, no. 2, pp. 262–272, 2001. View at Publisher · View at Google Scholar · View at Scopus
  20. G. A. Funk, A. Oxenius, M. Fischer et al., “HIV replication elicits little cytopathic effects in vivo: analysis of surrogate markers for virus production, cytotoxic T cell response and infected cell death,” Journal of Medical Virology, vol. 78, no. 9, pp. 1141–1146, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Peeters, R. Vincent, J. L. Perret et al., “Evidence for differences in MT2 cell tropism according to genetic subtypes of HIV-1: syncytium-inducing variants seem rare among subtype C HIV-1 viruses,” Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology, vol. 20, no. 2, pp. 115–121, 1999. View at Google Scholar
  22. C. Tscherning, A. Alaeus, R. Fredriksson et al., “Differences in chemokine coreceptor usage between genetic subtypes of HIV-1,” Virology, vol. 241, no. 2, pp. 181–188, 1998. View at Publisher · View at Google Scholar · View at Scopus
  23. M. H. Naghavi, S. Schwartz, A. Sönnerborg, and A. Vahlne, “Long terminal repeat promoter/enhancer activity of different subtypes of HIV type 1,” AIDS Research and Human Retroviruses, vol. 15, no. 14, pp. 1293–1303, 1999. View at Publisher · View at Google Scholar · View at Scopus
  24. R. E. Jeeninga, M. Hoogenkamp, M. Armand-Ugon, M. De Baar, K. Verhoef, and B. Berkhout, “Functional differences between the long terminal repeat transcriptional promoters of human immunodeficiency virus type 1 subtypes A through G,” Journal of Virology, vol. 74, no. 8, pp. 3740–3751, 2000. View at Publisher · View at Google Scholar · View at Scopus
  25. M. A. Montano, C. P. Nixon, T. Ndung'u et al., “Elevated tumor necrosis factor-α activation of human immunodeficiency virus type 1 subtype C in southern Africa is associated with an NF-κB enhancer gain-of-function,” Journal of Infectious Diseases, vol. 181, no. 1, pp. 76–81, 2000. View at Publisher · View at Google Scholar · View at Scopus
  26. F. Gao, D. L. Robertson, C. D. Carruthers et al., “A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1,” Journal of Virology, vol. 72, no. 7, pp. 5680–5698, 1998. View at Google Scholar · View at Scopus
  27. L. V. Wain, E. Bailes, F. Bibollet-Ruche et al., “Adaptation of HIV-1 to Its Human Host,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1853–1860, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. E. Domingo, E. Baranowski, C. M. Ruiz-Jarabo, A. M. Martin-Hernandez, J. C. Saiz, and C. Escarmis, “Quasispecies structure and persistence of RNA viruses,” Emerging Infectious Diseases, vol. 4, no. 4, pp. 521–527, 1998. View at Google Scholar
  29. A. S. Lauring and R. Andino, “Quasispecies theory and the behavior of RNA viruses,” PLoS Pathogens, vol. 6, no. 7, Article ID e1001005, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. J. Ji and L. A. Loeb, “Fidelity of HIV-1 reverse transcriptase copying RNA in vitro,” Biochemistry, vol. 31, no. 4, pp. 954–958, 1992. View at Google Scholar · View at Scopus
  31. V. K. Pathak and W. S. Hu, “‘Might as well jump!’ template switching by retroviral reverse transcriptase, defective genome formation, and recombination,” Seminars in Virology, vol. 8, no. 2, pp. 141–150, 1997. View at Publisher · View at Google Scholar · View at Scopus
  32. B. F. Keele, E. E. Giorgi, J. F. Salazar-Gonzalez et al., “Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 21, pp. 7552–7557, 2008. View at Publisher · View at Google Scholar · View at Scopus
  33. M. R. Abrahams, J. A. Anderson, E. E. Giorgi et al., “Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants,” Journal of Virology, vol. 83, no. 8, pp. 3556–3567, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. W. Fischer, V. V. Ganusov, E. E. Giorgi et al., “Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing,” PLoS One, vol. 5, no. 8, Article ID e12303, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. B. Gaschen, C. Kuiken, B. Korber, and B. Foley, “Retrieval and on-the-fly alignment of sequence fragments from the HIV database,” Bioinformatics, vol. 17, no. 5, pp. 415–418, 2001. View at Google Scholar · View at Scopus
  36. J. T. Herbeck, G. S. Gottlieb, X. Li et al., “Lack of evidence for changing virulence of HIV-1 in North America,” PLoS One, vol. 3, no. 2, Article ID e1525, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. N. Crum-Cianflone, L. Eberly, Y. Zhang et al., “Is HIV becoming more virulent? Initial CD4 cell counts among HIV seroconverters during the course of the HIV epidemic: 1985–2007,” Clinical Infectious Diseases, vol. 48, no. 9, pp. 1285–1292, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. J. D. Altman and M. B. Feinberg, “HIV escape: there and back again,” Nature Medicine, vol. 10, no. 3, pp. 229–230, 2004. View at Publisher · View at Google Scholar · View at Scopus
  39. S. Alizon, V. von Wyl, T. Stadler et al., “Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load,” PLoS Pathogens, vol. 6, no. 9, Article ID e01123, 2010. View at Publisher · View at Google Scholar · View at Scopus
  40. F. D. Bushman, C. Hoffmann, K. Ronen et al., “Massively parallel pyrosequencing in HIV research,” AIDS, vol. 22, no. 12, pp. 1411–1415, 2008. View at Publisher · View at Google Scholar · View at Scopus
  41. “454 Sequencing, GS FLX+ System, Roche,” December 2011, http://my454.com/downloads/GSFLXApplicationFlyer_FINALv2.pdf.
  42. C. S. Pareek, R. Smoczynski, and A. Tretyn, “Sequencing technologies and genome sequencing,” Journal of Applied Genetics, vol. 52, no. 4, pp. 413–435, 2011. View at Google Scholar
  43. A. M. N. Tsibris, B. Korber, R. Arnaout et al., “Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo,” PLoS One, vol. 4, no. 5, Article ID e5683, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. B. Liang, M. Luo, J. Scott-Herridge et al., “A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1,” PLoS One, vol. 6, no. 10, Article ID e26745, 2011. View at Google Scholar
  45. S. Palmer, M. Kearney, F. Maldarelli et al., “Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis,” Journal of Clinical Microbiology, vol. 43, no. 1, pp. 406–413, 2005. View at Publisher · View at Google Scholar · View at Scopus
  46. J. Zhang, “Host RNA polymerase II makes minimal contributions to retroviral frame-shift mutations,” Journal of General Virology, vol. 85, no. 8, pp. 2389–2395, 2004. View at Publisher · View at Google Scholar · View at Scopus
  47. A. C. van der Kuyl and M. Cornelissen, “Identifying HIV-1 dual infections,” Retrovirology, vol. 4, article no. 67, 2007. View at Publisher · View at Google Scholar · View at Scopus
  48. A. R. Templeton, M. G. Kramer, J. Jarvis et al., “Multiple-infection and recombination in HIV-1 within a longitudinal cohort of women,” Retrovirology, vol. 6, article no. 54, 2009. View at Publisher · View at Google Scholar · View at Scopus
  49. D. Shriner, A. G. Rodrigo, D. C. Nickle, and J. I. Mullins, “Pervasive genomic recombination of HIV-1 in vivo,” Genetics, vol. 167, no. 4, pp. 1573–1583, 2004. View at Publisher · View at Google Scholar · View at Scopus
  50. N. N. V. Vijay, Vasantika, R. Ajmani, A. S. Perelson, and N. M. Dixit, “Recombination increases human immunodeficiency virus fitness, but not necessarily diversity,” Journal of General Virology, vol. 89, no. 6, pp. 1467–1477, 2008. View at Publisher · View at Google Scholar · View at Scopus
  51. A. M. Land, T. B. Ball, M. Luo et al., “Full-length HIV type 1 proviral sequencing of 10 highly exposed women from Nairobi, Kenya reveals a high proportion of intersubtype recombinants,” AIDS Research and Human Retroviruses, vol. 24, no. 6, pp. 865–872, 2008. View at Publisher · View at Google Scholar · View at Scopus
  52. A. M. Land, M. Luo, R. Pilon et al., “High prevalence of genetically similar HIV-1 recombinants among infected sex workers in Nairobi, Kenya,” AIDS Research and Human Retroviruses, vol. 24, no. 11, pp. 1455–1460, 2008. View at Publisher · View at Google Scholar · View at Scopus
  53. K. Delviks-Frankenberry, A. Galli, O. Nikolaitchik, H. Mens, V. K. Pathak, and W. S. Hu, “Mechanisms and factors that influence high frequency retroviral recombination,” Viruses, vol. 3, no. 9, pp. 1650–1680, 2011. View at Google Scholar
  54. K. Motomura, J. Chen, and W. S. Hu, “Genetic recombination between human immunodeficiency virus type 1 (HIV-1) and HIV-2, two distinct human lentiviruses,” Journal of Virology, vol. 82, no. 4, pp. 1923–1933, 2008. View at Publisher · View at Google Scholar · View at Scopus
  55. B. Ramratnam, S. Bonhoeffer, J. Binley et al., “Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis,” Lancet, vol. 354, no. 9192, pp. 1782–1785, 1999. View at Publisher · View at Google Scholar · View at Scopus
  56. L. M. Mansky and L. C. Bernard, “3'-Azido-3'-deoxythymidine (AZT) and AZT-resistant reverse transcriptase can increase the in vivo mutation rate of human immunodeficiency virus type 1,” Journal of Virology, vol. 74, no. 20, pp. 9532–9539, 2000. View at Publisher · View at Google Scholar · View at Scopus
  57. J. Martinez-Picado and M. A. Martínez, “HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo,” Virus Research, vol. 134, no. 1-2, pp. 104–123, 2008. View at Publisher · View at Google Scholar · View at Scopus
  58. J. M. Coffin, “HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy,” Science, vol. 267, no. 5197, pp. 483–489, 1995. View at Google Scholar · View at Scopus
  59. K. J. Metzner, S. Bonhoeffer, M. Fischer et al., “Emergence of minor populations of human immunodeficiency virus type 1 carrying the M184V and L90M mutations in subjects undergoing structured treatment interruptions,” Journal of Infectious Diseases, vol. 188, no. 10, pp. 1433–1443, 2003. View at Publisher · View at Google Scholar · View at Scopus
  60. “Stanford HIV Drug Resistance Database,” February 2012, http://hivdb.stanford.edu.
  61. J. Fellay, K. V. Shianna, D. Ge et al., “A whole-genome association study of major determinants for host control of HIV-1,” Science, vol. 317, no. 5840, pp. 944–947, 2007. View at Publisher · View at Google Scholar · View at Scopus
  62. J. Klein and A. Sato, “The HLA system: first of two parts,” New England Journal of Medicine, vol. 343, no. 10, pp. 702–709, 2000. View at Publisher · View at Google Scholar · View at Scopus
  63. K. J. M. Jeffery and C. R. M. Bangham, “Do infectious diseases drive MHC diversity?” Microbes and Infection, vol. 2, no. 11, pp. 1335–1341, 2000. View at Publisher · View at Google Scholar · View at Scopus
  64. M. Carrington and S. J. O'Brien, “The Influence of HLA Genotype on AIDS,” Annual Review of Medicine, vol. 54, pp. 535–551, 2003. View at Publisher · View at Google Scholar · View at Scopus
  65. H. A. F. Stephens, “HIV-1 diversity versus HLA class I polymorphism,” Trends in Immunology, vol. 26, no. 1, pp. 41–47, 2005. View at Publisher · View at Google Scholar · View at Scopus
  66. C. M. Rousseau, M. G. Daniels, J. M. Carlson et al., “HLA class I-driven evolution of human immunodeficiency virus type 1 subtype C proteome: immune escape and viral load,” Journal of Virology, vol. 82, no. 13, pp. 6434–6446, 2008. View at Publisher · View at Google Scholar · View at Scopus
  67. Y. Kawashima, K. Pfafferott, J. Frater et al., “Adaptation of HIV-1 to human leukocyte antigen class I,” Nature, vol. 458, no. 7238, pp. 641–645, 2009. View at Publisher · View at Google Scholar · View at Scopus
  68. Y. Zhang, Y. Peng, H. Yan et al., “Multilayered defense in HLA-B51-associated HIV viral control,” Journal of Immunology, vol. 187, no. 2, pp. 684–691, 2011. View at Publisher · View at Google Scholar · View at Scopus
  69. J. N. Blankson, J. R. Bailey, and R. F. Siliciano, “Crosscurrents in HIV-1 evolution,” Nature Immunology, vol. 7, no. 2, pp. 121–122, 2006. View at Publisher · View at Google Scholar · View at Scopus
  70. B. Liang, M. Luo, T. B. Ball, and F. A. Plummer, “QUASI analysis of the HIV-1 envelope sequences in the Los Alamos National Laboratory HIV sequence database: pattern and distribution of positive selection sites and their frequencies over years,” Biochemistry and Cell Biology, vol. 85, no. 2, pp. 259–264, 2007. View at Publisher · View at Google Scholar · View at Scopus
  71. H. O. Peters, M. G. Mendoza, R. E. Capina et al., “An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani sex worker cohort,” Journal of Virology, vol. 82, no. 4, pp. 1980–1992, 2008. View at Publisher · View at Google Scholar · View at Scopus
  72. B. Liang, M. Luo, T. B. Ball et al., “Systematic analysis of host immunological pressure on the envelope gene of human immunodeficiency virus type 1 by an immunobioinformatics approach,” Current HIV Research, vol. 6, no. 4, pp. 370–379, 2008. View at Publisher · View at Google Scholar · View at Scopus
  73. C. A. Semeniuk, L. McKinnon, H. O. Peters et al., “Multiple T-cell epitopes overlap positively-selected residues in the p1 spacer protein of HIV-1 gag,” AIDS, vol. 23, no. 7, pp. 771–777, 2009. View at Publisher · View at Google Scholar · View at Scopus
  74. B. Liang, M. Luo, T. B. Ball, S. J. M. Jones, and F. A. Plummer, “QUASI analysis of host immune responses to Gag polyproteins of human immunodeficiency virus type 1 by a systematic bioinformatics approach,” Biochemistry and Cell Biology, vol. 88, no. 4, pp. 671–681, 2010. View at Publisher · View at Google Scholar · View at Scopus
  75. J. Snoeck, J. Fellay, I. Bartha, D. C. Douek, and A. Telenti, “Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints,” Retrovirology, vol. 8, no. 1, article 87, 2011. View at Google Scholar
  76. H. Barroso and N. Taveira, “Evidence for negative selective pressure in HIV-2 evolution in vivo,” Infection, Genetics and Evolution, vol. 5, no. 3, pp. 239–246, 2005. View at Publisher · View at Google Scholar · View at Scopus
  77. S. J. O'Brien and G. W. Nelson, “Human genes that limit AIDS,” Nature Genetics, vol. 36, no. 6, pp. 565–574, 2004. View at Publisher · View at Google Scholar · View at Scopus
  78. P. An and C. A. Winkler, “Host genes associated with HIV/AIDS: advances in gene discovery,” Trends in Genetics, vol. 26, no. 3, pp. 119–131, 2010. View at Publisher · View at Google Scholar · View at Scopus
  79. S. Neil and P. Bieniasz, “Human immunodeficiency virus, restriction factors, and interferon,” Journal of Interferon and Cytokine Research, vol. 29, no. 9, pp. 569–580, 2009. View at Publisher · View at Google Scholar · View at Scopus
  80. A. M. Land, T. B. Ball, M. Luo et al., “Human immunodeficiency virus (HIV) type 1 proviral hypermutation correlates with CD4 count in HIV-infected women from Kenya,” Journal of Virology, vol. 82, no. 16, pp. 8172–8182, 2008. View at Publisher · View at Google Scholar · View at Scopus
  81. R. S. Harris and M. T. Liddament, “Retroviral restriction by APOBEC proteins,” Nature Reviews Immunology, vol. 4, no. 11, pp. 868–877, 2004. View at Publisher · View at Google Scholar · View at Scopus
  82. P. Jern, R. A. Russell, V. K. Pathak, and J. M. Coffin, “Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance,” PLoS Pathogens, vol. 5, no. 4, Article ID e1000367, 2009. View at Publisher · View at Google Scholar · View at Scopus
  83. S. Fourati, I. Malet, M. Binka et al., “Partially active HIV-1 Vif alleles facilitate viral escape from specific antiretrovirals,” AIDS, vol. 24, no. 15, pp. 2313–2321, 2010. View at Publisher · View at Google Scholar · View at Scopus
  84. N. Wood, T. Bhattacharya, B. F. Keele et al., “HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC,” PLoS Pathogens, vol. 5, no. 5, Article ID e1000414, 2009. View at Publisher · View at Google Scholar · View at Scopus
  85. E. Y. Kim, T. Bhattacharya, K. Kunstman et al., “Human APOBEC3G-mediated editing can promote HIV-1 sequence diversification and accelerate adaptation to selective pressure,” Journal of Virology, vol. 84, no. 19, pp. 10402–10405, 2010. View at Publisher · View at Google Scholar · View at Scopus
  86. H. A. Sadler, M. D. Stenglein, R. S. Harris, and L. M. Mansky, “APOBEC3G contributes to HIV-1 variation through sublethal mutagenesis,” Journal of Virology, vol. 84, no. 14, pp. 7396–7404, 2010. View at Publisher · View at Google Scholar · View at Scopus
  87. L. C. F. Mulder, A. Harari, and V. Simon, “Cytidine deamination induced HIV-1 drug resistance,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 14, pp. 5501–5506, 2008. View at Publisher · View at Google Scholar · View at Scopus
  88. J. M. Norman, M. Mashiba, L. A. McNamara et al., “The antiviral factor APOBEC3G enhances the recognition of HIV-infected primary T cells by natural killer cells,” Nature Immunology, vol. 12, no. 10, pp. 975–983, 2011. View at Google Scholar
  89. N. Van Damme, D. Goff, C. Katsura et al., “The interferon-induced protein BST-2 restricts HIV-1 release and is downregulated from the cell surface by the viral Vpu protein,” Cell Host and Microbe, vol. 3, no. 4, pp. 245–252, 2008. View at Publisher · View at Google Scholar · View at Scopus
  90. S. J. Yang, L. A. Lopez, C. M. Exline, K. G. Haworth, and P. M. Cannon, “Lack of adaptation to human tetherin in HIV-1 group O and P,” Retrovirology, vol. 8, article 78, 2011. View at Google Scholar
  91. L. Liu, N. M. Oliveira, K. M. Cheney et al., “A whole genome screen for HIV restriction factors,” Retrovirology, vol. 8, article 94, 2011. View at Google Scholar
  92. A. Telenti, “HIV-1 host interactions: integration of large-scale datasets,” F1000 Biology Reports, vol. 1, article 71, 2009. View at Google Scholar
  93. N. Goonetilleke, M. K. P. Liu, J. F. Salazar-Gonzalez et al., “The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection,” Journal of Experimental Medicine, vol. 206, no. 6, pp. 1253–1272, 2009. View at Publisher · View at Google Scholar · View at Scopus
  94. J. Da Silva and A. L. Hughes, “Conservation of cytotoxic T lymphocyte (CTL) epitopes as a host strategy to constrain parasite adaptation: evidence from the nef gene of human immunodeficiency virus 1 (HIV-1),” Molecular Biology and Evolution, vol. 15, no. 10, pp. 1259–1268, 1998. View at Google Scholar · View at Scopus
  95. A. J. Leslie, K. J. Pfafferott, P. Chetty et al., “HIV evolution: CTL escape mutation and reversion after transmission,” Nature Medicine, vol. 10, no. 3, pp. 282–289, 2004. View at Publisher · View at Google Scholar · View at Scopus
  96. M. Altfeld, M. M. Addo, E. S. Rosenberg et al., “Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection,” AIDS, vol. 17, no. 18, pp. 2581–2591, 2003. View at Publisher · View at Google Scholar · View at Scopus
  97. M. Rotger, J. Dalmau, A. Rauch et al., “Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque,” Journal of Clinical Investigation, vol. 121, no. 6, pp. 2391–2400, 2011. View at Publisher · View at Google Scholar · View at Scopus
  98. H. N. Kloverpris, A. Stryhn, M. Harndahl et al., “HLA-B57 Micropolymorphism shapes HLA allele-specific epitope immunogenicity, selection pressure, and HIV immune control,” Journal of Virology, vol. 86, no. 2, pp. 919–929, 2012. View at Google Scholar
  99. T. Dong, Y. Zhang, K. Y. Xu et al., “Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China,” Blood, vol. 118, no. 1, pp. 98–106, 2011. View at Publisher · View at Google Scholar · View at Scopus
  100. International HIVCS, F. Pereyra, X. Jia et al., “The major genetic determinants of HIV-1 control affect HLA class I peptide presentation,” Science, vol. 330, no. 6010, pp. 1551–1557, 2010. View at Google Scholar
  101. P. Kiepiela, A. J. Leslie, I. Honeyborne et al., “Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA,” Nature, vol. 432, no. 7018, pp. 769–774, 2004. View at Publisher · View at Google Scholar · View at Scopus
  102. A. I. Fontaine Costa, X. Rao, E. Lechenadec, D. Van Baarle, and C. Keşmir, “HLA-B molecules target more conserved regions of the HIV-1 proteome,” AIDS, vol. 24, no. 2, pp. 211–215, 2010. View at Publisher · View at Google Scholar · View at Scopus
  103. M. Ciccozzi, I. Bon, and M. Ciotti, “Do the HIV-1 subtypes circulating in Italy resemble the Red Queen running in Carroll's novel?” New Microbiologica, vol. 33, no. 2, pp. 179–181, 2010. View at Google Scholar · View at Scopus
  104. M. Luo, J. Kimani, N. J. Nagelkerke et al., “Rapid selection for HLA alleles that protect against HIV-1 infection correlates significantly to the declining incidence of HIV-1 in an East African sex worker population,” in 16th Annual Canadian Conference on HIV/AIDS Research (CAHR '07), Toronto, Canada, April 2007.
  105. A. A. Bashirova, R. Thomas, and M. Carrington, “HLA/KIR restraint of HIV: surviving the fittest,” Annual Review of Immunology, vol. 29, pp. 295–317, 2011. View at Publisher · View at Google Scholar · View at Scopus
  106. E. Battivelli, J. Migraine, D. Lecossier, P. Yeni, F. Clavel, and A. J. Hance, “Gag cytotoxic T lymphocyte escape mutations can increase sensitivity of HIV-1 to human TRIM5alpha, linking intrinsic and acquired immunity,” Journal of Virology, vol. 85, no. 22, pp. 11846–11854, 2011. View at Google Scholar
  107. O. O. Yang, J. Church, C. M. R. Kitchen et al., “Genetic and stochastic influences on the interaction of human immunodeficiency virus type 1 and cytotoxic T lymphocytes in identical twins,” Journal of Virology, vol. 79, no. 24, pp. 15368–15375, 2005. View at Publisher · View at Google Scholar · View at Scopus
  108. R. Draenert, T. M. Allen, Y. Liu et al., “Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus,” Journal of Experimental Medicine, vol. 203, no. 3, pp. 529–539, 2006. View at Publisher · View at Google Scholar · View at Scopus
  109. D. H. O'Connor and D. R. Burton, “Immune responses and HIV: a little order from the chaos,” Journal of Experimental Medicine, vol. 203, no. 3, pp. 501–503, 2006. View at Publisher · View at Google Scholar · View at Scopus
  110. V. Dahirel, K. Shekhar, F. Pereyra et al., “Coordinate linkage of HIV evolution reveals regions of immunological vulnerability,” Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 28, pp. 11530–11535, 2011. View at Publisher · View at Google Scholar · View at Scopus
  111. J. J. Just, “Genetic predisposition to HIV-1 infection and acquired immune deficiency virus syndrome: a review of the literature examining associations with HLA,” Human Immunology, vol. 44, no. 3, pp. 156–169, 1995. View at Google Scholar
  112. A. T. Makadzange, G. Gillespie, T. Dong et al., “Characterization of an HLA-C-restricted CTL response in chronic HIV infection,” European Journal of Immunology, vol. 40, no. 4, pp. 1036–1041, 2010. View at Publisher · View at Google Scholar · View at Scopus
  113. J. K. Wright, Z. L. Brumme, B. Julg et al., “Lack of association between HLA class II alleles and in vitro replication capacities of recombinant viruses encoding HIV-1 subtype C Gag-protease from chronically infected individuals,” Journal of Virology, vol. 86, no. 2, pp. 1273–1276, 2012. View at Google Scholar
  114. G. C. Harcourt, S. Garrard, M. P. Davenport, A. Edwards, and R. E. Phillips, “HIV-1 variation diminishes CD4 T lymphocyte recognition,” Journal of Experimental Medicine, vol. 188, no. 10, pp. 1785–1793, 1998. View at Publisher · View at Google Scholar · View at Scopus
  115. G. Ahlenstiel, K. Roomp, M. Däumer et al., “Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level,” Clinical and Vaccine Immunology, vol. 14, no. 10, pp. 1266–1273, 2007. View at Publisher · View at Google Scholar · View at Scopus
  116. R. A. Hardie, E. Knight, B. Bruneau et al., “A common human leucocyte antigen-DP genotype is associated with resistance to HIV-1 infection in Kenyan sex workers,” AIDS, vol. 22, no. 15, pp. 2038–2042, 2008. View at Publisher · View at Google Scholar · View at Scopus
  117. R. A. Hardie, M. Luo, B. Bruneau et al., “Human leukocyte antigen-DQ alleles and haplotypes and their associations with resistance and susceptibility to HIV-1 infection,” AIDS, vol. 22, no. 7, pp. 807–816, 2008. View at Publisher · View at Google Scholar · View at Scopus
  118. P. A. Lacap, J. D. Huntington, M. Luo et al., “Associations of human leukocyte antigen DRB with resistance or susceptibility to HIV-1 infection in the Pumwani Sex Worker Cohort,” AIDS, vol. 22, no. 9, pp. 1029–1038, 2008. View at Publisher · View at Google Scholar · View at Scopus
  119. S. Raghavan, K. Alagarasu, and P. Selvaraj, “Immunogenetics of HIV and HIV associated tuberculosis,” Tuberculosis (Edinb), vol. 92, no. 1, pp. 18–30, 2012. View at Google Scholar
  120. B. Julg, E. S. Moodley, Y. Qi et al., “Possession of HLA class II DRB1*1303 associates with reduced viral loads in chronic HIV-1 clade C and B infection,” Journal of Infectious Diseases, vol. 203, no. 6, pp. 803–809, 2011. View at Publisher · View at Google Scholar · View at Scopus
  121. B. T. Korber, N. L. Letvin, and B. F. Haynes, “T-cell vaccine strategies for human immunodeficiency virus, the virus with a thousand faces,” Journal of Virology, vol. 83, no. 17, pp. 8300–8314, 2009. View at Publisher · View at Google Scholar · View at Scopus
  122. L. R. McKinnon, R. Kaul, M. Herman, F. A. Plummer, and T. B. Ball, “HIV-specific T cells: strategies for fighting a moving target,” Current HIV Research, vol. 8, no. 8, pp. 587–595, 2010. View at Publisher · View at Google Scholar · View at Scopus
  123. S. Kulkarni, M. P. Martin, and M. Carrington, “The Yin and Yang of HLA and KIR in human disease,” Seminars in Immunology, vol. 20, no. 6, pp. 343–352, 2008. View at Google Scholar
  124. K. M. Jamil and S. I. Khakoo, “KIR/HLA interactions and pathogen immunity,” Journal of Biomedicine and Biotechnology, vol. 2011, Article ID 298348, 9 pages, 2011. View at Publisher · View at Google Scholar
  125. G. B. Cohen, R. T. Gandhi, D. M. Davis et al., “The selective downregulation of class I major histocompatibility complex proteins by HIV-1 protects HIV-infected cells from NK cells,” Immunity, vol. 10, no. 6, pp. 661–671, 1999. View at Publisher · View at Google Scholar · View at Scopus
  126. S. Gaudieri, D. DeSantis, E. McKinnon et al., “Killer immunoglobulin-like receptors and HLA act both independently and synergistically to modify HIV disease progression,” Genes and Immunity, vol. 6, no. 8, pp. 683–690, 2005. View at Publisher · View at Google Scholar · View at Scopus
  127. M. P. Martin, Y. Qi, X. Gao et al., “Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1,” Nature Genetics, vol. 39, no. 6, pp. 733–740, 2007. View at Publisher · View at Google Scholar · View at Scopus
  128. K. Pelak, A. C. Need, J. Fellay et al., “Copy number variation of KIR genes influences HIV-1 control,” PLoS Biology, vol. 9, no. 11, Article ID e1001208, 2011. View at Google Scholar
  129. G. Alter, D. Heckerman, A. Schneidewind et al., “HIV-1 adaptation to NK-cell-mediated immune pressure,” Nature, vol. 476, no. 7358, pp. 96–100, 2011. View at Publisher · View at Google Scholar · View at Scopus
  130. G. B. Karlsson Hedestam, R. A. M. Fouchier, S. Phogat, D. R. Burton, J. Sodroski, and R. T. Wyatt, “The challenges of eliciting neutralizing antibodies to HIV-1 and to influenza virus,” Nature Reviews Microbiology, vol. 6, no. 2, pp. 143–155, 2008. View at Publisher · View at Google Scholar · View at Scopus
  131. L. Stamatatos, L. Morris, D. R. Burton, and J. R. Mascola, “Neutralizing antibodies generated during natural HIV-1 infection: good news for an HIV-1 vaccine?” Nature medicine, vol. 15, no. 8, pp. 866–870, 2009. View at Google Scholar · View at Scopus
  132. M. J. McElrath and B. F. Haynes, “Induction of immunity to human immunodeficiency virus type-1 by vaccination,” Immunity, vol. 33, no. 4, pp. 542–554, 2010. View at Publisher · View at Google Scholar · View at Scopus
  133. J. Cohen, “AIDS research. Novel antibody response may explain HIV vaccine success,” Science, vol. 333, no. 6049, p. 1560, 2011. View at Google Scholar
  134. D. D. Richman, T. Wrin, S. J. Little, and C. J. Petropoulos, “Rapid evolution of the neutralizing antibody response to HIV type 1 infection,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 7, pp. 4144–4149, 2003. View at Publisher · View at Google Scholar · View at Scopus
  135. X. Wei, J. M. Decker, S. Wang et al., “Antibody neutralization and escape by HIV-1,” Nature, vol. 422, no. 6929, pp. 307–312, 2003. View at Publisher · View at Google Scholar · View at Scopus
  136. X. Wu, Z. Y. Yang, Y. Li et al., “Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1,” Science, vol. 329, no. 5993, pp. 856–861, 2010. View at Publisher · View at Google Scholar · View at Scopus
  137. X. Wu, T. Zhou, J. Zhu et al., “Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing,” Science, vol. 333, no. 6049, pp. 1593–1602, 2011. View at Google Scholar
  138. J. F. Scheid, H. Mouquet, B. Ueberheide et al., “Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding,” Science, vol. 333, no. 6049, pp. 1633–1637, 2011. View at Publisher · View at Google Scholar · View at Scopus
  139. A. Rauch, D. Nolan, H. Furrer et al., “HLA-Bw4 homozygosity is associated with an impaired CD4 T cell recovery after initiation of antiretroviral therapy,” Clinical Infectious Diseases, vol. 46, no. 12, pp. 1921–1925, 2008. View at Google Scholar
  140. M. H. Kuniholm, X. Gao, X. Xue et al., “Human leukocyte antigen genotype and risk of HIV disease progression before and after initiation of antiretroviral therapy,” Journal of Virology, vol. 85, no. 20, pp. 10826–10833, 2011. View at Google Scholar
  141. M. Koga, A. Kawana-Tachikawa, D. Heckerman et al., “Changes in impact of HLA class I allele expression on HIV-1 plasma virus loads at a population level over time,” Microbiology and Immunology, vol. 54, no. 4, pp. 196–205, 2010. View at Google Scholar
  142. J. K. Carr, “Viral diversity as a challenge to HIV-1 vaccine development,” Current Opinion in HIV and AIDS, vol. 1, no. 4, pp. 294–300, 2006. View at Google Scholar
  143. W. A. Burgers, A. Manrique, D. Masopust et al., “Measurements of immune responses for establishing correlates of vaccine protection against HIV,” AIDS Research and Human Retroviruses. In press. View at Publisher · View at Google Scholar
  144. M. P. Davenport, R. M. Ribeiro, D. L. Chao, and A. S. Perelson, “Predicting the impact of a nonsterilizing vaccine against human immunodeficiency virus,” Journal of Virology, vol. 78, no. 20, pp. 11340–11351, 2004. View at Publisher · View at Google Scholar · View at Scopus
  145. S. K. Lakhashe, G. Silvestri, and R. M. Ruprecht, “No acquisition: a new ambition for HIV vaccine development?” Current Opinion in Virology, vol. 1, no. 4, pp. 246–253, 2011. View at Google Scholar
  146. F. A. Plummer, T. B. Ball, J. Kimani, and K. R. Fowke, “Resistance to HIV-1 infection among highly exposed sex workers in Nairobi: what mediates protection and why does it develop?” Immunology Letters, vol. 66, no. 1–3, pp. 27–34, 1999. View at Publisher · View at Google Scholar · View at Scopus
  147. L. Piacentini, C. Fenizia, V. Naddeo, and M. Clerici, “Not just sheer luck! Immune correlates of protection against HIV-1 infection,” Vaccine, vol. 26, no. 24, pp. 3002–3007, 2008. View at Publisher · View at Google Scholar · View at Scopus
  148. J. N. Blankson, “Effector mechanisms in HIV-1 infected elite controllers: highly active immune responses?” Antiviral Research, vol. 85, no. 1, pp. 295–302, 2010. View at Publisher · View at Google Scholar · View at Scopus
  149. A. Burgener, J. Sainsbury, F. A. Plummer, and T. Blake Ball, “Systems biology-based approaches to understand HIV-exposed uninfected women,” Current HIV/AIDS Reports, vol. 7, no. 2, pp. 53–59, 2010. View at Publisher · View at Google Scholar · View at Scopus
  150. B. Autran, B. Descours, V. Avettand-Fenoel, and C. Rouzioux, “Elite controllers as a model of functional cure,” Current Opinion in HIV and AIDS, vol. 6, no. 3, pp. 181–187, 2011. View at Publisher · View at Google Scholar · View at Scopus
  151. J. M. Young, J. A. Turpin, R. Musib, and O. K. Sharma, “Outcomes of a national institute of allergy and infectious diseases workshop on understanding HIV-exposed but seronegative individuals,” AIDS Research and Human Retroviruses, vol. 27, no. 7, pp. 737–743, 2011. View at Publisher · View at Google Scholar · View at Scopus
  152. L. M. Luft, M. J. Gill, and D. L. Church, “HIV-1 viral diversity and its implications for viral load testing: review of current platforms,” International Journal of Infectious Diseases, vol. 15, no. 10, pp. e661–e670, 2011. View at Publisher · View at Google Scholar · View at Scopus
  153. M. S. Cohen, Y. Q. Chen, M. McCauley et al., “Prevention of HIV-1 infection with early antiretroviral therapy,” New England Journal of Medicine, vol. 365, no. 6, pp. 493–505, 2011. View at Google Scholar
  154. C. Deleage, M. Moreau, N. Rioux-Leclercq, A. Ruffault, B. Jegou, and N. Dejucq-Rainsford, “Human immunodeficiency virus infects human seminal vesicles in vitro and in vivo,” The American Journal of Pathology, vol. 179, no. 5, pp. 2397–2408, 2011. View at Google Scholar
  155. V. Cobos-Jiménez, T. Booiman, J. Hamann, and N. A. Kootstra, “Macrophages and HIV-1,” Current Opinion in HIV and AIDS, vol. 6, no. 5, pp. 385–390, 2011. View at Publisher · View at Google Scholar · View at Scopus
  156. J. K. Wong, M. Hezareh, H. F. Günthard et al., “Recovery of replication-competent HIV despite prolonged suppression of plasma viremia,” Science, vol. 278, no. 5341, pp. 1291–1295, 1997. View at Publisher · View at Google Scholar · View at Scopus
  157. L. Zhang, B. Ramratnam, K. Tenner-Racz et al., “Quantifying residual HIV-1 replication in patients receiving combination antiretroviral therapy,” New England Journal of Medicine, vol. 340, no. 21, pp. 1605–1613, 1999. View at Publisher · View at Google Scholar · View at Scopus
  158. J. Stebbing, B. Gazzard, and D. C. Douek, “Where does HIV live?” The New England journal of medicine, vol. 350, no. 18, pp. 1872–1880, 2004. View at Google Scholar · View at Scopus
  159. S. K. Choudhary and D. M. Margolis, “Curing HIV: pharmacologic approaches to target HIV-1 Latency,” Annual Review of Pharmacology and Toxicology, vol. 51, pp. 397–418, 2011. View at Publisher · View at Google Scholar · View at Scopus
  160. E. H. Gisolf, R. H. Enting, S. Jurriaans et al., “Cerebrospinal fluid HIV-1 RNA during treatment with ritonavir/saquinavir or ritonavir/saquinavir/stavudine,” AIDS, vol. 14, no. 11, pp. 1583–1589, 2000. View at Publisher · View at Google Scholar · View at Scopus
  161. C. Solas, A. Lafeuillade, P. Halfon, S. Chadapaud, G. Hittinger, and B. Lacarelle, “Discrepancies between protease inhibitor concentrations and viral load in reservoirs and sanctuary sites in human immunodeficiency virus-infected patients,” Antimicrobial Agents and Chemotherapy, vol. 47, no. 1, pp. 238–243, 2003. View at Publisher · View at Google Scholar · View at Scopus
  162. K. M. McGrath, N. G. Hoffman, W. Resch, J. A. E. Nelson, and R. Swanstrom, “Using HIV-1 sequence variability to explore virus biology,” Virus Research, vol. 76, no. 2, pp. 137–160, 2001. View at Publisher · View at Google Scholar · View at Scopus
  163. J. J. Eron, P. L. Vernazza, D. M. Johnston et al., “Resistance of HIV-1 to antiretroviral agents in blood and seminal plasma: implications for transmission,” AIDS, vol. 12, no. 15, pp. F181–F189, 1998. View at Google Scholar · View at Scopus
  164. R. W. Coombs, C. E. Speck, J. P. Hughes et al., “Association between culturable human immunodeficiency virus type 1 (HIV- 1) in semen and HIV-1 RNA levels in semen and blood: evidence for compartmentalization of HIV-1 between semen and blood,” Journal of Infectious Diseases, vol. 177, no. 2, pp. 320–330, 1998. View at Google Scholar · View at Scopus
  165. L. H. Ping, M. S. Cohen, I. Hoffman et al., “Effects of genital tract inflammation on human immunodeficiency virus type 1 V3 populations in blood and semen,” Journal of Virology, vol. 74, no. 19, pp. 8946–8952, 2000. View at Publisher · View at Google Scholar · View at Scopus
  166. G. Venturi, M. Catucci, L. Romano et al., “Antiretroviral resistance mutations in human immunodeficiency virus type 1 reverse transcriptase and protease from paired cerebrospinal fluid and plasma samples,” Journal of Infectious Diseases, vol. 181, no. 2, pp. 740–745, 2000. View at Publisher · View at Google Scholar · View at Scopus
  167. Y. Quan, B. G. Brenner, A. Dascal, and M. A. Wainberg, “Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report,” Retrovirology, vol. 5, article no. 43, 2008. View at Publisher · View at Google Scholar · View at Scopus
  168. P. R. Harrigan, M. Whaley, and J. S. G. Montaner, “Rate of HIV-1 RNA rebound upon stopping antiretroviral therapy,” AIDS, vol. 13, no. 8, pp. F59–F62, 1999. View at Publisher · View at Google Scholar · View at Scopus
  169. J. Z. Li, R. Paredes, H. J. Ribaudo et al., “Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: a systematic review and pooled analysis,” Journal of the American Medical Association, vol. 305, no. 13, pp. 1327–1335, 2011. View at Publisher · View at Google Scholar · View at Scopus
  170. V. Jain, M. C. Sucupira, P. Bacchetti et al., “Differential persistence of transmitted HIV-1 drug resistance mutation classes,” Journal of Infectious Diseases, vol. 203, no. 8, pp. 1174–1181, 2011. View at Publisher · View at Google Scholar · View at Scopus
  171. M. Saag, R. Balu, E. Phillips et al., “High sensitivity of human leukocyte antigen-B*5701 as a marker for immunologically confirmed abacavir hypersensitivity in white and black patients,” Clinical Infectious Diseases, vol. 46, no. 7, pp. 1111–1118, 2008. View at Publisher · View at Google Scholar · View at Scopus
  172. M. Chaponda and M. Pirmohamed, “Hypersensitivity reactions to HIV therapy,” British Journal of Clinical Pharmacology, vol. 71, no. 5, pp. 659–671, 2011. View at Publisher · View at Google Scholar · View at Scopus
  173. A. R. Hughes, W. R. Spreen, M. Mosteller et al., “Pharmacogenetics of hypersensitivity to abacavir: from PGx hypothesis to confirmation to clinical utility,” Pharmacogenomics Journal, vol. 8, no. 6, pp. 365–374, 2008. View at Publisher · View at Google Scholar · View at Scopus
  174. M. He, Y. H. Zheng, H. Y. Zhou et al., “Prospective observation for seven-year's highly active antiretroviral therapy in Chinese HIV-1 infected patients,” Current HIV Research, vol. 9, no. 3, pp. 160–165, 2011. View at Publisher · View at Google Scholar · View at Scopus
  175. G. Hirnschall and B. Schwartländer, “Treatment 2.0: catalysing the next phase of scale-up.,” Lancet, vol. 378, no. 9787, pp. 209–211, 2011. View at Publisher · View at Google Scholar · View at Scopus
  176. WHO, “Antiretroviral therapy for HIV infection in adults and adolescents: recommendations for a public health approach,” 2010.
  177. WHO, “HIV Drug resistance fact sheet,” April 2011, http://www.who.int/hiv/facts/drug_resistance/en/index.html.
  178. D. E. Bennett, R. J. Camacho, D. Otelea et al., “Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update,” PLoS One, vol. 4, no. 3, Article ID e4724, 2009. View at Publisher · View at Google Scholar · View at Scopus
  179. T. Hinkley, J. Martins, C. Chappey et al., “A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase,” Nature Genetics, vol. 43, no. 5, pp. 487–489, 2011. View at Publisher · View at Google Scholar · View at Scopus
  180. O. Carlborg and C. S. Haley, “Epistasis: too often neglected in complex trait studies?” Nature Reviews Genetics, vol. 5, no. 8, pp. 618–625, 2004. View at Publisher · View at Google Scholar · View at Scopus
  181. P. C. Phillips, “The language of gene interaction,” Genetics, vol. 149, no. 3, pp. 1167–1171, 1998. View at Google Scholar · View at Scopus
  182. S. Swaminathan, R. Ramachandran, G. Baskaran et al., “Risk of development of tuberculosis in HIV-infected patients,” International Journal of Tuberculosis and Lung Disease, vol. 4, no. 9, pp. 839–844, 2000. View at Google Scholar · View at Scopus
  183. K. K. Venkatesh, S. Swaminathan, J. R. Andrews, and K. H. Mayer, “Tuberculosis and HIV co-infection: screening and treatment strategies,” Drugs, vol. 71, no. 9, pp. 1133–1152, 2011. View at Publisher · View at Google Scholar · View at Scopus
  184. M. Jones and M. Nunez, “HIV and hepatitis C co-infection: the role of HAART in HIV/hepatitis C virus management,” Current Opinion in HIV and AIDS, vol. 6, no. 6, pp. 546–552, 2011. View at Google Scholar
  185. R. F. Siliciano and W. C. Greene, “HIV latency,” Cold Spring Harbor Perspectives in Medicine, vol. 1, Article ID a007096, 2011. View at Google Scholar
  186. J. Cohen, “Understanding HIV latency to undo it,” Science, vol. 332, no. 6031, p. 786, 2011. View at Publisher · View at Google Scholar · View at Scopus
  187. S. Ganeshan, R. E. Dickover, B. T. M. Korber, Y. J. Bryson, and S. M. Wolinsky, “Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease,” Journal of Virology, vol. 71, no. 1, pp. 663–677, 1997. View at Google Scholar · View at Scopus
  188. K. Metzner, “The significance of minority drug-resistant quasispecies,” in Antiretroviral Resistance in Clinical Practice, A. M. Geretti, Ed., Mediscript, London, UK, 2006. View at Google Scholar
  189. C. M. Rousseau, G. H. Learn, T. Bhattacharya et al., “Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections,” Journal of Virology, vol. 81, no. 9, pp. 4492–4500, 2007. View at Publisher · View at Google Scholar · View at Scopus
  190. P. C. Aulicino, E. C. Holmes, C. Rocco, A. Mangano, and L. Sen, “Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina,” Journal of Virology, vol. 81, no. 1, pp. 427–429, 2007. View at Publisher · View at Google Scholar · View at Scopus
  191. P. Frange, J. Galimand, N. Vidal et al., “New and old complex recombinant HIV-1 strains among patients with primary infection in 1996-2006 in France: the French ANRS CO06 primo cohort study,” Retrovirology, vol. 5, article no. 69, 2008. View at Publisher · View at Google Scholar · View at Scopus
  192. P. A. Volberding and S. G. Deeks, “Antiretroviral therapy and management of HIV infection,” The Lancet, vol. 376, no. 9734, pp. 49–62, 2010. View at Publisher · View at Google Scholar · View at Scopus
  193. S. Rerks-Ngarm, P. Pitisuttithum, S. Nitayaphan et al., “Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand,” New England Journal of Medicine, vol. 361, no. 23, pp. 2209–2220, 2009. View at Publisher · View at Google Scholar · View at Scopus
  194. Q. A. Karim, S. S. A. Karim, J. A. Frohlich et al., “Effectiveness and safety of tenofovir gel, an antiretroviral microbicide, for the prevention of HIV infection in women,” Science, vol. 329, no. 5996, pp. 1168–1174, 2010. View at Publisher · View at Google Scholar · View at Scopus
  195. K. Allers, G. Hütter, J. Hofmann et al., “Evidence for the cure of HIV infection by CCR5Δ32/Δ32 stem cell transplantation,” Blood, vol. 117, no. 10, pp. 2791–2799, 2011. View at Publisher · View at Google Scholar · View at Scopus
  196. G. Hutter and S. Ganepola, “Eradication of HIV by transplantation of CCR5-deficient hematopoietic stem cells,” TheScientificWorldJournal, vol. 11, pp. 1068–1076, 2011. View at Google Scholar
  197. G. Hütter and E. Thiel, “Allogeneic transplantation of CCR5-deficient progenitor cells in a patient with HIV infection: an update after 3 years and the search for patient no. 2,” AIDS, vol. 25, no. 2, pp. 273–274, 2011. View at Publisher · View at Google Scholar · View at Scopus
  198. L. R. McKinnon and C. M. Card, “HIV vaccine efficacy trials: a brief history, and options for going forward,” AIDS Reviews, vol. 12, no. 4, pp. 209–217, 2010. View at Google Scholar · View at Scopus
  199. C. W. Dieffenbach and A. S. Fauci, “Thirty years of HIV and AIDS: future challenges and opportunities,” Annals of Internal Medicine, vol. 154, no. 11, pp. 766–771, 2011. View at Google Scholar · View at Scopus
  200. L. J. Picker, S. G. Hansen, and J. D. Lifson, “New paradigms for HIV/AIDS vaccine development,” Annual Review of Medicine, vol. 63, pp. 95–111, 2012. View at Google Scholar
  201. J. Cohen, “The emerging race to cure HIV infections,” Science, vol. 332, no. 6031, pp. 784–789, 2011. View at Publisher · View at Google Scholar · View at Scopus
  202. Y. Gali, B. Berkhout, G. Vanham, M. Bakker, N. K. T. Back, and K. K. Ariën, “Survey of the temporal changes in HIV-1 replicative fitness in the Amsterdam Cohort,” Virology, vol. 364, no. 1, pp. 140–146, 2007. View at Publisher · View at Google Scholar · View at Scopus
  203. K. K. Arien, G. Vanham, and E. J. Arts, “Is HIV-1 evolving to a less virulent form in humans?” Nature Reviews Microbiology, vol. 5, no. 2, pp. 141–151, 2007. View at Google Scholar