Impact of genetic diversity of HIV-1 on diagnosis, antiretroviral therapy & vaccine development

Indian Journal of Medical Research

Volumn 121, Issue 4, 2005, Pages 287-314

  Lal, Renu B ^b   Chakrabarti, Sekhar ^a   Yang, Chunfu ^b  

^a NATIONAL INSTITUTE OF CHOLERA AND ENTERIC DISEASES   (India)

^b CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; CD4 ANTIGEN; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; PROTEINASE INHIBITOR; RECOMBINANT VACCINE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; VIRUS GLYCOPROTEIN;

AFRICA; CELL REGENERATION; CLINICAL TRIAL; CYTOTOXIC T LYMPHOCYTE; DISEASE COURSE; DRUG DESIGN; EPIDEMIC; GENE MUTATION; GENETIC VARIABILITY; GENOTYPE; HELPER CELL; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOGENICITY; IN VIVO STUDY; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; REVIEW; VIRION; VIRUS NEUTRALIZATION; VIRUS PATHOGENESIS; VIRUS RECOMBINATION; VIRUS REPLICATION; VIRUS STRAIN; VIRUS TRANSMISSION; VIRUS TYPING;

AIDS VACCINES; ANIMALS; DISEASE PROGRESSION; HIV INFECTIONS; HIV-1; HIV-2; HUMANS; RECOMBINATION, GENETIC; VARIATION (GENETICS); ZOONOSES;

EID: 18844435415     PISSN: 09715916     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (215)

1. Gallo RC, Montagnier L. The discovery of HIV as the cause of AIDS. N Engl J Med 2003; 349 : 2283-5.
2. Gottlieb MS. AIDS - past and future. N Engl J Med 2001; 344 : 1788-91.
3. Schim van der Loeff MF, Aaby P. Towards a better understanding of the epidemiology of HIV-2. AIDS 1999; 13 (Suppl A) : S69-84.
4. UNAIDS. 2004 report on the global AIDS epidemic: Executive Summary. UNAIDS, 20 Avenue Appia, 1211 Geneva 27, Switzerland; 2004 p. 1-18.
5. Keulen W, Nijhuis M, Schuurman R, et al. Reverse transcriptase fidelity and HIV-1 variation. Science 1997; 275 : 229-1.
6. Drosopoulos WC, Rezende LF, Wainberg MA, Prasad VR. Virtues of being faithful: can we limit the genetic variation in human immunodeficiency virus? J Mol Med 1998; 76 : 604-12.
7. Hahn BH, Shaw GM, De Cock KM, et al. AIDS as a zoonosis: scientific and public health implications. Science 2000; 287 : 607-14.
8. Peters M. Cross-species transmissions of simian retroviruses in Africa and risk for human health. Lancet 2004; 363 : 911-2.
9. Sharp PM, Bailes E, Robertson DL, et al. Origins and evolution of AIDS viruses. Biol Bull 1999; 196 : 338-42.
10. Brander C, Walker BD. Gradual adaptation of HIV to human host populations: good or bad news? Nat Med 2003; 9 : 1359-62.
11. Rowland-Jones SL. Timeline: AIDS pathogenesis: what have two decades of HIV research taught us? Nat Rev Immunol 2003; 3 : 343-8.
12. Apetrei C, Marx PA, Smith SM. The evolution of HIV and its consequences. Infect Dis Clin North Am 2004; 18 : 369-94.
13. Spira S, Wainberg MA, Loemba H, et al. Impact of clade diversity on HIV-1 virulence, antiretroviral drug sensitivity and drug resistance. J Antimicrob Chemother 2003; 51 : 229-40.
14. McCutchan FE. Understanding the genetic diversity of HIV-1. AIDS 2000; 14 (Suppl 3) : S31-44.
15. Peeters M, Sharp PM. Genetic diversity of HIV-1: the moving target. AIDS 2000; 14 (Suppl 3) : S129-40.
16. Peeters, M. Recombinant HIV sequences: their role in the global epidemic. In: Kuiken C, Foley B, Hahn B, et al, editors. The HIV sequence compendium 2000. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory; 2000 p. 139-54.
17. Apetrei C, Robertson DL, Marx PA. The history of SIVS and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa. Front Biosci 2004; 9 : 225-54.
18. Peeters M, Courgnaud V, Abela B, et al. Risk to human health from a plethora of simian immunodeficiency viruses in primate bushmeat. Emerg Infect Dis 2002; 8 : 451-7.
19. Wolfe ND, Switzer WM, Carr JK, et al. Naturally acquired simian retrovirus infections in central African hunters. Lancet 2004; 363 : 932-7.
20. Gao F, Bailes E, Robertson DL, et al. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 1999; 397 : 436-41.
21. Gao F, Yue L, White AT, et al. Human infection by genetically diverse SIVSM-related HIV-2 in west Africa. Nature 1992; 358 : 495-9.
22. Sharp PM, Bailes E, Gao F, et al. Origins and evolution of AIDS viruses: estimating the time-scale. Biochem Soc Trans 2000; 28 : 275-82.
23. Lemey P, Pybus OG, Rambaut A, Drummond AJ, Robertson DL, Roques P, et al. The molecular population genetics of HIV-1 group O. Genetics 2004; 167 : 1059-68.
24. Roques P, Robertson DL, Souquiere S, et al. Phylogenetic characteristics of three new HIV-1 N strains and implications for the origin of group N. AIDS 2004; 18 : 1371-81.
25. Gao F, Yue L, Robertson DL, et al. Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology. J Virol 1994; 68 : 7433-47.
26. Lemey P, Pybus OG, Wang B, et al. Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci USA 2003; 100 : 6588-92.
27. Damond F, Worobey M, Campa P, et al. Identification of a highly divergent HIV type 2 and proposal for a change in HIV type 2 classification. AIDS Res Hum Retroviruses 2004; 20 : 666-72.
28. Korber B, Muldoon M, Theiler J, et al. Timing the ancestor of the HIV-1 pandemic strains. Science 2000; 288 : 1789-96.
29. Salemi M, Strimmer K, Hall WW, et al. Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution. FASEB J 2001; 15 : 276-8.
30. Vidal N, Peeters M, Mulanga-Kabeya C, et al. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J Virol 2000; 74 : 10498-507.
31. Yang C, Dash B, Hanna SL, et al. Predominance of HIV type 1 subtype G among commercial sex workers from Kinshasa, Democratic Republic of Congo. AIDS Res Hum Retroviruses 2001; 17 : 361-5.
32. Robbins KE, Lemey P, Pybus OG, et al. US Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol 2003; 77 : 6359-66.
33. Kalish ML, Robbins KE, Pieniazek D, et al. Recombinant viruses and early global HIV-1 epidemic. Emerg Infect Dis 2004; 10 : 1227-34.
34. Zhu T, Korber BT, Nahmias AJ, et al. An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 1998; 391 : 594-7.
35. Simon F, Mauclere P, Roques P, et al. Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nat Med 1998; 4 : 1032-7.
36. Robertson DL, Sharp PM, McCutchan FE, et al. Recombination in HIV-1. Nature 1995; 374 : 124-6.
37. Jetzt AE, Yu H, Klarmann GJ, et al. High rate of recombination throughout the human immunodeficiency virus type 1 genome. J Virol 2000; 74 : 1234-40.
38. Thomson MM, Perez-Alvarez L, Najera R. Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy. Lancet Infect Dis 2002; 2 : 461-71.
39. Robertson DL, Anderson JP, Bradac JA, et al. HIV-1 nomenclature proposal. Science 2000; 288 : 55-6. 2000; 288 : 55-6.
40. Stebbing J, Moyle G. The clades of HIV: their origins and clinical significance. AIDS Rev 2003; 5 : 205-13.
41. Gao F, Vidal N, Li Y, et al. Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. AIDS Res Hum Retroviruses 2001; 17 : 675-88.
42. Triques K, Bourgeois A, Saragosti S, et al. High diversity of HIV-1 subtype F strains in Central Africa. Virology 1999; 259 : 99-109.
43. Pollakis G, Abebe A, Kliphuis A, et al. Recombination of HIV type 1C (C′/C″) in Ethiopia: possible link of EthHIV-1C′ to subtype C sequences from the high-prevalence epidemics in India and Southern Africa. AIDS Res Hum Retroviruses 2003; 19 : 999-1008.
44. Peeters M, Gueye A, Mboup S, et al. Geographical distribution of HIV-1 group O viruses in Africa. AIDS 1997; 11 : 493-8.
45. Rayfield MA, Sullivan P, Bandea CI, et al. HIV-1 group O virus identified for the first time in the United States. Emerg Infect Dis 1996; 2 : 209-12.
46. Bodelle P, Vallari A, Coffey R, et al. Identification and genomic sequence of an HIV type 1 group N isolate from Cameroon. AIDS Res Hum Retroviruses 2004; 20 : 902-8.
47. Fonjungo PN, Mpoudi EN, Torimiro JN, et al. Presence of diverse human immunodeficiency virus type 1 viral variants in Cameroon. AIDS Res Hum Retroviruses 2000; 16 : 1319-24.
48. Hoelscher M, Dowling WE, Sanders-Buell E, et al. Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assay. AIDS 2002; 16 : 2055-64.
49. Altfeld M, Allen TM, Yu XG, et al. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 2002; 420 : 434-9.
50. Ramos A, Hu DJ, Nguyen L, et al. Intersubtype human immunodeficiency virus type 1 superinfection following seroconversion to primary infection in two injection drug users. J Virol 2002; 76 : 7444-52.
51. Blackard JT, Cohen DE, Mayer KH. Human immunodeficiency virus superinfection and recombination: current state of knowledge and potential clinical consequences. Clin Infect Dis 2002; 34 : 1108-14.
52. Fang G, Weiser B, Kuiken C, et al. Recombination following superinfection by HIV-1. AIDS 2004; 18 : 153-9.
53. Achkar JM, Burda ST, Konings FA, et al. Infection with HIV type 1 group M non-B subtypes in individuals living in New York city. J Acquir Immune Defic Syndr 2004; 36 : 835-44.
54. Brodine SK, Starkey MJ, Shaffer RA, et al. Diverse HIV-1 subtypes and clinical, laboratory and behavioral factors in a recently infected US military cohort. AIDS 2003; 17 : 2521-7.
55. Carrion G, Hierholzer J, Montano S, et al. Circulating recombinant form CRF02_AG in South America. AIDS Res Hum Retroviruses 2003; 19 : 329-32.
56. Vachot L, Ataman-Onal Y, Terrat C, et al. Retrospective study to time the introduction of HIV type 1 non-B subtypes in Lyon, France, using env genes obtained from primary infection samples. AIDS Res Hum Retroviruses 2004; 20 : 687-91.
57. Liitsola K, Tashkinova I, Laukkanen T, et al. HIV-1 genetic subtype A/B recombinant strain causing an explosive epidemic in injecting drug users in Kaliningrad. AIDS 1998; 12 : 1907-19.
58. Lukashov VV, Huismans R, Rakhmanova AG, et al. Circulation of subtype A and gagA/envB recombinant HIV type 1 strains among injecting drug users in St. Petersburg, Russia, correlates with geographical origin of infections. AIDS Res Hum Retroviruses 1999; 15 : 1577-83.
59. Gao F, Robertson DL, Carruthers CD, et al. An isolate of human immunodeficiency virus type I originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). J Virol 1998; 72 : 10234-41.
60. Nasioulas G, Paraskevis D, Magiorkinis E, et al. Molecular analysis of the full-length genome of HIV type 1 subtype 1: evidence of A/G/I recombination. AIDS Res Hum Retroviruses 1999; 15 : 745-58.
61. Laukkanen T, Carr JK, Janssens W, et al. Virtually full-length subtype F and F/D recombinant HIV-1 from Africa and South America. Virology 2000; 269 : 95-104.
62. Montavon C, Bibollet-Ruche F, Robertson D, et al. The identification of a complex A/G/I/J recombinant HIV type 1 virus in various West African countries. AIDS Res Hum Retroviruses 1999; 15 : 1707-12.
63. Oelrichs RB, Workman C, Laukkanen T, et al. A novel subtype A/G/J recombinant full-length HIV type 1 genome from Burkina Faso. AIDS Res Hum Retroviruses 1998; 14 : 1495-500.
64. Piyasirisilp S, McCutchan FE, Carr JK, et al. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. J Virol 2000; 74 : 11286-95.
65. Rodenburg CM, Li Y, Trask SA, et al. Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. AIDS Res Hum Retroviruses 2001; 17 : 161-8.
66. Yang R, Kusagawa S, Zhang C, et al. Identification and characterization of a new class of human immunodeficiency virus type 1 recombinants comprised of two circulating recombinant forms, CRF07_BC and CRF08_BC, in China. J Virol 2003; 77 : 685-95.
67. McCutchan FE, Sankale JL, M'Boup S, et al. HIV type 1 circulating recombinant form CRF09∐x from west Africa combines subtypes A, F, G, and may share ancestors with CRF02_AG and Z321. AIDS Res Hum Retroviruses 2004; 20 : 819-26.
68. Koulinska IN, Ndung'u T, Mwakagile D, et al. A new human immunodeficiency virus type 1 circulating recombinant form from Tanzania. AIDS Res Hum Retroviruses 2001; 17 : 423-31.
69. Koulinska IN, Msamanga G, Mwakagile D, et al. Common genetic arrangements among human immunodeficiency virus type 1 subtype A and D recombinant genomes vertically transmitted in Tanzania. AIDS Res Hum Retroviruses 2002; 18 : 947-56.
70. Montavon C, Vergne L, Bourgeois A, et al. Identification of a new circulating recombinant form of HIV type 1, CRF11-cpx, involving subtypes A, G, J, and CRF01-AE, in Central Africa. AIDS Res Hum Retroviruses 2002; 18 : 231-6.
71. Paraskevis D, Magiorkinis M, Paparizos V, et al. Molecular characterization of a recombinant HIV type 1 isolate (A/G/E/?): unidentified regions may be derived from parental subtype E sequences. AIDS Res Hum Retroviruses 2000; 16 : 845-55.
72. Carr JK, Avila M, Gomez CM, et al. Diverse BF recombinants have spread widely since the introduction of HIV-1 into South America. AIDS 2001; 15 : F41-7.
73. Wilbe K, Casper C, Albert J, et al. Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon. AIDS Res Hum Retroviruses 2002; 18 : 849-56.
74. Delgado E, Thomson MM, Villahermosa ML, et al. Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure. J Acquir Immune Defic Syndr 2002; 29 : 536-43.
75. Tovanabutra S, Watanaveeradej V, Viputtikul K, et al. A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in Thailand. AIDS Res Hum Retroviruses 2003; 19 : 561-7.
76. Gomez-Carrillo M, Quarleri JF, Rubio AE, et al. Drug resistance testing provides evidence of the globalization of HIV type 1: a new circulating recombinant form. AIDS Res Hum Retroviruses 2004; 20 : 885-8.
77. Yang R, Xia X, Kusagawa S, et al. On-going generation of multiple forms of HIV-1 intersubtype recombinants in the Yunnan Province of China. AIDS 2002; 16 : 1401-7.
78. Mamadou S, Vidal N, Montavon C, et al. Emergence of complex and diverse CRF02-AG/CRF06-cpx recombinant HIV type 1 strains in Niger, West Africa. AIDS Res Hum Retroviruses 2003; 19 : 77-82.
79. Perez-Alvarez L, Carmona R, Munoz M, et al. High incidence of non-B and recombinant HIV-1 strains in newly diagnosed patients in Galicia, Spain: study of genotypic resistance. Antivir Ther 2003; 8 : 355-60.
80. Turner BG, Summers MF. Structural biology of HIV. J Mol Biol 1999; 285 : 1-32.
81. Peeters M, Liegeois F, Torimiro N, et al. Characterization of a highly replicative intergroup M/O human immunodeficiency virus type 1 recombinant isolated from a Cameroonian patient. J Virol 1999; 73 : 7368-75.
82. Takehisa J, Zekeng L, Ido E, et al. Human immunodeficiency virus type 1 intergroup (M/O) recombination in cameroon. J Virol 1999; 73 : 6810-20.
83. Descamps D, Collin G, Letourneur F, et al. Susceptibility of human immunodeficiency virus type 1 group O isolates to antiretroviral agents: in vitro phenotypic and genotypic analyses. J Virol 1997; 71 : 8893-8.
84. Corbet S, Muller-Trutwin MC, Versmisse P, et al. env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area. J Virol 2000; 74 : 529-34.
85. De Cock KM, Adjorlolo G, Ekpini E, et al. Epidemiology and transmission of HIV-2. Why there is no HIV-2 pandemic. J Am Med Assoc 1993; 270 : 2083-6.
86. Kanki PJ, Peeters M, Gueye-Ndiaye A. Virology of HIV-1 and HIV-2: implications for Africa. AIDS 1997; 11 (Suppl B) : S33-42.
87. Reeves JD, Doms RW. Human immunodeciency virus type 2. J Gen Virol 2002; 83 : 1253-65.
88. Pieniazek D, Ellenberger D, Janini LM, et al. Predominance of human immunodeficiency virus type 2 subtype B in Abidjan, Ivory Coast. AIDS Res Hum Retroviruses 1999; 15 : 603-8.
89. Choisy M, Woelk CH, Guegan JF, Robertson DL. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol 2004; 78 : 1962-70. Erratum in: J Virol 2004; 78 : 4381-2.
90. da Silva J. The evolutionary adaptation of HIV-1 to specific immunity. Curr HIV Res 2003; 1 : 363-71.
91. Gadkari DA, Moore D, Sheppard HW, Kulkarni SS, Mehendale SM, Bollinger RC. Transmission of genetically diverse strains of HIV-1 in Pune, India. Indian J Med Res 1998; 107 : 1-9.
92. Lole KS, Bollinger RC, Paranjape RS, et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999; 73 : 152-60.
93. Chakrabarti S, Panda S, Chatterjee A, et al. HIV-1 subtypes in injecting drug users & their non-injecting wives in Manipur, India. Indian J Med Res 2000; 111 : 189-94.
94. Choudhury S, Montano MA, Womack C, Blackard JT, Maniar JK, Saple DG, et al. Increased promoter diversity reveals a complex phylogeny of human immunodeficiency virus type 1 subtype C in India. J Hum Virol 2000; 3 : 35-43.
95. Mandal D, Jana S, Panda S, et al. Distribution of HIV-1 subtypes in female sex workers of Calcutta, India. Indian J Med Res 2000; 112 : 165-72, 165-72.
96. Halani N, Wang B, Ge YC, et al. Changing epidemiology of HIV type 1 infections in India: evidence of subtype B introduction in Bombay from a common source. AIDS Res Hum Retroviruses 2001; 17 : 637-42.
97. Shankarappa R, Chatterjee R, Learn GH, et al. Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: identification of features that distinguish subtype C sequences in India from other subtype C sequences. J Virol 2001; 75 : 10479-87.
98. Sahni AK, Prasad VV, Seth P. Genomic diversity of human immunodeficiency virus type-1 in India. Int J STD AIDS 2002; 13 : 115-8.
99. Mandal D, Jana S, Bhattacharya SK, et al. HIV type 1 subtypes circulating in eastern and northeastern regions of India. AIDS Res Hum Retroviruses 2002; 18 : 1219-27.
100. Siddappa NB, Dash PK, Mahadevan A, et al. Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India. J Clin Microbiol 2004; 42 : 2742-51.
101. Deshpande A, Recordon-Pinson P, Deshmukh R, et al. Molecular charaterization of HIV type 1 isolates from untreated patients of Mumbai (Bombay), India, and detection of rare resistance mutations. AIDS Res Hum Retroviruses 2004; 20 : 1032-5.
102. Kannangai R, Shaji RV, Ramalingam S, et al. HIV-2 subtype circulating in India (south). J Acquir Immune Defic Syndr 2003; 33 : 219-22.
103. Bhanja P, Mandal DK, Jana S, Bhattacharya SK, Chakrabarti S. Detection and characterization of HIV type 2 in Calcutta, India. AIDS Res Hum Retroviruses 2004; 20 : 101-4.
104. Harris ME, Maayan S, Kim B, et al. A cluster of HIV type 1 subtype C sequences from Ethiopia, observed in full genome analysis, is not sustained in subgenomic regions. AIDS Res Hum Retroviruses 2003; 19 : 1125-33.
105. Grez M, Dietrich U, Balfe P, et al. Genetic analysis of human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2) mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses. J Virol 1994; 68 : 2161-8.
106. Beyrer C, Razak MH, Lisam K, Chen J, Lui W, Yu XF. Overland heroin trafficking routes and HIV-1 spread in south and south-east Asia. AIDS 2000; 14 : 75-83.
107. Gupta P, Kingsley L, Sheppard HW, et al. High incidence and prevalence of HIV-1 infection in high risk population in Calcutta, India. Int J STD AIDS 2003; 14 : 463-8.
108. Ljungberg K, Hassan MS, Islam MN, et al. Subtypes A, C, G, and recombinant HIV type 1 are circulating in Bangladesh. AIDS Res Hum Retroviruses 2002; 18 : 667-70.
109. Motomura K, Kusagawa S, Kato K, et al. Emergence of new forms of human immunodeficiency virus type 1 intersubtype recombinants in central Myanmar. AIDS Res Hum Retroviruses 2000; 16 : 1831-43.
110. Tovanabutra S, Beyrer C, Sakkhachornphop S, et al. The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002. AIDS Res Hum Retroviruses 2004; 20 : 465-75.
111. Novitsky V, Smith UR, Gilbert P, et al. Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design? J Virol 2002; 76 : 5435-51.
112. Mullins JI, Nickle DC, Heath L, et al. Immunogen sequence: the fourth tier of AIDS vaccine design. Expert Rev Vaccines 2004; 3 : S151-9.
113. Parry JV, Mortimer PP, Perry KR, Pillay D, Zuckerman M, Health Protection Agency HIV Laboratory Diagnosis Forum. Towards error-free HIV diagnosis: guidelines on laboratory practice. Commun Dis Public Health 2003; 6 : 334-50.
114. Zhang M, Versalovic J. HIV update. Diagnostic tests and markers of disease progression and response to therapy. Am J Clin Pathol 2002; 118 (Suppl) : S26-32.
115. Eberle J, Loussert-Ajaka I, Brust S, et al. Diversity of the immunodominant epitope of gp41 of HIV-1 subtype O and its validity for antibody detection. J Virol Methods 1997; 67 : 85-91.
116. Koch WH, Sullivan PS, Roberts C, Francis K, Downing R, Mastro TD, et al. Evaluation of United States-licensed human immunodeficiency virus immunoassays for detection of group M viral variants. J Clin Microbiol 2001; 39 : 1017-20.
117. Rouet F, Ekouevi DK, Inwoley A, et al. Field evaluation of a rapid human immunodeficiency virus (HIV) serial serologic testing algorithm for diagnosis and differentiation of HIV type 1 (HIV-1), HIV-2, and dual HIV-1-HIV-2 infections in West African pregnant women. J Clin Microbiol 2004; 42 : 4147-53.
118. Koblavi-Deme S, Maurice C, Yavo D, et al. Sensitivity and specificity of human immunodeficiency virus rapid serologic assays and testing algorithms in an antenatal clinic in Abidjan, Ivory Coast. J Clin Microbiol 2001; 39 : 1808-12.
119. Sickinger E, Stieler M, Kaufman B, et al. Multicenter evaluation of a new, automated enzyme-linked immunoassay for detection of human immunodeficiency virus-specific antibodies and antigen. J Clin Microbiol 2004; 42 : 21-9.
120. Yang C, Dash BC, Simon F, et al. Detection of diverse variants of human immunodeficiency virus-1 groups M, N, and O and simian immunodeficiency viruses from chimpanzees by using generic pol and env primer pairs. J Infect Dis 2000; 1791-5.
121. Yang C, Pieniazek D, Owen SM, et al. Detection of phylogenetically diverse human immunodeficiency virus type 1 groups M and O from plasma by using highly sensitive and specific generic primers. J Clin Microbiol 1999; 37 : 2581-86.
122. Elbeik T, Alvord WG, Trichavaroj R, et al. Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5. J Acquir Immune Defic Syndr 2002; 29 : 330-9.
123. Elbeik T, Charlebois E, Nassos P, et al. Quantitative and cost comparison of ultrasensitive human immunodeficiency virus type 1 RNA viral load assays: Bayer bDNA quantiplex versions 3.0 and 2.0 and Roche PCR Amplicor monitor version 1.5. J Clin Microbiol 2000; 38 : 1113-20.
124. Lyamuya E, Olausson-Hansson E, Albert J, et al. Evaluation of a prototype Amplicor PCR assay for detection of human immunodeficiency virus type 1 DNA in blood samples from Tanzanian adults infected with HIV-1 subtypes A, C and D. J Clin Virol 2000; 17 : 57-63.
125. Triques K, Coste J, Perret JL, et al. Efficiencies of four versions of the AMPLICOR HIV-1 MONITOR test for quantification of different subtypes of human immunodeficiency virus type 1. J Clin Microbiol 1999; 37 : 110-6.
126. de Mendoza C, Alcami J, Sainz M, et al. Evaluation of the Abbott LCx quantitative assay for measurement of human immunodeficiency virus RNA in plasma. J Clin Microbiol 2002; 40 : 1518-21.
127. Araujo FM, Henriques IS, Monteiro FP, et al. Detection of HIV-1 subtype G using Cobas Ampliscreen test. J Clin Virol 2004; 30 : 205-6.
128. Amendola A, Bordi L, Angeletti C, et al. Comparison of LCx with other current viral load assays for detecting and quantifying human immunodeficiency virus type 1 RNA in patients infected with the circulating recombinant form A/G (CRF02). J Clin Microbiol 2004; 42 : 811-5.
129. Amendola A, Bordi L, Angeletti C, et al. Underevaluation of HIV-1 plasma viral load by a commercially available assay in a cluster of patients infected with HIV-1 A/G circulating recombinant form (CRF02). J Acquir Immune Defic Syndr 2002; 31 : 488-94.
130. Gottesman BS, Grosman Z, Lorber M, et al. Measurement of HIV RNA in patients infected by subtype C by assays optimized for subtype B results in an underestimation of the viral load. J Med Virol 2004; 73 : 167-71.
131. Shafer RW. Genotypic testing for human immunodeficiency virus type 1 drug resistance. Clin Microbiol Rev 2002; 15 : 247-77.
132. Cheung PK, Wynhoven B, Harrigan PR. Which HIV-1 drug resistance mutations are common in clinical practice? AIDS Rev 2004; 6 : 107-16.
133. Parikh U, Calef C, Larder B, Schinazi R, Mellor JW. Mutations in retroviral genes associated with drug resistance. In: Kuiken C, Foley B, Freed E, et al, editors. HIV Sequence Compendium 2002. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, LA-UR number 03-3564, 2002 : 94-183.
134. Kantor R, Machekano R, Gonzales MJ, et al. Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs. Nucleic Acids Res 2001; 29 : 296-9.
135. Soriano V, de Mendoza C. Genetic mechanisms of resistance to NRTI and NNRTI. HIV Clin Trials 2002: 3 : 237-48.
136. Soriano V, de Mendoza C. Genetic mechanisms of resistance to protease inhibitors and entry inhibitors. HIV Clin Trials 2002; 3 : 249-57.
137. Holguin A, Soriano V. Resistance to antiretroviral agents in individuals with HIV-1 non-B subtypes. HIV Clin Trials 2002; 3 : 403-11.
138. Wainberg MA. HIV-1 subtype distribution and the problem of drug resistance. AIDS 2004; 18 (Suppl 3) : S63-8.
139. Kantor R, Katzenstein D. Drug resistance in non-subtype B HIV-1. J Clin Virol 2004; 29 : 152-9.
140. Frater AJ, Dunn DT, Beardall AJ, Ariyoshi K, Clarke JR, McClure MO, et al. Comparative response of African HIV-1-infected individuals to highly active antiretroviral therapy. AIDS 2002; 16 : 1139-46.
141. Vergne L, Peeters M, Mpoudi-Ngole E, et al. Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B HIV type 1 strains: evidence of many minor drug resistance mutations in treatment-naïve patients. J Clin Microbiol 2000; 38 : 3919-25.
142. Erickson JW, Gulnik SV, Markowitz M. Protease inhibitors: resistance, cross-resistance, fitness and the choice of initial and salvage therapies. AIDS 1999; 13 (Suppl A) : S189-204.
143. Pieniazek D, Rayfield M, Hu DJ, et al. Protease sequences from HIV-1 group M subtypes A-H reveal distinct amino acid mutation patterns associated with protease resistance in protease inhibitor-naive individuals worldwide. HIV Variant Working Group. AIDS 2000; 14 : 1489-95.
144. Velazquez-Campoy A, Todd MJ, Vega S, et al. Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes. Proc Natl Acad Sci USA 2001; 98 : 6062-7.
145. Velazquez-Campoy A, Vega S, Freire E. Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes. Biochemistry 2002; 41 : 8613-9.
146. Descamps D, Apetrei C, Collin G, Damond F, Simon F, Brun-Vezinet F. Naturally occurring decreased susceptibility of HIV-1 subtype G to protease inhibitors. AIDS 1998; 12 : 1109-11.
147. Vicente AC, Agwale SM, Otsuki K, Njouku OM, Jelpe D, Idoko JA, et al. Genetic variability of HIV-1 protease from Nigeria and correlation with protease inhibitors drug resistance. Virus Genes 2001; 22 : 181-6.
148. Maguire M, Shortino D, Klein A, et al. Emergence of resistance to protease inhibitor amprenavir in human immunode?ciency virus type 1-infected patients: selection of four alternative viral protease genotypes and in?uence of viral susceptibility to coadministered reverse transcriptase nucleoside inhibitors. Antimicrob Agents Chemother 2002; 46 : 731-8.
149. Deeks SG. Nonnucleoside Reverse Transcriptase Inhibitor Resistance. J Acquir Immune Defic Syndr 2001; 26 : S25-S33.
150. Clevenbergh P, Cua E, Dam E, et al. Prevalence of nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance-associated mutations and polymorphisms in NNRTI-naive HIV-infected patients. HIV Clin Trials 2002; 3 : 36-44.
151. Kaufmann GR, Suzuki K, Cunningham P, Mukaide M, Kondo M, Imai M, et al. Impact of HIV type 1 protease, reverse transcriptase, cleavage site, and p6 mutations on the virological response to quadruple therapy with saquinavir, ritonavir, and two nucleoside analogs. AIDS Res Hum Retroviruses 2001; 17 : 487-97.
152. Hu DJ, Vanichseni S, Mastro TD, et al. Viral load differences in early infection with two HIV-1 subtypes. AIDS 2001; 15 : 683-91.
153. Tscherning C, Alaeus A, Fredriksson R, et al. Differences in chemokine coreceptor usage between genetic subtypes of HIV-1. Virology 1998; 241 : 181-8.
154. Jeeninga RE, Hoogenkamp M, Armand-Ugon M, et al. Functional differences between the long terminal repeat transcriptional promoters of human immunodeficiency virus type 1 subtypes A through G. J Virol 2000; 74 : 3740-51.
155. Kanki PJ, Hamel DJ, Sankale JL, et al. Human immunodeficiency virus type 1 subtypes differ in disease progression. J Infect Dis 1999; 179 : 68-73.
156. Renjifo B, Fawzi W, Mwakagile D, et al. Differences in perinatal transmission among human immunodeficiency virus type 1 genotypes. J Hum Virol 2001; 4 : 16-25.
157. Yang C, Li M, Newman RD, et al. Genetic diversity of HIV-1 in western Kenya: subtype-specific differences in mother-to-child transmission. AIDS 2003; 17 : 1667-74.
158. Kaleebu P, French N, Mahe C, et al. Effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression in a large cohort of HIV-1-positive persons in Uganda. J Infect Dis 2002: 185 : 1244-50.
159. Weisman Z, Kalinkovich A, Borkow G, et al. Infection by different HIV-1 subtypes (B and C) results in a similar immune activation profile despite distinct immune backgrounds. J Acquir Immune Defic Syndr 1999; 21 : 157-63.
160. Alaeus A, Lidman K, Bjorkman A, et al. Similar rate of disease progression among individuals infected with HIV-1 genetic subtypes A-D. AIDS 1999; 13 : 901-7.
161. Amornkul PN, Tansuphasawadikul S, Limpakarnjanarat K et al. Clinical disease associated with HIV-1 subtype B′ and E infection among 2104 patients in Thailand. AIDS 1999; 13 : 1963-9.
162. Laurent C, Bourgeois A, Faye MA, et al. No difference in clinical progression between patients infected with the predominant human immunodeficiency virus type 1 circulating recombinant form (CRF) 02_AG strain and patients not infected with CRF02_AG, in Western and West-Central Africa: a four-year prospective multicenter study. J Infect Dis 2002; 186 : 486-92.
163. Galai N, Kalinkovich A, Burstein R, et al. African HIV-1 subtype C and rate of progression among Ethiopian immigrants in Israel. Lancet 1997; 349 : 180-1.
164. van der GG, Nyambi PN, Beirnaert E, et al. Genetic variation of HIV type 1: relevance of interclade variation to vaccine development. AIDS Res Hum Retroviruses 1998; 14 (Suppl 3) : S211-21.
165. Gaschen B, Taylor J, Yusim K, et al. Diversity considerations in HIV-1 vaccine selection. Science 2002; 296 : 2354-60.
166. Garber DA, Silvestri G, Feinberg MB. Prospects for an AIDS vaccine: three big questions, no easy answers. Lancet Infect Dis 2004; 4 : 397-413.
167. Estcourt MJ, McMichael AJ, Hanke T. DNA vaccines against human immunodeficiency virus type 1. Immunol Rev 2004; 199 : 144-55.
168. Soudeyns H, Pantaleo G. The moving target: mechanisms of HIV persistence during primary infection. Immunol Today 1999; 20 : 446-50.
169. Mascola JR, Montefiori DC. HIV-1: nature's master of disguise. Nat Med 2003; 9 : 393-4.
170. Klenerman P, Wu Y, Phillips R. HIV: current opinion in escapology. Curr Opin Microbiol 2002; 5 : 408-13.
171. Goulder PJ, Watkins DI. HIV and SIV CTL escape: implications for vaccine design. Nat Rev Immunol 2004; 4 : 630-40.
172. Pantaleo G, Koup RA. Correlates of immune protection in HIV-1 infection: what we know, what we don't know, what we should know. Nat Med 2004; 10 : 806-10.
173. Malkevitch NV, Robert-Guroff M. A call for replicating vector prime-protein boost strategies in HIV vaccine design. Expert Rev Vaccines 2004; 3 : S105-17.
174. Esparza J, Osmanov S. HIV vaccines: a global perspective. Curr Mol Med 2003; 3 : 183-93.
175. Stratov I, DeRose R, Purcell DF, et al. Vaccines and vaccine strategies against HIV. Curr Drug Targets 2004; 5 : 71-88.
176. Gao F, Korber BT, Weaver E, et al. Centralized immunogens as a vaccine strategy to overcome HIV-1 diversity. Expert Rev Vaccines 2004; 3 : S161-8.
177. Nunberg JH, Follis KE, Trahey M, et al. Turning a corner on HIV neutralization? Microbes Infect 2000; 2 : 213-21.
178. Zolla-Pazner S, Gorny MK, Nyambi PN, et al. Immunotyping of human immunodeficiency virus type 1 (HIV): an approach to immunologic classification of HIV. J Virol 1999; 73 : 4042-51.
179. Mascola JR, Louwagie J, McCutchan FE, et al. Two antigenically distinct subtypes of human immunodeficiency virus type 1: viral genotype predicts neutralization serotype. J Infect Dis 1994; 169 : 48-54.
180. Lee SA, Orque R, Escarpe PA, et al. Vaccine-induced antibodies to the native, oligomeric envelope glycoproteins of primary HIV-1 isolates. Vaccine 2001; 20 : 563-76.
181. Pitisuttithum P, Berman PW, Phonrat B, et al. Phase I/II Study of a Candidate Vaccine Designed Against the B and E Subtypes of HIV-1. J Acquir Immune Defic Syndr 2004; 37 : 1160-5.
182. Zhang YJ, Fracasso C, Fiore JR, et al. Augmented serum neutralizing activity against primary human immunodeficiency virus type 1 (HIV-1) isolates in two groups of HIV-1-infected long-term nonprogressors. J Infect Dis 1997; 176 : 1180-7.
183. Wei X, Decker JM, Wang S, et al. Antibody neutralization and escape by HIV-1. Nature 2003; 422 : 307-12.
184. Derdeyn CA, Decker JM, Bibollet-Ruche F, et al. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004; 303 : 2019-22.
185. Price DA, Meier UC, Klenerman P, Purbhoo MA, Phillips RE, Sewell AK. The influence of antigenic variation on cytotoxic T lymphocyte responses in HIV-1 infection. J Mol Med 1998; 76 : 699-708.
186. Betts MR, Krowka J, Santamaria C, et al. Cross-clade human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte responses in HIV-infected Zambians. J Virol 1997; 71 : 8908-11.
187. Dorrell L, Dong T, Ogg GS, et al. Distinct recognition of non-clade B human immunodeficiency virus type 1 epitopes by cytotoxic T lymphocytes generated from donors infected in Africa. J Virol 1999; 73 : 1708-14.
188. Thakar MR, Patke D, Lakhashe SK, et al. Consistent subtype-specific anti-HIV type 1 T lymphocyte responses in Indian subjects recently infected with HIV type 1. AIDS Res Hum Retroviruses 2002; 18 : 1389-93.
189. Cao H, Kanki P, Sankale JL, et al. Cytotoxic T-lymphocyte cross-reactivity among different human immunodeficiency virus type 1 clades: implications for vaccine development. J Virol 1997; 71 : 8615-23.
190. McAdam S, Kaleebu P, Krausa P, et al. Cross-clade recognition of p55 by cytotoxic T lymphocytes in HIV-1 infection. AIDS 1998; 12 : 571-9.
191. Dorrell L, Willcox BE, Jones EY, et al. Cytotoxic T lymphocytes recognize structurally diverse, clade-specific and cross-reactive peptides in human immunodeficiency virus type-1 gag through HLA-B53. Eur J Immunol 2001; 31 : 1747-56.
192. Fukada K, Tomiyama H, Wasi C, et al. Cytotoxic T-cell recognition of HIV-1 cross-clade and clade-specific epitopes in HIV-1-infected Thai and Japanese patients. AIDS 2002; 16 : 701-11.
193. Ferrari G, Currier JR, Harris ME, et al. HLA-A and -B allele expression and ability to develop anti-Gag cross-clade responses in subtype C HIV-1-infected Ethiopians. Hum Immunol 2004; 65 : 648-59.
194. Masemola AM, Mashishi TN, Khoury G, et al. Novel and promiscuous CTL epitopes in conserved regions of Gag targeted by individuals with early subtype C HIV type 1 infection from Southern Africa. J Immunol 2004; 173 : 4607-17.
195. McKinney DM, Skvoretz R, Livingston BD, et al. Recognition of variant HIV-1 epitopes from diverse viral subtypes by vaccine-induced CTL. J Immunol 2004; 173 : 1941-50.
196. De Groot AS, Jesdale B, Martin W, et al. Mapping cross-clade HIV-1 vaccine epitopes using a bioinformatics approach. Vaccine 2003; 21 : 4486-504.
197. Moore CB, John M, James IR, Christiansen FT, Witt CS, Mallal SA. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 2002; 296 : 1439-43.1.
198. McMichael A, Klenerman P. HIV/AIDS. HLA leaves its footprints on HIV. Science 2002; 296 : 1410-1.
199. Walker BD, Korber BT. Immune control of HIV: the obstacles of HLA and viral diversity. Nat Immunol 2001; 2 : 473-5.
200. Excler JL. AIDS vaccine development: perspectives, challenges & hopes. Indian J Med Res 2005; 121 : 568-81.
201. Ball SC, Abraha A, Collins KR, et al. Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes B and C. J Virol 2003; 77 : 1021-38.
202. Quinones-Mateu ME, Ball SC, Marozsan AJ, et al. A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression. J Virol 2000; 74 : 9222-3.
203. Hunt G, Tiemessen CT. Occurrence of additional NF-kappaB-binding motifs in the long terminal repeat region of South African HIV type 1 subtype C isolates. AIDS Res Hum Retroviruses 2000; 16 : 305-6.
204. Montano MA, Nixon CP, Ndung'u T, et al. Elevated tumor necrosis factor-alpha activation of human immunodeficiency virus type 1 subtype C in Southern Africa is associated with an NF-kappaB enhancer gain-of-function. J Infect Dis 2000; 181 : 76-81.
205. Roof P, Ricci M, Genin P, et al. Differential regulation of HIV-1 clade-specific B, C, and E long terminal repeats by NF-kappaB and the Tat transactivator. Virology 2002; 296 : 77-83.
206. Dandekar DH, Ganesh KN, Mitra D. HIV-1 Tat directly binds to NFkappaB enhancer sequence: role in viral and cellular gene expression. Nucleic Acids Res 2004; 32 : 1270-8.
207. van Opijnen T, Jeeninga RE, Boerlijst MC, et al. Human immunodeficiency virus type 1 subtypes have a distinct long terminal repeat that determines the replication rate in a host-cell-specific manner. J Virol 2004; 78 : 3675-83.
208. Ranga U, Shankarappa R, Siddappa NB, et al. Tat protein of human immunodeficiency virus type 1 subtype C strains is a defective chemokine. J Virol 2004; 78 : 2586-90.
209. De Oliveira T, Engelbrecht S, Janse VR, et al. Variability at human immunodeficiency virus type 1 subtype C protease cleavage sites: an indication of viral fitness? J Virol 2003; 77 : 9422-30.
210. Gonzalez LM, Brindeiro RM, Aguiar RS, et al. Impact of nelfinavir resistance mutations on in vitro phenotype, fitness, and replication capacity of human immunodeficiency virus type 1 with subtype B and C proteases. Antimicrob Agents Chemother 2004; 48 : 3552-5.
211. Cecilia D, Kulkarni SS, Tripathy SP, et al. Absence of coreceptor switch with disease progression in human immunodeficiency virus infections in India. Virology 2000; 271 : 253-8.
212. Xiao L, Rudolph DL, Owen SM, et al. Adaptation to promiscuous usage of CC and CXC-chemokine coreceptors in vivo correlates with HIV-1 disease progression, AIDS 1998; 12 : F137-43.
213. Cilliers T, Nhlapo J, Coetzer M, et al. The CCR5 and CXCR4 coreceptors are both used by human immunodeficiency virus type 1 primary isolates from subtype C. J Virol 2003; 77 : 4449-56.
214. Pollakis G, Abebe A, Kliphuis A, et al. Phenotypic and genotypic comparisons of CCR5- and CXCR4-tropic human immunodeficiency virus type 1 biological clones isolated from subtype C-infected individuals. J Virol 2004; 78 : 2841-52.
215. Johnston ER, Zijenah LS, Mutetwa S, et al. High frequency of syncytium-inducing and CXCR4-tropic viruses among human immunodeficiency virus type 1 subtype C-infected patients receiving antiretroviral treatment. J Virol 2003; 77: 7682-8.