Selective pressures of human immunodeficiency virus type 1 (HIV-1) during pediatric infection

Infection, Genetics and Evolution

Volumn 7, Issue 6, 2007, Pages 694-707

  Leal, Élcio ^a   Janini, Mario ^a   Diaz, Ricardo S ^a  

^a FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

HIV 1; Pediatric infection; Population genetics; Positive selection; Viral evolution

Indexed keywords

GAG PROTEIN; POL PROTEIN; VIRUS ENVELOPE PROTEIN; VIRUS PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CHILD; CLINICAL FEATURE; CODON; CYTOTOXIC T LYMPHOCYTE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; IMMUNE RESPONSE; MAXIMUM LIKELIHOOD METHOD; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; VERTICAL TRANSMISSION; VIRUS CELL INTERACTION; VIRUS LOAD; VIRUS TRANSMISSION;

ADULT; AGE FACTORS; CHILD; CHILD, PRESCHOOL; CODON; FEMALE; GENE PRODUCTS, ENV; GENES, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; INFANT; INFANT, NEWBORN; PHYLOGENY; VARIATION (GENETICS);

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 35448977610     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2007.07.008     Document Type: Article

References (71)

1. Adkins B. T-cell function in newborn mice and humans. Immunol. Today 20 (1999) 330-335
2. Bhattacharya T., Daniels M., Hecherman D., Foley B., Frahm N., Kadie C., Carlson J., Yusim K., MacMahon B., Gaschen B., Mallal S., Mullins J.I., Nickle D.C., Herbeck J., Rousseau C., Learn G.H., Miura T., Brander C., Walker B., and Korber B. Founder effect in the assessment of HIV polymorphisms and HLA allele associations. Science 315 (2007) 1583-1586
3. Bebenek K., Abbotts J., Roberts J.D., Wilson S.H., and Kunkel T.A. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J. Biol. Chem. 264 (1989) 16948-16956
4. Betts M.R., Ambrozak D.R., Douek D.C., Bonhoeffer S., Brenchley J.M., Casazza J.P., Koup R.A., and Picker L.J. Analysis of total human immunodeficiency virus (HIV)-specific CD4(+) and CD8(+) T-cell responses: relationship to viral load in untreated HIV infection. J. Virol. 75 (2001) 11983-11991
5. Borrow P., Lewicki H., Hahn B.H., Shaw G.M., and Oldstone M.B. Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection. J. Virol. 68 (1994) 6103-6110
6. Borrow P., Lewicki H., Wei X., Horwitz M.S., Peffer N., Meyers H., Nelson J.A., Gairin J.E., Hahn B.H., Oldstone M.B., and Shaw G.M. Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3 (1997) 205-211
7. Buseyne F., Chaix M.L., Fleury B., Manigard O., Burgard M., Blanche S., Rouzioux C., and Riviere Y. Cross-clade-specific cytotoxic T lymphocytes in HIV-1-infected children. Virology 250 (1998) 316-324
8. Chandwani R., Jordan K.A., Shacklett B.L., Papasavvas E., Montaner L.J., Rosenberg M.G., Nixon D.F., and Sandberg J.K. Limited magnitude and breadth in the HLA-A2-restricted CD8 T-Cell response to Nef in children with vertically acquired HIV-1 infection. Scand. J. Immunol. 59 (2004) 109-114
9. Cheynier R., Langlade-Demoyen P., Marescot M.R., Blanche S., Blondin G., Wain-Hobson S., Griscelli C., Vilmer E., and Plata F. Cytotoxic T lymphocyte responses in the peripheral blood of children born to human immunodeficiency virus-1-infected mothers. Eur. J. Immunol. 22 (1992) 2211-2217
10. Choe H., Farzan M., Sun Y., Sullivan N., Rollins B., Ponath P.D., Wu L., Mackay C.R., LaRosa G., Newman W., Gerard N., Gerard C., and Sodroski J. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 85 (1996) 1135-1148
11. Choisy M., Woelk C.H., Guegan J.F., and Robertson D.L. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J. Virol. 78 (2004) 1962-1970
12. Dickover R., Garratty E., Yusim K., Miller C., Korber B., and Bryson Y. Role of maternal autologous neutralizing antibody in selective perinatal transmission of human immunodeficiency virus type 1 escape variants. J. Virol. 80 (2006) 6525-6533
13. Draenert R., Le Gall S., Pfafferott K.J., Leslie A.J., Chetty P., Brander C., Holmes E.C., Chang S.C., Feeney M.E., Addo M.M., Ruiz L., Ramduth D., Jeena P., Altfeld M., Thomas S., Tang Y., Verrill C.L., Dixon C., Prado J.G., Kiepiela P., Martinez-Picado J., Walker B.D., and Goulder P.J. Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. J. Exp. Med. 199 (2004) 905-915
14. Drummond A., Pybus O.G., and Rambaut A. Inference of viral evolutionary rates from molecular sequences. Adv. Parasitol. 54 (2003) 331-358
15. Edwards C.T., Holmes E.C., Wilson D.J., Viscidi R.P., Abrams E.J., Phillips R.E., and Drummond A.J. Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol. Biol. 6 (2006) 28
16. Feeney M.E., Roosevelt K.A., Tang Y., Pfafferott K.J., McIntosh K., Burchett S.K., Mao C., Walker B.D., and Goulder P.J. Comprehensive screening reveals strong and broadly directed human immunodeficiency virus type 1-specific CD8 responses in perinatally infected children. J. Virol. 77 (2003) 7492-7501
17. Frost S.D., Wrin T., Smith D.M., Pond S.L.K., Liu Y., Paxinos E., Chappey C., Galovich J., Beauchaine J., Petropoulos C.J., Little S.J., and Richman D.D. Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 18514-18519
18. Ganeshan S., Dickover R.E., Korber B.T., Bryson Y.J., and Wolinsky S.M. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virol. 71 (1997) 663-677
19. Goulder P.J., Pasquier C., Holmes E.C., Liang B., Tang Y., Izopet J., Saune K., Rosenberg E.S., Burchett S.K., McIntosh K., Barnardo M., Bunce M., Walker B.D., Brander C., and Phillips R.E. Mother-to-child transmission of HIV infection and CTL escape through HLA-A2-SLYNTVATL epitope sequence variation. Immunol. Lett. 79 (2001) 109-116
20. Grenfell B.T., Pybus O.G., Gog J.R., Wood J.L., Daly J.M., Mumford J.A., and Holmes E.C. Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303 (2004) 327-332
21. Harrer T., Harrer E., Kalams S.A., Barbosa P., Trocha A., Johnson R.P., Elbeik T., Feinberg M.B., Buchbinder S.P., and Walker B.D. Cytotoxic T lymphocytes in asymptomatic long-term nonprogressing HIV-1 infection. Breadth and specificity of the response and relation to in vivo viral quasispecies in a person with prolonged infection and low viral load. J. Immunol. 156 (1996) 2616-2623
22. Herbeck J.T., Nickle D.C., Learn G.H., Gottlieb G.S., Curlin M.E., Heath L., and Mullins J.I. Human Immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. J. Virol. 80 (2006) 1637-1644
23. Holmes E.C., Zhang L.Q., Simmonds P., Ludlam C.A., and Brown A.J. Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. U.S.A. 89 (1992) 4835-4839
24. Huang C.C., Tang M., Zhang M.Y., Majeed S., Montabana E., Stanfield R.L., Dimitrov D.S., Korber B., Sodroski J., Wilson I.A., Wyatt R., and Kwong P.D. Structure of a V3-containing HIV-1 gp120 core. Science 310 (2005) 1025-1028
25. Jamieson B.D., Yang O.O., Hultin L., Hausner M.A., Hultin P., Matud J., Kunstman K., Killian S., Altman J., Kommander K., Korber B., Giorgi J., and Wolinsky S. Epitope escape mutation and decay of human immunodeficiency virus type 1-specific CTL responses. J. Immunol. 171 (2003) 5372-5379
26. Kalams S.A., Buchbinder S.P., Rosenberg E.S., Billingsley J.M., Colbert D.S., Jones N.G., Shea A.K., Trocha A.K., and Walker B.D. Association between virus-specific cytotoxic T-lymphocyte and helper responses in human immunodeficiency virus type 1 infection. J. Virol. 73 (1999) 6715-6720
27. Kelleher A.D., Long C., Holmes E.C., Allen R.L., Wilson J., Conlon C., Workman C., Shaunak S., Olson K., Goulder P., Brander C., Ogg G., Sullivan J.S., Dyer W., Jones I., McMichael A.J., Rowland-Jones S., and Phillips R.E. Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses. J. Exp. Med. 193 (2001) 375-386
28. Koup R.A., Safrit J.T., Cao Y., Andrews C.A., McLeod G., Borkowsky W., Farthing C., and Ho D.D. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J. Virol. 68 (1994) 4650-4655
29. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5 (2004) 150-163
30. Leal E.S., Holmes E.C., and Zanotto P.M. Distinct patterns of natural selection in the reverse transcriptase gene of HIV-1 in the presence and absence of antiretroviral therapy. Virology 325 (2004) 181-191
31. Leslie A.J., Pfafferott K.J., Chetty P., Draenert R., Addo M.M., Feeney M., Tang Y., Holmes E.C., Allen T., Prado J.G., Altfeld M., Brander C., Dixon C., Ramduth D., Jeena P., Thomas S.A., St John A., Roach T.A., Kupfer B., Luzzi G., Edwards A., Taylor G., Lyall H., Tudor-Williams G., Novelli V., Martinez-Picado J., Kiepiela P., Walker B.D., and Goulder P.J. HIV evolution: CTL escape mutation and reversion after transmission. Nat. Med. 10 (2004) 282-289
32. Leslie A., Kavanagh D., Honeyborne I., Pfafferott K., Edwards C., Pillay T., Hilton L., Thobakgale C., Ramduth D., Draenert R., Le Gall S., Luzzi G., Edwards A., Brander C., Sewell A.K., Moore S., Mullins J., Moore C., Mallal S., Bhardwaj N., Yusim K., Phillips R., Klenerman P., Korber B., Kiepiela P., Walker B., and Goulder P. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J. Exp. Med. 201 (2005) 891-902
33. Li B., Gladden A.D., Altfeld M., Kaldor J.M., Cooper D.A., Kelleher A.D., and Allen T.M. Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution. J. Virol. 81 (2007) 193-201
34. Lusso P., Earl P.L., Sironi F., Santoro F., Ripamonti C., Scarlatti G., Longhi R., Berger E.A., and Burastero S.E. Cryptic nature of a conserved, CD4-inducible V3 loop neutralization epitope in the native envelope glycoprotein oligomer of CCR5-restricted, but not CXCR4-using, primary human immunodeficiency virus type 1 strains. J. Virol. 79 (2005) 6957-6968
35. Luzuriaga K., Holmes D., Hereema A., Wong J., Panicali D.L., and Sullivan J.L. HIV-1-specific cytotoxic T lymphocyte responses in the first year of life. J. Immunol. 154 (1995) 433-443
36. Mansky L.M., and Temin H.M. Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol. 69 (1995) 5087-5094
37. McFarland E.J., Harding P.A., Luckey D., Conway B., Young R.K., and Kuritzkes D.R. High frequency of Gag- and envelope-specific cytotoxic T lymphocyte precursors in children with vertically acquired human immunodeficiency virus type 1 infection. J. Infect. Dis. 170 (1994) 766-774
38. McIntosh K., Shevitz A., Zaknun D., Kornegay J., Chatis P., Karthas N., and Burchett S.K. Age- and time-related changes in extracellular viral load in children vertically infected by human immunodeficiency virus. Pediatr. Infect. Dis. J. 15 (1996) 1087-1091
39. McMichael A.J., and Rowland-Jones S.L. Cellular immune responses to HIV. Nature 410 (2001) 980-987
40. Mofenson L.M., Korelitz J., Meyer III W.A., Bethel J., Rich K., Pahwa S., Moye Jr. J., Nugent R., and Read J. The relationship between serum human immunodeficiency virus type 1 (HIV-1) RNA level, CD4 lymphocyte percent, and long-term mortality risk in HIV-1-infected children. National Institute of Child Health and Human Development Intravenous Immunoglobulin Clinical Trial Study Group. J. Infect. Dis. 175 (1997) 1029-1038
41. Moore C.B., John M., James I.R., Christiansen F.T., Witt C.S., and Mallal S.A. Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science 296 (2002) 1439-1443
42. Muse S.V., and Gaut B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11 (1994) 715-724
43. Musey L., Hu Y., Eckert L., Christensen M., Karchmer T., and McElrath M.J. HIV-1 induces cytotoxic T lymphocytes in the cervix of infected women. J. Exp. Med. 185 (1997) 293-303
44. Nielsen R., and Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
45. Nowak M. HIV mutation rate. Nature 347 (1990) 522
46. Ogg G.S., Jin X., Bonhoeffer S., Dunbar P.R., Nowak M.A., Monard S., Segal J.P., Cao Y., Rowland-Jones S.L., Cerundolo V., Hurley A., Markowitz M., Ho D.D., Nixon D.F., and McMichael A.J. Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. Science 279 (1998) 2103-2106
47. Perelson A.S., Neumann A.U., Markowitz M., Leonard J.M., and Ho D.D. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271 (1996) 1582-1586
48. Pillay T., and Phillips R.E. Adaptive evolution in perinatal HIV-1. Best Pract. Res. Clin. Obstet. Gynaecol. 19 (2005) 211-229
49. Pond S.L., Frost S.D., Grossman Z., Gravenor M.B., Richman D.D., and Brown A.J. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput. Biol. 2 (2006) e62
50. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
51. Price D.A., Goulder P.J., Klenerman P., Sewell A.K., Easterbrook P.J., Troop M., Bangham C.R., and Phillips R.E. Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 1890-1895
52. Ross H.A., and Rodrigo A.G. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J. Virol. 76 (2002) 11715-11720
53. Sabbaj S., Edwards B.H., Ghosh M.K., Semrau K., Cheelo S., Thea D.M., Kuhn L., Ritter G.D., Mulligan M.J., Goepfert P.A., and Aldrovandi G.M. Human immunodeficiency virus-specific CD8(+) T cells in human breast milk. J. Virol. 76 (2002) 7365-7373
54. Sandberg J.K., Fast N.M., Jordan K.A., Furlan S.N., Barbour J.D., Fennelly G., Dobroszycki J., Spiegel H.M., Wiznia A., Rosenberg M.G., and Nixon D.F. HIV-specific CD8+ T cell function in children with vertically acquired HIV-1 infection is critically influenced by age and the state of the CD4+ T cell compartment. J. Immunol. 170 (2003) 4403-4410
55. Schmitz J.E., Kuroda M.J., Santra S., Sasseville V.G., Simon M.A., Lifton M.A., Racz P., Tenner-Racz K., Dalesandro M., Scallon B.J., Ghrayeb J., Forman M.A., Montefiori D.C., Rieber E.P., Letvin N.L., and Reimann K.A. Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes. Science 283 (1999) 857-860
56. Scott Z.A., Chadwick E.G., Gibson L.L., Catalina M.D., McManus M.M., Yogev R., Palumbo P., Sullivan J.L., Britto P., Gay H., and Luzuriaga K. Infrequent detection of HIV-1-specific, but not cytomegalovirus-specific, CD8(+) T cell responses in young HIV-1-infected infants. J. Immunol. 167 (2001) 7134-7140
57. Shankarappa R., Margolick J.B., Gange S.J., Rodrigo A.G., Upchurch D., Farzadegan H., Gupta P., Rinaldo C.R., Learn G.H., He X., Huang X.L., and Mullins J.I. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73 (1999) 10489-10502
58. Shearer W.T., Quinn T.C., LaRussa P., Lew J.F., Mofenson L., Almy S., Rich K., Handelsman E., Diaz C., Pagano M., Smeriglio V., and Kalish L.A. Viral load and disease progression in infants infected with human immunodeficiency virus type 1. Women and Infants Transmission Study Group. N. Engl. J. Med. 336 (1997) 1337-1342
59. Strunnikova N., Ray S.C., Livingston R.A., Rubalcaba E., and Viscidi R.P. Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression. J. Virol. 69 (1995) 7548-7558
60. Suzuki Y., and Gojobori T. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16 (1999) 1315-1328
61. Swofford D.L. PAUP*. Plylogenetic Analysis Using Parsimony (*and Other Methods) (2002), Sinauer Associates, Sunderlands, Massachusetts
62. Travers S.A.A., O'Connel M.J., McCormack G.P., and McInerney J.O. Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. J. Virol. 79 (2005) 1836-1841
63. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
64. Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20 (2003) 1318-1325
65. Wilson C.C., Brown R.C., Korber B.T., Wilkes B.M., Ruhl D.J., Sakamoto D., Kunstman K., Luzuriaga K., Hanson I.C., Widmayer S.M., Wiznia A., Clapp S., Ammann A.J., Koup R.A., Wolinsky S.M., and Walker B.D. Frequent detection of escape from cytotoxic T-lymphocyte recognition in perinatal human immunodeficiency virus (HIV) type 1 transmission: the ariel project for the prevention of transmission of HIV from mother to infant. J. Virol. 73 (1999) 3975-3985
66. Wolinsky S.M., Wike C.M., Korber B.T., Hutto C., Parks W.P., Rosenblum L.L., Kunstman K.J., Furtado M.R., and Munoz J.L. Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science 255 (1992) 1134-1137
67. Wolinsky S.M., Korber B.T., Neumann A.U., Daniels M., Kunstman K.J., Whetsell A.J., Furtado M.R., Cao Y., Ho D.D., and Safrit J.T. Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272 (1996) 537-542
68. Woolhouse M.E., Webster J.P., Domingo E., Charlesworth B., and Levin B.R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32 (2002) 569-577
69. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
70. Yang Z., and Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19 (2002) 908-917
71. Yang W., Bielawski J.P., and Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57 (2003) 212-221