Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California

Journal of Infectious Diseases

Volumn 205, Issue 10, 2012, Pages 1529-1533

  Mehta, Sanjay R ^a   Kosakovsky Pond, Sergei L ^a   Young, Jason A ^a   Richman, Douglas ^a,b   Little, Susan ^a   Smith, Davey M ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DRB1 ANTIGEN; POL PROTEIN;

ALLELE; ARTICLE; CONTROLLED STUDY; FEMALE; GENE CLUSTER; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC DISTANCE; GENOTYPE; HLA SYSTEM; HOMOZYGOSITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INFECTION RISK; MAJOR CLINICAL STUDY; MALE; MALE HOMOSEXUAL; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; UNITED STATES; VIRUS MUTATION; VIRUS TRANSMISSION; VIRUS VIRULENCE;

ALLELES; CALIFORNIA; CLUSTER ANALYSIS; COHORT STUDIES; DEMOGRAPHY; FEMALE; GENES, POL; HIV INFECTIONS; HIV-1; HLA-A ANTIGENS; HLA-B ANTIGENS; HOMOSEXUALITY, MALE; HOMOZYGOTE; HUMANS; IMMUNE EVASION; MALE; MUTATION; PHYLOGENY; RISK FACTORS;

EID: 84860376773     PISSN: 00221899     EISSN: None     Source Type: Journal    
DOI: 10.1093/infdis/jis231     Document Type: Article

References (35)

1. McMichael AJ, Borrow P, Tomaras GD, Goonetilleke N, Haynes BF. The immune response during acute HIV-1 infection: clues for vaccine development. Nat Rev Immunol Jan; 10:11-23.
2. Manosuthi W, Butler DM, Perez-Santiago J, et al. Protease polymorphisms in HIV-1 subtype CRF01AE represent selection by antiretroviral therapy and host immune pressure. AIDS Jan 28; 24:411-6.
3. Gesprasert G, Wichukchinda N, Mori M, et al. HLA-associated immune pressure on Gag protein in CRF01AE-infected individuals and its association with plasma viral load. PLoS One 2010; 5:e11179.
4. Matthews PC, Leslie AJ, Katzourakis A, et al. HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering. J Virol 2009; 83:4605-15.
5. McMichael A, Klenerman P. HIV/AIDS. HLA leaves its footprints on HIV. Science 2002; 296:1410-1.
6. Shiina T, Hosomichi K, Inoko H, Kulski JK. The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet 2009; 54:15-39.
7. Mackelprang RD, John-Stewart G, Carrington M, et al. Maternal HLA homozygosity and mother-child HLA concordance increase the risk of vertical transmission of HIV-1. J Infect Dis 2008; 197:1156-61.
8. Tang J, Costello C, Keet IP, et al. HLA class I homozygosity accelerates disease progression in human immunodeficiency virus type 1 infection. AIDS Res Hum Retroviruses 1999; 15:317-24.
9. Kroner BL, Goedert JJ, Blattner WA, Wilson SE, Carrington MN, Mann DL. Concordance of human leukocyte antigen haplotypesharing, CD4 decline and AIDS in hemophilic siblings. Multicenter Hemophilia Cohort and Hemophilia Growth and Development Studies. AIDS 1995; 9:275-80.
10. Lockett SF, Robertson JR, Brettle RP, Yap PL, Middleton D, Leigh Brown AJ. Mismatched human leukocyte antigen alleles protect against heterosexual HIV transmission. J Acquir Immune Defic Syndr 2001; 27:277-80.
11. MacDonald KS, Embree J, Njenga S, et al. Mother-child class I HLA concordance increases perinatal human immunodeficiency virus type 1 transmission. J Infect Dis 1998; 177:551-6.
12. Polycarpou A, Ntais C, Korber BT, et al. Association between maternal and infant class I and II HLA alleles and of their concordance with the risk of perinatal HIV type 1 transmission. AIDS Res Hum Retroviruses 2002; 18:741-6.
13. Smith DM, May SJ, Tweeten S, et al. A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS 2009; 23:225-32.
14. Chalmet K, Staelens D, Blot S, et al. Epidemiological study of phylogenetic transmission clusters in a local HIV-1 epidemic reveals distinct differences between subtype B and non-B infections. BMC Infect Dis 10:262.
15. Lewis F, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 2008; 5:e50.
16. Altfeld M, Addo MM, Rosenberg ES, et al. Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. AIDS 2003; 17:2581-91.
17. Prado JG, Prendergast A, Thobakgale C, et al. Replicative capacity of human immunodeficiency virus type 1 transmitted from mother to child is associated with pediatric disease progression rate. J Virol 2010; 84:492-502.
18. de Oliveira T, Pybus OG, Rambaut A, et al. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 2006; 444: 836-7.
19. Ou CY, Ciesielski CA, Myers G, et al. Molecular epidemiology of HIV transmission in a dental practice. Science 1992; 256:1165-71.
20. Morris SR, Little SJ, Cunningham T, Garfein RS, Richman DD, Smith DM. Evaluation of an HIV nucleic acid testing program with automated Internet and voicemail systems to deliver results. Ann Intern Med 2009; 152:778-85.
21. Little SJ, Frost SD, Wong JK, et al. Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J Virol 2008; 82:5510-8.
22. Ahuja SK, Kulkarni H, Catano G, et al. CCL3L1-CCR5 genotype influences durability of immune recovery during antiretroviral therapy of HIV-1-infected individuals. Nat Med 14:413-20.
23. Brenner BG, Roger M, Routy JP, et al. High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 2007; 195:951-9.
24. Laboratory LAN. HLA comparison tool. [cited 2010 October 1]; Statistical tool for comparing HLA frequencies]. Available from: http://www.hiv.lanl.gov/ content/immunology/hla/hla-compare.html.
25. LANL. HLA linkage disequilibirum. [cited 2011 January 7]; Statistical Tool]. Available from: http://www.hiv.lanl.gov/content/immunology/hla/hla- linkage.html.
26. LANL. Epitope map. [cited 2010 October 30]; Epitope Maps of HIV proteome]. Available from: http://www.hiv.lanl.gov/content/immunology/maps/maps. html.
27. Database IE. MHC-1 processing predictions. [cited 2010 September 10, 2010]. Available from: http://tools.immuneepitope.org/analyze/html/mhc- processing.html.
28. Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M. NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res 2008; 36:W509-12.
29. Lundegaard C, Lund O, Nielsen M. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers. Bioinformatics 2008; 24:1397-8.
30. Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 2003; 171:1741-9.
31. Tenzer S, Peters B, Bulik S, et al. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci 2005; 62:1025-37.
32. San Diego County. HIV/AIDS Surveillance Program Epidemiology Report 2010. San Diego County Helath and Human Services: County of San Diego, 2010.
33. Dorak MT, Tang J, Penman-Aguilar A, et al. Transmission of HIV-1 and HLA-B allele-sharing within serodiscordant heterosexual Zambian couples. Lancet 2004; 363:2137-9.
34. Ober C, Weitkamp LR, Cox N, Dytch H, Kostyu D, Elias S. HLA and mate choice in humans. Am J Hum Genet 1997; 61:497-504.
35. Wedekind C, Seebeck T, Bettens F, Paepke AJ. MHC-dependent mate preferences in humans. Proc Biol Sci 1995; 260:245-9.