HIV-1 Progression Links with Viral Genetic Variability and Subtype, and Patient's HLA Type: Analysis of a Nairobi-Kenyan Cohort

Overview

Journal Med Microbiol Immunol

Specialty Allergy & Immunology

Date 2013 Oct 22

PMID 24142198

Citations 9

Authors

Syed Hani Abidi

Aniqa Shahid

Laila S Lakhani

Reena Shah

Nancy Okinda

Peter Ojwang

Farhat Abbas

Sarah Rowland-Jones

Syed Ali

Affiliations

Soon will be listed here.

Abstract

In a Nairobi-Kenyan cohort of 50 HIV-1 positive patients, we analysed the prevalence of HIV-1 subtypes and human leucocyte antigen (HLA) alleles. From this cohort, 33 patients were selected for the analysis of HIV-1 infection progression markers (i.e. CD4 cell counts and viral loads) and their association with HIV-1 genetic variability and subtype, and patient's HLA type. HIV-1 gag genetic variability, analysed using bioinformatics tools, showed an inverse relationship with CD4 cell count whereas with viral load that relationship was direct. Certain HLA types and viral subtypes were also found to associate with patients' viral load. Associations between disease parameters and the genetic makeup of the host and virus may be crucial in determining the outcome of HIV-1 infection.

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References

Reekie J, Gatell J, Yust I, Bakowska E, Rakhmanova A, Losso M . Fatal and nonfatal AIDS and non-AIDS events in HIV-1-positive individuals with high CD4 cell counts according to viral load strata. AIDS. 2011; 25(18):2259-68. DOI: 10.1097/QAD.0b013e32834cdb4b. View

Kaur G, Mehra N . Genetic determinants of HIV-1 infection and progression to AIDS: immune response genes. Tissue Antigens. 2009; 74(5):373-85. DOI: 10.1111/j.1399-0039.2009.01337.x. View

Arien K, Vanham G, Arts E . Is HIV-1 evolving to a less virulent form in humans?. Nat Rev Microbiol. 2007; 5(2):141-51. PMC: 7097722. DOI: 10.1038/nrmicro1594. View

Bettinotti M, Mitsuishi Y, Bibee K, Lau M, Terasaki P . Comprehensive method for the typing of HLA-A, B, and C alleles by direct sequencing of PCR products obtained from genomic DNA. J Immunother. 1997; 20(6):425-30. DOI: 10.1097/00002371-199711000-00001. View

Khoja S, Ojwang P, Khan S, Okinda N, Harania R, Ali S . Genetic analysis of HIV-1 subtypes in Nairobi, Kenya. PLoS One. 2008; 3(9):e3191. PMC: 2527130. DOI: 10.1371/journal.pone.0003191. View

Carrington M, Nelson G, Martin M, Kissner T, Vlahov D, Goedert J . HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science. 1999; 283(5408):1748-52. DOI: 10.1126/science.283.5408.1748. View

Pereyra F, Jia X, McLaren P, de Bakker P, Walker B, Ripke S . The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010; 330(6010):1551-7. PMC: 3235490. DOI: 10.1126/science.1195271. View

Kiwanuka N, Robb M, Laeyendecker O, Kigozi G, Wabwire-Mangen F, Makumbi F . HIV-1 viral subtype differences in the rate of CD4+ T-cell decline among HIV seroincident antiretroviral naive persons in Rakai district, Uganda. J Acquir Immune Defic Syndr. 2009; 54(2):180-4. PMC: 2877752. DOI: 10.1097/QAI.0b013e3181c98fc0. View

Yang O . Candidate vaccine sequences to represent intra- and inter-clade HIV-1 variation. PLoS One. 2009; 4(10):e7388. PMC: 2753653. DOI: 10.1371/journal.pone.0007388. View

10.

Cao K, Moormann A, Lyke K, Masaberg C, Sumba O, Doumbo O . Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. Tissue Antigens. 2004; 63(4):293-325. DOI: 10.1111/j.0001-2815.2004.00192.x. View

11.

Trachtenberg E, Korber B, Sollars C, Kepler T, Hraber P, Hayes E . Advantage of rare HLA supertype in HIV disease progression. Nat Med. 2003; 9(7):928-35. DOI: 10.1038/nm893. View

12.

Tang J, Tang S, Lobashevsky E, Myracle A, Fideli U, Aldrovandi G . Favorable and unfavorable HLA class I alleles and haplotypes in Zambians predominantly infected with clade C human immunodeficiency virus type 1. J Virol. 2002; 76(16):8276-84. PMC: 155130. DOI: 10.1128/jvi.76.16.8276-8284.2002. View

13.

Rose P, Korber B . Detecting hypermutations in viral sequences with an emphasis on G --> A hypermutation. Bioinformatics. 2000; 16(4):400-1. DOI: 10.1093/bioinformatics/16.4.400. View

14.

Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh S . The IMGT/HLA database. Nucleic Acids Res. 2010; 39(Database issue):D1171-6. PMC: 3013815. DOI: 10.1093/nar/gkq998. View

15.

Baeten J, Chohan B, Lavreys L, Chohan V, McClelland R, Certain L . HIV-1 subtype D infection is associated with faster disease progression than subtype A in spite of similar plasma HIV-1 loads. J Infect Dis. 2007; 195(8):1177-80. DOI: 10.1086/512682. View

16.

Hewitt E . The MHC class I antigen presentation pathway: strategies for viral immune evasion. Immunology. 2003; 110(2):163-9. PMC: 1783040. DOI: 10.1046/j.1365-2567.2003.01738.x. View

17.

Haynes B, Pantaleo G, Fauci A . Toward an understanding of the correlates of protective immunity to HIV infection. Science. 1996; 271(5247):324-8. DOI: 10.1126/science.271.5247.324. View

18.

Bird T, Kaul R, Rostron T, Kimani J, Embree J, Dunn P . HLA typing in a Kenyan cohort identifies novel class I alleles that restrict cytotoxic T-cell responses to local HIV-1 clades. AIDS. 2002; 16(14):1899-904. DOI: 10.1097/00002030-200209270-00006. View