Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants

Dowling, William E.; Kim, Bohye; Mason, Carl J.; Wasunna, K.; Alam, Uzma; Elson, Lynne; Birx, Deborah L.; Robb, Merlin L.; McCutchan, Francine E.; Carr, Jean K.

doi:10.1097/00002030-200209060-00015

Cited by 100 publications

(74 citation statements)

References 40 publications

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“…Other subtypes are C, D and G with other recombinant which account for about 30% [29]. The origin of HIV-1 Subtype G is believed to be introduced into Kenya from West Africa through Lake Victoria shore near Uganda.…”

Section: Hiv-1 Diversity In East Africamentioning

confidence: 99%

HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article

2014

J Vaccines Vaccin

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Background: Human immunodeficiency viruses (HIV) are characterized by extremely high genetic variability. This extensive heterogeneity resulted from high error rate of reverse transcriptase enzyme in combination with fast turnover of virions among HIV-infected individuals. With geographical distribution of subtypes its evolution and unpredictable process and intermixing of HIV-1 variants is inevitable. Recombinant viruses contribute already substantially to the global pandemic especially in sub-Saharan African. East Africa studies has shown more complex mixture of HIV-1 Subtypes and associated recombinant virus especially in Tanzania.

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Section: Hiv-1 Diversity In East Africamentioning

confidence: 99%

HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article

2014

J Vaccines Vaccin

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“…Naturally occurring variations (four to six per epitope) of optimal epitopes were selected on the basis of frequency in selected Kenyan sequences (Ref. 32 and F. A. Plummer, unpublished data), and on variant frequencies in available HIV-1 group M sequences (http://hiv-web.lanl.gov/ content/hiv-db/mainpage.html) ( Table II). Peptides were synthesized via Fmoc chemistry (Sigma-Genosys) and diluted in RPMI 1640 and DMSO (Ͻ1% final concentration).…”

Section: Peptidesmentioning

confidence: 99%

Epitope Cross-Reactivity Frequently Differs between Central and Effector Memory HIV-Specific CD8+ T Cells

McKinnon

Ball

Wachihi

et al. 2007

The Journal of Immunology

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HIV diversity may limit the breadth of vaccine coverage due to epitope sequence differences between strains. Although amino acid substitutions within CD8+ T cell HIV epitopes can result in complete or partial abrogation of responses, this has primarily been demonstrated in effector CD8+ T cells. In an HIV-infected Kenyan cohort, we demonstrate that the cross-reactivity of HIV epitope variants differs dramatically between overnight IFN-γ and longer-term proliferation assays. For most epitopes, particular variants (not the index peptide) were preferred in proliferation in the absence of corresponding overnight IFN-γ responses and in the absence of the variant in the HIV quasispecies. Most proliferating CD8+ T cells were polyfunctional via cytokine analyses. A trend to positive correlation was observed between proliferation (but not IFN-γ) and CD4 counts. We present findings relevant to the assessment of HIV vaccine candidates and toward a better understanding of how viral diversity is tolerated by central and effector memory CD8+ T cells.

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“…Each strain was characterized by sequencing of the complete genome, except for a small portion of the long terminal repeat. Thirty-nine viruses were sequenced previously (2,11,12,19,(21)(22)(23)(24)60). Twenty-one new complete genome sequences were generated for this study.…”

Section: Collection Of Isolatesmentioning

confidence: 99%

Biologic and Genetic Characterization of a Panel of 60 Human Immunodeficiency Virus Type 1 Isolates, Representing Clades A, B, C, D, CRF01_AE, and CRF02_AG, for the Development and Assessment of Candidate Vaccines

Brown

Darden

Tovanabutra

et al. 2005

J Virol

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122

104

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A critical priority for human immunodeficiency virus type 1 (HIV-1) vaccine development is standardization of reagents and assays for evaluation of immune responses elicited by candidate vaccines. To provide a panel of viral reagents from multiple vaccine trial sites, 60 international HIV-1 isolates were expanded in peripheral blood mononuclear cells and characterized both genetically and biologically. Ten isolates each from clades A, B, C, and D and 10 isolates each from CRF01_AE and CRF02_AG were prepared from individuals whose HIV-1 infection was evaluated by complete genome sequencing. The main criterion for selection was that the candidate isolate was pure clade or pure circulating recombinant. After expansion in culture, the complete envelope (gp160) of each isolate was verified by sequencing. The 50% tissue culture infectious dose and p24 antigen concentration for each viral stock were determined; no correlation between these two biologic parameters was found. Syncytium formation in MT-2 cells and CCR5 or CXCR4 coreceptor usage were determined for all isolates. Isolates were also screened for neutralization by soluble CD4, a cocktail of monoclonal antibodies, and a pool of HIV-1-positive patient sera. The panel consists of 49 nonsyncytium-inducing isolates that use CCR5 as a major coreceptor and 11 syncytium-inducing isolates that use only CXCR4 or both coreceptors. Neutralization profiles suggest that the panel contains both neutralization-sensitive and -resistant isolates. This collection of HIV-1 isolates represents the six major globally prevalent strains, is exceptionally large and well characterized, and provides an important resource for standardization of immunogenicity assessment in HIV-1 vaccine trials.

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Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants

Cited by 100 publications

References 40 publications

HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article

HIV-1 Diversity in Tanzania and its Implication toward Development of Effective Vaccines: A Review Article

Epitope Cross-Reactivity Frequently Differs between Central and Effector Memory HIV-Specific CD8+ T Cells

Biologic and Genetic Characterization of a Panel of 60 Human Immunodeficiency Virus Type 1 Isolates, Representing Clades A, B, C, D, CRF01_AE, and CRF02_AG, for the Development and Assessment of Candidate Vaccines

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