AEGiS-13IAC: Conservation of South African HIV-1 subtype C Nef sequences at different stages of disease progression: implications for vaccine strategies.

13th International AIDS Conference

Durban, South Africa - July 9-July 14, 2000

Conservation of South African HIV-1 subtype C Nef sequences at different stages of disease progression: implications for vaccine strategies.

Int Conf AIDS 2000 Jul 9-14; 13:(abstract no. WeOrA598)

Mashishi T, Hunt G, Bredell H, Morris L, Ramjee G, Abdool-Karim S, Gray C
T. Mashishi, National Institute for Virology, Private Bag X4, Sandringham 2131, Johannesburg, South Africa, Tel.: +27 11 321 4292, Fax: +27 11 321 4325, E-mail: tumelom@niv.ac.za

BACKGROUND: Cytotoxic T lymphocytes (CTL) that recognise specific viral epitopes are thought to provide the most effective control of viral replication and spread. The accessory viral protein, Nef has been shown to contain conserved regions rich in CTL epitopes in subtype B viruses. Subtype C HIV-1 is the most prevalent subtype in South Africa. We analysed subtype C HIV-1 Nef sequences derived from individuals during early and late stage disease. Our aim was to show whether Nef is conserved, irrespective of disease status.

METHODS: Nef was sequenced by direct PCR product sequencing from either proviral DNA or viral RNA. A Nef PCR reaction was designed to result in two short fragments that overlap by 96 bases and incorporate the whole Nef region. Nef was sequenced from 12 acute seroconverters and 6 AIDS patients. Nucleotide and amino acid sequences were used to construct phylogenetic trees to assess if there was distinct grouping between these cohorts. CTL epitopes (9-mer) were predicted from RNA sequences, where host HLA genetics were known.

RESULTS: Phylogenetic analysis showed significant (83-100% bootstrap values) grouping for South African subtype C isolates. Nef amino acid alignments showed a high degree of conservation from early to late stage disease, showing a range of 1.5%-9% amino acid variation. In contrast, the V3 loop region from the same isolates had amino acid variation as high as 50%. By comparison, the amino acid variation between South African subtype C and subtype B Nef sequences (from Los Alamos database) ranged between 15-20%. Subtype C CTL epitopes were predicted to be in regions known to be rich in CTL epitopes for subtype B, despite the relatively increased variability in subtype B Nef sequences.

CONCLUSIONS: These preliminary results show that Nef is well conserved from early infection to AIDS. The stability of subtype C Nef, which contains multiple CTL epitopes, makes it a good candidate for inclusion in a CTL-based vaccine.

Keywords: AEGIS, HIV-1, Disease Progression, Acquired Immunodeficiency Syndrome, T-Lymphocytes, Cytotoxic, AIDS Vaccines, Epitopes, Amino Acid Sequence, Vaccines, South Africa, Human, immunology
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