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263 Full-Length 5 LTRs and Regulatory Genes from South African HIV-1 Subtype C Strains
F. Treurnicht*1, T. de Villiers1, T. Scriba1, J. zur Megede2, S. Barnett2, S. Engelbrecht1, and E. Janse van Rensburg1
1Tygerberg Hosp. and Univ. of Stellenbosch, South Africa and 2Chiron Corp., Emeryville, CA, USA
Background: HIV-1 subtype C has been characterized by intrasubtype diversity that remains unparalleled.
Methods: Nearly 9-kb amplicons amplified from cellular DNA prepared from HIV-1-positive primary cultures were use to amplify tat and rev exons 1 and 2. The complete 5 LTRs were amplified directly from the cellular DNA. Sequence analysis were performed with the CLUSTALX, GENEDOC, and TREECONW software packages.
Results: South African LTR sequences form a distinct cluster that branch from the other subtypes with a bootstrap value of 100. Twelve of our isolates have 3 NF-kappaB sites. TV019 has a NF-kappaB-like site in addition to 3 NF-kappaB sites. The NF-kappaB I and II sites in isolates TV008 and TV012, respectively, is changed to NF-kappaB-like sites by point mutations. The functional domains in Tat are highly conserved in all isolates. The critical cysteine residue motif at positions 22 to 37 were 100% conserved in most C strains, yet at position 31 isolates TV004, TV010, and TV014 have an additional cysteine residue. The basic domain and the ESKKKVE motif were also 100% conserved except in TV012, which has an EPKKKVE motif. The consensus sequence in the activation domain of Tat for our isolates and 8 reference sequences is PVDPNLEPWNHPGSQPK. Similarly to Tat, Rev shows well-conserved amino acid sequences with some variation in the C-terminal region. A premature stop codon in Rev at position 108 in most isolates results in a truncated protein. TV005 do not contain this stop codon and thus encode Rev proteins of 126 residues. Isolates TV014 and TV019 have 7-residue deletions directly following the nuclear export signal.
Conclusions: Most of our subtype C isolates have 3 NF-kappaB sites which is contrary to previous studies that found that only 50% of C strains have 3 NF-kappaB sites. Most Rev proteins are well conserved at the NH terminus with a signature truncation at position 108. The functional domains of Tat are also highly conserved and the role of regulatory gene conservation, truncated Rev proteins, and the extra NF-kappaB binding site in the successful transmission of subtype C strains needs to be studied.
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