AEGiS-11IAC: First full length sequence prototypes of HIV-1 clades C, E and G: two of three are mosaic genomes.

11th International AIDS Conference


Vancouver, British Columbia — July 7-12, 1996

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First full length sequence prototypes of HIV-1 clades C, E and G: two of three are mosaic genomes.

Int Conf AIDS 1996 Jul 7-12; 11:216 (abstract no. Tu.A.100)
Carr JK, Salminen MO, Leinikki P, Johansson B, Burke DS, McCutchan FE; Henry M. Jackson Foundation Rockville, MD, USA. Fax: 301-762-7460. E-mail: jcarr@hiv.hjf.org.

OBJECTIVE: To obtain the initial prototypic full length genomic sequences of HIV-1 isolates of clades C, E and G.

METHODS: DNA from primary virus cultures on donor peripheral blood mononuclear cells from HIV-1 infections acquired in Ethiopia (C2220, clade C), Thailand (CM240, clade E) and Kenya (HH8793, clade G) was isolated and used as template for long PCR amplification of virtually full length HIV-1 genomes. PCR products were molecularly cloned and fully sequenced using fluorescent dye terminators and an Applied Biosystems automated sequencer. An alignment was built, segmented and the segments analysed using maximum likelihood and maximum parsimony.

RESULTS: The full length sequence of the Thai and Kenyan viruses revealed both to be mosaics between clade A and clade E, on the one hand, and clade A and clade G, on the other. Their structure is diagrammed below: The Thai virus is predominantly clade A(grey) except for the extracellular portion of env and the U3 region of the LTR. The kenyan virus is predominantly G (white) except for vif and vpr, and the internal portion of env. It appears that both viruses have common breakpoints at the 3' end of the viral RNA. The clade C virus from Ethiopia was not apparently recombinant and had the same genomic organization as that of the previously sequenced isolates of clades A,B and D. However, the C virus has three NF-kB binding sites in the core promoter instead of the usual two, and the Thai virus has only one.

CONCLUSION: The only full length sequences of clades E and G suggest that these 'clades' are recombinant.

Keywords: AEGIS, HIV-1, HIV Infections, Mosaicism, Genome, Genome, Viral, Thailand, Ethiopia, Kenya, genetics, ICA11KWDaegis,hiv-1,hivinfections,mosaicism,genome,genome,viral,thailand,ethiopia,kenya,genetics,ica11

960707
TuA100

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