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272 First Full-Genome Sequences of Intersubtype Recombinants Circulating in South Africa
M. A. Papathanasopoulos*1, T. Cilliers1, L. Morris1, J. Mokili2, W. Dowling3, J. K. Carr2, and F. McCutchan2
1Natl. Inst. for Virology, Johannesburg, South Africa; 2Henry M. Jackson Fndn., Rockville, MD, USA; and 3Walter Reed Army Inst. of Res., Washington, DC, USA
Background: The prevalence of non-subtype C HIV-1 infection in South Africa has not been widely and systematically investigated. HIV-1 circulating in South Africa has mainly been subtyped by partial rather than full-length genome sequencing. The large movement of people into and out of South Africa in recent years, particularly from neighboring countries where many recombinant forms are known to predominate could have an impact on the molecular epidemiology. There is therefore a need to ascertain and fully characterize recombinants. Recent analysis of several unusual isolates by gag and env HMA identified 2 recombinants, which were characterized in this study by full genome sequencing.
Methods: Proviral DNA from strains CM4 (AIDS patient with cryptococcal meningitis) and Du178 (commercial sex worker in Durban) was isolated from coculture. Coreceptor usage was established by infecting U87.CD4.CCR5 and U87.CD4.CXCR4 cells. Virtually full-length genomes were PCR amplified and sequenced. LTR regions were amplified separately and assembled to generate the complete genomes. A multiple alignment with all available HIV-1 subtypes was generated. Phylogenetic trees were constructed to determine subtype, and recombination was identified and confirmed by distance scanning and bootscanning.
Results: Du178 is a recombinant between the recently defined sub-subtype A2 and subtype C, with at least 4 breakpoints. The virus is predominantly subtype C, with the accessory/envelope region being subtype A2. CM4 is a very complex recombinant, with multiple breakpoints containing segments of A, C, D, K, and apparently CRF02_AGIbNG. Preliminary analysis of the subtype C sections resemble circulating South African HIV-1 subtype C, suggesting that recombination occurred within the country. Both isolates use the CCR5 coreceptor.
Conclusions: Results confirm the presence of recombinants in South Africa. Ongoing surveillance for these recombinants is necessary, particularly since the Du178 virus is in a high transmission setting.
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