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275 Full Documentation of HIV-1 Subtype J with Additional Full Genome Sequences from the Democratic Republic of Congo
J. L. K. Mokili*1, M. Rogers1, N. Lubaki2, M. Milangu2, M. Kashamuka2,3, N. Nzila3, R. Bollinger2, D. Birx4, and F. E. McCutchan1
1Henry M. Jackson Fndn., Rockville, MD, USA; 2Johns Hopkins Sch. of Med., Baltimore, MD, USA; 3Projet SIDA, Kinshasa, Democratic Republic of the Congo; and 4Walter Reed Army Inst. of Res., Washington, DC, USA
Background: At least 10 HIV-1 group M subtypes, called A through K, are recognized. Whereas most subtypes show a wide geographic distribution and are documented with 3 or more near-full genome sequences, subtypes J and K have only been identified in limited numbers of people and in highly circumscribed geographic areas. Furthermore, subtype J is known only from 2 closely related full genomes from individuals infected in DRC. Here we report 3 additional subtype J or J-containing sequences from DRC.
Materials and Methods: Blood samples were collected from a husband and wife, aged 45 and 29, respectively, attending an HIV clinic in Kinshasa in 1998. Another sample originated from a patient attending an antenatal clinic in Kimpese, a rural area south of Kinshasa, in 1991. DNA was extracted from PBMCs and the nearly complete provirus was amplified by nested PCR. The PCR products were directly sequenced and the sequences aligned with group M HIV-1 reference sequences and analyzed by neighbor-joining trees. To investigate the possibility of recombination, bootscan and distance scan were performed.
Results: The 3 sequences clustered with subtype J with a significant bootstrap value. By bootscan and distance scan, 2 of the genomes, those from the couple from Kinshasa, showed no sign of recombination, confirming them as "pure" subtype J. The sequence from Kimpese proved to contain unclassified fragments within the genome. The new subtype J sequences establish a similar diversity within subtype as found in other HIV-1 subtypes.
Conclusions: Subtype J is circulating at some level in DRC, both as a pure subtype and as subtype-J containing recombinants. At lease 1 circulating recombinant form, CRF06_cpx, found in Mali and Burkina Faso, also incorporates subtype J. Recombinants with subtype J may have a wider geographic range than the pure subtype J.
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