Background: The patterns of different genetic forms of HIV-1 in Africa are correlated with geography. In Nigeria, two genetic forms have been thought to be responsible for the majority of the infections: subtype G and the circulating recombinant form CRF02_AG. These observations, however, have been derived from small sample sets. For the first time, over 100 patients from Nigeria have been sequenced and classified according to subtype.
Methods: The sera from 199 patients clinically failing antiretroviral drug therapy were used for automated sequencing of the protease gene and part of the reverse transcriptase gene. RNA was reverse transcribed, PCR amplified, sequenced and then phylogenetically analyzed with sequences representing the pandemic.
Results: The most common genetic form identified was CRF02_AG (41.7%), followed by subtype G (25.1%). A newly identified circulating recombinant form, CRF43_G02, a recombinant between CRF02_AG and subtype G, was discovered recently in Saudi Arabia. Surprisingly, CRF43_G02 represented 14.6% of the study population. In the region sequenced, CRF43_G02, is entirely subtype G, but forms a genetic cluster within subtype G that is significant based on bootstrap value. The remaining 18% of the samples were either unique recombinant forms or other subtypes.
Conclusions: Nigeria, the most populous country in Africa, has a diverse HIV-1 population as well, based predominantly on subtype G and CRF02_AG. A new recombinant of these two genetic forms, CRF43_G02, represented close to 15% of this population of viruses based on the sequence of protease and RT. Because the two components of the recombinant are the two most common genetic forms in Nigeria, this CRF may have arisen in Nigeria, before its detection in Saudi Arabia.