Circulating Recombinant Form (CRF) 37_cpx: An Old Strain in Cameroon Composed of Diverse,Genetically Distant Lineages of Subtypes A and G

HIV-1 in Cameroon is genetically diverse, but is predominated by the circulating recombinant form (CRF) 02_AG, which cocirculates among an array of other CRFs, unique recombinant forms (URFs), and all group M subtypes. In particular, our studies of HIV-1 diversity in the East Province found a high proportion of URFs and second generation recombinants (SGRs), suggesting this region of Cameroon may be a breading ground for new CRFs. Herein we present the full-length sequence analysis of one such CRF, composed primarily (66%) of unique, distant lineages of subtypes A and G in alternating regions throughout the genome. This CRF also combines segments in pol and env genes possessing intrasubtype distance (<15%) to the CRF01_AE and CRF02_AG radiations. The genomic composition of this strain comprising gene segments of subtypes A and G as well as CRF01_AE and CRF02_AG defines this strain as a circulating SGR (CSGR), and the 37th CRF to be identified. Furthermore, more than half of CRF19_cpx, a CRF identified in Cuba, clusters with CRF37_cpx, and the clear genetic distance among the viruses in this cluster suggests this strain has been in circulation since the early days of the epidemic. The genetically distant segments comprising CRF37_cpx, which were found to cluster outside the crown groups of previously described viruses, may represent a link to very rare or extinct strains, and, potentially, to understanding the evolutionary history of HIV-1 in this region.