HIV/AIDS was first identified in Cameroon during 1985  and the epidemic has continued to increase with the identification of multiple, divergent HIV subtypes and circulating recombinant forms (CRFs) . According to a recent epidemiological surveillance report, 10,625 new infections were diagnosed in Cameroon during 2007 in comparison with 8,596 new infections during 2006 . Furthermore, about 5.1% (ages 15-49) of adults are living with HIV/AIDS; among them, 60% (ages 15-49) were women. The majority of HIV infections in Cameroon are due to heterosexual transmission and high rates (40-50%) of infection have been observed among risk groups such as commercial sex workers and long distance truck drivers (UNAIDS/WHO) . Antiretroviral therapy (ART) was initiated in Cameroon during 2001 and later decentralized to district level hospitals by the WHO 3by5 initiative (treating 3 million by 2005). In a study from Yaounde, Cameroon it was reported that 2.6% protease drug resistance and 9.3% major reverse transcriptase drug resistance were detected among patients who never received therapy, a finding that has implications for the efficacy of first line therapies . Further in a study conducted at Doula, Cameroon  out of 819 patients who received first line ART, 36% had virological failure after 6 months or more. About 80% of drug resistance was detected for Nucleoside Reverse Transcriptase Inhibitors (NRTI) class, followed by the non-nucleoside reverse transcriptase Inhibitors (NNRTI) (76%) and Protease Inhibitor (PI) class (19%) drugs.
HIV infection in Cameroon is characterized by highly diversified strains including Circulatory Recombinant Forms (CRFs), Group O and N  which pose a challenge for diagnosis, vaccines and treatment . Recently a new HIV strain, group P of gorilla origin, was identified in a Cameroonian woman  and shown to be distinct from other HIV groups O and N identified earlier in Cameroon [10, 11]. Although new strains have been shown to emerge in Cameroon, studies that analyzed three immunodominant regions gag/pol/env have documented that 60-70% of infections continue to be CRF02_AG [12, 13]. The current HIV molecular epidemic in Cameroon is predominantly based on CRF02_AG (65-75%), pure subtypes A1, A2, C, F2, G and H(1-5%), 6 different CRFs (-01, -11, -13, -18, -25, -37), divergent forms group O (2.2-3.8%) and HIV-2 (0.4-1.2%) [13–15]. Several previous reports on molecular epidemiology in Cameroon were from urban area using phylogenetic analysis of only gag and env gene sequences. In the first study it was reported that CRF02_AG accounted for 60%, followed by URFs(26%), 12 pure subtypes and CRFs  and in another study CRF02_AG accounted for 58.2% of infections followed by 14.8% of URFs, 0.2 - 6.1% of subtypes, A, B, C, D, F2, G and CRFs 01, 06, 09, 11, 13, 22, and 37 . Both studies confirmed CRF02_AG is a dominant strain in urban Cameroon. However rural Cameroon comprises the majority of the country's population and in certain rural areas HIV prevalence has been found to be double the national rate (8-10%) . In recent studies from rural Cameroon, CRF02_AG was shown to be a dominant strain 66.5% whether analyzed from a single pol fragment  or individual fragments of gag (65%), pol (75%) and env (55%)  followed by a second dominant strain CRF22_01_A1 in 5-10% of infections [14, 18]. CRF22_01_A1 had been detected earlier  as a URF and later by full genome sequencing in two studies [14, 18] and was found to be 2nd dominant circulating strain in Cameroon. It is interesting to note that along with these subtypes and CRFs about 10-20% of strains were unique recombinant forms (URFs) that were likely generated by recombination of existing strains [12, 19].
CRF02_AG recombinant viruses have become well established in the Cameroonian population possibly due to a founder effect from parent strains subtype A [20.21] and G  and/or a higher replicative advantage of CRF02_AG over other co-circulating recombinants [23, 24]. A prospective study confirmed that CRF02_AG is the predominant strain in blood donors in Yaoundé, Cameroon ; however, other CRFs and Unique Recombinant Forms (URFs) have also been detected [25–27]. The ongoing evolution of HIV and emergence of new recombinant forms are a major concern for the global AIDS pandemic. Several factors may contribute to the emergence of recombinant viruses or URFs but most importantly, recombination provides a mechanism to increase viral sequence diversity rapidly, unlike the slow accumulation of mutations that occurs through replication errors . For recombination to occur between distinct HIV-1 strains, a cell needs to be dually infected with different viruses the progeny virions that result possess RNA genomes from each virus, permitting strand-switching to occur during the next round of reverse transcription. Therefore, recombination requires co-infection of viral strains in an individual. This dual infection may occur during the primary infection period, before the immune response is fully developed, or it may occur as a superinfection with a new viral strain after the initial strain has established a chronic infection. Super infection with a different strain is thought to be the most predominant contributor to viral recombination . The possibility for superinfection among high risk individuals has been reported in Cameroon . Both superinfection and recombination have the potential to complicate efforts to develop vaccines, and reinfection with a drug-resistant virus could jeopardize available treatment options. To date 49 CRFs have been identified  and recombination between the URFs and existing CRFs results in Second Generation Recombinants (SGRs)  which would further complicate the phylogenetic nature of the epidemic. In the present study we have analyzed recent trends in the genetic evolution of the HIV epidemic in different regions of Cameroon and demonstrated the ongoing emergence of new recombinants and prevalence of multi-drug resistant viruses in the population.