HIV-1CRF09_cpx circulates in the North West province of Cameroon where CRF02_AG infections predominate and recombinant strains are common

This study describes the HIV-1 genetic diversity that currently circulates in Bamenda, the provincial capital of the North West province of Cameroon. Phylogenetic analysis of the protease (pro) gene of 20 HIV-1-seropositive individuals identified 11 (55%) CRF02_ AG, one D, one F2, one J, and four (20%) unclassifiable strains. Interestingly, the remaining two (10%) samples, 02CMNYU3072 and 03CMNYU3224, originating from epidemiologically unlinked individuals, were classified as CRF09_ cpx, representing the first reported cases of this complex circulating recombinant form (CRF) in Cameroon. Additional analysis of the C2V5 portion of the envelope (env) gene confirmed the CRF09_ cpx identity of these isolates and classified the remaining isolates as CRF02_ AG (n = 12, 63%), subtype D ( n = 2, 11%), subtype F2 ( n = 2, 11%), and subtype A1 (n = 1). In combination, the pro and env subtyping results revealed three (16%) isolates with discordant subtypes including J(pro)CRF02_ AG(env), CRF02_ AG(pro)D(env), and CRF02_ AG(pro)F2(env). In conclusion, this study highlights the presence of HIV-1 CRF09_ cpx in Cameroon and identifies three possible intersubtype recombinants (ISRs) containing CRF02_ AG in a town where CRF02_ AG infections predominate, and stresses the commonness of HIV-1 recombinant strains in a region where broad genetic diversity exists.