Spread of distinct human immunodeficiency virus type 1 AG recombinant lineages in Africa

To identify new subtype G human immunodeficiency virus type 1 (HIV-1) strai ns and AG recombinant forms, we collected 28 serum samples from immigrants to the Netherlands from 12 countries throughout Africa. Based on the gag se quences 22 isolates were identified as subtype A or G. Phylogenetic analysi s of discontinuous regions of the gag (726 nt), pol (1176 nt) and env (276 nt) genes revealed 13 AG recombinants with the mosaic structure A(gag)/G(po l)/A(env), three with A(gag)/G(pol)/G(env) and one other with A(gag)/G(pol) /G(env), in addition to 'pure' subtypes A(gag)/A(pol)/A(env) (n = 1) and G( gag)/G(pol)/G(env) (n = 4). To analyse the crossover points in more detail, a new RT-PCR was developed resulting in a large contiguous sequence of 260 0 nt from the gag region to half the pol region. All the 13 A(gag)/G(pol)/A (env) recombinants appeared to belong to the circulating recombinant form ( CRF) AG (IbNG). The three A(gag)/G(pol)/G(env) recombinants differed from t he CRF AG (IbNG) subtype, suggesting the identification of a new CRF subtyp e. The recovery of AG recombinants from African countries a thousand miles apart indicates the active spread of new recombinants.