Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants

Multiple genetic subtypes and intersubtype recombinant strains have been identified among isolates of HIV-1. The greatest diversity of strains has been recovered from Central Africa, where mixtures of subtypes and recombinant forms have been recovered. However, many of the HIV-1 subtypes and recombinants have been characterized by partial rather than full-length genome sequencing. Here we report the first two virtually full-length genome sequences from HIV-1 subtype G, isolated in Sweden and Finland but originating in Congo and Kenya, and from two Djibouti isolates sharing the A/G recombinant structure of Nigerian isolate, IbNG. By comparison with reference sequences of other subtypes, it appears that the subtype G strains are largely nonrecombinant, while the Djibouti strains show alternating segments from subtypes A and G. In the cytoplasmic domain of the gp41 protein of the Djibouti viruses the E, G, and IbNG strains form a single cluster, separate from subtype A, clouding the subtype origin of these particular segments. Within the resolution of current technology, the structure of the Djibouti strains is identical to that of IbNG, establishing for the first time the geographic spread of this recombinant in Africa. The geographic spread of the IbNG-like strains suggests that, like the subtype E recombinants, these should be given a specific name to facilitate future identification and tracking; the name "IbNG subtype" is proposed.