HIV-1 subtype H near-full length genome reference strains and analysis of subtype-H-containing inter-subtype recombinants.

Objective: To characterize near-full-length genomes of two HIV-1 subtype H strains. To extend sequence data to include full env and gag, and analyse and redefine, previously documented subtype H strains. Design: Near-full-length genomes of HIV-1 env subtype H strains V1991 and V1997 were amplified, cloned, sequenced, phylogenetically analysed and compared with a panel of 23 HIV-1 group M reference isolates. The mosaic nature of previously published subtype H strains V1557 and CA13 was reanalysed. Materials and methods: Peripheral blood mononuclear cells (PBMC) from individuals harbouring strains V1991 and V1997 were co-cultivated with PHA stimulated donor PBMC. Near-full-length genomes of V1991 and V1997, and gag and env genes of CA13 and V1557, were amplified by polymerase chain reaction, cloned and sequenced. Intersubtype recombination analyses were performed by similarity plot, bootscanning and phylogenetic analysis. Results: Near-full-length clones of HIV-1 V1991 and V1997 are representative of subtype H. They form a phylogenetic cluster with the only previously described subtype H representative HIV-1 90CF056.1, regardless of the genome region analysed. V1557 is redefined as a gag and env subtype H mosaic virus containing unclassified fragments. CA13 is a complex intersubtype recombinant between subtypes A, H and unclassified strains Conclusion: Near-full-length genome analysis identified HIV-1 V1991 and V1997 as two new subtype H representatives. These reagents will allow defining and classifying non-recombinant as well as recombinant HIV-1, eventually helping to solve the puzzle of HIV-1 subtypes.