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 a nd redefine, previously documented subtype H strains. Design: Near-full-length genomes of HIV-1 env subtype H strains V1991 and V 1997 were amplified, cloned, sequenced, phylogenetically analysed and compa red 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 indiv iduals harbouring strains V1991 and V1997 were co-cultivated with PHA stimu lated 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, c loned 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 representativ e of subtype H. They form a phylogenetic cluster with the only previously d escribed subtype H representative HIV-1 90CF056.1, regardless of the genome region analysed. V1557 is redefined as a gag and env subtype H mosaic viru s containing unclassified fragments. CA13 is a complex intersubtype recombi nant between subtypes A, H and unclassified strains Conclusion: Near-full-length genome analysis identified HIV-1 V1991 and V19 97 as two new subtype H representatives. These reagents will allow defining and classifying non-recombinant as well as recombinant HIV-1, eventually h elping to solve the puzzle of HIV-1 subtypes. (C) 2000 Lippincott Williams & Wilkins.