AEGiS-12IAC: Full-length sequences of HIV-1 subtypes A-J: inter-subtype recombination plays a significant role on global HIV-1 evolution.

12th International AIDS Conference

Geneva, Switzerland - June 28-July 3, 1998

Full-length sequences of HIV-1 subtypes A-J: inter-subtype recombination plays a significant role on global HIV-1 evolution.

Int Conf AIDS 1998 Jun 28-Jul 3; 12:17-8 (abstract no. 11177)

Salminen MO, Laukkanen T, Janssen W, Albert J, Leinikki PO, Carr J, McCutchan FE
Nat'l. Publ. Inst. HIV-Labotory, Helsinki, Finland.

BACKGROUND: Multiple genetic subtypes of the Human Immunodeficiency Virus Type 1 (HIV-1) have been found among internationally collected strains. Subtypes A through J comprise the prevalent, main (M) group and a small proportion of strains are group O (outlier). The recent identification of inter-subtype recombinants, which contain interspersed segments of genome from two different subtypes, has added a new level of complexity to the genetic diversity of HIV-1. Within the M group of HIV-1, inter-subtype recombination between many different pairs of subtypes has already been documented. Until recently, it has been believed that recombinant viruses are exceptions from the globally prevalent strains. This has partially been the result of fragmentary sequencing of subgenomic regions of the virus.

METHODS: We have recently developed full-length PCR and sequencing techniques as well as sequence analysis methods that have allowed us to rapidly clone and analyse many new full-length HIV-1 genomes.

RESULTS: Multiple new full length clones (> 10) of viruses representing subtypes A-J were generated and sequenced. Analysis of the sequences by the bootscanning technique, which we have developed, reveals that subtypes G, F, H and J are classical subtypes, since they form highly supported monophyletic clusters in phylogenetic analysis, regardless of genomic region used. However, some viruses, believed to represent additional subtypes or members of a previously described subtype, were found to be intersubtype recombinant strains.

CONCLUSIONS: The generation of reference clones for the globally prevalent F and G subtypes of HIV-1 will aid in work targeted for vaccine and treatment, as well as basic science. The finding of many recombinant viruses among randomly selected strains argues for frequent occurrence of co-infections, and emphasizes the need for sequencing full genomes in situations where viruses are used for clinical research.

Keywords: AEGIS, HIV-1, Recombination, Genetic, Evolution, Variation (Genetics), Phylogeny, HIV-1 Reverse Transcriptase, Greece, Human, genetics, ICA12
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