AEGiS-14IAC: Preliminary evidence for another HIV-1 circulating recombinant form containing segments from an unknown subtype.

14th International AIDS Conference

Barcelona, Spain - July 7-12, 2002

Preliminary evidence for another HIV-1 circulating recombinant form containing segments from an unknown subtype.

Int Conf AIDS 2002 Jul 7-12; 14:(abstract no. A10038)

Snoeck J, Riva C, Carr JK, McCutchan FE, Vandamme AM
Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium

BACKGOUND: The high genetic diversity of HIV is well documented and has led to the classification of the virus into several genetic types and subtypes. Recombination between subtypes is frequently detected, and some key strains in the pandemic are circulating recombinant forms (CRF). A partial viral sequence from a patient in Leuven, who probably acquired HIV-1 in Africa, did not cluster with any known subtypes or CRF of HIV-1, and was investigated.

METHODS: A pol sequence of 1392 nucleotides was obtained using plasma viral RNA by RNA-PCR amplification and sequencing. An alignment was made with reference sequences of all subtypes in the Dambe program and was edited using Genedoc. Simplot was used for creating similarity plots and bootscanning. Phylogenetic trees were created with the PHILYP program.

RESULTS: The similarity plot and phylogenetic tree showed no clustering with any of the currently known HIV-1 subtypes or CRF. Using a BLAST search, we found a high similarity with a complex recombinant sequence, CAM53379, from Cameroon (AF377959). This sequence has 2 breakpoints in pol, 2586 and 3078 with respect to HXB2, of which the first part is subtype G, the second part subtype F and the third part is of an unknown subtype. Analyses of our sequence revealed the same clustering, although the bootstrap support for the second part with subtype F was low (55%). In the third part, the previously reported and our new sequence cluster together with 100% bootstrap support, and separately from all other subtypes.

CONCLUSION: This pol sequence raises the possibility that CAM53379 represents a new circulating recombinant form with most of the pol region belonging to a unknown subtype of HIV-1. Complete sequencing of the strain reported here is underway, but a third strain would also be required to definitively establish a new CRF.

Keywords: AEGIS, HIV-1, HIV Infections, HIV Seropositivity, Variation (Genetics), HIV-1 Reverse Transcriptase, Recombination, Genetic, Polymerase Chain Reaction, Cameroon, Africa, Human, genetics

020707
A10038