Dating the origin of HIV-1 group M and HIV-1 group M/SIVcpz separation

Anne-Mieke Vandamme1, Korbinian Strimmer2, William W. Hall3, Eric Delaporte4, Souleymane Mboup5, Martine Peeters4, and Marco Salemi1.

1: Rega Institute for Medical Research, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium; 2: MIPS/GSF, Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany; 3: Department of Medical Microbiology, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland; 4: Laboratoire Retrovirus, IRD, Montpellier, France; 5: African Network of HIV variability, Senegal.

Dating events in the history of SIV/HIV are not straightforward since different HIV-1 lineages and their currently closest simian counterpart, SIVcpz from Pan troglodytes troglodytes, have different evolutionary rates. That is, they do not follow a molecular clock. Using a newly developed method, called site stripping for clock detection (SSCD), which allows selection of nucleotide sites in a set of aligned sequences evolving at an equal rate in different lineages, we investigated particular dates in the history of HIV-1. Two separate gene regions were used to estimate dates on the nodes of the HIV-1 tree, a set of pol sequences isolated in 1998, and a set of env sequences, isolated in 1992. The molecular clock was calibrated using all available pol and env strains of known isolation year. The results from both datasets were very concordant. Subtype B originated in the early 1970s, and the separation between the B and D subtype dates from the early 1950s. The most recent common ancestor of group M has to be placed in the 1930s. Interestingly, our analysis uncovered sites in the pol and env region for which HIV-1 group M and SIVcpz strains accumulate mutations following the same molecular clock. As a consequence, it was possible to estimate that the most recent common ancestor of HIV-1 group M and SIVcpz dates from around 1800. These results shed new light on the origin of AIDS pandemic and seem to indicate a long time interval between HIV-1 origin and the first reported waves of the AIDS epidemic.

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