Background: To combat the pandemic of human immunodeficiency virus 1 (HIV-1), a successful vaccine will need
to cope with the variability of transmissible viruses. Human hosts infected with HIV-1 potentially harbour many viral
variants but very little is known about viruses that are likely to be transmitted, or even if there are viral
characteristics that predict enhanced transmission in vivo. We show for the first time that genetic divergence
consistent with a single transmission event in vivo can represent several years of pre-transmission evolution.
Results: We describe a highly unusual case consistent with a single donor transmitting highly related but distinct
HIV-1 variants to two individuals on the same evening. We confirm that the clustering of viral genetic sequences,
present within each recipient, is consistent with the history of a single donor across the viral env, gag and pol
genes by maximum likelihood and Bayesian Markov Chain Monte Carlo based phylogenetic analyses. Based on an
uncorrelated, lognormal relaxed clock of env gene evolution calibrated with other datasets, the time since the
most recent common ancestor is estimated as 2.86 years prior to transmission (95% confidence interval 1.28 to
4.54 years).
Conclusion: Our results show that an effective design for a preventative vaccine will need to anticipate extensive
HIV-1 diversity within an individual donor as well as diversity at the population level.