Max-Planck-Institut für Informatik
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Viral Recombination

Our goal is to extract details on the recombination process from molecular sequence data. To be more specific, we want to find out which sequences are subject to recombination and where recombination breakpoints occurred. As sequence variation can arise both due to mutation and recombination, it is crucial to develop statistical tests that quantify the support of the generated recombination hypotheses. The statistical nature of the problem also makes validation a necessity.

An important application for our method is the analysis of rapidly evolving pathogens such as HIV. Due to its highly variable genome, HIV has a striking ability to cause persistent infections, develop drug resistance and evade immune response. Interestingly, an important source for genetic variation in HIV is not only point mutation, but also recombination with estimates indicating a 10-fold higher frequency of recombination over mutation [1].

Figure 1:
HIV (upper left) virions budding from an infected human immune cell (lower right). Image courtesy of Dr. Rolf Kaiser, Institute for Virology, Cologne University

Figure 2:
An ancestral recombination graph describing the evolution of a set of sequences.
R1 is a recombinant derived from the ancestors of A1 and B1, with a recombination breakpoint in the middle of the sequence.



  1. A. Jung, R. Maier, J.P. Vartanian, G. Bocharov, V. Jung, U. Fischer, E. Meese, S. Wain-Hobson and A. Meyerhans, “Multiply infected spleen cells in HIV patients, Nature, 418:133, 2002.