Reconstruction of the Genealogy of Recombining Viruses using Phylogenetic Networks

• Applicant: Dr. Ingo Bulla
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2013 to 2015
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 237440467

The aim of the project is the development of an algorithm for the reconstruction of the genealogy of highly recombining viruses (or other species), in particular human immunodeficiency virus 1 (HIV-1). In detail, a Markov Chain Monte Carlo (MCMC) algorithm is employed to sample ancestral recombination graphs (ARGs), i.e. phylogenetic networks, proportionally to their likelihood for given input sequences of a species. Due to the high number of possible crossovers during recombination events of HIV, the modifications made during the run of the MCMC algorithm which involve recombination events have to be guided by their plausibility with respect to the input sequences. This process is carried out using a Hidden Markov Model (HMM) approach.The developed algorithm then is applied for - estimation of the probability of taxonomic features, - systematic deduction of a classification system for recombinant species, - classification of new sequences with respect to a given classification system, - estimation of evolutionary parameters (like mutation rate, recombination rate, growth rate, etc.) of recombinant species. Reliable execution of these tasks on recombining viruses (in particular HIV-1) is important for- studying the geographic epidemiology, - reconstructing their origin, - deciphering the interaction of their evolution with the immune system and drug resistances,- developing effective control strategies. The target species comprise HIV-1, hepatitis B virus (HBV), human enterovirus (HEV), white spot syndrome virus (WSSV), influenza virus, and escherichia coli (E. Coli).

• DFG Programme: Research Fellowships
• International Connection: USA
• Host: Thomas Leitner, Ph.D.