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The evolution of HPV by means of a phylogenetic study
R. Isea1, J.L. Chaves2, E. Montes3, A.J. Rubio-Montero3 and R. Mayo3
Fundación IDEA, Baruta 1080 (Venezuela)
Corp. Parque Tecnológico Mérida, Mérida 5101 (Venezuela)
3 CIEMAT, Avda. Complutense, 22, 28040 Madrid (Spain)
1
2
Abstract
In this work we calculate the evolution of the Human papillomavirus (HPV). To do so, we have analysed several phylogenetic trees which
have been calculated with the PhyloGrid tool, a workflow developed in the framework of the EELA-2 Project
The Biological problem
 20% of the female Human Being is carrier of the Human Papillomavirus (HPV)
 Cervical cancer [1] and the most transmitted sexual disease
 HPV is a double DNA circular chain (~ 8000 pair of basis)
 Genes of early expression E1, E2, E4-E7: virus regulation and replication
 Genes of late expression L1-L2: virus capsid assembly
 Currently, the virus classification is done according to L1 similarity
 Oncogenic potential
The Molecular Phylogenetic Calculation
 By means of the PhyloGrid application [2]
 Based on Bayesian statistics (MrBayes [3])
 Performed with a workflow based on Taverna [4]
 web service
 Capabilities
Definition of the parameters for doing the Bayesian calculation
 Determination of the model of evolution
 Multiple alignment of the sequences previously to the final result
Fig. 1 The Taverna workflow used for calculating with MrBayes
Results
 The EELA-2 Project e-Infrastructure has been used
 On average, one tree has consumed more than 91 hours on nine Intel Xeon X5365 3 GHz
 121 sequences from different HPVs based on the nucleotide sequence of the major capsid gene
 The phylogenetic trees derived from L1, L2 and E7 genes are showed in Figures 1 to 3
 These trees have been calculated independently and put in order for its representation
 There is a topology similarity score of 85% between genes
 There is no consistency in the derived topology  the classification based on the variability of the L1 gene is not correct
a
b
c
Fig. 2. Phylogenetic trees obtained of: a) L1 and its difference with L2 (broader lines) ; b) L1 with E7; and, c) L2 with E7
References
[1] D. R. Lowy and J. T. Schiller. J. Clin. Invest. 116 (5), 1167 (2006)
[2] R. Isea et al. Proc. First EELA-2 Conf., 139 (2009)
[3] F. Ronquist and J.P. Huelsenbeck. Bioinformatics 19, 1572 (2003)
[4] T. Oinn et al. Concurrency and Computation: Prac. Exp. 18, 1067 (2006)