Modeling viral coevolution HIV multi-clonal persistence and competition dynamics.pdf

Modeling viral coevolution: HIV multi-clonal persistence and competition dynamics F. Bagnoli a,c,1, P. Li`o b,2 , L. Sguanci a,c,3 5 0 0 aDipartimento di Energetica, Universit`a di Firenze, Via S. Marta 3, 50139 2 Firenze, Italy. p b e Computer Laboratory, University of Cambridge, CB3 0FD Cambridge, UK. S c INFN, sezione di Firenze and CSDC. 7 ] E P . o Abstract i b - The coexistence of different viral strains (quasispecies) within the same host are q [ nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have 1 v not yet been understood. We present a model of HIV quasispecies competition, 6 that describes the conditions of viral quasispecies coexistence under different im- 0 mune system conditions. Our model incorporates both T and B cells responses, 0 9 and we show that the role of B cells is important and additive to that of T cells. 0 Simulations of coinfection (simultaneous infection) and superinfection (delayed sec- 5 ondary infection) scenarios in the early stages (days) and in the late stages of the 0 / infection (years) are in agreement with emerging molecular biology findings. The o i immune response induces a competition among similar phenotypes, leading to dif- b- ferentiation (quasi-speciation), escape dynamics and complex oscillations of viral q strain abundance. We found that the quasispecies dynamics after superinfection or : v coinfection has time scal