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The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations.

TitleThe route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations.
Publication TypeJournal Article
Year of Publication2014
AuthorsBatorsky, R, Sergeev, RA, IM Rouzine
JournalPLoS Comput Biol
Volume10
Issue10
Paginatione1003878
Date Published2014 Oct
ISSN1553-7358
KeywordsComputational Biology, Genetic Fitness, HIV Infections, HIV-1, Humans, Mutation, T-Lymphocytes, Cytotoxic
Abstract

Cytotoxic T lymphocytes (CTL) are a major factor in the control of HIV replication. CTL arise in acute infection, causing escape mutations to spread rapidly through the population of infected cells. As a result, the virus develops partial resistance to the immune response. The factors controlling the order of mutating epitope sites are currently unknown and would provide a valuable tool for predicting conserved epitopes. In this work, we adapt a well-established mathematical model of HIV evolution under dynamical selection pressure from multiple CTL clones to include partial impairment of CTL recognition, [Formula: see text], as well as cost to viral replication, [Formula: see text]. The process of escape is described in terms of the cost-benefit tradeoff of escape mutations and predicts a trajectory in the cost-benefit plane connecting sequentially escaped sites, which moves from high recognition loss/low fitness cost to low recognition loss/high fitness cost and has a larger slope for early escapes than for late escapes. The slope of the trajectory offers an interpretation of positive correlation between fitness costs and HLA binding impairment to HLA-A molecules and a protective subset of HLA-B molecules that was observed for clinically relevant escape mutations in the Pol gene. We estimate the value of [Formula: see text] from published experimental studies to be in the range (0.01-0.86) and show that the assumption of complete recognition loss ([Formula: see text]) leads to an overestimate of mutation cost. Our analysis offers a consistent interpretation of the commonly observed pattern of escape, in which several escape mutations are observed transiently in an epitope. This non-nested pattern is a combined effect of temporal changes in selection pressure and partial recognition loss. We conclude that partial recognition loss is as important as fitness loss for predicting the order of escapes and, ultimately, for predicting conserved epitopes that can be targeted by vaccines.

DOI10.1371/journal.pcbi.1003878
Alternate JournalPLoS Comput. Biol.
PubMed ID25356981
PubMed Central IDPMC4214571
Grant ListR01AI 063926 / AI / NIAID NIH HHS / United States
R37CA 089441 / CA / NCI NIH HHS / United States