Estimating selection pressures on HIV-1 using phylogenetic likelihood models
| Autor: | Ronald J. Ellis, Selene Zárate, A. J. Leigh Brown, Satish K. Pillai, Joseph K. Wong, S. L. Kosakovsky Pond, Simon D. W. Frost, Douglas D. Richman, Art F. Y. Poon, Susan J. Little, Davey M. Smith |
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| Rok vydání: | 2008 |
| Předmět: |
Statistics and Probability
Likelihood Functions Models Statistical Phylogenetic tree Epidemiology Extramural Human immunodeficiency virus (HIV) virus diseases Computational biology Group-specific antigen Biology medicine.disease_cause Virology gag Gene Products Human Immunodeficiency Virus Virus Article Data sequences Phylogenetics medicine HIV-1 Humans Selection Genetic Selection (genetic algorithm) Phylogeny |
| Zdroj: | Statistics in medicine. 27(23) |
| ISSN: | 0277-6715 |
| Popis: | Human immunodeficiency virus (HIV-1) can rapidly evolve due to selection pressures exerted by HIV-specific immune responses, antiviral agents, and to allow the virus to establish infection in different compartments in the body. Statistical models applied to HIV-1 sequence data can help to elucidate the nature of these selection pressures through comparisons of non-synonymous (or amino acid changing) and synonymous (or amino acid preserving) substitution rates. These models also need to take into account the non-independence of sequences due to their shared evolutionary history. We review how we have developed these methods and have applied them to characterize the evolution of HIV-1 in vivo. To illustrate our methods, we present an analysis of compartment-specific evolution of HIV-1 env in blood and cerebrospinal fluid and of site-to-site variation in the gag gene of subtype C HIV-1. |
| Databáze: | OpenAIRE |
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