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J Theor Biol. 2013 Jul 21;329:82-93. doi: 10.1016/j.jtbi.2013.03.026. Epub 2013 Apr 6.

Modeling sequence evolution in HIV-1 infection with recombination.

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  • 1Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Abstract

Previously we proposed two simplified models of early HIV-1 evolution. Both showed that under a model of neutral evolution and exponential growth, the mean Hamming distance (HD) between genetic sequences grows linearly with time. In this paper we describe a more realistic continuous-time, age-dependent mathematical model of infection and viral replication, and show through simulations that even in this more complex description, the mean Hamming distance grows linearly with time. This remains unchanged when we introduce recombination, though the confidence intervals of the mean HD obtained ignoring recombination are overly conservative.

PMID:
23567647
PMCID:
PMC3667750
DOI:
10.1016/j.jtbi.2013.03.026
[PubMed - indexed for MEDLINE]
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