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Intrahost simian immunodeficiency virus (SIV) evolution is marked by repeatedviral escape from cytotoxic T-lymphocyte (CTLs) response. Typically, the firstsuch CTL escape occurs in a matter of days, starting around the time of peakviral load. Many authors have developed methods to quantify the strength of CTLresponse by measuring the rate at which CTL escape occurs, but such methodsusually depend on sampling at two or more timepoints, while many datasetscapture the dynamics of the first CTL escape at only a single timepoint. Here,we develop inference methods for CTL escape rates applicable to singletimepoint datasets. Through a model of early infection dynamics, we constructconfidence intervals for escape rates, but since early infection dynamics arenot completely understood, we also develop a one-sided confidence intervalserving as a lower bound for escape rates over a collection of early infectionmodels. We apply our methods to two SIV datasets, using our lower bounds andexisting methods to show that escape rates are relatively high during theinitial days of the first CTL escape and then drop to lower levels as theescape proceeds. We also compare escape in the lymph nodes and the rectalmucosa, showing that escape in the lymph nodes is initially faster, but as thefirst escape proceeds, the rate of escape in the lymph nodes drops below therate seen in the rectal mucosa.

Constructing Lower-Bounds for CTL Escape Rates in Early HIV and SIV Infection