(Short-term) viral dynamics.

<p>Left panels (A-C): Viral decay. Right panels (D-F): Viral growth. <b>A:</b> Data used for estimating viral decay parameters <i>δ</i>_<i>h</i>, <i>δ</i>_<i>m</i>. Blue circles indicate viral decay profiles from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref041" target="_blank">41</a>], green upward pointing triangles denote data from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref042" target="_blank">42</a>], black squares denote data from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref043" target="_blank">43</a>] and red downward pointing triangles denote data from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref004" target="_blank">4</a>]. Horizontal dashed lines and background shading indicates the assignment of the depicted data to the sets ℋ (> 4000 viral RNA/mL)), ℳ and ℒ (≤ 50 viral RNA/mL) of our model. <b>B:</b> When assuming 100% effective treatment (<i>η</i> = 1), the model shown in panel B is derived. This model is used to identify decay parameters <i>δ</i>_<i>h</i> and <i>δ</i>_<i>m</i> (circled parameters in panel B). <b>C:</b> Data-derived (error bars, dashed lines) and predicted (solid lines) probabilities of states ℋ and ℒ using the model in panel B with estimated parameters <i>δ</i>_<i>h</i> and <i>δ</i>_<i>m</i>. <b>D:</b> Data from treatment interruption trials [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref043" target="_blank">43</a>–<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref045" target="_blank">45</a>] used for estimating viral growth parameters <i>k</i>_ℓ,∅, <i>k</i>_<i>m</i>,∅. Magenta diamonds indicate viral rebound profiles from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref044" target="_blank">44</a>], cyan pentagrams indicate data from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref045" target="_blank">45</a>] and black left-pointing triangles indicate data from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004200#pcbi.1004200.ref043" target="_blank">43</a>]. Horizontal dashed lines and background shading indicates the assignment of the depicted viral growth data to the sets ℋ, ℳ and ℒ. <b>E:</b> We assumed the absence of treatment (<i>η</i> = 0), such that the model shown in panel E is sufficient to decribe the data and allows identifying growth parameters <i>k</i>_ℓ,∅ and <i>k</i>_<i>m</i>,∅ (circled parameters in panel E). <b>F:</b> Data-derived (error bars, dashed lines) and predicted (solid lines) probabilities of states ℋ and ℒ using the model in panel E with <i>δ</i>_<i>h</i> and <i>δ</i>_<i>m</i> and estimated parameters <i>k</i>_ℓ,∅ and <i>k</i>_<i>m</i>,∅. The parameter estimation procedure is exemplified in the <i>Material and Methods</i> section.