As Fig 1 but for DENV2-infected subjects.

<p>The left hand axis shows log₁₀ viral copies/ml of plasma in black. The right hand axis shows IgG titres in red and IgM titres in purple (both on a linear scale). Each box represents the viral and antibody measurements of a different individual. Unfilled marker symbols show measurements below the assay limit of detection for virus and above the upper limit of reliable (linear) quantification for IgG and IgM [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004951#pcbi.1004951.ref013" target="_blank">13</a>]. All subjects were classified as secondary infections.</p

Summary of data characteristics.

<p>Summary of data characteristics.</p

The parameters of the model and values if fixed.

<p>References for fixed parameter assignments are given.</p

Parameter estimates for the model with virus neutralisation, in which antibody removes virus (Model 2).

<p>The model was separately fitted to IgM data for DENV1 and DENV2 infections. For immune response parameters and the incubation period which are patient specific parameters, median (IQR) and min and max are reported. For the group-level parameter <i>δ</i>, the median and (95% CI) are reported. Parameters z₀, <i>η</i>_<i>1</i>, <i>η</i>_<i>2</i>, <i>IP</i> and <i>SF</i> were fitted as patient specific and others as common to all patients in the fitted group.</p

Measured RNA and antibody titres over time for DENV1-infected subjects.

<p>The left hand axis shows log₁₀ RNA copies/ml of plasma in black. The right hand axis shows IgG titres in red and IgM titres in purple (both on a linear scale). Each box represents the viral and antibody measurements of a different individual. Unfilled marker symbols show measurements below the assay limit of detection for virus and above the upper limit of reliable (linear) quantification for IgG and IgM [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004951#pcbi.1004951.ref013" target="_blank">13</a>]. Subjects classified as primary infections are outlined in green. Patient 15, who shows the lowest RNA titres overall, is outlined in black.</p

As Fig 5 but for DENV2-infected subjects.

<p>Fit of the model to virus and IgM measurements for DENV1-infected subjects for the ADCC model variant. Each plot shows an individual patient. Virus data is shown in black and IgM data in purple. Parameters <i>z</i>_<i>0</i>, <i>η</i>_<i>1</i>, <i>η</i>_<i>2</i>, <i>IP</i> and <i>SF</i> fitted as patient specific, other parameters fitted per group. Mauve, grey and blue curves show 100 samples from the posterior distributions of antibody, virus and target cell trajectories, respectively. Median fits are shown as bold lines (purple shows IgM, black shows virus). Parameter estimates are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004951#pcbi.1004951.t003" target="_blank">Table 3</a>. All subjects were classified as secondary infections.</p

Fit of the model to virus and IgM measurements for DENV1-infected subjects for the ADCC model variant.

<p>Each plot shows an individual patient. Virus data is shown in black and IgM data in purple. Parameters <i>z</i>_<i>0</i>, <i>η</i>_<i>1</i>, <i>η</i>_<i>2</i>, <i>IP</i> and <i>SF</i> fitted as patient specific, other parameters fitted per group. Mauve, grey and blue curves show 100 samples from the posterior distributions of antibody, virus and target cell trajectories, respectively. Median fits are shown as bold lines (purple shows IgM, black shows virus). Parameter estimates are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004951#pcbi.1004951.t003" target="_blank">Table 3</a>. Subjects classified as primary infections highlighted with green outline.</p

Fit of the model to virus and IgM measurements for DENV1-infected subjects for the model variant in which antibody removed virus.

<p>Each plot shows an individual patient. Virus data is shown in black and IgM data in purple. Parameters <i>z</i>_<i>0</i>, <i>η</i>_<i>1</i>, <i>η</i>_<i>2</i>, <i>IP</i> and <i>SF</i> fitted as patient specific, other parameters fitted per group. Mauve, grey and blue curves show 100 samples from the posterior distributions of antibody, virus and target cell trajectories, respectively. Median fits are shown as bold lines (purple shows IgM, black shows virus). Parameter estimates are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004951#pcbi.1004951.t002" target="_blank">Table 2</a>. Subjects classified as primary infections highlighted with green outline.</p

Parameter estimates for the model with ADCC, in which antibody removes infected cells (Model 1).

<p>The model was separately fitted to IgM data for DENV1 and DENV2 infections. For patient specific parameters (i.e. the immune response parameters and the incubation period, IP), median [IQR] and {minimum, maximum} estimates across subjects are reported. For parameters assumed to be the same for all infections with the same serotype (<i>κ</i>), the median posterior estimate and 95% CI are reported. Parameters z₀, <i>η</i>_<i>1</i>, <i>η</i>_<i>2</i>, <i>IP</i> and <i>SF</i> were fitted as patient-specific and others as common to all patients in the fitted group.</p

As Fig 3 but for DENV2-infected subjects.

<p>Fit of the model to virus and IgM measurements for DENV1-infected subjects for the model variant in which antibody removed virus. Each plot shows an individual patient. Virus data is shown in black and IgM data in purple. Parameters <i>z</i>_<i>0</i>, <i>η</i>_<i>1</i>, <i>η</i>_<i>2</i>, <i>IP</i> and <i>SF</i> fitted as patient specific, other parameters fitted per group. Mauve, grey and blue curves show 100 samples from the posterior distributions of antibody, virus and target cell trajectories, respectively. Median fits are shown as bold lines (purple shows IgM, black shows virus). Parameter estimates are shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004951#pcbi.1004951.t002" target="_blank">Table 2</a>. All subjects were classified as secondary infections.</p