Fig 1.
Viral shedding patterns of study participants.
Viral loads in the saliva of study participants were measured daily via qPCR for a median of 29 days. Swabs up to 30 days post initiating observation are shown. Each plot represents the shedding pattern of a separate participant. Patients are arranged according to their median viral load. The grey horizontal line represents the threshold of EBV detection (150 EBV copies/ml).
Fig 2.
Impact of HIV-1 coinfection on oral EBV replication.
A. Percentages of saliva samples that tested positive for EBV for each participant. Black dots indicate the percentage of samples that tested positive for EBV when pooling participant samples. In HIV-1 uninfected participants, the median percentage of swabs positive for EBV was 86% (range 0–100%, interquartile range (IQR) 33%), while in HIV-1 coinfected participants, the median percentage of swabs positive for EBV was 100% (range 27–100%, IQR 0%). B. Median EBV viral loads/ml in oral swabs testing positive for EBV for each participant. All graphs stratify participants by HIV-1 infection status. Coloured dots show the median value of the statistic for each participant, while bars and whiskers show the spread across participants. C. Distributions of participants’ oral swab viral loads. Each box and whisker represents the viral loads of EBV-positive oral swabs for an individual participant. The percentage of oral swabs that tested positive for EBV for each participant is indicated by the colour of the box. Of swabs that tested positive for EBV, viral loads varied over time by a median of 3.49 orders of magnitude (range 0.34–5.27, IQR 1.32) within individual HIV-1 uninfected participants and a median of 2.30 orders of magnitude (range 0.95–5.93, IQR 1.15) within individual HIV-1 coinfected participants. The red horizontal line represents the threshold of EBV detection (150 EBV copies/ml). D. Participants’ BAFF levels, CD4+ T cell counts, and HIV-1 RNA loads correlated against median EBV copies/ml of saliva.
Fig 3.
Description of single crypt dynamics.
Waldeyer’s ring is represented as a series of 240 individual crypts in which infection dynamics occur. Within each crypt, the population dynamics of infected epithelial cells (I), cytotoxic T cells (T) and EBV (V) are described. The viral load detected in saliva is represented by the total virus aggregated across all crypts.
Fig 4.
The impact of varying b and θ on model simulation trajectories.
Model simulations for different pairings of values for parameters b and θ are shown (units of cell day−1 and day−1 respectively). Simulations reproduce the stochastic nature of the data and are able to capture a wide variety of EBV shedding traits. For all simulations, β = 50 day−1, f = 0.1 day−1cell−1, α = 200 cells, δ = 0.1 day−1, p = 104 virions day−1 ml−1 cell−1, and c = 6 day−1. The grey horizontal line represents the qPCR threshold of detection. All simulated viral loads below this threshold were set to zero to match with participant data.
Fig 5.
Cumulative distribution of parameters b and θ, stratified by HIV-1 status and median EBV viral load in saliva.
Fitting our mathematical model to participant data revealed that parameter b is usually greater in HIV-1 coinfected participants (A) and increases with median EBV viral load (B). Parameter θ is usually lower in HIV-1 coinfected participants (C) and decreases with median saliva EBV viral load (D). Directional arrows and numbers by figure legends indicate the probability that a randomly selected individual of one group has a higher parameter value (be it b or θ) than a randomly selected individual in a second group. Arrows show the direction of comparison.
Fig 6.
Correlation between parameters b and θ.
Obtained densities of parameters b and θ are plotted, stratified by HIV-1 infection status and median oral EBV viral load group. Across all participants, or when stratifying by HIV-1 infection status, b and θ are negatively correlated (grey lines in top plots and blue line in bottom plot). However, since b and θ have opposite effects on viral load, positive correlations are seen within each viral load group (grey lines, lower plot).
Fig 7.
Predicted numbers of active crypts and viral load per active crypt.
Cumulative distributions of the median number of crypts actively producing EBV (A and B) and the median EBV viral load produced by an active crypt at any given time (C and D) are shown stratified by participant HIV-1 status and EBV median viral load in the saliva. Increases in median salivary EBV viral load are caused by a higher number of crypts having active (B) and more extensive (D) infection. This trend translates to HIV-1 coinfected participants having more infected crypts infected, and each infected crypt producing more virus. We see that HIV-1 uninfected individuals usually have more actively infected crypts and more virus per active crypt than HIV-1 coinfected individuals. Similarly, we see that individuals with higher median viral loads in their saliva usually have more actively infected crypts and more virus per active crypt than individuals with lower median viral loads. Directional arrows and numbers by figure legends indicate the probability that a randomly selected individual of one group has a higher parameter value (be it the number of active crypts or the viral load per active crypt) compared with a randomly selected individual in a second group. Arrows show the direction of comparison.
Table 1.
Effects of plasma HIV-1 load, CD4+ T cell count and BAFF amount on the Ugandan cohort participants’ median viral load and median values of parameters b and θ.
In cohort participants, median viral load detected via qPCR and values of parameters b and θ are influenced by the CD4+ T cell count, HIV-1 plasma viral load, and the amount of BAFF in serum. The fold-change (FC) in participants’ median viral load, or model-fit b and θ values for every log10 increase in HIV-1 RNA copies/mL, every 100 CD4+ T cell/mm3 increase, and every 100 pg/ml increase in BAFF is shown. Note that data on CD4+ T cell count and HIV-1 RNA was only available for HIV-1 coinfected participants.