Fig. 2: Model fits quantify heterogeneity in viral dynamics and discordance in genome shedding between nasal and saliva samples.
a, Diagrams outlining structures of the refractory cell and immune effector cell models that best fit nasal swab and saliva RT–qPCR data, respectively. In the refractory cell model, target cells (T) are infected by viruses (V) at rate β. Infected cells first become eclipse cells (E) and do not produce viruses; at rate k, eclipse cells become productively infected cells (I) producing both viruses and interferon (F) at rates π and s, respectively; they die at rate δ. Binding of interferons with target cells induces an antiviral response that converts target cells into cells refractory to infection (R). The rate of induction of the antiviral response is Φ. Refractory cells can revert to target cells at rate ρ. In the effector cell model we assume that, over the course of infection, immune effector cells (X) that clear infected cells are activated and recruited, leading to an increase in infected cell death rate from δ1 to δ1 + δ2. b, Model fits to nasal sample (navy blue) and saliva (teal) RT–qPCR results from the same subset of individuals shown in Fig. 1a; includes last recorded negative saliva RT–qPCR result before study enrolment. Dotted lines represent the limit of detection (LoD) for RT–qPCR assays; dots on dotted lines denote measurements under LoD. c,d, Distributions of exponential viral growth rates, days from infection to peak viral genome load and days from peak to undetectable viral genome loads predicted by the refractory cell model (nasal data, c) and the immune effector model (saliva data, d) across 56 individuals in this cohort. e, Association between age and the estimated strength of innate immune response (Φ) based on nasal sample data. The y axis is shown on a log10 scale. Associations were examined using standard linear regression analysis, with R2 and P values reported. f, Distribution of differences in estimated times of peak viral genome loads between saliva and nasal samples. Bars coloured teal and navy blue represent estimated saliva peaks that occurred at least 0.5 day earlier or later than nasal samples, respectively; grey bar indicates the number of individuals with similar timing in peaks.
