Within-Host Viral Growth and Immune Response Rates Predict Foot-and-Mouth Disease Virus Transmission Dynamics for African Buffalo

AbstractInfectious disease dynamics operate across biological scales: pathogens replicate within hosts but transmit among populations. Functional changes in the pathogen-host interaction thus generate cascading effects across organizational scales. We investigated within-host dynamics and among-host transmission of three strains (SAT-1, -2, -3) of foot-and-mouth disease viruses (FMDVs) in their wildlife host, African buffalo. We combined data on viral dynamics and host immune responses with mathematical models to ask the following questions: How do viral and immune dynamics vary among strains? Which viral and immune parameters determine viral fitness within hosts? And how do within-host dynamics relate to virus transmission? Our data reveal contrasting within-host dynamics among viral strains, with SAT-2 eliciting more rapid and effective immune responses than SAT-1 and SAT-3. Within-host viral fitness was overwhelmingly determined by variation among hosts in immune response activation rates but not by variation among individual hosts in viral growth rate. Our analyses investigating across-scale linkages indicate that viral replication rate in the host correlates with transmission rates among buffalo and that adaptive immune activation rate determines the infectious period. These parameters define the virus's relative basic reproductive number (ℛ0), suggesting that viral invasion potential may be predictable from within-host dynamics.

Disparity-driven heterogeneous nucleation in finite-size adaptive networks

Phase transitions are crucial in shaping the collective dynamics of a broad spectrum of natural systems across disciplines. Here, we report two distinct heterogeneous nucleation facilitating single step and multistep phase transitions to global synchronization in a finite-size adaptive network due to the trade off between time scale adaptation and coupling strength disparities. Specifically, small intracluster nucleations coalesce either at the population interface or within the populations resulting in the two distinct phase transitions depending on the degree of the disparities. We find that the coupling strength disparity largely controls the nature of phase transition in the phase diagram irrespective of the adaptation disparity. We provide a mesoscopic description for the cluster dynamics using the collective coordinates approach that brilliantly captures the multicluster dynamics among the populations leading to distinct phase transitions. Further, we also deduce the upper bound for the coupling strength for the existence of two intraclusters explicitly in terms of adaptation and coupling strength disparities. These insights may have implications across domains ranging from neurological disorders to segregation dynamics in social networks.

Compositional modelling of immune response and virus transmission dynamics

Transmission models for infectious diseases are typically formulated in terms of dynamics between individuals or groups with processes such as disease progression or recovery for each individual captured phenomenologically, without reference to underlying biological processes. Furthermore, the construction of these models is often monolithic: they do not allow one to readily modify the processes involved or include the new ones, or to combine models at different scales. We show how to construct a simple model of immune response to a respiratory virus and a model of transmission using an easily modifiable set of rules allowing further refining and merging the two models together. The immune response model reproduces the expected response curve of PCR testing for COVID-19 and implies a long-tailed distribution of infectiousness reflective of individual heterogeneity. This immune response model, when combined with a transmission model, reproduces the previously reported shift in the population distribution of viral loads along an epidemic trajectory. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Tracking the national and regional COVID-19 epidemic status in the UK using weighted principal component analysis

One of the difficulties in monitoring an ongoing pandemic is deciding on the metric that best describes its status when multiple intercorrelated measurements are available. Having a single measure, such as the effective reproduction number [Formula: see text], has been a simple and useful metric for tracking the epidemic and for imposing policy interventions to curb the increase when [Formula: see text]. While [Formula: see text] is easy to interpret in a fully susceptible population, it is more difficult to interpret for a population with heterogeneous prior immunity, e.g. from vaccination and prior infection. We propose an additional metric for tracking the UK epidemic that can capture the different spatial scales. These are the principal scores from a weighted principal component analysis. In this paper, we have used the methodology across the four UK nations and across the first two epidemic waves (January 2020-March 2021) to show that first principal score across nations and epidemic waves is a representative indicator of the state of the pandemic and is correlated with the trend in R. Hospitalizations are shown to be consistently representative; however, the precise dominant indicator, i.e. the principal loading(s) of the analysis, can vary geographically and across epidemic waves. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Estimation and optimal control of the multiscale dynamics of Covid-19: a case study from Cameroon

This work aims at a better understanding and the optimal control of the spread of the new severe acute respiratory corona virus 2 (SARS-CoV-2). A multi-scale model giving insights on the virus population dynamics, the transmission process and the infection mechanism is proposed first. Indeed, there are human to human virus transmission, human to environment virus transmission, environment to human virus transmission and self-infection by susceptible individuals. The global stability of the disease-free equilibrium is shown when a given threshold T 0 is less or equal to 1 and the basic reproduction number R 0 is calculated. A convergence index T 1 is also defined in order to estimate the speed at which the disease extincts and an upper bound to the time of infectious extinction is given. The existence of the endemic equilibrium is conditional and its description is provided. Using Partial Rank Correlation Coefficient with a three levels fractional experimental design, the sensitivity of  R 0 , T 0 and T 1 to control parameters is evaluated. Following this study, the most significant parameter is the probability of wearing mask followed by the probability of mobility and the disinfection rate. According to a functional cost taking into account economic impacts of SARS-CoV-2, optimal fighting strategies are determined and discussed. The study is applied to real and available data from Cameroon with a model fitting. After several simulations, social distancing and the disinfection frequency appear as the main elements of the optimal control strategy against SARS-CoV-2.