Staff

Abstract:
When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells. The model enables investigation of the impact of immunostimulatory defective viral particles and signaling network perturbations that could potentially facilitate containment or clearance of the viral infection.

Abstract:
Resolving practical non-identifiability of computational models typically requires either additional data or non-algorithmic model reduction, which frequently results in models containing parameters lacking direct interpretation. Here, instead of reducing models, we explore an alternative, Bayesian approach, and quantify the predictive power of non-identifiable models. We considered an example biochemical signalling cascade model as well as its mechanical analogue. For these models, we demonstrated that by measuring a single variable in response to a properly chosen stimulation protocol, the dimensionality of the parameter space is reduced, which allows for predicting the measured variable’s trajectory in response to different stimulation protocols even if all model parameters remain unidentified. Moreover, one can predict how such a trajectory will transform in the case of a multiplicative change of an arbitrary model parameter. Successive measurements of remaining variables further reduce the dimensionality of the parameter space and enable new predictions. We analysed potential pitfalls of the proposed approach that can arise when the investigated model is oversimplified, incorrect, or when the training protocol is inadequate. The main advantage of the suggested iterative approach is that the predictive power of the model can be assessed and practically utilised at each step.

Abstract:
Omicron, the novel highly mutated SARS-CoV-2 Variant of Concern (VOC, Pango lineage B.1.1.529) was first collected in early November 2021 in South Africa. By the end of November 2021, it had spread and approached fixation in South Africa, and had been detected on all continents. We analyzed the exponential growth of Omicron over four-week periods in the two most populated of South Africa’s provinces, Gauteng and KwaZulu-Natal, arriving at the doubling time estimates of, respectively, 3.3 days (95% CI: 3.2–3.4 days) and 2.7 days (95% CI: 2.3–3.3 days). Similar or even shorter doubling times were observed in other locations: Australia (3.0 days), New York State (2.5 days), UK (2.4 days), and Denmark (2.0 days). Log–linear regression suggests that the spread began in Gauteng around 11 October 2021; however, due to presumable stochasticity in the initial spread, this estimate can be inaccurate. Phylogenetics-based analysis indicates that the Omicron strain started to diverge between 6 October and 29 October 2021. We estimated that the weekly growth of the ratio of Omicron to Delta is in the range of 7.2–10.2, considerably higher than the growth of the ratio of Delta to Alpha (estimated to be in in the range of 2.5–4.2), and Alpha to pre-existing strains (estimated to be in the range of 1.8–2.7). High relative growth does not necessarily imply higher Omicron infectivity. A two-strain SEIR model suggests that the growth advantage of Omicron may stem from immune evasion, which permits this VOC to infect both recovered and fully vaccinated individuals. As we demonstrated within the model, immune evasion is more concerning than increased transmissibility, because it can facilitate larger epidemic outbreaks.

Keywords:
COVID-19 pandemic, SARS-CoV-2, Omicron variant, genome sequencing, mutation

Abstract:
The novel SARS-CoV-2 Variant of Concern (VOC)-202012/01 (also known as B.1.1.7), first collected in United Kingdom on 20 September 2020, is a rapidly growing lineage that in January 2021 constituted 86% of all SARS-CoV-2 genomes sequenced in England. The VOC has been detected in 40 out of 46 countries that reported at least 50 genomes in January 2021. We have estimated that the replicative advantage of the VOC is in the range 1.83–2.18 [95% CI: 1.71–2.40] with respect to the 20A.EU1 variant that dominated in England in November 2020, and in range 1.65–1.72 [95% CI: 1.46–2.04] in Wales, Scotland, Denmark, and USA. As the VOC strain will likely spread globally towards fixation, it is important to monitor its molecular evolution. We have estimated growth rates of expanding mutations acquired by the VOC lineage to find that the L18F substitution in spike has initiated a fast growing VOC substrain. The L18F substitution is of significance because it has been found to compromise binding of neutralizing antibodies. Of concern are immune escape mutations acquired by the VOC: E484K, F490S, S494P (in the receptor binding motif of spike) and Q677H, Q675H (in the proximity of the polybasic cleavage site at the S1/S2 boundary). These mutants may hinder efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine-induced seroprevalence.

Keywords:
COVID-19 pandemic, SARS-CoV-2, spike protein, VOC-202012/01, spike L18F, genome sequencing, mutation

Abstract:
The basic reproduction number R0 of the coronavirus disease 2019 has been estimated to range between 2 and 4. Here, we used an SEIR model that properly accounts for the distribution of the latent period and, based on empirical estimates of the doubling time in the near-exponential phases of epidemic progression in China, Italy, Spain, France, UK, Germany, Switzerland and New York State, we estimated that R0 lies in the range 4.7-11.4. We explained this discrepancy by performing stochastic simulations of model dynamics in a population with a small proportion of super-spreaders. The simulations revealed two-phase dynamics, in which an initial phase of relatively slow epidemic progression diverts to a faster phase upon appearance of infectious super-spreaders. Early estimates obtained for this initial phase may suggest lower R0.

Keywords:
COVID-19, reproduction number

Abstract:
We constructed a simple Susceptible−Exposed–Infectious–Removed model of the spread of COVID-19. The model is parametrised only by the average incubation period, τ, and two rate parameters: contact rate, β, and exclusion rate, γ. The rates depend on nontherapeutic interventions and determine the basic reproduction number, R0 = β/γ, and, together with τ, the daily multiplication coefficient in the early exponential phase, θ. Initial R0 determines the reduction of β required to contain the spread of the epidemic. We demonstrate that introduction of a cascade of multiple exposed states enables the model to reproduce the distributions of the incubation period and the serial interval reported by epidemiologists. Using the model, we consider a hypothetical scenario in which β is modulated solely by anticipated changes of social behaviours: first, β decreases in response to a surge of daily new cases, pressuring people to self-isolate, and then, over longer time scale, β increases as people gradually accept the risk. In this scenario, initial abrupt epidemic spread is followed by a plateau and slow regression, which, although economically and socially devastating, grants time to develop and deploy vaccine or at least limit daily cases to a manageable number.

Keywords:
basic reproduction number, novel coronavirus

Abstract:
Two important signalling pathways of NF-κB and ERK transmit merely 1 bit of information about the level of extracellular stimulation. It is thus unclear how such systems can coordinate complex cell responses to external cues. We analyse information transmission in the MAPK/ERK pathway that converts both constant and pulsatile EGF stimulation into pulses of ERK activity. Based on an experimentally verified computational model, we demonstrate that, when input consists of sequences of EGF pulses, transmitted information increases nearly linearly with time. Thus, pulse-interval transcoding allows more information to be relayed than the amplitude–amplitude transcoding considered previously for the ERK and NF-κB pathways. Moreover, the information channel capacity C, or simply bitrate, is not limited by the bandwidth B = 1/τ, where τ ≈ 1 h is the relaxation time. Specifically, when the input is provided in the form of sequences of short binary EGF pulses separated by intervals that are multiples of τ/n (but not shorter than τ), then for n = 2, C ≈ 1.39 bit/h^-1; and for n = 4, C ≈ 1.86 bit/h^-1. The capability to respond to random sequences of EGF pulses enables cells to propagate spontaneous ERK activity waves across tissue.

Keywords:
cellular signal transduction, pulsatile stimulation, pulse-interval transcoding, bandwidth, representation problem

Abstract:
Mutual information is a general statistical dependency measure which has found applications in representation learning, causality, domain generalization and computational biology. However, mutual information estimators are typically evaluated on simple families of probability distributions, namely multivariate normal distribution and selected distributions with one-dimensional random variables. In this paper, we show how to construct a diverse family of distributions with known ground-truth mutual information and propose a language-independent benchmarking platform for mutual information estimators. We discuss the general applicability and limitations of classical and neural estimators in settings involving high dimensions, sparse interactions, long-tailed distributions, and high mutual information. Finally, we provide guidelines for practitioners on how to select appropriate estimator adapted to the difficulty of problem considered and issues one needs to consider when applying an estimator to a new data set.