Modeling the heterogeneity in COVID-19's reproductive number and its impact on predictive scenarios

The correct evaluation of the reproductive number $R$ for COVID-19 -- which characterizes the average number of secondary cases generated by each typical primary case -- is central in the quantification of the potential scope of the pandemic and the selection of an appropriate course of action. In most models, $R$ is modeled as a ``universal" constant for the virus across outbreak clusters and individuals -- effectively averaging the effect of the inherent variability of the transmission process due to varying population densities, demographics, temporal factors, etc. Yet, due to the exponential nature of epidemics growth, this simplification can lead to inaccurate predictions and/or risk evaluation, thus begging the question: how large is the impact of this simplification on predictions and risk estimates? How can this variability be percolated in the projections for the pandemics so as to provide a more accurate uncertainty quantification? In this perspective, instead of considering a single, fixed $R$, we model the reproductive number as a distribution sampled from a simple Bayesian hierarchical model. Using our fitted model, we then simulate the spread of the epidemic as well as the impact of different social distancing strategies, and highlight the strong impact of this added variability on the reported results. We emphasize that our goal is not to replace benchmark methods for estimating the reproductive numbers, nor to pretend to more accurate predictive scenarios. Rather, we focus solely on discussing the importance of the impact of $R$'s heterogeneity on uncertainty quantification for the current COVID-19 pandemic.

[1]  G. Danuser,et al.  Estimation of the fraction of COVID-19 infected people in U.S. states and countries worldwide. , 2021, PloS one.

[2]  P. Nouvellet,et al.  Estimation of Transmissibility in the Early Stages of a Disease Outbreak [R package earlyR version 0.0.5] , 2020 .

[3]  Quentin J. Leclerc,et al.  Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections , 2020, BMC Medicine.

[4]  G. Danuser,et al.  Estimation of the fraction of COVID-19 infected people in U.S. states and countries worldwide , 2020, medRxiv.

[5]  A. Salas,et al.  Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders , 2020, Genome research.

[6]  L. Dwivedi,et al.  Estimates of serial interval for COVID-19: A systematic review and meta-analysis , 2020, Clinical Epidemiology and Global Health.

[7]  Claire Donnat,et al.  A Bayesian Hierarchical Network for Combining Heterogeneous Data Sources in Medical Diagnoses , 2020, 2007.13847.

[8]  K. Khunti,et al.  Socio-demographic heterogeneity in the prevalence of COVID-19 during lockdown is associated with ethnicity and household size: Results from an observational cohort study , 2020, EClinicalMedicine.

[9]  Mikhail Prokopenko,et al.  Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling , 2020, Nature Medicine.

[10]  Shaobo He,et al.  SEIR modeling of the COVID-19 and its dynamics , 2020, Nonlinear Dynamics.

[11]  Petrônio C. L. Silva,et al.  COVID-ABS: An agent-based model of COVID-19 epidemic to simulate health and economic effects of social distancing interventions , 2020, Chaos, Solitons & Fractals.

[12]  A. Marzuoli,et al.  Socioeconomic Network Heterogeneity and Pandemic Policy Response , 2020, SSRN Electronic Journal.

[13]  Jean Dolbeault,et al.  Social heterogeneity and the COVID-19 lockdown in a multi-group SEIR model , 2020, medRxiv.

[14]  COVID-19 Super-spreaders: Definitional Quandaries and Implications , 2020, Asian bioethics review.

[15]  Eleanor M. Rees,et al.  Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study , 2020, BMC Medicine.

[16]  Lu Wang,et al.  Evaluating Transmission Heterogeneity and Super-Spreading Event of COVID-19 in a Metropolis of China , 2020, medRxiv.

[17]  J. Dolbeault,et al.  Heterogeneous social interactions and the COVID-19 lockdown outcome in a multi-group SEIR model , 2020, Mathematical Modelling of Natural Phenomena.

[18]  K. Deforche An age-structured epidemiological model of the Belgian COVID-19 epidemic , 2020, medRxiv.

[19]  Anna Rotkirch,et al.  Universal Masking is Urgent in the COVID-19 Pandemic: SEIR and Agent Based Models, Empirical Validation, Policy Recommendations , 2020, ArXiv.

[20]  Wladimir Lyra,et al.  COVID-19 pandemics modeling with SEIR(+CAQH), social distancing, and age stratification. The effect of vertical confinement and release in Brazil. , 2020, medRxiv.

[21]  Yanjun Shi,et al.  Impact of meteorological factors on the COVID-19 transmission: A multi-city study in China , 2020, Science of The Total Environment.

[22]  Alastair Grant,et al.  Dynamics of COVID‐19 epidemics: SEIR models underestimate peak infection rates and overestimate epidemic duration , 2020, medRxiv.

[23]  A. Notari Temperature dependence of COVID-19 transmission , 2020, Science of The Total Environment.

[24]  Ming Wang,et al.  Identification of a super-spreading chain of transmission associated with COVID-19 , 2020, medRxiv.

[25]  Mikhail Prokopenko,et al.  Modelling transmission and control of the COVID-19 pandemic in Australia , 2020, Nature Communications.

[26]  L. Meyers,et al.  Serial Interval of COVID-19 among Publicly Reported Confirmed Cases , 2020, Emerging infectious diseases.

[27]  Hiroshi Nishiura,et al.  Ascertainment rate of novel coronavirus disease (COVID-19) in Japan , 2020, International Journal of Infectious Diseases.

[28]  Shilei Zhao,et al.  Modeling the epidemic dynamics and control of COVID-19 outbreak in China , 2020, Quantitative Biology.

[29]  G. Leung,et al.  Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study , 2020, The Lancet.

[30]  L. Yang,et al.  Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak , 2020, bioRxiv.

[31]  D. Cummings,et al.  Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions , 2020, medRxiv.

[32]  Timothy F. Leslie,et al.  Complexity of the Basic Reproduction Number (R0) , 2019, Emerging infectious diseases.

[33]  Jiqiang Guo,et al.  Stan: A Probabilistic Programming Language. , 2017, Journal of statistical software.

[34]  Michael Betancourt,et al.  A Conceptual Introduction to Hamiltonian Monte Carlo , 2017, 1701.02434.

[35]  Andrew Gelman,et al.  The No-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo , 2011, J. Mach. Learn. Res..

[36]  C. Fraser,et al.  A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics , 2013, American journal of epidemiology.

[37]  C. Fraser Estimating Individual and Household Reproduction Numbers in an Emerging Epidemic , 2007, PloS one.

[38]  B. Finkenstädt,et al.  Statistical Inference in a Stochastic Epidemic SEIR Model with Control Intervention: Ebola as a Case Study , 2006, Biometrics.

[39]  Herbert W. Hethcote,et al.  The Mathematics of Infectious Diseases , 2000, SIAM Rev..

[40]  Daryl J. Daley,et al.  Epidemic Modelling: An Introduction , 1999 .

[41]  HighWire Press Proceedings of the Royal Society of London. Series A, Containing papers of a mathematical and physical character , 1934 .

[42]  W. O. Kermack,et al.  A contribution to the mathematical theory of epidemics , 1927 .