| Literature DB >> 35018194 |
Abstract
How will the novel coronavirus evolve? I study a simple epidemiological model, in which mutations may change the properties of the virus and its associated disease stochastically and antigenic drifts allow new variants to partially evade immunity. I show analytically that variants with higher infectiousness, longer disease duration, and shorter latent period prove to be fitter. "Smart" containment policies targeting symptomatic individuals may redirect the evolution of the virus, as they give an edge to variants with a longer incubation period and a higher share of asymptomatic infections. Reduced mortality, on the other hand, does not per se prove to be an evolutionary advantage. I then implement this model as an agent-based simulation model in order to explore its aggregate dynamics. Monte Carlo simulations show that a) containment policy design has an impact on both speed and direction of viral evolution, b) the virus may circulate in the population indefinitely, provided that containment efforts are too relaxed and the propensity of the virus to escape immunity is high enough, and crucially c) that it may not be possible to distinguish between a slowly and a rapidly evolving virus by looking only at short-term epidemiological outcomes. Thus, what looks like a successful mitigation strategy in the short run, may prove to have devastating long-run effects. These results suggest that optimal containment policy must take the propensity of the virus to mutate and escape immunity into account, strengthening the case for genetic and antigenic surveillance even in the early stages of an epidemic.Entities:
Keywords: Agent-based model; Covid-19; Pandemic; Phylodynamic model; SARS-CoV2; SIR model
Year: 2022 PMID: 35018194 PMCID: PMC8739737 DOI: 10.1007/s11403-021-00344-3
Source DB: PubMed Journal: J Econ Interact Coord ISSN: 1860-711X
Fig. 1Variant-specific SEPAIRD model
Fig. 2Example phylogenetic tree of different variants. Different colors denote different antigenic clusters
Parameters of the simulation
| Parameter | Symbol | Value |
|---|---|---|
| human agents | 10,000 | |
| initially infected agents | 10 | |
| daily contacts | 10 | |
| initial infectiousness | 6.25% | |
| initial end of the latent period | 4 | |
| initial end of the incubation period | 6 | |
| initial duration | 8 | |
| initial fatality rate | 1% | |
| initial symptomatic chance | 70% | |
| actual time standard deviation | 0.1 | |
| probability of a mutation | 0/0.5/1/2% | |
| mutation mean | 0 | |
| mutation standard deviation | 0.05 | |
| cross immunity between antigenic clusters | 0/50/90% | |
| cross protection against a lethal infection | 90/99% | |
| probability of antigenic drift during a mutation | 10% | |
| Isolation upon developing symptoms | yes / no | |
| social distancing | 0–80% |
Fig. 3Mean R0 of active (or, in case of extinction, last surviving) variants at simulation step 500 without isolation of symptomatic individuals and with 99% cross protection against a lethal infection (notched box plot)
Fig. 4Mean R0 of active (or, in case of extinction, last surviving) variants at simulation step 500 with isolation of symptomatic individuals and with 99% cross protection against a lethal infection (notched box plot)
Fig. 5Mean of active (or, in case of extinction, last surviving) variants at simulation step 500 without isolation of symptomatic individuals and with 99% cross protection against a lethal infection (notched box plot)
Fig. 6Mean of active (or, in case of extinction, last surviving) variants at simulation step 500 with isolation of symptomatic individuals and with 99% cross protection against a lethal infection (notched box plot)
Fig. 7Mortality rate in the first 100 simulation steps with 99% cross protection against a lethal infection (quantile regressions)
Fig. 8Share of infected agents in the first 100 simulation steps with 99% cross protection against a lethal infection (quantile regressions)
Fig. 9Share of infected agents in the first 500 simulation steps with 99% cross protection against a lethal infection (quantile regressions)
Fig. 10Mortality rate in the first 500 simulation steps with 99% cross protection against a lethal infection (quantile regressions)
Fig. 11Mortality rate in the first 500 simulation steps with 90% cross protection against a lethal infection (quantile regressions)
Fig. 12Maximum antigenic distance to wild-type in the first 500 simulation steps with 99% cross protection against a lethal infection (quantile regressions)
Fig. 13Mean phylogenetic distance of active variants to wild-type in the first 500 simulation steps with 99% cross protection against a lethal infection (quantile regressions)