Microsimulation based quantitative analysis of COVID-19 management strategies

Abstract

SummaryBackgroundPandemic management includes a variety of control measures, such as social distancing, testing/quarantining and vaccination applied to a population where the virus is circulating. The COVID-19 (SARS-CoV-2) pandemic is mitigated by several non-pharmaceutical interventions, but it is hard to predict which of these regulations are the most effective for a given population.MethodsWe developed a computationally effective and scalable, agent-based microsimulation framework. This unified framework was fitted to realistic data to enable us to test control measures (closures, quarantining, testing, vaccination) in multiple infection waves caused by the spread of a new virus variant in a city-sized societal environment. Our framework is capable of simulating nine billion agent-steps per minute, allowing us to model interactions in populations with up to 90 million individuals.FindingsWe show that vaccination strategies prioritising occupational risk groups minimise the number of infections but allow higher mortality while prioritising vulnerable groups minimises mortality but implies increased infection rate. We also found that intensive vaccination and non-pharmaceutical interventions can substantially suppress the spread of the virus, while low levels of vaccination and premature reopening may easily revert the epidemic to an uncontrolled state.InterpretationOur analysis highlights that while vaccination protects the elderly from COVID-19, a large percentage of children will contract and spread the virus, and we also show the benefits and limitations of various quarantine and testing scenarios.FundingThis work was carried out within the framework of the Hungarian National Development, Research, and Innovation (NKFIH) Fund 2020-2.1.1-ED-2020-00003.Research in contextEvidence before this studyWe still do not have an effective medical treatment against COVID-19 (SARS-CoV-2), thus the majority of the efforts to stop the pandemic focuses on non-pharmaceutical interventions. Each country came up with a local solution to stop the spread of the virus by increased testing, quarantining, lock-down of various events and institutions or early vaccination. There is no clear way how these interventions can be compared, and it is especially challenging to predict how combinations of interventions could influence the pandemic. Various mathematical modelling approaches helped decision-makers to foresee the effects of their decisions. Most of these models rely on classical, deterministic compartmental “SEIR” models, which can be solved easily but cannot take into account spatial effects and most non-pharmaceutical interventions affect the same parameters, so there is no way to analyse their separate or joint effects. Agent-based microsimulations are harder to solve but can consider far more details. Several models were developed on these lines focusing on questions about ideal vaccination, lock-down or other specific problems, but none of these studies evaluated and compared the individual and mixed effects of a wide variety of control measures.Added-value of this studyHere we present PanSim, a framework where we introduce a detailed infection event simulation step and the possibility to control specific workplaces individually (schools, hospitals, etc.), test various vaccination, testing and quarantine scenarios while considering preconditions, age, sex, residence and workplace of individuals and mutant viruses with various infectivity. The level of details and granularity of simulations allow our work to evaluate this wide range of scenarios and control measures accurately and directly compare them with one another to provide quantitative evidence to support decision-makers. Analysis of our simulations also provides emergent results on the risks children and non-vaccinated individuals face.Implications of all the available evidenceThe agent-based microsimulation framework allows us to evaluate the risk and possible consequences of particular interventions precisely. Due to the outstanding efficiency of the computations, it is possible to apply scenario-based analysis and control design methods which require a high number of simulation runs to obtain results on a given confidence level. This will enable us to design and quantitatively assess control measures in case of new waves of COVID-19 or new pandemic outbreaks.

A SARS-COV-2 vírus magyarországi terjedésének ágens alapú modellezése – az első járványhullám tapasztalatai

“…Magyarországon emellett a Pázmány Péter Katolikus Egyetem Információs Technológiai és Bionikai Karának munkatársai foglalkoznak a koronavírus ágens alapú modellezésével. Virtuális Szegedet szimuláló modelljük a településeken belüli fertőzésterjesztési mintázatok feltérképezéséhez is kulcsfontosságú inputokat ad, valamint alkalmas különböző korlátozási, karantén és vakcinációs forgatókönyvek tesztelésére (Csikász-Nagy, Pongor 2021; Reguly et al 2021). E kutatócsoport a modell országos léptékű adaptációján is dolgozik.…”