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Grass D, Wrzaczek S, Caulkins JP, Feichtinger G, Hartl RF, Kort PM, Kuhn M, Prskawetz A, Sanchez-Romero M, Seidl A. Riding the waves from epidemic to endemic: Viral mutations, immunological change and policy responses. Theor Popul Biol 2024; 156:46-65. [PMID: 38310975 DOI: 10.1016/j.tpb.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/06/2024]
Abstract
Nonpharmaceutical interventions (NPI) are an important tool for countering pandemics such as COVID-19. Some are cheap; others disrupt economic, educational, and social activity. The latter force governments to balance the health benefits of reduced infection and death against broader lockdown-induced societal costs. A literature has developed modeling how to optimally adjust lockdown intensity as an epidemic evolves. This paper extends that literature by augmenting the classic SIR model with additional states and flows capturing decay over time in vaccine-conferred immunity, the possibility that mutations create variants that erode immunity, and that protection against infection erodes faster than protecting against severe illness. As in past models, we find that small changes in parameter values can tip the optimal response between very different solutions, but the extensions considered here create new types of solutions. In some instances, it can be optimal to incur perpetual epidemic waves even if the uncontrolled infection prevalence would settle down to a stable intermediate level.
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Affiliation(s)
- D Grass
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria; Research Group Economics, Institute of Statistics and Mathematical Methods in Economics, TU Wien, Vienna, Austria
| | - S Wrzaczek
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria; Wittgenstein Centre for Demography and Global Human Capital (IIASA, VID/OeAW, University of Vienna), Austria.
| | - J P Caulkins
- Heinz College, Carnegie Mellon University, Pittsburgh, USA
| | - G Feichtinger
- Wittgenstein Centre for Demography and Global Human Capital (IIASA, VID/OeAW, University of Vienna), Austria; Research Group Variational Analysis, Dynamics & Operations Research, Institute of Statistics and Mathematical Methods in Economics, TU Wien, Vienna, Austria
| | - R F Hartl
- Department of Business Decisions and Analytics, University of Vienna, Vienna, Austria
| | - P M Kort
- Tilburg School of Economics and Management, Tilburg University, Tilburg, Netherlands
| | - M Kuhn
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria; Wittgenstein Centre for Demography and Global Human Capital (IIASA, VID/OeAW, University of Vienna), Austria
| | - A Prskawetz
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria; Wittgenstein Centre for Demography and Global Human Capital (IIASA, VID/OeAW, University of Vienna), Austria; Research Group Economics, Institute of Statistics and Mathematical Methods in Economics, TU Wien, Vienna, Austria
| | - M Sanchez-Romero
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria; Research Group Economics, Institute of Statistics and Mathematical Methods in Economics, TU Wien, Vienna, Austria; Vienna Institute of Demography (VID), Austrian Academy of Sciences (OeAW), Vienna, Austria
| | - A Seidl
- Department of Business Decisions and Analytics, University of Vienna, Vienna, Austria; Faculty of Management, Seeburg Castle University, Seekirchen am Wallersee, Austria
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Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Cell 2023; 186:5151-5164.e13. [PMID: 37875109 PMCID: PMC10964984 DOI: 10.1016/j.cell.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, and antigenic changes that reduce cross-immunity induced by previous infections or vaccinations. How this functional variation shapes global evolution has remained unclear. Here, we establish a predictive fitness model for SARS-CoV-2 that integrates antigenic and intrinsic selection. The model is informed by tracking of time-resolved sequence data, epidemiological records, and cross-neutralization data of viral variants. Our inference shows that immune pressure, including contributions of vaccinations and previous infections, has become the dominant force driving the recent evolution of SARS-CoV-2. The fitness model can serve continued surveillance in two ways. First, it successfully predicts the short-term evolution of circulating strains and flags emerging variants likely to displace the previously predominant variant. Second, it predicts likely antigenic profiles of successful escape variants prior to their emergence.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany.
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Chardès V, Mazzolini A, Mora T, Walczak AM. Evolutionary stability of antigenically escaping viruses. Proc Natl Acad Sci U S A 2023; 120:e2307712120. [PMID: 37871216 PMCID: PMC10622963 DOI: 10.1073/pnas.2307712120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/24/2023] [Indexed: 10/25/2023] Open
Abstract
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the coevolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other nonantigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of nonantigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low.
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Affiliation(s)
- Victor Chardès
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
- Center for Computational Biology, Flatiron Institute, New York, NY10010
| | - Andrea Mazzolini
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
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Gutierrez MA, Gog JR. The importance of vaccinated individuals to population-level evolution of pathogens. J Theor Biol 2023; 567:111493. [PMID: 37054971 DOI: 10.1016/j.jtbi.2023.111493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/17/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
Virus evolution shapes the epidemiological patterns of infectious disease, particularly via evasion of population immunity. At the individual level, host immunity itself may drive viral evolution towards antigenic escape. Using compartmental SIR-style models with imperfect vaccination, we allow the probability of immune escape to differ in vaccinated and unvaccinated hosts. As the relative contribution to selection in these different hosts varies, the overall effect of vaccination on the antigenic escape pressure at the population level changes. We find that this relative contribution to escape is important for understanding the effects of vaccination on the escape pressure and we draw out some fairly general patterns. If vaccinated hosts do not contribute much more than unvaccinated hosts to the escape pressure, then increasing vaccination always reduces the overall escape pressure. In contrast, if vaccinated hosts contribute significantly more than unvaccinated hosts to the population level escape pressure, then the escape pressure is maximised for intermediate vaccination levels. Past studies find only that the escape pressure is maximal for intermediate levels with fixed extreme assumptions about this relative contribution. Here we show that this result does not hold across the range of plausible assumptions for the relative contribution to escape from vaccinated and unvaccinated hosts. We also find that these results depend on the vaccine efficacy against transmission, particularly through the partial protection against infection. This work highlights the potential value of understanding better how the contribution to antigenic escape pressure depends on individual host immunity.
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Affiliation(s)
- Maria A Gutierrez
- Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge, United Kingdom.
| | - Julia R Gog
- Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Cambridge, United Kingdom; Joint UNIversities Pandemic and Epidemiological Research (JUNIPER) Consortium, United Kingdom.
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Bull JJ, Antia R. Which 'imperfect vaccines' encourage the evolution of higher virulence? Evol Med Public Health 2022; 10:202-213. [PMID: 35539897 PMCID: PMC9081871 DOI: 10.1093/emph/eoac015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Background and objectives Theory suggests that some types of vaccines against infectious pathogens may lead to the evolution of variants that cause increased harm, particularly when they infect unvaccinated individuals. This theory was supported by the observation that the use of an imperfect vaccine to control Marek's disease virus in chickens resulted in the virus evolving to be more lethal to unvaccinated birds. This raises the concern that the use of some other vaccines may lead to similar pernicious outcomes. We examine that theory with a focus on considering the regimes in which such outcomes are expected. Methodology We evaluate the plausibility of assumptions in the original theory. The previous theory rested heavily on a particular form of transmission-mortality-recovery trade-off and invoked other assumptions about the pathways of evolution. We review alternatives to mortality in limiting transmission and consider evolutionary pathways that were omitted in the original theory. Results The regime where the pernicious evolutionary outcome occurs is narrowed by our analysis but remains possible in various scenarios. We propose a more nuanced consideration of alternative models for the within-host dynamics of infections and for factors that limit virulence. Our analysis suggests imperfect vaccines against many pathogens will not lead to the evolution of pathogens with increased virulence in unvaccinated individuals. Conclusions and implications Evolution of greater pathogen mortality driven by vaccination remains difficult to predict, but the scope for such outcomes appears limited. Incorporation of mechanistic details into the framework, especially regarding immunity, may be requisite for prediction accuracy. Lay Summary A virus of chickens appears to have evolved high mortality in response to a vaccine that merely prevented disease symptoms. Theory has predicted this type of evolution in response to a variety of vaccines and other interventions such as drug treatment. Under what circumstances is this pernicious result likely to occur? Analysis of the theory in light of recent changes in our understanding of viral biology raises doubts that medicine-driven, pernicious evolution is likely to be common. But we are far from a mechanistic understanding of the interaction between pathogen and host that can predict when vaccines and other medical interventions will lead to the unwanted evolution of more virulent pathogens. So, while the regime where a pernicious result obtains may be limited, caution remains warranted in designing many types of interventions.
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Affiliation(s)
- James J Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA,Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA. E-mail:
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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