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Williams B, Carruthers J, Gillard JJ, Lythe G, Perelson AS, Ribeiro RM, Molina-París C, López-García M. The reproduction number and its probability distribution for stochastic viral dynamics. J R Soc Interface 2024; 21:20230400. [PMID: 38264928 PMCID: PMC10806437 DOI: 10.1098/rsif.2023.0400] [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: 07/12/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
We consider stochastic models of individual infected cells. The reproduction number, R, is understood as a random variable representing the number of new cells infected by one initial infected cell in an otherwise susceptible (target cell) population. Variability in R results partly from heterogeneity in the viral burst size (the number of viral progeny generated from an infected cell during its lifetime), which depends on the distribution of cellular lifetimes and on the mechanism of virion release. We analyse viral dynamics models with an eclipse phase: the period of time after a cell is infected but before it is capable of releasing virions. The duration of the eclipse, or the subsequent infectious, phase is non-exponential, but composed of stages. We derive the probability distribution of the reproduction number for these viral dynamics models, and show it is a negative binomial distribution in the case of constant viral release from infectious cells, and under the assumption of an excess of target cells. In a deterministic model, the ultimate in-host establishment or extinction of the viral infection depends entirely on whether the mean reproduction number is greater than, or less than, one, respectively. Here, the probability of extinction is determined by the probability distribution of R, not simply its mean value. In particular, we show that in some cases the probability of infection is not an increasing function of the mean reproduction number.
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Affiliation(s)
- Bevelynn Williams
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | | | - Joseph J. Gillard
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
| | - Alan S. Perelson
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Ruy M. Ribeiro
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carmen Molina-París
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, UK
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Alamil M, Thébaud G, Berthier K, Soubeyrand S. Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics. Front Microbiol 2022; 13:983938. [PMID: 36274731 PMCID: PMC9581327 DOI: 10.3389/fmicb.2022.983938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has opened the route for a deep assessment of within-host genetic diversity that can be used, e.g., to characterize microbial communities and to infer transmission links in infectious disease outbreaks. The performance of such characterizations and inferences cannot be analytically assessed in general and are often grounded on computer-intensive evaluations. Then, being able to simulate within-host genetic diversity across time under various demo-genetic assumptions is paramount to assess the performance of the approaches of interest. In this context, we built an original model that can be simulated to investigate the temporal evolution of genotypes and their frequencies under various demo-genetic assumptions. The model describes the growth and the mutation of genotypes at the nucleotide resolution conditional on an overall within-host viral kinetics, and can be tuned to generate fast non-equilibrium demo-genetic dynamics. We ran simulations of this model and computed classic diversity indices to characterize the temporal variation of within-host genetic diversity (from high-throughput amplicon sequences) of virus populations under three demographic kinetic models of viral infection. Our results highlight how demographic (viral load) and genetic (mutation, selection, or drift) factors drive variations in within-host diversity during the course of an infection. In particular, we observed a non-monotonic relationship between pathogen population size and genetic diversity, and a reduction of the impact of mutation on diversity when a non-specific host immune response is activated. The large variation in the diversity patterns generated in our simulations suggests that the underlying model provides a flexible basis to produce very diverse demo-genetic scenarios and test, for instance, methods for the inference of transmission links during outbreaks.
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Affiliation(s)
- Maryam Alamil
- INRAE, BioSP, Avignon, France
- Department of Mathematics and Computer Science, Alfaisal University, Riyadh, Saudi Arabia
- *Correspondence: Maryam Alamil ;
| | - Gaël Thébaud
- PHIM Plant Health Institute, INRAE, Univ Montpellier, CIRAD, Institut Agro, IRD, Montpellier, France
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Nurtay A, Hennessy MG, Alsedà L, Elena SF, Sardanyés J. Host-virus evolutionary dynamics with specialist and generalist infection strategies: Bifurcations, bistability, and chaos. CHAOS (WOODBURY, N.Y.) 2020; 30:053128. [PMID: 32491911 DOI: 10.1063/1.5144875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
In this work, we have investigated the evolutionary dynamics of a generalist pathogen, e.g., a virus population, that evolves toward specialization in an environment with multiple host types. We have particularly explored under which conditions generalist viral strains may rise in frequency and coexist with specialist strains or even dominate the population. By means of a nonlinear mathematical model and bifurcation analysis, we have determined the theoretical conditions for stability of nine identified equilibria and provided biological interpretation in terms of the infection rates for the viral specialist and generalist strains. By means of a stability diagram, we identified stable fixed points and stable periodic orbits, as well as regions of bistability. For arbitrary biologically feasible initial population sizes, the probability of evolving toward stable solutions is obtained for each point of the analyzed parameter space. This probability map shows combinations of infection rates of the generalist and specialist strains that might lead to equal chances for each type becoming the dominant strategy. Furthermore, we have identified infection rates for which the model predicts the onset of chaotic dynamics. Several degenerate Bogdanov-Takens and zero-Hopf bifurcations are detected along with generalized Hopf and zero-Hopf bifurcations. This manuscript provides additional insights into the dynamical complexity of host-pathogen evolution toward different infection strategies.
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Affiliation(s)
- Anel Nurtay
- Centre de Recerca Matemàtica (CRM), Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Matthew G Hennessy
- Centre de Recerca Matemàtica (CRM), Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Lluís Alsedà
- Centre de Recerca Matemàtica (CRM), Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UV, Paterna 46980 València, Spain
| | - Josep Sardanyés
- Centre de Recerca Matemàtica (CRM), Campus de Bellaterra, Edifici C, 08193 Bellaterra, Spain
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Nedellec R, Herbeck JT, Hunt PW, Deeks SG, Mullins JI, Anton ED, Reeves JD, Mosier DE. High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia. AIDS Res Hum Retroviruses 2017; 33:234-245. [PMID: 27604829 DOI: 10.1089/aid.2016.0153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coreceptor switching from CCR5 to CXCR4 is common during chronic HIV-1 infection, but is even more common in individuals who have failed antiretroviral therapy (ART). Prior studies have suggested rapid mutation and/or recombination of HIV-1 envelope (env) genes during coreceptor switching. We compared the functional and genotypic changes in env of viruses from viremic subjects who had failed ART just before and after coreceptor switching and compared those to viruses from matched subjects without coreceptor switching. Analysis of multiple unique functional env clones from each subject revealed extensive diversity at both sample time points and rapid diversification of sequences during the 4-month interval in viruses from both 9 subjects with coreceptor switching and 15 control subjects. Only two subjects had envs with evidence of recombination. Three findings distinguished env clones from subjects with coreceptor switching from controls: (1) lower entry efficiency via CCR5; (2) longer V1/V2 regions; and (3), lower nadir CD4 T cell counts during prior years of infection. Most of these subjects harbored virus with lower replicative capacity associated with protease (PR) and/or reverse transcriptase inhibitor resistance mutations, and the extensive diversification tended to lead either to improved entry efficiency via CCR5 or the gain of entry function via CXCR4. These results suggest that R5X4 or X4 variants emerge from a diverse, low-fitness landscape shaped by chronic infection, multiple ART resistance mutations, the availability of target cells, and reduced entry efficiency via CCR5.
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Affiliation(s)
- Rebecca Nedellec
- Department of Immunology and Microbial Science, IMM-7, The Scripps Research Institute, La Jolla, California
| | - Joshua T. Herbeck
- International Clinical Research Center, Department of Global Health, University of Washington, Seattle, Washington
| | - Peter W. Hunt
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington
| | - Elizabeth D. Anton
- Monogram Biosciences, Laboratory Corporation of America® Holding, Virology Research and Development, South San Francisco, California
| | - Jacqueline D. Reeves
- Monogram Biosciences, Laboratory Corporation of America® Holding, Virology Research and Development, South San Francisco, California
| | - Donald E. Mosier
- Department of Immunology and Microbial Science, IMM-7, The Scripps Research Institute, La Jolla, California
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da Silva J, Wyatt SK. Fitness valleys constrain HIV-1's adaptation to its secondary chemokine coreceptor. J Evol Biol 2014; 27:604-15. [DOI: 10.1111/jeb.12329] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/04/2014] [Indexed: 12/15/2022]
Affiliation(s)
- J. da Silva
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide SA Australia
| | - S. K. Wyatt
- School of Molecular and Biomedical Science; University of Adelaide; Adelaide SA Australia
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Restif O. An offer you cannot refuse: down-regulation of immunity in response to a pathogen's retaliation threat. J Evol Biol 2013; 26:2021-30. [PMID: 23927686 PMCID: PMC4274018 DOI: 10.1111/jeb.12209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/16/2013] [Accepted: 05/28/2013] [Indexed: 12/15/2022]
Abstract
According to the Red Queen hypothesis, hosts and pathogens are engaged in an escalating coevolutionary arms race between resistance and virulence. However, the vast majority of symbionts colonize their hosts' mucosal compartments without triggering any immune response, resulting in durable commensal associations. Here, I propose a simple extension of previous mathematical models for antagonistic coevolution in which the host can mount a delayed immune response; in response, the symbiont can change its virulence following this activation. Even though the levels of virulence in both phases are assumed to be genetically determined, this simple form of plasticity can select for commensal associations. In particular, coevolution can result in hosts that do not activate their immune response, thus preventing phenotypically plastic pathogens from switching to a higher virulence level. I argue that, from the host's point of view, this state is analogous to the mafia behaviour previously described in avian brood parasites. More importantly, this study provides a new hypothesis for the maintenance of a commensal relationship through antagonistic coevolution.
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Affiliation(s)
- O Restif
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
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Abstract
The Human Immunodeficiency Virus (HIV) is one of the most threatening viral agents. This virus infects approximately 33 million people, many of whom are unaware of their status because, except for flu-like symptoms right at the beginning of the infection during the acute phase, the disease progresses more or less symptom-free for 5 to 10 years. During this asymptomatic phase, the virus slowly destroys the immune system until the onset of AIDS when opportunistic infections like pneumonia or Kaposi’s sarcoma can overcome immune defenses. Mathematical models have played a decisive role in estimating important parameters (e.g., virion clearance rate or life-span of infected cells). However, most models only account for the acute and asymptomatic latency phase and cannot explain the progression to AIDS. Models that account for the whole course of the infection rely on different hypotheses to explain the progression to AIDS. The aim of this study is to review these models, present their technical approaches and discuss the robustness of their biological hypotheses. Among the few models capturing all three phases of an HIV infection, we can distinguish between those that mainly rely on population dynamics and those that involve virus evolution. Overall, the modeling quest to capture the dynamics of an HIV infection has improved our understanding of the progression to AIDS but, more generally, it has also led to the insight that population dynamics and evolutionary processes can be necessary to explain the course of an infection.
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Affiliation(s)
- Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, B.P. 64501, 34394 Montpellier Cedex 5, France
- Authors to whom correspondence should be addressed; (S.A.); (C.M.); Tel.: +33-4674-16436; Fax: +33-4674-16330
| | - Carsten Magnus
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
- Authors to whom correspondence should be addressed; (S.A.); (C.M.); Tel.: +33-4674-16436; Fax: +33-4674-16330
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Boldin B, Kisdi É. ON THE EVOLUTIONARY DYNAMICS OF PATHOGENS WITH DIRECT AND ENVIRONMENTAL TRANSMISSION. Evolution 2012; 66:2514-27. [DOI: 10.1111/j.1558-5646.2012.01613.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Alizon S, Luciani F, Regoes RR. Epidemiological and clinical consequences of within-host evolution. Trends Microbiol 2010; 19:24-32. [PMID: 21055948 DOI: 10.1016/j.tim.2010.09.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 09/14/2010] [Accepted: 09/28/2010] [Indexed: 11/18/2022]
Abstract
Many viruses and bacteria are known to evolve rapidly over the course of an infection. However, epidemiological studies generally assume that within-host evolution is an instantaneous process. We argue that the dynamics of within-host evolution has implications at the within-host and at the between-host levels. We first show that epidemiologists should consider within-host evolution, notably because it affects the genotype of the pathogen that is transmitted. We then present studies that investigate evolution at the within-host level and examine the extent to which these studies can help to understand infection traits involved in the epidemiology (e.g. transmission rate, virulence, recovery rate). Finally, we discuss how new techniques for data acquisition can open new perspectives for empirical and theoretical research.
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Affiliation(s)
- Samuel Alizon
- Laboratoire Génétique et Évolution des Maladies Infectieuses, Unité Mixte de Recherche du Centre national de la Recherche Scientifique et de l'Institut de Recherche pour le Développement 2724, 911 avenue Agropolis, BP 64501, 34394 Montpellier CEDEX 5, France.
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