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Ashby B, Smith CA, Thompson RN. Non-pharmaceutical interventions and the emergence of pathogen variants. Evol Med Public Health 2022; 11:80-89. [PMID: 37007165 PMCID: PMC10052376 DOI: 10.1093/emph/eoac043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Non-pharmaceutical interventions (NPIs), such as social distancing and contact tracing, are important public health measures that can reduce pathogen transmission. In addition to playing a crucial role in suppressing transmission, NPIs influence pathogen evolution by mediating mutation supply, restricting the availability of susceptible hosts, and altering the strength of selection for novel variants. Yet it is unclear how NPIs might affect the emergence of novel variants that are able to escape pre-existing immunity (partially or fully), are more transmissible or cause greater mortality. We analyse a stochastic two-strain epidemiological model to determine how the strength and timing of NPIs affect the emergence of variants with similar or contrasting life-history characteristics to the wild type. We show that, while stronger and timelier NPIs generally reduce the likelihood of variant emergence, it is possible for more transmissible variants with high cross-immunity to have a greater probability of emerging at intermediate levels of NPIs. This is because intermediate levels of NPIs allow an epidemic of the wild type that is neither too small (facilitating high mutation supply), nor too large (leaving a large pool of susceptible hosts), to prevent a novel variant from becoming established in the host population. However, since one cannot predict the characteristics of a variant, the best strategy to prevent emergence is likely to be an implementation of strong, timely NPIs.
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Affiliation(s)
- Ben Ashby
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Mathematical Sciences, University of Bath, Bath, UK
- The Pacific Institute on Pathogens, Pandemics and Society (PIPPS), Simon Fraser University, Burnaby, BC, Canada
| | - Cameron A Smith
- Department of Mathematical Sciences, University of Bath, Bath, UK
| | - Robin N Thompson
- Mathematics Institute, University of Warwick, Coventry, UK
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
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2
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McLeod DV, Gandon S. Effects of epistasis and recombination between vaccine-escape and virulence alleles on the dynamics of pathogen adaptation. Nat Ecol Evol 2022; 6:786-793. [PMID: 35437006 DOI: 10.1038/s41559-022-01709-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022]
Abstract
Pathogen adaptation to public health interventions such as vaccination may take tortuous routes and involve multiple mutations at different locations in the pathogen genome, acting on distinct phenotypic traits. Yet how these multi-locus adaptations jointly evolve is poorly understood. Here we consider the joint evolution of two adaptations: pathogen escape from the vaccine-induced immune response and adjustments to pathogen virulence affecting transmission or clearance. We elucidate the role played by epistasis and recombination, with an emphasis on the different protective effects of vaccination. We show that vaccines blocking infection, reducing transmission and/or increasing clearance generate positive epistasis between the vaccine-escape and virulence alleles, favouring strains that carry both mutations, whereas vaccines reducing virulence mortality generate negative epistasis, favouring strains that carry either mutation but not both. High rates of recombination can affect these predictions. If epistasis is positive, frequent recombination can prevent the transient build-up of more virulent escape strains. If epistasis is negative, frequent recombination between loci can create an evolutionary bistability, favouring whichever adaptation is more accessible. Our work provides a timely alternative to the variant-centred perspective on pathogen adaptation and captures the effect of different types of vaccine on the interference between multiple adaptive mutations.
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Affiliation(s)
- David V McLeod
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France. .,Institute of Ecology and Evolution, Universität Bern, Bern, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.
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3
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Rochman N, Wolf YI, Koonin EV. Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics. F1000Res 2021; 10:315. [PMID: 34504684 PMCID: PMC8406440 DOI: 10.12688/f1000research.52341.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Background: The start of 2021 was marked by the initiation of a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods: A deterministic model of epidemic evolution is analyzed, with seven compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results: When an escape variant is only modestly less infectious than the originating strain within a naïve population, the cumulative number of infections does not monotonically decrease with the rate of vaccine distribution. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host-host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions: Mathematical modeling shows that limiting post-vaccination contacts can perceptibly affect the course of an epidemic. The consideration of limitations on post-vaccination contacts remains relevant for the entire duration of any vaccination campaign including the current status of SARS-CoV-2 vaccination.
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Affiliation(s)
- Nash Rochman
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
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4
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Rochman N, Wolf YI, Koonin EV. Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics. F1000Res 2021; 10:315. [PMID: 34504684 PMCID: PMC8406440 DOI: 10.12688/f1000research.52341.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 07/20/2023] Open
Abstract
Background: The start of 2021 was marked by the initiation of a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods: A deterministic model of epidemic evolution is analyzed, with seven compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results: When an escape variant is only modestly less infectious than the originating strain within a naïve population, there exists an optimal rate of vaccine distribution. Exceeding this rate increases the cumulative number of infections due to vaccine escape. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host-host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions: Mathematical modeling shows that optimization of the vaccination rate and limiting post-vaccination contacts can perceptibly affect the course of an epidemic. The consideration of limitations on post-vaccination contacts remains relevant for the entire duration of any vaccination campaign including the current status of SARS-CoV-2 vaccination.
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Affiliation(s)
- Nash Rochman
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NIH, Bethesda, MD, 20894, USA
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5
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Rochman ND, Wolf YI, Koonin EV. Substantial Impact of Post Vaccination Contacts on Cumulative Infections during Viral Epidemics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.12.19.20248554. [PMID: 33398300 PMCID: PMC7781343 DOI: 10.1101/2020.12.19.20248554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The start of 2021 will be marked by a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods A deterministic model of epidemic evolution is analyzed, with 7 compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results When an escape variant is only modestly less infectious than the originating strain within a naïve population, there exists an optimal rate of vaccine distribution. Exceeding this rate increases the cumulative number of infections due to vaccine escape. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host-host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions Mathematical modeling shows that optimization of the vaccination rate and limiting post-vaccination contacts can affect the course of an epidemic. Given the relatively short window between inoculation and the acquisition of immunity, these results might merit consideration for an immediate, practical public health response.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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Leung T, Campbell PT, Hughes BD, Frascoli F, McCaw JM. Infection-acquired versus vaccine-acquired immunity in an SIRWS model. Infect Dis Model 2018; 3:118-135. [PMID: 30839933 PMCID: PMC6326260 DOI: 10.1016/j.idm.2018.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/18/2018] [Accepted: 06/05/2018] [Indexed: 12/02/2022] Open
Abstract
In some disease systems, the process of waning immunity can be subtle, involving a complex relationship between the duration of immunity-acquired either through natural infection or vaccination-and subsequent boosting of immunity through asymptomatic re-exposure. We present and analyse a model of infectious disease transmission where primary and secondary infections are distinguished to examine the interplay between infection and immunity. Additionally we allow the duration of infection-acquired immunity to differ from that of vaccine-acquired immunity to explore the impact on long-term disease patterns and prevalence of infection in the presence of immune boosting. Our model demonstrates that vaccination may induce cyclic behaviour, and the ability of vaccinations to reduce primary infections may not lead to decreased transmission. Where the boosting of vaccine-acquired immunity delays a primary infection, the driver of transmission largely remains primary infections. In contrast, if the immune boosting bypasses a primary infection, secondary infections become the main driver of transmission under a sufficiently long duration of immunity. Our results show that the epidemiological patterns of an infectious disease may change considerably when the duration of vaccine-acquired immunity differs from that of infection-acquired immunity. Our study highlights that for any particular disease and associated vaccine, a detailed understanding of the waning and boosting of immunity and how the duration of protection is influenced by infection prevalence are important as we seek to optimise vaccination strategies.
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Affiliation(s)
- Tiffany Leung
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Patricia T. Campbell
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Parkville, Victoria 3010, Australia
- Infection and Immunity Research Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Barry D. Hughes
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Federico Frascoli
- Department of Mathematics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122, Australia
| | - James M. McCaw
- School of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3010, Australia
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Parkville, Victoria 3010, Australia
- Infection and Immunity Research Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria 3010, Australia
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Domenech de Cellès M, Magpantay FMG, King AA, Rohani P. The pertussis enigma: reconciling epidemiology, immunology and evolution. Proc Biol Sci 2016; 283:rspb.2015.2309. [PMID: 26763701 DOI: 10.1098/rspb.2015.2309] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Pertussis, a highly contagious respiratory infection, remains a public health priority despite the availability of vaccines for 70 years. Still a leading cause of mortality in developing countries, pertussis has re-emerged in several developed countries with high vaccination coverage. Resurgence of pertussis in these countries has routinely been attributed to increased awareness of the disease, imperfect vaccinal protection or high infection rates in adults. In this review, we first present 1980-2012 incidence data from 63 countries and show that pertussis resurgence is not universal. We further argue that the large geographical variation in trends probably precludes a simple explanation, such as the transition from whole-cell to acellular pertussis vaccines. Reviewing available evidence, we then propose that prevailing views on pertussis epidemiology are inconsistent with both historical and contemporary data. Indeed, we summarize epidemiological evidence showing that natural infection and vaccination both appear to provide long-term protection against transmission and disease, so that previously infected or vaccinated adults contribute little to overall transmission at a population level. Finally, we identify several promising avenues that may lead to a consistent explanation of global pertussis epidemiology and to more effective control strategies.
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Affiliation(s)
| | - Felicia M G Magpantay
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aaron A King
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pejman Rohani
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Odum School of Ecology, University of Georgia, Athens, GA 30602, USA College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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8
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van Twillert I, Bonačić Marinović AA, van Gaans-van den Brink JAM, Kuipers B, Berbers GAM, van der Maas NAT, Verheij TJM, Versteegh FGA, Teunis PFM, van Els CACM. The Use of Innovative Two-Component Cluster Analysis and Serodiagnostic Cut-Off Methods to Estimate Prevalence of Pertussis Reinfections. PLoS One 2016; 11:e0148507. [PMID: 26848833 PMCID: PMC4743910 DOI: 10.1371/journal.pone.0148507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/19/2016] [Indexed: 01/13/2023] Open
Abstract
Bordetella pertussis circulates even in highly vaccinated countries affecting all age groups. Insight into the scale of concealed reinfections is important as they may contribute to transmission. We therefore investigated whether current single-point serodiagnostic methods are suitable to estimate the prevalence of pertussis reinfection. Two methods based on IgG-Ptx plasma levels alone were used to evaluate the proportion of renewed seroconversions in the past year in a cohort of retrospective pertussis cases ≥ 24 months after a proven earlier symptomatic infection. A Dutch population database was used as a baseline. Applying a classical 62.5 IU/ml IgG-Ptx cut-off, we calculated a seroprevalence of 15% in retrospective cases, higher than the 10% observed in the population baseline. However, this method could not discriminate between renewed seroconversion and waning of previously infection-enhanced IgG-Ptx levels. Two-component cluster analysis of the IgG-Ptx datasets of both pertussis cases and the general population revealed a continuum of intermediate IgG-Ptx levels, preventing the establishment of a positive population and the comparison of prevalence by this alternative method. Next, we investigated the complementary serodiagnostic value of IgA-Ptx levels. When modelling datasets including both convalescent and retrospective cases we obtained new cut-offs for both IgG-Ptx and IgA-Ptx that were optimized to evaluate renewed seroconversions in the ex-cases target population. Combining these cut-offs two-dimensionally, we calculated 8.0% reinfections in retrospective cases, being below the baseline seroprevalence. Our study for the first time revealed the shortcomings of using only IgG-Ptx data in conventional serodiagnostic methods to determine pertussis reinfections. Improved results can be obtained with two-dimensional serodiagnostic profiling. The proportion of reinfections thus established suggests a relatively increased period of protection to renewed infection after clinical pertussis.
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Affiliation(s)
- Inonge van Twillert
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Axel A. Bonačić Marinović
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Betsy Kuipers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Guy A. M. Berbers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Nicoline A. T. van der Maas
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Theo J. M. Verheij
- Julius Center Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Florens G. A. Versteegh
- Department of Pediatrics, Groene Hart Ziekenhuis, Gouda, the Netherlands
- Ghent University Hospital, department of pediatrics, Ghent, Belgium
| | - Peter F. M. Teunis
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- RSPH, Emory University, Atlanta, United States of America
| | - Cécile A. C. M. van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- * E-mail:
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Abstract
Why is it that some parasites cause high levels of host damage (i.e. virulence) whereas others are relatively benign? There are now numerous reviews of virulence evolution in the literature but it is nevertheless still difficult to find a comprehensive treatment of the theory and data on the subject that is easily accessible to non-specialists. Here we attempt to do so by distilling the vast theoretical literature on the topic into a set of relatively few robust predictions. We then provide a comprehensive assessment of the available empirical literature that tests these predictions. Our results show that there have been some notable successes in integrating theory and data but also that theory and empiricism in this field do not ‘speak’ to each other very well. We offer a few suggestions for how the connection between the two might be improved.
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Althouse BM, Scarpino SV. Asymptomatic transmission and the resurgence of Bordetella pertussis. BMC Med 2015; 13:146. [PMID: 26103968 PMCID: PMC4482312 DOI: 10.1186/s12916-015-0382-8] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/22/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The recent increase in whooping cough incidence (primarily caused by Bordetella pertussis) presents a challenge to both public health practitioners and scientists trying to understand the mechanisms behind its resurgence. Three main hypotheses have been proposed to explain the resurgence: 1) waning of protective immunity from vaccination or natural infection over time, 2) evolution of B. pertussis to escape protective immunity, and 3) low vaccine coverage. Recent studies have suggested a fourth mechanism: asymptomatic transmission from individuals vaccinated with the currently used acellular B. pertussis vaccines. METHODS Using wavelet analyses of B. pertussis incidence in the United States (US) and United Kingdom (UK) and a phylodynamic analysis of 36 clinical B. pertussis isolates from the US, we find evidence in support of asymptomatic transmission of B. pertussis. Next, we examine the clinical, public health, and epidemiological consequences of asymptomatic B. pertussis transmission using a mathematical model. RESULTS We find that: 1) the timing of changes in age-specific attack rates observed in the US and UK are consistent with asymptomatic transmission; 2) the phylodynamic analysis of the US sequences indicates more genetic diversity in the overall bacterial population than would be suggested by the observed number of infections, a pattern expected with asymptomatic transmission; 3) asymptomatic infections can bias assessments of vaccine efficacy based on observations of B. pertussis-free weeks; 4) asymptomatic transmission can account for the observed increase in B. pertussis incidence; and 5) vaccinating individuals in close contact with infants too young to receive the vaccine ("cocooning" unvaccinated children) may be ineffective. CONCLUSIONS Although a clear role for the previously suggested mechanisms still exists, asymptomatic transmission is the most parsimonious explanation for many of the observations surrounding the resurgence of B. pertussis in the US and UK. These results have important implications for B. pertussis vaccination policy and present a complicated scenario for achieving herd immunity and B. pertussis eradication.
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Bourget R, Chaumont L, Durel CE, Sapoukhina N. Sustainable deployment of QTLs conferring quantitative resistance to crops: first lessons from a stochastic model. THE NEW PHYTOLOGIST 2015; 206:1163-1171. [PMID: 25623549 DOI: 10.1111/nph.13295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Quantitative plant disease resistance is believed to be more durable than qualitative resistance, since it exerts less selective pressure on the pathogens. However, the process of progressive pathogen adaptation to quantitative resistance is poorly understood, which makes it difficult to predict its durability or to derive principles for its sustainable deployment. Here, we study the dynamics of pathogen adaptation in response to quantitative plant resistance affecting pathogen reproduction rate and its colonizing capacity. We developed a stochastic model for the continuous evolution of a pathogen population within a quantitatively resistant host. We assumed that pathogen can adapt to a host by the progressive restoration of reproduction rate or of colonizing capacity, or of both. Our model suggests that a combination of quantitative trait loci (QTLs) affecting distinct pathogen traits was more durable if the evolution of repressed traits was antagonistic. Otherwise, quantitative resistance that depressed only pathogen reproduction was more durable. In order to decelerate the progressive pathogen adaptation, QTLs that decrease the pathogen's maximum capacity to colonize must be combined with QTLs that decrease the spore production per lesion or the infection efficiency or that increase the latent period. Our theoretical framework can help breeders to develop principles for sustainable deployment of QTLs.
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Affiliation(s)
- Romain Bourget
- Département de Mathématiques, LAREMA, Université d'Angers, 2 Blvd Lavoisier, F-49045, Angers Cedex 01, France
- INRA, UMR1345, Institut de Recherches en Horticulture et Semences (IRHS), SFR 4207 QUASAV, 42 rue Georges Morel, F-49071, Beaucouzé cedex, France
- AgroCampus-Ouest, UMR1345, Institut de Recherche en Horticulture et Semences (IRHS), F-49045, Angers, France
- Université d'Angers, UMR1345, Institut de Recherche en Horticulture et Semences (IRHS), F-49045, Angers, France
| | - Loïc Chaumont
- Département de Mathématiques, LAREMA, Université d'Angers, 2 Blvd Lavoisier, F-49045, Angers Cedex 01, France
| | - Charles-Eric Durel
- INRA, UMR1345, Institut de Recherches en Horticulture et Semences (IRHS), SFR 4207 QUASAV, 42 rue Georges Morel, F-49071, Beaucouzé cedex, France
- AgroCampus-Ouest, UMR1345, Institut de Recherche en Horticulture et Semences (IRHS), F-49045, Angers, France
- Université d'Angers, UMR1345, Institut de Recherche en Horticulture et Semences (IRHS), F-49045, Angers, France
| | - Natalia Sapoukhina
- INRA, UMR1345, Institut de Recherches en Horticulture et Semences (IRHS), SFR 4207 QUASAV, 42 rue Georges Morel, F-49071, Beaucouzé cedex, France
- AgroCampus-Ouest, UMR1345, Institut de Recherche en Horticulture et Semences (IRHS), F-49045, Angers, France
- Université d'Angers, UMR1345, Institut de Recherche en Horticulture et Semences (IRHS), F-49045, Angers, France
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12
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Bordetella pertussis naturally occurring isolates with altered lipooligosaccharide structure fail to fully mature human dendritic cells. Infect Immun 2014; 83:227-38. [PMID: 25348634 DOI: 10.1128/iai.02197-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bordetella pertussis is a Gram-negative bacterium and the causative agent of whooping cough. Despite high vaccination coverage, outbreaks are being increasingly reported worldwide. Possible explanations include adaptation of this pathogen, which may interfere with recognition by the innate immune system. Here, we describe innate immune recognition and responses to different B. pertussis clinical isolates. By using HEK-Blue cells transfected with different pattern recognition receptors, we found that 3 out of 19 clinical isolates failed to activate Toll-like receptor 4 (TLR4). These findings were confirmed by using the monocytic MM6 cell line. Although incubation with high concentrations of these 3 strains resulted in significant activation of the MM6 cells, it was found to occur mainly through interaction with TLR2 and not through TLR4. When using live bacteria, these 3 strains also failed to activate TLR4 on HEK-Blue cells, and activation of MM6 cells or human monocyte-derived dendritic cells was significantly lower than activation induced by the other 16 strains. Mass spectrum analysis of the lipid A moieties from these 3 strains indicated an altered structure of this molecule. Gene sequence analysis revealed mutations in genes involved in lipid A synthesis. Findings from this study indicate that B. pertussis isolates that do not activate TLR4 occur naturally and that this phenotype may give this bacterium an advantage in tempering the innate immune response and establishing infection. Knowledge on the strategies used by this pathogen in evading the host immune response is essential for the improvement of current vaccines or for the development of new ones.
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13
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JACKSON DW, ROHANI PEJMAN. Perplexities of pertussis: recent global epidemiological trends and their potential causes. Epidemiol Infect 2014; 142:672-84. [PMID: 23324361 PMCID: PMC9151176 DOI: 10.1017/s0950268812003093] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/10/2012] [Accepted: 12/10/2012] [Indexed: 12/11/2022] Open
Abstract
Recent much-publicized increases in pertussis case reports in some countries with high vaccine coverage have raised concerns about its current and future control. The ubiquity of this trend, however, remains unexamined. In an attempt to paint a global picture, we used case counts to determine which countries experienced statistically significant trends in incidence over the past two decades and to map changes in incidence during this period. These data reveal that pertussis resurgence is not a universal phenomenon. The heterogeneity in incidence trends, even in countries with superficially similar demography, socioeconomic conditions and vaccination programmes, is striking and requires explanation. In this opinion piece, we review and assess the multifaceted proposed explanations incorporating evolution, population dynamics, and the details of immunization programmes. While we do not solve the riddle that is pertussis epidemiology, we highlight critical aspects that are likely to hold the key to understanding its worldwide epidemiology.
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Affiliation(s)
- D. W. JACKSON
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - PEJMAN ROHANI
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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van Twillert I, van Gaans-van den Brink JAM, Poelen MCM, Helm K, Kuipers B, Schipper M, Boog CJP, Verheij TJM, Versteegh FGA, van Els CACM. Age related differences in dynamics of specific memory B cell populations after clinical pertussis infection. PLoS One 2014; 9:e85227. [PMID: 24454823 PMCID: PMC3890308 DOI: 10.1371/journal.pone.0085227] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/26/2013] [Indexed: 01/10/2023] Open
Abstract
For a better understanding of the maintenance of immune mechanisms to Bordetella pertussis (Bp) in relation to age, we investigated the dynamic range of specific B cell responses in various age-groups at different time points after a laboratory confirmed pertussis infection. Blood samples were obtained in a Dutch cross sectional observational study from symptomatic pertussis cases. Lymphocyte subpopulations were phenotyped by flowcytometry before and after culture. Memory B (Bmem) cells were differentiated into IgG antibody secreting cells (ASC) by polyclonal stimulation and detected by an ELISPOT assay specific for pertussis antigens pertussis toxin (Ptx), filamentous haemagglutinin (FHA) and pertactin (Prn). Bp antigen specific IgG concentrations in plasma were determined using multiplex technology. The majority of subjects having experienced a clinical pertussis episode demonstrated high levels of both Bp specific IgG and Bmem cell levels within the first 6 weeks after diagnosis. Significantly lower levels were observed thereafter. Waning of cellular and humoral immunity to maintenance levels occurred within 9 months after antigen encounter. Age was found to determine the maximum but not base-line frequencies of Bmem cell populations; higher levels of Bmem cells specific for Ptx and FHA were reached in adults and (pre-) elderly compared to under-fours and schoolchildren in the first 6 weeks after Bp exposure, whereas not in later phases. This age effect was less obvious for specific IgG levels. Nonetheless, subjects' levels of specific Bmem cells and specific IgG were weakly correlated. This is the first study to show that both age and closeness to last Bp encounter impacts the size of Bp specific Bmem cell and plasma IgG levels.
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Affiliation(s)
- Inonge van Twillert
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Martien C. M. Poelen
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Kina Helm
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Betsy Kuipers
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Maarten Schipper
- Department of Statistics, Mathematical Modelling and Data Logistics, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Theo J. M. Verheij
- Julius Center Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Cécile A. C. M. van Els
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- * E-mail:
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15
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van der Ark AAJ, Hozbor DF, Boog CJP, Metz B, van den Dobbelsteen GPJM, van Els CACM. Resurgence of pertussis calls for re-evaluation of pertussis animal models. Expert Rev Vaccines 2014; 11:1121-37. [DOI: 10.1586/erv.12.83] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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16
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Berbers GAM, van de Wetering MSE, van Gageldonk PGM, Schellekens JFP, Versteegh FGA, Teunis PFM. A novel method for evaluating natural and vaccine induced serological responses to Bordetella pertussis antigens. Vaccine 2013; 31:3732-8. [PMID: 23742995 DOI: 10.1016/j.vaccine.2013.05.073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/26/2013] [Accepted: 05/17/2013] [Indexed: 11/17/2022]
Abstract
We studied the time course of serum IgG antibodies against 3 different pertussis vaccine antigens: PT (pertussis toxin), FHA (filamentous hemagglutinin), Prn (pertactin) in sera from individuals vaccinated with four different pertussis vaccines at 4 years of age: (N=44, 44, 23 and 23, respectively,) and compared the responses to/after natural infection with Bordetella pertussis (N=44, age 1-8 years). These longitudinal data were analyzed with a novel method, using a mathematical model to describe the observed responses, and their variation among subjects. This allowed us to estimate biologically meaningful characteristics of the serum antibody response, like peak level and decay rate, and to compare these among natural infections and vaccine responses. Compared to natural infection, responses to PT after vaccination with the tested vaccines are smaller in magnitude and tend to decay slightly faster. When present in vaccines, FHA and Prn tend to produce high peak levels, higher than those in naturally infected patients, but these decay faster. As expected, the Dutch whole cell vaccine produced lower antibody responses than the acellular vaccines. This model allows a better comparison of the kinetics of vaccine induced antibody responses and after natural infection over a long follow up period.
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Affiliation(s)
- G A M Berbers
- Center for Infectious Disease Control, National Institute of Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands
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17
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Lavine JS, Rohani P. Resolving pertussis immunity and vaccine effectiveness using incidence time series. Expert Rev Vaccines 2013; 11:1319-29. [PMID: 23249232 DOI: 10.1586/erv.12.109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Resolving the long-term, population-level consequence of vaccine-induced immunity to pertussis is a key challenge for control strategies and vaccine development. Controlled vaccine efficacy studies provide invaluable information; however, they are limited in scope by their sample size and follow-up duration. Long-term time series of incidence data collected by public health institutions provide insight at a broader scale, especially when the data are spatially explicit and age stratified. By using modern ecological and statistical methodolgies, which are reviewed in this paper, new insights into the duration of transmission-blocking immunity and the age-specific patterns of transmission can be gained. Recent advances in computing power and statistical software development will increasingly make these methods available to public health practitioners, vaccine developers and academics alike.
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Affiliation(s)
- Jennie S Lavine
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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18
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Pathogen-host-environment interplay and disease emergence. Emerg Microbes Infect 2013; 2:e5. [PMID: 26038452 PMCID: PMC3630490 DOI: 10.1038/emi.2013.5] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/07/2012] [Accepted: 01/07/2013] [Indexed: 12/13/2022]
Abstract
Gaining insight in likely disease emergence scenarios is critical to preventing such events from happening. Recent focus has been on emerging zoonoses and on identifying common patterns and drivers of emerging diseases. However, no overarching framework exists to integrate knowledge on all emerging infectious disease events. Here, we propose such a conceptual framework based on changes in the interplay of pathogens, hosts and environment that lead to the formation of novel disease patterns and pathogen genetic adjustment. We categorize infectious disease emergence events into three groups: (i) pathogens showing up in a novel host, ranging from spill-over, including zoonoses, to complete species jumps; (ii) mutant pathogens displaying novel traits in the same host, including an increase in virulence, antimicrobial resistance and host immune escape; and (iii) disease complexes emerging in a new geographic area, either through range expansion or through long distance jumps. Each of these categories is characterized by a typical set of drivers of emergence, matching pathogen trait profiles, disease ecology and transmission dynamics. Our framework may assist in disentangling and structuring the rapidly growing amount of available information on infectious diseases. Moreover, it may contribute to a better understanding of how human action changes disease landscapes globally.
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Pitman R, Fisman D, Zaric GS, Postma M, Kretzschmar M, Edmunds J, Brisson M. Dynamic transmission modeling: a report of the ISPOR-SMDM Modeling Good Research Practices Task Force Working Group-5. Med Decis Making 2013; 32:712-21. [PMID: 22990086 DOI: 10.1177/0272989x12454578] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The transmissible nature of communicable diseases is what sets them apart from other diseases modeled by health economists. The probability of a susceptible individual becoming infected at any one point in time (the force of infection) is related to the number of infectious individuals in the population, will change over time, and will feed back into the future force of infection. These nonlinear interactions produce transmission dynamics that require specific consideration when modeling an intervention that has an impact on the transmission of a pathogen. Best practices for designing and building these models are set out in this paper.
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Affiliation(s)
| | - David Fisman
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada (DF)
| | - Gregory S Zaric
- Ivey School of Business, University of Western Ontario, London, Canada (GSZ)
| | - Maarten Postma
- Unit of PharmacoEpidemiology and PharmacoEconomics, Department of Pharmacy, University of Groningen, Groningen, Netherlands (MP)
| | - Mirjam Kretzschmar
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, and Center for Infectious Disease Control, RIVM, Bilthoven, Netherlands (MK)
| | - John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine,
London, United Kingdom (JE)
| | - Marc Brisson
- URESP, Centre de Recherche FRSQ du CHA Universitaire de Que´ bec and De´ partement de Me´ decine Sociale et Pre´ ventive, Laval University, Quebec City, Canada (MB)
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20
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Chang Z, Lu S, Chen L, Jin Q, Yang J. Causative species and serotypes of shigellosis in mainland China: systematic review and meta-analysis. PLoS One 2012; 7:e52515. [PMID: 23285073 PMCID: PMC3527545 DOI: 10.1371/journal.pone.0052515] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 11/14/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Shigella, the causative agent of shigellosis, is a major global public health concern, particularly in developing countries with poor sanitation. A comprehensive and current understanding of the prevalent species and serotypes of shigellosis is essential for both disease prevention and vaccine development. However, no current data are available on the causative species/serotypes of shigellosis in mainland China during the past decade. METHODS AND FINDINGS Relevant studies addressing the prevalent species of shigellosis in mainland China from January 2001 to December 2010 were identified from PubMed and the Chinese BioMedical Literature Database (in Chinese) until April 2012. A total of 131 eligible articles (136 studies) were included in this review. Meta-analyses showed that the prevalences of S. flexneri and S. sonnei were 76.2% (95% CI, 73.7%-78.5%) and 21.3% (95% CI, 19.0%-23.7%), respectively. Stratified analyses indicated a decrease in the prevalence of S. flexneri cases and an increase in the prevalence of S. sonnei cases concurrent with the rapid economic growth experienced by China in recent years. Moreover, significantly higher rates of S. sonnei were observed in the East, North and Northeast regions of China, as compared to the rest of the country. These phenomena imply the possible association between the prevalent species of Shigella and regional economic status; however, additional factors also exist and require further investigations. Moreover, the two major serotypes S. flexneri 2a and 4c accounted for 21.5% (95% CI, 16.7%-27.4%) and 12.9% (95% CI 9.8%-16.9%) of S. flexneri infections, respectively, in the past decade. However, these results were found to be frequently heterogeneous (p for Q tests <0.01). CONCLUSIONS This study provides an updated review of the causative agents of shigellosis in mainland China and focuses on the importance of strengthening prevention and research efforts on S. sonnei and the newly emerged S. flexneri serotype 4c.
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Affiliation(s)
- Zhili Chang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuting Lu
- Institute of Medical Information/Medical Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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21
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Safan M, Kretzschmar M, Hadeler KP. Vaccination based control of infections in SIRS models with reinfection: special reference to pertussis. J Math Biol 2012; 67:1083-110. [PMID: 22948407 DOI: 10.1007/s00285-012-0582-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 08/09/2012] [Indexed: 11/26/2022]
Abstract
The aim of this paper is to study the impact of introducing a partially protective vaccine on the dynamics of infection in SIRS models where primary and secondary infections are distinguished. We investigate whether a public health strategy based solely on vaccinating a proportion of newborns can lead to an effective control of the disease. In addition to carrying out the qualitative analysis, the findings are further explained by numerical simulations. The model exhibits backward bifurcation for certain values of the parameters. In these cases the standard basic reproduction number (obtained by inspection of the uninfected state) is not significant. The key threshold is the reinfection level which depends on the relative transmissibility (susceptibility) of secondary, with respect to primary, infected (susceptible) individuals and the relative loss of immunity of vaccinated, with respect to recovered, individuals. If one or all of these ratios decrease, then the threshold increases which increases the possibility to contain the infection by vaccination. The analysis shows further that symptomatic infections can be eliminated by vaccination solely.
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Affiliation(s)
- Muntaser Safan
- Mathematics Department, Faculty of Science, Mansoura University, 35516 , Mansoura, Egypt,
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22
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Pitman R, Fisman D, Zaric GS, Postma M, Kretzschmar M, Edmunds J, Brisson M. Dynamic transmission modeling: a report of the ISPOR-SMDM Modeling Good Research Practices Task Force--5. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2012; 15:828-34. [PMID: 22999132 PMCID: PMC7110742 DOI: 10.1016/j.jval.2012.06.011] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 06/21/2012] [Indexed: 05/17/2023]
Abstract
The transmissible nature of communicable diseases is what sets them apart from other diseases modeled by health economists. The probability of a susceptible individual becoming infected at any one point in time (the force of infection) is related to the number of infectious individuals in the population, will change over time, and will feed back into the future force of infection. These nonlinear interactions produce transmission dynamics that require specific consideration when modeling an intervention that has an impact on the transmission of a pathogen. Best practices for designing and building these models are set out in this article.
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23
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The decline and resurgence of pertussis in the US. Epidemics 2011; 3:183-8. [DOI: 10.1016/j.epidem.2011.10.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/17/2011] [Accepted: 08/18/2011] [Indexed: 11/22/2022] Open
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Laboratory adaptation of Bordetella pertussis is associated with the loss of type three secretion system functionality. Infect Immun 2011; 79:3677-82. [PMID: 21730086 DOI: 10.1128/iai.00136-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although Bordetella pertussis contains and transcribes loci encoding type III secretion system (TTSS) homologues, expression of TTSS-associated proteins has been reported only for non-laboratory-adapted Irish clinical isolates. Here we confirm such a result for clinical isolates obtained from patients treated in Argentinean hospitals. Moreover, we demonstrate that the expression of TTSS-associated proteins is independent both of the year in which the isolate was obtained and of the types of polymorphic alleles for other virulence factors but is dependent on environmental growth conditions. Interestingly, we observed that TTSS-associated protein expression is lost after successive in vitro passages but becomes operative again when bacteria come into contact with the host. This in vivo activation of TTSS expression was observed not only for clinical isolates previously adapted to the laboratory after successive in vitro passages but also for vaccine strains that did not express the system in vitro. The reversibility of TTSS expression, demonstrated by its switching off-on when the bacterium comes into contact with the host, appears to be an adaptive response of this pathogen.
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25
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Complete genome sequence of Bordetella pertussis CS, a Chinese pertussis vaccine strain. J Bacteriol 2011; 193:4017-8. [PMID: 21622744 DOI: 10.1128/jb.05184-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis is the causative agent of pertussis. Here, we report the genome sequence of Bordetella pertussis strain CS, isolated from an infant patient in Beijing and widely used as a vaccine strain for production of an acellular pertussis vaccine in China.
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26
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van Gent M, Bart MJ, van der Heide HGJ, Heuvelman KJ, Kallonen T, He Q, Mertsola J, Advani A, Hallander HO, Janssens K, Hermans PW, Mooi FR. SNP-based typing: a useful tool to study Bordetella pertussis populations. PLoS One 2011; 6:e20340. [PMID: 21647370 PMCID: PMC3103551 DOI: 10.1371/journal.pone.0020340] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA). In this study, a single nucleotide polymorphism (SNP) typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in the Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis.
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Affiliation(s)
- Marjolein van Gent
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marieke J. Bart
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Han G. J. van der Heide
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kees J. Heuvelman
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Teemu Kallonen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
- Turku Graduate School for Biomedical Sciences, University of Turku, Turku, Finland
| | - Qiushui He
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
| | - Jussi Mertsola
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Turku, Finland
| | - Abdolreza Advani
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Hans O. Hallander
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | | | - Peter W. Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Nijmegen Medical Center, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Frits R. Mooi
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
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de Greeff SC, de Melker HE, van Gageldonk PGM, Schellekens JFP, van der Klis FRM, Mollema L, Mooi FR, Berbers GAM. Seroprevalence of pertussis in The Netherlands: evidence for increased circulation of Bordetella pertussis. PLoS One 2010; 5:e14183. [PMID: 21152071 PMCID: PMC2995730 DOI: 10.1371/journal.pone.0014183] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/24/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In many countries, the reported pertussis has increased despite high vaccination coverage. However, accurate determination of the burden of disease is hampered by reporting artifacts. The infection frequency is more reliably estimated on the basis of the prevalence of high IgG concentrations against pertussis toxin (IgG-Ptx). We determined whether the increase in reported pertussis in the last decade is associated with an increase in the number of infections. METHODOLOGY/PRINCIPAL FINDINGS In a cross-sectional population-based serosurveillance study conducted in 2006-07, from a randomly selected age-stratified sample of 7,903 persons, serum IgG-Ptx concentrations were analyzed using a fluorescent bead-based multiplex immuno assay. In 2006-07, 9.3% (95%CI 8.5-10.1) of the population above 9 years of age had an IgG-Ptx concentration above 62.5 EU/ml (suggestive for pertussis infection in the past year), which was more than double compared to 1995-96 (4.0%; 95%CI 3.3-4.7). The reported incidence showed a similar increase as the seroprevalence between both periods. CONCLUSIONS Although changes in the vaccination program have reduced pertussis morbidity in childhood, they have not affected the increased infection rate in adolescent and adult pertussis. Indeed, the high circulation of B. pertussis in the latter age-categories may limit the effectiveness of pediatric vaccination.
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Affiliation(s)
- Sabine C de Greeff
- Epidemiology and Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
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Broutin H, Viboud C, Grenfell BT, Miller MA, Rohani P. Impact of vaccination and birth rate on the epidemiology of pertussis: a comparative study in 64 countries. Proc Biol Sci 2010; 277:3239-45. [PMID: 20534609 DOI: 10.1098/rspb.2010.0994] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bordetella pertussis infection remains an important public health problem worldwide despite decades of routine vaccination. A key indicator of the impact of vaccination programmes is the inter-epidemic period, which is expected to increase with vaccine uptake if there is significant herd immunity. Based on empirical data from 64 countries across the five continents over the past 30-70 years, we document the observed relationship between the average inter-epidemic period, birth rate and vaccine coverage. We then use a mathematical model to explore the range of scenarios for duration of immunity and transmission resulting from repeat infections that are consistent with empirical evidence. Estimates of pertussis periodicity ranged between 2 and 4.6 years, with a strong association with susceptible recruitment rate, defined as birth rate × (1 - vaccine coverage). Periodicity increased by 1.27 years on average after the introduction of national vaccination programmes (95% CI: 1.13, 1.41 years), indicative of increased herd immunity. Mathematical models suggest that the observed patterns of pertussis periodicity are equally consistent with loss of immunity that is not as rapid as currently thought, or with negligible transmission generated by repeat infections. We conclude that both vaccine coverage and birth rate drive pertussis periodicity globally and that vaccination induces strong herd immunity effects. A better understanding of the role of repeat infections in pertussis transmission is critical to refine existing control strategies.
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Affiliation(s)
- H Broutin
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
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Williams PD. Darwinian interventions: taming pathogens through evolutionary ecology. Trends Parasitol 2009; 26:83-92. [PMID: 20036799 DOI: 10.1016/j.pt.2009.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/27/2009] [Accepted: 11/26/2009] [Indexed: 01/23/2023]
Abstract
From the seemingly inevitable emergence of antibiotic resistance following drug use to the necessity of annual influenza vaccine updates, the ability of pathogens to evolve appears to preclude the development of effective, long-term interventions for many diseases. Despite this gloomy forecast, recent research explores how various principles and concepts from evolutionary ecology might inform practical attempts to bring these disease-causing agents under greater human control. By utilizing evolutionary and ecological information at various scales, these works investigate some promising avenues of disease intervention, from trapping pathogens in evolutionary dead ends, through slowing or inhibiting the process of pathogen adaptation, to more accurate forecasting of pathogen evolutionary trajectories. Thus, an evolutionary ecology perspective might ultimately provide powerful new tools in the pursuit of enduring solutions to the problem of treatment-driven pathogen evolution.
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Affiliation(s)
- Paul David Williams
- University of California at Davis, Environmental Science and Policy, 1 Shields Avenue, Davis, California 95616, USA.
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Abstract
To gain insight into pertussis disease dynamics, we studied age-specific long-term periodicity and seasonality of pertussis in The Netherlands. Hierarchical time-series models were used to analyse the monthly reported pertussis incidence in January 1996-June 2006 by age group. The incidence of pertussis showed a slightly increasing long-term trend with highest incidence rates seen in 1996, 1999, 2001 and 2004. For all age groups the annual peak incidence was found in August, except for the 13-18 years age group where the peak occurred in November. Monthly trends in adults showed high correlation with trends in age groups 0-4 years (0.94) and 5-12 years (0.92). We found no evidence for a relationship between annual rises in pertussis and the opening of schools. Concurrent annual fluctuations of pertussis incidence in adults and infants suggest frequent transmission within and between these age groups. Studying trends offers insight into transmission dynamics and may facilitate decisions on future vaccination strategies.
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van Gent M, de Greeff SC, van der Heide HGJ, Mooi FR. An investigation into the cause of the 1983 whooping cough epidemic in the Netherlands. Vaccine 2009; 27:1898-903. [PMID: 19368769 DOI: 10.1016/j.vaccine.2009.01.111] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/13/2009] [Accepted: 01/22/2009] [Indexed: 10/21/2022]
Abstract
Despite more than 50 years of vaccination, whooping cough is still an endemic disease in the Netherlands with regular epidemic outbreaks. In the last 20 years, two periods of increased notifications were observed. The causes of the increased notifications in the first period, from 1983 to 1987, are contentious. At the time it was suggested to be a surveillance artifact, caused by changes in diagnostic procedures and increased awareness. An alternative explanation, a reduction in the vaccine dose, was downplayed at the time. The aim of this study was to reinvestigate the causes of the increased notifications by identifying changes in the Bordetella pertussis population. B. pertussis strains, isolated from 1965 to 1992, were characterized by means of fimbrial serotyping, multiple-locus sequence typing of virulence genes (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Shifts in fimbrial serotypes and MLVA types were associated with changes in vaccine dose and increased number of notifications. One to three years after lowering of the vaccine dose, the predominant fimbrial serotype changed from Fim3 to Fim2, and the reverse trend was observed when the vaccine dose was increased. Significantly, changes in fimbrial serotypes were evident at least seven years before the increase in notifications. Our results provide evidence that the change in vaccine dose affected host immunity and, consequently, contributed to an increase in pertussis morbidity. Further, we show that MLVA and fimbrial serotyping of strains can be used as early warning for pertussis epidemics.
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Affiliation(s)
- Marjolein van Gent
- Laboratory for Infectious Diseases and Screening, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, The Netherlands
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Day T, Galvani A, Struchiner C, Gumel A. The evolutionary consequences of vaccination. Vaccine 2008; 26 Suppl 3:C1-3. [DOI: 10.1016/j.vaccine.2008.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Gimeno IM. Marek's disease vaccines: A solution for today but a worry for tomorrow? Vaccine 2008; 26 Suppl 3:C31-41. [DOI: 10.1016/j.vaccine.2008.04.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Vaccination leads to dramatic perturbations of the environment of parasite populations and this can have both demographic and evolutionary consequences. We present a theoretical framework for modelling the short- and long-term epidemiological and evolutionary consequences of vaccination. This framework integrates previous theoretical studies of vaccine-induced parasite evolution, and it allows one to make some useful qualitative predictions regarding the outcome of the competition between different types of vaccine-favoured variants. It can also be used to make quantitative predictions about the speed of such evolutionary processes. This work may help define the relevant parameters that need to be measured in specific parasite populations in order to evaluate the potential evolutionary consequences of vaccination. In particular, we argue that more work should be done evaluating the nature and magnitude of parasite fitness costs associated with adaptation to vaccinated hosts.
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Affiliation(s)
- Sylvain Gandon
- Génétique et Evolution des Maladies Infectieuses, UMR CNRS/IRD 2724, IRD, 911 Avenue Agropolis, 34394 Montpellier Cedex 5, France.
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DNA fingerprinting analysis of breakthrough outbreaks in vaccine-protected poultry stocks. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2007; 14:1649-51. [PMID: 17928428 DOI: 10.1128/cvi.00159-07] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report recurrent outbreaks of Yersinia pseudotuberculosis conjunctivitis in ducks and of fowl cholera in geese, occurring in stocks previously vaccinated with inactivated autogenous vaccines. Enterobacterial repetitive intergenic consensus sequence-based PCR and pulsed-field gel electrophoresis indicated reinfection with a new Y. pseudotuberculosis strain and vaccine evasion by the same Pasteurella multocida strain.
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Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. THE LANCET. INFECTIOUS DISEASES 2007; 7:328-37. [PMID: 17448936 DOI: 10.1016/s1473-3099(07)70108-1] [Citation(s) in RCA: 509] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
New tools for controlling tuberculosis are urgently needed. Despite our emerging understanding of the biogeography of Mycobacterium tuberculosis, the implications for development of new diagnostics, drugs, and vaccines is unknown. M tuberculosis has a clonal genetic population structure that is geographically constrained. Evidence suggests strain-specific differences in virulence and immunogenicity in light of this global phylogeography. We propose a strain selection framework, based on robust phylogenetic markers, which will allow for systematic and comprehensive evaluation of new tools for tuberculosis control.
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Safan M, Heesterbeek H, Dietz K. The minimum effort required to eradicate infections in models with backward bifurcation. J Math Biol 2006; 53:703-18. [PMID: 16897013 DOI: 10.1007/s00285-006-0028-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 04/28/2006] [Indexed: 11/27/2022]
Abstract
We study an epidemiological model which assumes that the susceptibility after a primary infection is r times the susceptibility before a primary infection. For r = 0 (r = 1) this is the SIR (SIS) model. For r > 1 + (mu/alpha) this model shows backward bifurcations, where mu is the death rate and alpha is the recovery rate. We show for the first time that for such models we can give an expression for the minimum effort required to eradicate the infection if we concentrate on control measures affecting the transmission rate constant beta. This eradication effort is explicitly expressed in terms of alpha,r, and mu As in models without backward bifurcation it can be interpreted as a reproduction number, but not necessarily as the basic reproduction number. We define the relevant reproduction numbers for this purpose. The eradication effort can be estimated from the endemic steady state. The classical basic reproduction number R0 is smaller than the eradication effort for r > 1 + (mu/alpha) and equal to the effort for other values of r. The method we present is relevant to the whole class of compartmental models with backward bifurcation.
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Affiliation(s)
- Muntaser Safan
- Department of Medical Biometry, Eberhard-Karls-University Tübingen, Westbahnhofstr. 55, 72070, Tübingen, Germany.
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Restif O, Grenfell BT. Integrating life history and cross-immunity into the evolutionary dynamics of pathogens. Proc Biol Sci 2006; 273:409-16. [PMID: 16615206 PMCID: PMC1560197 DOI: 10.1098/rspb.2005.3335] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Models for the diversity and evolution of pathogens have branched into two main directions: the adaptive dynamics of quantitative life-history traits (notably virulence) and the maintenance and invasion of multiple, antigenically diverse strains that interact with the host's immune memory. In a first attempt to reconcile these two approaches, we developed a simple modelling framework where two strains of pathogens, defined by a pair of life-history traits (infectious period and infectivity), interfere through a given level of cross-immunity. We used whooping cough as a potential example, but the framework proposed here could be applied to other acute infectious diseases. Specifically, we analysed the effects of these parameters on the invasion dynamics of one strain into a population, where the second strain is endemic. Whereas the deterministic version of the model converges towards stable coexistence of the two strains in most cases, stochastic simulations showed that transient epidemic dynamics can cause the extinction of either strain. Thus ecological dynamics, modulated by the immune parameters, eventually determine the adaptive value of different pathogen genotypes. We advocate an integrative view of pathogen dynamics at the crossroads of immunology, epidemiology and evolution, as a way towards efficient control of infectious diseases.
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Affiliation(s)
- Olivier Restif
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
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Brinig MM, Cummings CA, Sanden GN, Stefanelli P, Lawrence A, Relman DA. Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation. J Bacteriol 2006; 188:2375-82. [PMID: 16547023 PMCID: PMC1428402 DOI: 10.1128/jb.188.7.2375-2382.2006] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bordetella pertussis, an obligate human pathogen and the agent of whooping cough, is a clonal species, despite the dynamic selection pressures imposed by host immunity and vaccine usage. Because the generation of variation is critical for species evolution, we employed a variety of approaches to examine features of B. pertussis genetic variation. We found a high level of conservation of gene content among 137 B. pertussis strains with different geographical, temporal, and epidemiological associations, using comparative genomic hybridization. The limited number of regions of difference were frequently located adjacent to copies of the insertion element IS481, which is present in high numbers in the B. pertussis chromosome. This repeated sequence appears to provide targets for homologous recombination, resulting in deletion of intervening sequences. Using subtractive hybridization, we searched for previously undetected genes in diverse clinical isolates but did not detect any new genes, indicating that gene acquisition is rare in B. pertussis. In contrast, we found evidence of altered gene order in the several strains that were examined and again found an association of IS481 with sites of rearrangement. Finally, we compared whole-genome expression profiles of different strains and found significant changes in transcript abundance, even in the same strain after as few as 12 laboratory passages. This combination of approaches provides a detailed picture of a pathogenic species with little gene loss or gain but with the capacity to generate variation by rearranging its chromosome and altering gene expression. These findings have broad implications for host adaptation by microbial pathogens.
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Affiliation(s)
- Mary M Brinig
- Department of Microbiology and Immunology, Stanford University School of Medicine, California 94305, USA.
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