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Gardini Sanches Palasio R, Marques Moralejo Bermudi P, Luiz de Lima Macedo F, Reis Santana LM, Chiaravalloti-Neto F. Zika, chikungunya and co-occurrence in Brazil: space-time clusters and associated environmental-socioeconomic factors. Sci Rep 2023; 13:18026. [PMID: 37865641 PMCID: PMC10590386 DOI: 10.1038/s41598-023-42930-4] [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: 02/14/2023] [Accepted: 09/16/2023] [Indexed: 10/23/2023] Open
Abstract
Chikungunya and Zika have been neglected as emerging diseases. This study aimed to analyze the space-time patterns of their occurrence and co-occurrence and their associated environmental and socioeconomic factors. Univariate (individually) and multivariate (co-occurrence) scans were analyzed for 608,388 and 162,992 cases of chikungunya and Zika, respectively. These occurred more frequently in the summer and autumn. The clusters with the highest risk were initially located in the northeast, dispersed to the central-west and coastal areas of São Paulo and Rio de Janeiro (2018-2021), and then increased in the northeast (2019-2021). Chikungunya and Zika demonstrated decreasing trends of 13% and 40%, respectively, whereas clusters showed an increasing trend of 85% and 57%, respectively. Clusters with a high co-occurrence risk have been identified in some regions of Brazil. High temperatures are associated with areas at a greater risk of these diseases. Chikungunya was associated with low precipitation levels, more urbanized environments, and places with greater social inequalities, whereas Zika was associated with high precipitation levels and low sewage network coverage. In conclusion, to optimize the surveillance and control of chikungunya and Zika, this study's results revealed high-risk areas with increasing trends and priority months and the role of socioeconomic and environmental factors.
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Affiliation(s)
- Raquel Gardini Sanches Palasio
- Laboratory of Spatial Analysis in Health (LAES), Department of Epidemiology, School of Public Health, University of São Paulo (FSP/USP), São Paulo, SP, Brazil.
| | - Patricia Marques Moralejo Bermudi
- Laboratory of Spatial Analysis in Health (LAES), Department of Epidemiology, School of Public Health, University of São Paulo (FSP/USP), São Paulo, SP, Brazil
| | - Fernando Luiz de Lima Macedo
- Epidemiological Surveillance Center (CVE) Prof. Alexandre Vranjac, Coordination of Disease Control, Health Department of the State of São Paulo, São Paulo, SP, Brazil
| | - Lidia Maria Reis Santana
- Epidemiological Surveillance Center (CVE) Prof. Alexandre Vranjac, Coordination of Disease Control, Health Department of the State of São Paulo, São Paulo, SP, Brazil
- Federal University of Sao Paulo (Unifesp), São Paulo, SP, Brazil
| | - Francisco Chiaravalloti-Neto
- Laboratory of Spatial Analysis in Health (LAES), Department of Epidemiology, School of Public Health, University of São Paulo (FSP/USP), São Paulo, SP, Brazil
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2
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Southall E, Ogi-Gittins Z, Kaye AR, Hart WS, Lovell-Read FA, Thompson RN. A practical guide to mathematical methods for estimating infectious disease outbreak risks. J Theor Biol 2023; 562:111417. [PMID: 36682408 DOI: 10.1016/j.jtbi.2023.111417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Mathematical models are increasingly used throughout infectious disease outbreaks to guide control measures. In this review article, we focus on the initial stages of an outbreak, when a pathogen has just been observed in a new location (e.g., a town, region or country). We provide a beginner's guide to two methods for estimating the risk that introduced cases lead to sustained local transmission (i.e., the probability of a major outbreak), as opposed to the outbreak fading out with only a small number of cases. We discuss how these simple methods can be extended for epidemiological models with any level of complexity, facilitating their wider use, and describe how estimates of the probability of a major outbreak can be used to guide pathogen surveillance and control strategies. We also give an overview of previous applications of these approaches. This guide is intended to help quantitative researchers develop their own epidemiological models and use them to estimate the risks associated with pathogens arriving in new host populations. The development of these models is crucial for future outbreak preparedness. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
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Affiliation(s)
- E Southall
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - Z Ogi-Gittins
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - A R Kaye
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - W S Hart
- Mathematical Institute, University of Oxford, Oxford, UK
| | | | - R 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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3
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Thompson RN, Southall E, Daon Y, Lovell-Read FA, Iwami S, Thompson CP, Obolski U. The impact of cross-reactive immunity on the emergence of SARS-CoV-2 variants. Front Immunol 2023; 13:1049458. [PMID: 36713397 PMCID: PMC9874934 DOI: 10.3389/fimmu.2022.1049458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/05/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction A key feature of the COVID-19 pandemic has been the emergence of SARS-CoV-2 variants with different transmission characteristics. However, when a novel variant arrives in a host population, it will not necessarily lead to many cases. Instead, it may fade out, due to stochastic effects and the level of immunity in the population. Immunity against novel SARS-CoV-2 variants may be influenced by prior exposures to related viruses, such as other SARS-CoV-2 variants and seasonal coronaviruses, and the level of cross-reactive immunity conferred by those exposures. Methods Here, we investigate the impact of cross-reactive immunity on the emergence of SARS-CoV-2 variants in a simplified scenario in which a novel SARS-CoV-2 variant is introduced after an antigenically related virus has spread in the population. We use mathematical modelling to explore the risk that the novel variant invades the population and causes a large number of cases, as opposed to fading out with few cases. Results We find that, if cross-reactive immunity is complete (i.e. someone infected by the previously circulating virus is not susceptible to the novel variant), the novel variant must be more transmissible than the previous virus to invade the population. However, in a more realistic scenario in which cross-reactive immunity is partial, we show that it is possible for novel variants to invade, even if they are less transmissible than previously circulating viruses. This is because partial cross-reactive immunity effectively increases the pool of susceptible hosts that are available to the novel variant compared to complete cross-reactive immunity. Furthermore, if previous infection with the antigenically related virus assists the establishment of infection with the novel variant, as has been proposed following some experimental studies, then even variants with very limited transmissibility are able to invade the host population. Discussion Our results highlight that fast assessment of the level of cross-reactive immunity conferred by related viruses against novel SARS-CoV-2 variants is an essential component of novel variant risk assessments.
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Affiliation(s)
- Robin N. Thompson
- Mathematics Institute, University of Warwick, Coventry, United Kingdom,Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom,*Correspondence: Robin N. Thompson,
| | - Emma Southall
- Mathematics Institute, University of Warwick, Coventry, United Kingdom,Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Yair Daon
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Shingo Iwami
- Division of Natural Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Craig P. Thompson
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Uri Obolski
- School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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4
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Danesh G, Saulnier E, Gascuel O, Choisy M, Alizon S. TiPS
: Rapidly simulating trajectories and phylogenies from compartmental models. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gonché Danesh
- MIVEGEC, CNRS, IRD Université de Montpellier Montpellie France
| | - Emma Saulnier
- MIVEGEC, CNRS, IRD Université de Montpellier Montpellie France
| | | | - Marc Choisy
- Centre for Tropical Medicine and Global Health Nuffield Department of Medicine, University of Oxford Oxford UK
- Oxford University Clinical Research Unit Ho Chi Minh City Vietnam
| | - Samuel Alizon
- MIVEGEC, CNRS, IRD Université de Montpellier Montpellie France
- Center for Interdisciplinary Research in Biology (CIRB) College de France, CNRS, INSERM, Université PSL Paris France
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5
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Elie B, Selinger C, Alizon S. The source of individual heterogeneity shapes infectious disease outbreaks. Proc Biol Sci 2022; 289:20220232. [PMID: 35506229 PMCID: PMC9065969 DOI: 10.1098/rspb.2022.0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There is known heterogeneity between individuals in infectious disease transmission patterns. The source of this heterogeneity is thought to affect epidemiological dynamics but studies tend not to control for the overall heterogeneity in the number of secondary cases caused by an infection. To explore the role of individual variation in infection duration and transmission rate in parasite emergence and spread, while controlling for this potential bias, we simulate stochastic outbreaks with and without parasite evolution. As expected, heterogeneity in the number of secondary cases decreases the probability of outbreak emergence. Furthermore, for epidemics that do emerge, assuming more realistic infection duration distributions leads to faster outbreaks and higher epidemic peaks. When parasites require adaptive mutations to cause large epidemics, the impact of heterogeneity depends on the underlying evolutionary model. If emergence relies on within-host evolution, decreasing the infection duration variance decreases the probability of emergence. These results underline the importance of accounting for realistic distributions of transmission rates to anticipate the effect of individual heterogeneity on epidemiological dynamics.
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Affiliation(s)
- Baptiste Elie
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Christian Selinger
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France.,Swiss Tropical and Public Health Institute, Basel, Kreuzstrasse 2, Allschwil 4123, Switzerland
| | - Samuel Alizon
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France.,Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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6
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Shaw CL, Kennedy DA. What the reproductive number R 0 can and cannot tell us about COVID-19 dynamics. Theor Popul Biol 2021; 137:2-9. [PMID: 33417839 PMCID: PMC7785280 DOI: 10.1016/j.tpb.2020.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/02/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022]
Abstract
The reproductive number R (or R0, the initial reproductive number in an immune-naïve population) has long been successfully used to predict the likelihood of pathogen invasion, to gauge the potential severity of an epidemic, and to set policy around interventions. However, often ignored complexities have generated confusion around use of the metric. This is particularly apparent with the emergent pandemic virus SARS-CoV-2, the causative agent of COVID-19. We address some misconceptions about the predictive ability of the reproductive number, focusing on how it changes over time, varies over space, and relates to epidemic size by referencing the mathematical definition of R and examples from the current pandemic. We hope that a better appreciation of the uses, nuances, and limitations of R and R0 facilitates a better understanding of epidemic spread, epidemic severity, and the effects of interventions in the context of SARS-CoV-2.
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Affiliation(s)
- Clara L Shaw
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States of America.
| | - David A Kennedy
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, United States of America.
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7
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Morris DH, Petrova VN, Rossine FW, Parker E, Grenfell BT, Neher RA, Levin SA, Russell CA. Asynchrony between virus diversity and antibody selection limits influenza virus evolution. eLife 2020; 9:e62105. [PMID: 33174838 PMCID: PMC7748417 DOI: 10.7554/elife.62105] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously-infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within-host. They also suggest new avenues for improving influenza control.
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MESH Headings
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Biological Evolution
- Genetic Variation/genetics
- Humans
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A virus/genetics
- Influenza A virus/immunology
- Influenza, Human/immunology
- Influenza, Human/transmission
- Influenza, Human/virology
- Models, Statistical
- Selection, Genetic/genetics
- Selection, Genetic/immunology
- Virion/genetics
- Virion/immunology
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Affiliation(s)
- Dylan H Morris
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Velislava N Petrova
- Department of Human Genetics, Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Fernando W Rossine
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Edyth Parker
- Department of Veterinary Medicine, University of CambridgeCambridgeUnited Kingdom
- Department of Medical Microbiology, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Bryan T Grenfell
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
- Fogarty International Center, National Institutes of HealthBethesdaUnited States
| | | | - Simon A Levin
- Department of Ecology & Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - Colin A Russell
- Department of Medical Microbiology, Academic Medical Center, University of AmsterdamAmsterdamNetherlands
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Meehan MT, Cope RC, McBryde ES. On the probability of strain invasion in endemic settings: Accounting for individual heterogeneity and control in multi-strain dynamics. J Theor Biol 2019; 487:110109. [PMID: 31816294 PMCID: PMC7094110 DOI: 10.1016/j.jtbi.2019.110109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 01/21/2023]
Abstract
Endemic infection can insulate host populations from invasion by mutant variants. The timing of control implementation strongly influences its efficacy. Controls that exacerbate host heterogeneity outperform those that curtail it. Differential control can facilitate strain invasion and eventual replacement.
Pathogen evolution is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of new pathogens are often ignited by the emergence and transmission of mutant variants descended from wild-type strains circulating in the community. In this work we investigate the stochastic dynamics of the emergence of a novel disease strain, introduced into a population in which it must compete with an existing endemic strain. In analogy with past work on single-strain epidemic outbreaks, we apply a branching process approximation to calculate the probability that the new strain becomes established. As expected, a critical determinant of the survival prospects of any invading strain is the magnitude of its reproduction number relative to that of the background endemic strain. Whilst in most circumstances this ratio must exceed unity in order for invasion to be viable, we show that differential control scenarios can lead to less-fit novel strains invading populations hosting a fitter endemic one. This analysis and the accompanying findings will inform our understanding of the mechanisms that have led to past instances of successful strain invasion, and provide valuable lessons for thwarting future drug-resistant strain incursions.
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Affiliation(s)
- Michael T Meehan
- James Cook University, Australian Institute of Tropical Health and Medicine, Townsville, Australia.
| | - Robert C Cope
- The University of Adelaide, School of Mathematical Sciences, Adelaide, Australia
| | - Emma S McBryde
- James Cook University, Australian Institute of Tropical Health and Medicine, Townsville, Australia
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9
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Vissoci JRN, Rocha TAH, da Silva NC, de Sousa Queiroz RC, Thomaz EBAF, Amaral PVM, Lein A, Branco MDRFC, Aquino J, Rodrigues ZMR, da Silva AAM, Staton C. Zika virus infection and microcephaly: Evidence regarding geospatial associations. PLoS Negl Trop Dis 2018; 12:e0006392. [PMID: 29694351 PMCID: PMC5937996 DOI: 10.1371/journal.pntd.0006392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/07/2018] [Accepted: 03/18/2018] [Indexed: 01/06/2023] Open
Abstract
Background Although the Zika virus (ZIKV) epidemic ceased to be a public health emergency by the end of 2016, studies to improve knowledge about this emerging disease are still needed, especially those investigating a causal relationship between ZIKV in pregnant women and microcephaly in neonates. However, there are still many challenges in describing the relationship between ZIKV and microcephaly. The few studies focusing on the epidemiological profile of ZIKV and its changes over time are largely limited to systematic reviews of case reports and dispersal mapping of ZIKV spread over time without quantitative methods to analyze patterns and their covariates. Since Brazil has been at the epicenter of the ZIKV epidemic, this study examines the geospatial association between ZIKV and microcephaly in Brazil. Methods Our study is categorized as a retrospective, ecological study based on secondary databases. Data were obtained from January to December 2016, from the following data sources: Brazilian System for Epidemiological Surveillance, Disease Notification System, System for Specialized Management Support, and Brazilian Institute of Geography and Statistics. Data were aggregated by municipality. Incidence rates were estimated per 100,000 inhabitants. Analyses consisted of mapping the aggregated incidence rates of ZIKV and microcephaly, followed by a Getis-Ord-Gi spatial cluster analysis and a Bivariate Local Moran’s I analysis. Results The incidence of ZIKV cases is changing the virus’s spatial pattern, shifting from Brazil’s Northeast region to the Midwest and North regions. The number of municipalities in clusters of microcephaly incidence is also shifting from the Northeast region to the Midwest and North, after a time lag is considered. Our findings suggest an increase in microcephaly incidence in the Midwest and North regions, associated with high levels of ZIKV infection months before. Conclusion The greatest burden of microcephaly shifted from the Northeast to other Brazilian regions at the beginning of 2016. Brazil’s Midwest region experienced an increase in microcephaly incidence associated with ZIKV incidence. This finding highlights an association between an increase in ZIKV infection with a rise in microcephaly cases after approximately three months. The increasing evidence of a relationship between ZIKV in pregnant women and fetal congenital ZIKV syndrome with microcephaly has been reported in the literature over the last two years. Our findings suggest a spatial dependency between the diseases. Therefore, using the spatial pattern of ZIKV incidence to better understand risk areas for microcephaly may help the design of surveillance policies. Brazil had a large epidemic of ZIKV, leading to several important studies of the ZIKV outbreak and its association with microcephaly. This study used a geospatial analysis approach to examine the association between ZIKV and microcephaly in Brazilian regions. It was possible to highlight a spatial association between ZIKV and microcephaly considering a time lag between diseases. Brazilian regions with the highest incidences of microcephaly were the regions where the highest incidence of ZIKV occurred months before. This finding can help the organization and planning of health services to offer better screening actions dedicated to pregnant women in high-risk areas.
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Affiliation(s)
- João Ricardo Nickenig Vissoci
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Division of Emergency Medicine, Duke University Health System, Durham, North Carolina, United States of America
- * E-mail:
| | - Thiago Augusto Hernandes Rocha
- Federal University of Minas Gerais, School of Economics, Center of post-graduate and Research in Administration, Belo Horizonte, Minas Gerais, Brazil
| | - Núbia Cristina da Silva
- Federal University of Minas Gerais, Faculty of Economics, Observatory of Human Resources in Health, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Pedro Vasconcelos Maia Amaral
- Federal University of Minas Gerais, Centre for Development and Regional Planning, Belo Horizonte, Minas Gerais, Brazil
| | - Adriana Lein
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | | | - José Aquino
- Federal University of Maranhão, Department of Geosciences, São Luís, Maranhão, Brazil
| | | | | | - Catherine Staton
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Division of Emergency Medicine, Duke University Health System, Durham, North Carolina, United States of America
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Abstract
The continual emergence of new pathogens and the increased spread of antibiotic resistance in bacterial populations remind us that microbes are living entities that evolve at rates that impact public health interventions. Following the historical thread of the works of Pasteur and Darwin shows how reconciling clinical microbiology, ecology, and evolution can be instrumental to understanding pathology, developing new therapies, and prolonging the efficiency of existing ones.
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Affiliation(s)
- Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), Montpellier, France
- * E-mail:
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12
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Kautz TF, Díaz-González EE, Erasmus JH, Malo-García IR, Langsjoen RM, Patterson EI, Auguste DI, Forrester NL, Sanchez-Casas RM, Hernández-Ávila M, Alpuche-Aranda CM, Weaver SC, Fernández-Salas I. Chikungunya Virus as Cause of Febrile Illness Outbreak, Chiapas, Mexico, 2014. Emerg Infect Dis 2016; 21:2070-3. [PMID: 26488312 PMCID: PMC4622247 DOI: 10.3201/eid2111.150546] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Since chikungunya virus (CHIKV) was introduced into the Americas in 2013, its geographic distribution has rapidly expanded. Of 119 serum samples collected in 2014 from febrile patients in southern Mexico, 79% were positive for CHIKV or IgM against CHIKV. Sequencing results confirmed CHIKV strains closely related to Caribbean isolates.
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Abstract
Virulence is generally defined as the reduction in host fitness following infection by a parasite (see Box 1 for glossary) [1]. In general, parasite exploitation of host resources may reduce host survival (mortality virulence), decrease host fecundity (sterility virulence), or even have sub-lethal effects that disturb the way individuals interact within a community (morbidity) [2,3]. In fact, the virulence of many parasites involves a combination of these various effects (Box 2). In practice, however, virulence is most often defined as disease-induced mortality [1, 4–6]. This is especially true in the theoretical literature, where the evolution of sterility virulence, morbidity, and mixed strategies of host exploitation have received relatively little attention. While the focus on mortality effects has allowed for easy comparison between models and, thus, rapid advancement of the field, we ask whether these theoretical simplifications have led us to inadvertently minimize the evolutionary importance of host sterilization and secondary virulence effects. As explicit theoretical work on morbidity is currently lacking (but see [7]), our aim in this Opinion piece is to discuss what is understood about sterility virulence evolution, its adaptive potential, and the implications for parasites that utilize a combination of host survival and reproductive resources.
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Affiliation(s)
- Jessica L. Abbate
- Centre d’Écologie Fonctionnelle et Évolutive (CEFE), CNRS-Université de Montpellier- Université Paul-Valéry Montpellier-EPHE, Montpellier, France
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- * E-mail:
| | - Sarah Kada
- Centre d’Écologie Fonctionnelle et Évolutive (CEFE), CNRS-Université de Montpellier- Université Paul-Valéry Montpellier-EPHE, Montpellier, France
| | - Sébastien Lion
- Centre d’Écologie Fonctionnelle et Évolutive (CEFE), CNRS-Université de Montpellier- Université Paul-Valéry Montpellier-EPHE, Montpellier, France
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14
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Hartfield M, Alizon S. Within-host stochastic emergence dynamics of immune-escape mutants. PLoS Comput Biol 2015; 11:e1004149. [PMID: 25785434 PMCID: PMC4365036 DOI: 10.1371/journal.pcbi.1004149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/22/2015] [Indexed: 12/28/2022] Open
Abstract
Predicting the emergence of new pathogenic strains is a key goal of evolutionary epidemiology. However, the majority of existing studies have focussed on emergence at the population level, and not within a host. In particular, the coexistence of pre-existing and mutated strains triggers a heightened immune response due to the larger total pathogen population; this feedback can smother mutated strains before they reach an ample size and establish. Here, we extend previous work for measuring emergence probabilities in non-equilibrium populations, to within-host models of acute infections. We create a mathematical model to investigate the emergence probability of a fitter strain if it mutates from a self-limiting strain that is guaranteed to go extinct in the long-term. We show that ongoing immune cell proliferation during the initial stages of infection causes a drastic reduction in the probability of emergence of mutated strains; we further outline how this effect can be accurately measured. Further analysis of the model shows that, in the short-term, mutant strains that enlarge their replication rate due to evolving an increased growth rate are more favoured than strains that suffer a lower immune-mediated death rate (‘immune tolerance’), as the latter does not completely evade ongoing immune proliferation due to inter-parasitic competition. We end by discussing the model in relation to within-host evolution of human pathogens (including HIV, hepatitis C virus, and cancer), and how ongoing immune growth can affect their evolutionary dynamics. The ongoing evolution of infectious diseases provides a constant health threat. This evolution can either result in the production of new pathogens, or new strains of existing pathogens that escape prevailing drug treatments or immune responses. The latter process, also known as immune escape, is a predominant reason for the persistence of several viruses, including HIV and hepatitis C virus (HCV), in their human host. As a consequence, the within-host emergence of new strains has been the intense focus of modelling studies. However, existing models have neglected important feedbacks that affects this emergence probability. Specifically, once a mutated pathogen arises that spreads more quickly than the initial (resident) strain, it potentially triggers a heightened immune response that can eliminate the mutated strain before it spreads. Our study outlines novel mathematical modelling techniques that accurately quantify how ongoing immune growth reduces the emergence probability of mutated pathogenic strains over the course of an infection. Analysis of this model suggests that, in order to enlarge its emergence probability, it is evolutionary beneficial for a mutated strain to increase its growth rate rather than tolerate immunity by having a lower immune-mediated death-rate. Our model can be readily applied to existing within-host data, as demonstrated with application to HIV, HCV, and cancer dynamics.
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Affiliation(s)
- Matthew Hartfield
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, Montpellier, France
- * E-mail:
| | - Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2), 911 avenue Agropolis, Montpellier, France
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Evolution and emergence of infectious diseases in theoretical and real-world networks. Nat Commun 2015; 6:6101. [PMID: 25592476 PMCID: PMC4335509 DOI: 10.1038/ncomms7101] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 12/15/2014] [Indexed: 12/23/2022] Open
Abstract
One of the most important advancements in theoretical epidemiology has been the development of methods that account for realistic host population structure. The central finding is that heterogeneity in contact networks, such as the presence of 'superspreaders', accelerates infectious disease spread in real epidemics. Disease control is also complicated by the continuous evolution of pathogens in response to changing environments and medical interventions. It remains unclear, however, how population structure influences these adaptive processes. Here we examine the evolution of infectious disease in empirical and theoretical networks. We show that the heterogeneity in contact structure, which facilitates the spread of a single disease, surprisingly renders a resident strain more resilient to invasion by new variants. Our results suggest that many host contact structures suppress invasion of new strains and may slow disease adaptation. These findings are important to the natural history of disease evolution and the spread of drug-resistant strains.
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