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Bhoomiboonchoo P, Gibbons RV, Huang A, Yoon IK, Buddhari D, Nisalak A, Chansatiporn N, Thipayamongkolgul M, Kalanarooj S, Endy T, Rothman AL, Srikiatkhachorn A, Green S, Mammen MP, Cummings DA, Salje H. The spatial dynamics of dengue virus in Kamphaeng Phet, Thailand. PLoS Negl Trop Dis 2014; 8:e3138. [PMID: 25211127 PMCID: PMC4161352 DOI: 10.1371/journal.pntd.0003138] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 07/22/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Dengue is endemic to the rural province of Kamphaeng Phet, Northern Thailand. A decade of prospective cohort studies has provided important insights into the dengue viruses and their generated disease. However, as elsewhere, spatial dynamics of the pathogen remain poorly understood. In particular, the spatial scale of transmission and the scale of clustering are poorly characterized. This information is critical for effective deployment of spatially targeted interventions and for understanding the mechanisms that drive the dispersal of the virus. METHODOLOGY/PRINCIPAL FINDINGS We geocoded the home locations of 4,768 confirmed dengue cases admitted to the main hospital in Kamphaeng Phet province between 1994 and 2008. We used the phi clustering statistic to characterize short-term spatial dependence between cases. Further, to see if clustering of cases led to similar temporal patterns of disease across villages, we calculated the correlation in the long-term epidemic curves between communities. We found that cases were 2.9 times (95% confidence interval 2.7-3.2) more likely to live in the same village and be infected within the same month than expected given the underlying spatial and temporal distribution of cases. This fell to 1.4 times (1.2-1.7) for individuals living in villages 1 km apart. Significant clustering was observed up to 5 km. We found a steadily decreasing trend in the correlation in epidemics curves by distance: communities separated by up to 5 km had a mean correlation of 0.28 falling to 0.16 for communities separated between 20 km and 25 km. A potential explanation for these patterns is a role for human movement in spreading the pathogen between communities. Gravity style models, which attempt to capture population movement, outperformed competing models in describing the observed correlations. CONCLUSIONS There exists significant short-term clustering of cases within individual villages. Effective spatially and temporally targeted interventions deployed within villages may target ongoing transmission and reduce infection risk.
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Affiliation(s)
- Piraya Bhoomiboonchoo
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Faculty of Public Health, Mahidol University, Bangkok, Thailand
- * E-mail:
| | - Robert V. Gibbons
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Angkana Huang
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - In-Kyu Yoon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Darunee Buddhari
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Ananda Nisalak
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | | | - Timothy Endy
- Department of Infectious Diseases, State University of New York, Syracuse, New York, United States of America
| | - Alan L. Rothman
- University of Rhode Island, Providence, Rhode Island, United States of America
| | - Anon Srikiatkhachorn
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sharone Green
- Center for Infectious Disease and Vaccine Research, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Mammen P. Mammen
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Derek A. Cummings
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Henrik Salje
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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52
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Le MQ, Lam HM, Cuong VD, Lam TTY, Halpin RA, Wentworth DE, Hien NT, Thanh LT, Phuong HVM, Horby P, Boni MF. Migration and persistence of human influenza A viruses, Vietnam, 2001-2008. Emerg Infect Dis 2014; 19:1756-65. [PMID: 24188643 PMCID: PMC3837676 DOI: 10.3201/eid1911.130349] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year.
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53
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Nunes MRT, Palacios G, Faria NR, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DBA, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PFC, Lipkin WI. Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLoS Negl Trop Dis 2014; 8:e2769. [PMID: 24743730 PMCID: PMC3990485 DOI: 10.1371/journal.pntd.0002769] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/18/2014] [Indexed: 01/01/2023] Open
Abstract
Dengue virus and its four serotypes (DENV-1 to DENV-4) infect 390 million people and are implicated in at least 25,000 deaths annually, with the largest disease burden in tropical and subtropical regions. We investigated the spatial dynamics of DENV-1, DENV-2 and DENV-3 in Brazil by applying a statistical framework to complete genome sequences. For all three serotypes, we estimated that the introduction of new lineages occurred within 7 to 10-year intervals. New lineages were most likely to be imported from the Caribbean region to the North and Northeast regions of Brazil, and then to disperse at a rate of approximately 0.5 km/day. Joint statistical analysis of evolutionary, epidemiological and ecological data indicates that aerial transportation of humans and/or vector mosquitoes, rather than Aedes aegypti infestation rates or geographical distances, determine dengue virus spread in Brazil.
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Affiliation(s)
- Marcio R. T. Nunes
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Gustavo Palacios
- Center for Genomic Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, Maryland, United States of America
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | | | - Jamilla A. Pantoja
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Sueli G. Rodrigues
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Valéria L. Carvalho
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Daniele B. A. Medeiros
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Guy Baele
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California - Los Angeles, Los Angeles, California, United States of America
| | - Philippe Lemey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Pedro F. C. Vasconcelos
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
- Universidade do Estado do Pará, Belém, Pará, Brazil
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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Villabona-Arenas CJ, de Oliveira JL, Capra CDS, Balarini K, Loureiro M, Fonseca CRTP, Passos SD, Zanotto PMDA. Detection of four dengue serotypes suggests rise in hyperendemicity in urban centers of Brazil. PLoS Negl Trop Dis 2014; 8:e2620. [PMID: 24587454 PMCID: PMC3937275 DOI: 10.1371/journal.pntd.0002620] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Christian Julián Villabona-Arenas
- Laboratório de Evolução Molecular e Bioinformática, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Jessica Luana de Oliveira
- Laboratório de Evolução Molecular e Bioinformática, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Carla de Sousa Capra
- Laboratório de Saúde Pública, Secretaria da Saúde, Prefeitura Municipal de Guarujá, Guarujá, São Paulo, Brazil
| | - Karime Balarini
- Itapema Laboratório de Análises Clínicas, Guarujá, São Paulo, Brazil
| | - Mauricio Loureiro
- Laboratório de Infectologia Pedriátrica, Faculdade de Medicina de Jundiaí, Jundiaí, São Paulo, Brazil
| | | | - Saulo Duarte Passos
- Laboratório de Infectologia Pedriátrica, Faculdade de Medicina de Jundiaí, Jundiaí, São Paulo, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Laboratório de Evolução Molecular e Bioinformática, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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Messina JP, Brady OJ, Scott TW, Zou C, Pigott DM, Duda KA, Bhatt S, Katzelnick L, Howes RE, Battle KE, Simmons CP, Hay SI. Global spread of dengue virus types: mapping the 70 year history. Trends Microbiol 2014; 22:138-46. [PMID: 24468533 PMCID: PMC3946041 DOI: 10.1016/j.tim.2013.12.011] [Citation(s) in RCA: 438] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/20/2013] [Accepted: 12/23/2013] [Indexed: 12/28/2022]
Abstract
Since the first isolation of dengue virus (DENV) in 1943, four types have been identified. Global phenomena such as urbanization and international travel are key factors in facilitating the spread of dengue. Documenting the type-specific record of DENV spread has important implications for understanding patterns in dengue hyperendemicity and disease severity as well as vaccine design and deployment strategies. Existing studies have examined the spread of DENV types at regional or local scales, or described phylogeographic relationships within a single type. Here we summarize the global distribution of confirmed instances of each DENV type from 1943 to 2013 in a series of global maps. These show the worldwide expansion of the types, the expansion of disease hyperendemicity, and the establishment of an increasingly important infectious disease of global public health significance.
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Affiliation(s)
- Jane P Messina
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| | - Oliver J Brady
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Thomas W Scott
- Department of Entomology, University of California Davis, Davis, California 95616, USA; Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chenting Zou
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - David M Pigott
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Kirsten A Duda
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Samir Bhatt
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Leah Katzelnick
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Rosalind E Howes
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Katherine E Battle
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Cameron P Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK; Nossal Institute of Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Simon I Hay
- Spatial Ecology and Epidemiology Group, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK; Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
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56
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Guo RN, Lin JY, Li LH, Ke CW, He JF, Zhong HJ, Zhou HQ, Peng ZQ, Yang F, Liang WJ. The prevalence and endemic nature of dengue infections in Guangdong, South China: an epidemiological, serological, and etiological study from 2005-2011. PLoS One 2014; 9:e85596. [PMID: 24465613 PMCID: PMC3900419 DOI: 10.1371/journal.pone.0085596] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/29/2013] [Indexed: 11/30/2022] Open
Abstract
Objectives Frequent outbreaks of dengue are considered to be associated with an increased risk for endemicity of the disease. The occurrence of a large number of indigenous dengue cases in consecutive years indicates the possibility of a changing dengue epidemic pattern in Guangdong, China. Methods To have a clear understanding of the current dengue epidemic, a retrospective study of epidemiological profile, serological response, and virological features of dengue infections from 2005–2011 was conducted. Case data were collected from the National Notifiable Infectious Diseases Reporting Network. Serum samples were collected and prepared for serological verification and etiological confirmation. Incidence, temporal and spatial distribution, and the clinical manifestation of dengue infections were analyzed. Pearson's Chi-Square test was used to compare incidences between different age groups. A seroprevalence survey was implemented in local healthy inhabitants to obtain the overall positive rate for the specific immunoglobulin (Ig) G antibody against dengue virus (DENV). Results The overall annual incidence rate was 1.87/100000. A significant difference was found in age-specific incidence (Pearson's Chi-Square value 498.008, P<0.001). Children under 5 years of age had the lowest incidence of 0.28/100000. The vast majority of cases presented with a mild manifestation typical to dengue fever. The overall seroprevalence of dengue IgG antibody in local populations was 2.43% (range 0.28%–5.42%). DENV-1 was the predominant serotype in circulation through the years, while all 4 serotypes were identified in indigenous patients from different outbreak localities since 2009. Conclusions A gradual change in the epidemic pattern of dengue infection has been observed in recent years in Guangdong. With the endemic nature of dengue infections, the transition from a monotypic to a multitypic circulation of dengue virus in the last several years will have an important bearing on the prevention and control of dengue in the province and in the neighboring districts.
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Affiliation(s)
- Ru-Ning Guo
- Public Health Emergency management office, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Jin-Yan Lin
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Lin-Hui Li
- Public Health Emergency management office, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Chang-Wen Ke
- Institute of Pathogenic Microorganisms, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Jian-Feng He
- Institute of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Hao-Jie Zhong
- Institute of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Hui-Qiong Zhou
- Institute of Pathogenic Microorganisms, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Zhi-Qiang Peng
- Institute of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Fen Yang
- Institute of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Wen-Jia Liang
- Institute of Infectious Disease Prevention and Control, Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
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Rabaa MA, Simmons CP, Fox A, Le MQ, Nguyen TTT, Le HY, Gibbons RV, Nguyen XT, Holmes EC, Aaskov JG. Dengue virus in sub-tropical northern and central Viet Nam: population immunity and climate shape patterns of viral invasion and maintenance. PLoS Negl Trop Dis 2013; 7:e2581. [PMID: 24340118 PMCID: PMC3854975 DOI: 10.1371/journal.pntd.0002581] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 10/29/2013] [Indexed: 11/22/2022] Open
Abstract
Dengue virus transmission occurs in both epidemic and endemic cycles across tropical and sub-tropical regions of the world. Incidence is particularly high in much of Southeast Asia, where hyperendemic transmission plagues both urban and rural populations. However, endemicity has not been established in some areas with climates that may not support year-round viral transmission. An understanding of how dengue viruses (DENV) enter these environments and whether the viruses persist in inapparent local transmission cycles is central to understanding how dengue emerges in areas at the margins of endemic transmission. Dengue is highly endemic in tropical southern Vietnam, while increasingly large seasonal epidemics have occurred in northern Viet Nam over the last decade. We have investigated the spread of DENV-1 throughout Vietnam to determine the routes by which the virus enters northern and central regions of the country. Phylogeographic analysis of 1,765 envelope (E) gene sequences from Southeast Asia revealed frequent movement of DENV between neighboring human populations and strong local clustering of viral lineages. Long-distance migration of DENV between human population centers also occurred regularly and on short time-scales, indicating human-mediated viral invasion into northern Vietnam. Human populations in southern Vietnam were found to be the primary source of DENV circulating throughout the country, while central and northern Vietnam acted as sink populations, likely due to reduced connectedness to other populations in the case of the central regions and to the influence of temperature variability on DENV replication and vector survival and competence in the north. Finally, phylogeographic analyses suggested that viral movement follows a gravity model and indicates that population immunity and physical and economic connections between populations may play important roles in shaping patterns of DENV transmission. Reports from sub-tropical regions of the world suggest a growing risk of introduction and establishment of dengue viruses (DENV) in new locales. Recent dengue epidemics in northern Viet Nam present an opportunity to study how DENV invades and spreads in these environments. The proximity of this region to tropical areas experiencing year-round endemic DENV transmission makes it an ideal site for studying the effects of human population movement and climate on DENV emergence. We performed a phylogenetic analysis using DENV-1 envelope gene sequences from Southeast Asia. We show that DENV are regularly imported into northern and central Viet Nam from southern Vietnam, and that increasingly large seasonal epidemics in the north are caused by newly introduced viruses each year. While tropical Vietnam maintains localized virus populations for multiple years, cool winter temperatures in sub-tropical northern Viet Nam may reduce mosquito populations and virus replication to levels that are not conducive to year-round DENV transmission. Finally, we found that the dispersal of DENV across the region is well-described using human movement and immunity data, and believe that increased epidemiological, entomological, and virological surveillance are needed to understand the processes by which endemic DENV transmission becomes established in new populations.
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Affiliation(s)
- Maia A. Rabaa
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Cameron P. Simmons
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annette Fox
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Hanoi, Vietnam
| | - Mai Quynh Le
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Hai Yen Le
- Military Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Robert V. Gibbons
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Edward C. Holmes
- Marie Bashir Institute for Emerging Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John G. Aaskov
- Queensland University of Technology, Brisbane, Australia
- Australian Army Malaria Institute, Brisbane, Australia
- * E-mail:
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58
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Natural, persistent oscillations in a spatial multi-strain disease system with application to dengue. PLoS Comput Biol 2013; 9:e1003308. [PMID: 24204241 PMCID: PMC3812071 DOI: 10.1371/journal.pcbi.1003308] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 09/13/2013] [Indexed: 12/03/2022] Open
Abstract
Many infectious diseases are not maintained in a state of equilibrium but exhibit significant fluctuations in prevalence over time. For pathogens that consist of multiple antigenic types or strains, such as influenza, malaria or dengue, these fluctuations often take on the form of regular or irregular epidemic outbreaks in addition to oscillatory prevalence levels of the constituent strains. To explain the observed temporal dynamics and structuring in pathogen populations, epidemiological multi-strain models have commonly evoked strong immune interactions between strains as the predominant driver. Here, with specific reference to dengue, we show how spatially explicit, multi-strain systems can exhibit all of the described epidemiological dynamics even in the absence of immune competition. Instead, amplification of natural stochastic differences in disease transmission, can give rise to persistent oscillations comprising semi-regular epidemic outbreaks and sequential dominance of dengue's four serotypes. Not only can this mechanism explain observed differences in serotype and disease distributions between neighbouring geographical areas, it also has important implications for inferring the nature and epidemiological consequences of immune mediated competition in multi-strain pathogen systems. The population dynamics of multi-strain pathogens are often characterized by persistent and irregular fluctuations in disease incidence and strain prevalence levels over time. Previous theoretical approaches have often evoked strong immunological interactions between individual strains, such as cross-immunity, in order to explain these complex epidemiologies; however, spatial segregation between hosts and stochastic heterogeneities in transmission success are rarely considered in these studies. Here, with specific reference to dengue, we show that the stochasticities underlying disease transmission within a spatially explicit, agent-based model can give rise to multi-annual epidemic outbreaks and fluctuating pathogen population structures - even in the absence of immune competition. In contrast to previous modeling studies, which have resulted in ambiguous predictions about the exact nature and strength of interactions between dengue's four serotypes, our results present a parsimonious, demographic mechanism, that highlights the importance of spatial ecology for understanding and interpreting the epidemiological dynamics of dengue and other multi-strain pathogen systems.
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Rasmussen DA, Boni MF, Koelle K. Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam. Mol Biol Evol 2013; 31:258-71. [PMID: 24150038 PMCID: PMC3907054 DOI: 10.1093/molbev/mst203] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Coalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches—often referred to as phylodynamic methods—have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred from viral genealogies often differ widely from those observed from other sources of epidemiological data, such as hospitalization records. We demonstrate how a modeling framework that allows for the direct fitting of mechanistic epidemiological models to genealogies can be used to test different hypotheses about what ecological factors cause phylodynamic inferences to differ from observed dynamics. We use this framework to test different hypotheses about why dengue serotype 1 (DENV-1) population dynamics in southern Vietnam inferred using existing phylodynamic methods differ from hospitalization data. Specifically, we consider how factors such as seasonality, vector dynamics, and spatial structure can affect inferences drawn from genealogies. The coalescent models we derive to take into account vector dynamics and spatial structure reveal that these ecological complexities can substantially affect coalescent rates among lineages. We show that incorporating these additional ecological complexities into coalescent models can also greatly improve estimates of historical population dynamics and lead to new insights into the factors shaping viral genealogies.
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Cuong HQ, Vu NT, Cazelles B, Boni MF, Thai KTD, Rabaa MA, Quang LC, Simmons CP, Huu TN, Anders KL. Spatiotemporal dynamics of dengue epidemics, southern Vietnam. Emerg Infect Dis 2013; 19:945-53. [PMID: 23735713 PMCID: PMC3713821 DOI: 10.3201/eid1906.121323] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An improved understanding of heterogeneities in dengue virus transmission might provide insights into biological and ecologic drivers and facilitate predictions of the magnitude, timing, and location of future dengue epidemics. To investigate dengue dynamics in urban Ho Chi Minh City and neighboring rural provinces in Vietnam, we analyzed a 10-year monthly time series of dengue surveillance data from southern Vietnam. The per capita incidence of dengue was lower in Ho Chi Minh City than in most rural provinces; annual epidemics occurred 1-3 months later in Ho Chi Minh City than elsewhere. The timing and the magnitude of annual epidemics were significantly more correlated in nearby districts than in remote districts, suggesting that local biological and ecologic drivers operate at a scale of 50-100 km. Dengue incidence during the dry season accounted for 63% of variability in epidemic magnitude. These findings can aid the targeting of vector-control interventions and the planning for dengue vaccine implementation.
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Affiliation(s)
- Hoang Quoc Cuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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61
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Chu PY, Ke GM, Chen PC, Liu LT, Tsai YC, Tsai JJ. Spatiotemporal dynamics and epistatic interaction sites in dengue virus type 1: a comprehensive sequence-based analysis. PLoS One 2013; 8:e74165. [PMID: 24040199 PMCID: PMC3767619 DOI: 10.1371/journal.pone.0074165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/29/2013] [Indexed: 12/26/2022] Open
Abstract
The continuing threat of dengue fever necessitates a comprehensive characterisation of its epidemiological trends. Phylogenetic and recombination events were reconstructed based on 100 worldwide dengue virus (DENV) type 1 genome sequences with an outgroup (prototypes of DENV2-4). The phylodynamic characteristics and site-specific variation were then analysed using data without the outgroup. Five genotypes (GI-GV) and a ladder-like structure with short terminal branch topology were observed in this study. Apparently, the transmission of DENV1 was geographically random before gradual localising with human activity as GI-GIII in South Asia, GIV in the South Pacific, and GV in the Americas. Genotypes IV and V have recently shown higher population densities compared to older genotypes. All codon regions and all tree branches were skewed toward a negative selection, which indicated that their variation was restricted by protein function. Notably, multi-epistatic interaction sites were found in both PrM 221 and NS3 1730. Recombination events accumulated in regions E, NS3-NS4A, and particularly in region NS5. The estimated coevolution pattern also highlights the need for further study of the biological role of protein PrM 221 and NS3 1730. The recent transmission of emergent GV sublineages into Central America and Europe mandates closely monitoring of genotype interaction and succession.
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Affiliation(s)
- Pei-Yu Chu
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Guan-Ming Ke
- Graduate Institute of Animal Vaccine Technology, National Pingtung University of Science and Technology, Neipu, Pingtung, Taiwan
| | - Po-Chih Chen
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Li-Teh Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine and Life Science, Chung-Hwa University of Medical Technology, Tainan, Taiwan
| | - Yen-Chun Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Jih-Jin Tsai
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail:
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62
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Camargo A, Werneck FP, Morando M, Sites JW, Avila LJ. Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling. Mol Ecol 2013; 22:4038-54. [PMID: 23786355 DOI: 10.1111/mec.12369] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 04/25/2013] [Accepted: 04/25/2013] [Indexed: 12/29/2022]
Abstract
Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.
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Affiliation(s)
- Arley Camargo
- Unidad de Diversidad, Sistemática y Evolución, Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Boulevard Almirante Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
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63
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Villabona-Arenas CJ, de Brito AF, de Andrade Zanotto PM. Genomic mosaicism in two strains of Dengue virus type 3. INFECTION GENETICS AND EVOLUTION 2013; 18:202-12. [PMID: 23727343 DOI: 10.1016/j.meegid.2013.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 11/28/2022]
Abstract
Recombination is a significant factor driving genomic evolution, but it is not well understood in Dengue virus. We used phylogenetic methods to search for recombination in 636 Dengue virus type 3 (DENV-3) genomes and unveiled complex recombination patterns in two strains, which appear to be the outcome of recombination between genotype II and genotype I parental DENV-3 lineages. Our findings of genomic mosaic structures suggest that strand switching during RNA synthesis may be involved in the generation of genetic diversity in dengue viruses.
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Affiliation(s)
- Christian Julián Villabona-Arenas
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1734, CEP: 05508-000, São Paulo, SP, Brazil
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64
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Villabona-Arenas CJ, Zanotto PMDA. Worldwide spread of Dengue virus type 1. PLoS One 2013; 8:e62649. [PMID: 23675416 PMCID: PMC3652851 DOI: 10.1371/journal.pone.0062649] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/24/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND DENV-1 is one of the four viral serotypes that causes Dengue, the most common mosquito-borne viral disease of humans. The prevalence of these viruses has grown in recent decades and is now present in more than 100 countries. Limited studies document the spread of DENV-1 over the world despite its importance for human health. METHODOLOGY/PRINCIPAL FINDINGS We used representative DENV-1 envelope gene sequences to unravel the dynamics of viral diffusion under a Bayesian phylogeographic approach. Data included strains from 45 distinct geographic locations isolated from 1944 to 2009. The estimated mean rate of nucleotide substitution was 6.56 × 10⁻⁴ substitutions/site/year. The larger genotypes (I, IV and V) had a distinctive phylogenetic structure and since 1990 they experienced effective population size oscillations. Thailand and Indonesia represented the main sources of strains for neighboring countries. Besides, Asia broadcast lineages into the Americas and the Pacific region that diverged in isolation. Also, a transmission network analysis revealed the pivotal role of Indochina in the global diffusion of DENV-1 and of the Caribbean in the diffusion over the Americas. CONCLUSIONS/SIGNIFICANCE The study summarizes the spatiotemporal DENV-1 worldwide spread that may help disease control.
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Affiliation(s)
- Christian Julián Villabona-Arenas
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
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65
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Villabona-Arenas CJ, Mondini A, Bosch I, Schimitt D, Calzavara-Silva CE, de A Zanotto PM, Nogueira ML. Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006-2007. PLoS One 2013; 8:e63496. [PMID: 23667626 PMCID: PMC3646734 DOI: 10.1371/journal.pone.0063496] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022] Open
Abstract
Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.
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Affiliation(s)
- Christian Julian Villabona-Arenas
- Laboratório de Evolução Molecular e Bioinformática (LEMB), Departamento de Microbiologia, Instituto de Ciências Biomédicas. Universidade de São Paulo, São Paulo, Brazil
| | - Adriano Mondini
- Laboratório de Saúde Pública. Departamento de Ciências Biológicas. Faculdade de Ciências Farmacêuticas - Universidade Estadual Paulista “Júlio de Mesquita Filho” Araraquara/SP, Brazil
| | - Irene Bosch
- Division of Heath Science and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Diane Schimitt
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Carlos E. Calzavara-Silva
- Laboratório de Imunologia Celular e Molecular (LICM), Centro de Pesquisas Rene Rachou (CPqRR), Fundação Oswaldo Cruz (Fiocruz), Belo Horizonte, MG, Brazil
| | - Paolo M. de A Zanotto
- Laboratório de Evolução Molecular e Bioinformática (LEMB), Departamento de Microbiologia, Instituto de Ciências Biomédicas. Universidade de São Paulo, São Paulo, Brazil
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
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66
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Stadler T, Bonhoeffer S. Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120198. [PMID: 23382421 DOI: 10.1098/rstb.2012.0198] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).
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Affiliation(s)
- Tanja Stadler
- Institut für Integrative Biologie, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland.
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67
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Ward MJ, Lycett SJ, Kalish ML, Rambaut A, Leigh Brown AJ. Estimating the rate of intersubtype recombination in early HIV-1 group M strains. J Virol 2013; 87:1967-73. [PMID: 23236072 PMCID: PMC3571495 DOI: 10.1128/jvi.02478-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/06/2012] [Indexed: 11/20/2022] Open
Abstract
West Central Africa has been implicated as the epicenter of the HIV-1 epidemic, and almost all group M subtypes can be found there. Previous analysis of early HIV-1 group M sequences from Kinshasa in the Democratic Republic of Congo, formerly Zaire, revealed that isolates from a number of individuals fall in different positions in phylogenetic trees constructed from sequences from opposite ends of the genome as a result of recombination between viruses of different subtypes. Here, we use discrete ancestral trait mapping to develop a procedure for quantifying HIV-1 group M intersubtype recombination across phylogenies, using individuals' gag (p17) and env (gp41) subtypes. The method was applied to previously described HIV-1 group M sequences from samples obtained in Kinshasa early in the global radiation of HIV. Nine different p17 and gp41 intersubtype recombinant combinations were present in the data set. The mean number of excess ancestral subtype transitions (NEST) required to map individuals' p17 subtypes onto the gp14 phylogeny samples, compared to the number required to map them onto the p17 phylogenies, and vice versa, indicated that excess subtype transitions occurred at a rate of approximately 7 × 10(-3) to 8 × 10(-3) per lineage per year as a result of intersubtype recombination. Our results imply that intersubtype recombination may have occurred in approximately 20% of lineages evolving over a period of 30 years and confirm intersubtype recombination as a substantial force in generating HIV-1 group M diversity.
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Affiliation(s)
- Melissa J. Ward
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Samantha J. Lycett
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
| | - Marcia L. Kalish
- Vanderbilt University, Vanderbilt Institute for Global Health, Nashville, Tennessee, USA
| | - Andrew Rambaut
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew J. Leigh Brown
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Edinburgh, United Kingdom
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68
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Rabaa MA, Klungthong C, Yoon IK, Holmes EC, Chinnawirotpisan P, Thaisomboonsuk B, Srikiatkhachorn A, Rothman AL, Tannitisupawong D, Aldstadt J, Nisalak A, Mammen MP, Gibbons RV, Endy TP, Fansiri T, Scott TW, Jarman RG. Frequent in-migration and highly focal transmission of dengue viruses among children in Kamphaeng Phet, Thailand. PLoS Negl Trop Dis 2013; 7:e1990. [PMID: 23350000 PMCID: PMC3547850 DOI: 10.1371/journal.pntd.0001990] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/16/2012] [Indexed: 12/15/2022] Open
Abstract
Revealing the patterns and determinants of the spread of dengue virus (DENV) at local scales is central to understanding the epidemiology and evolution of this major human pathogen. We performed a phylogenetic analysis of the envelope (E) genes of DENV-1, -2, -3, and -4 isolates (involving 97, 23, 5, and 74 newly collected sequences, respectively) sampled from school-based cohort and village-based cluster studies in Kamphaeng Phet, Thailand, between 2004 and 2007. With these data, we sought to describe the spatial and temporal patterns of DENV spread within a rural population where a future vaccine efficacy trial is planned. Our analysis revealed considerable genetic diversity within the study population, with multiple lineages within each serotype circulating for various lengths of time during the study period. These results suggest that DENV is frequently introduced into both semi-urban and rural areas in Kamphaeng Phet from other populations. In contrast, the persistence of viral lineages across sampling years was observed less frequently. Analysis of phylogenetic clustering indicated that DENV transmission was highly spatially and temporally focal, and that it occurred in homes rather than at school. Overall, the strength of temporal clustering suggests that seasonal bottlenecks in local DENV populations facilitate the invasion and establishment of viruses from outside of the study area, in turn reducing the extent of lineage persistence.
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Affiliation(s)
- Maia A. Rabaa
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anon Srikiatkhachorn
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Alan L. Rothman
- Institute for Immunology and Informatics, University of Rhode Island, Providence, Rhode Island, United States of America
| | - Darunee Tannitisupawong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jared Aldstadt
- Department of Geography, University at Buffalo, Buffalo, New York, United States of America
| | - Ananda Nisalak
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mammen P. Mammen
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Robert V. Gibbons
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy P. Endy
- Department of Infectious Diseases, State University of New York at Syracuse, Syracuse, New York, United States of America
| | - Thanyalak Fansiri
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Thomas W. Scott
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Entomology, University of California Davis, Davis, California, United States of America
| | - Richard G. Jarman
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- * E-mail:
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69
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Hughes J, Allen RC, Baguelin M, Hampson K, Baillie GJ, Elton D, Newton JR, Kellam P, Wood JLN, Holmes EC, Murcia PR. Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathog 2012; 8:e1003081. [PMID: 23308065 PMCID: PMC3534375 DOI: 10.1371/journal.ppat.1003081] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/25/2012] [Indexed: 12/30/2022] Open
Abstract
The ability of influenza A viruses (IAVs) to cross species barriers and evade host immunity is a major public health concern. Studies on the phylodynamics of IAVs across different scales – from the individual to the population – are essential for devising effective measures to predict, prevent or contain influenza emergence. Understanding how IAVs spread and evolve during outbreaks is critical for the management of epidemics. Reconstructing the transmission network during a single outbreak by sampling viral genetic data in time and space can generate insights about these processes. Here, we obtained intra-host viral sequence data from horses infected with equine influenza virus (EIV) to reconstruct the spread of EIV during a large outbreak. To this end, we analyzed within-host viral populations from sequences covering 90% of the infected yards. By combining gene sequence analyses with epidemiological data, we inferred a plausible transmission network, in turn enabling the comparison of transmission patterns during the course of the outbreak and revealing important epidemiological features that were not apparent using either approach alone. The EIV populations displayed high levels of genetic diversity, and in many cases we observed distinct viral populations containing a dominant variant and a number of related minor variants that were transmitted between infectious horses. In addition, we found evidence of frequent mixed infections and loose transmission bottlenecks in these naturally occurring populations. These frequent mixed infections likely influence the size of epidemics. Influenza A viruses (IAVs) are major pathogens of humans and animals. Understanding how IAVs spread and evolve at different scales (individual, regional, global) in natural conditions is critical for preventing or managing influenza epidemics. A vast body of knowledge has been generated on the evolution of IAVs at the global scale. Additionally, recent experimental transmission studies have examined the diversity and transmission of influenza viruses within and between hosts. However, most studies on the spread of IAVs during epidemics have been based on consensus viral sequences, an approach that does not have enough discriminatory power to reveal exact transmission pathways. Here, we analyzed multiple within-host viral populations from different horses infected with equine influenza virus (EIV) during the course of an outbreak in a population within a confined area. This provided an opportunity to examine the genetic diversity of the viruses within single animals, the transmission of the viruses between each closely confined population within a yard, and the transmission between horses in different yards. We show that individual horses can be infected by viruses from more than one other horse, which has important implications for facilitating segment reassortment and the evolution of EIV. Additionally, by combining viral sequencing data and epidemiological data we show that the high levels of mixed infections can reveal the underlying epidemiological dynamics of the outbreak, and that epidemic size could be underestimated if only epidemiological data is considered. As sequencing technologies become cheaper and faster, these analyses could be undertaken almost in real-time and help control future outbreaks.
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Affiliation(s)
- Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard C. Allen
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Marc Baguelin
- Immunisation, Hepatitis and Blood Safety Department, Health Protection Agency, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Katie Hampson
- Boyd Orr Centre for Population and Ecosystem Health, Institute for Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Gregory J. Baillie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Debra Elton
- Animal Health Trust, Centre for Preventive Medicine, Lanwades Park, Newmarket, United Kingdom
| | - J. Richard Newton
- Animal Health Trust, Centre for Preventive Medicine, Lanwades Park, Newmarket, United Kingdom
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - James L. N. Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, United States of America
| | - Pablo R. Murcia
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Tibayrenc M, Ayala FJ. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A 2012; 109:E3305-13. [PMID: 22949662 PMCID: PMC3511763 DOI: 10.1073/pnas.1212452109] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, Institut de Rercherche pour le Développement 224, Centre National de la Recherche Scientifique 5290, Universités Montpellier 1 and 2, 34394 Montpellier Cedex 5, France; and
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
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71
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Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P, McCauley JW, Wood JLN, Brown IH, Pybus OG, Leigh Brown AJ, for the Combating Swine Influenza Initiative (COSI) Consortium. Estimating reassortment rates in co-circulating Eurasian swine influenza viruses. J Gen Virol 2012; 93:2326-2336. [PMID: 22971819 PMCID: PMC3542128 DOI: 10.1099/vir.0.044503-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/24/2012] [Indexed: 12/22/2022] Open
Abstract
Swine have often been considered as a mixing vessel for different influenza strains. In order to assess their role in more detail, we undertook a retrospective sequencing study to detect and characterize the reassortants present in European swine and to estimate the rate of reassortment between H1N1, H1N2 and H3N2 subtypes with Eurasian (avian-like) internal protein-coding segments. We analysed 69 newly obtained whole genome sequences of subtypes H1N1-H3N2 from swine influenza viruses sampled between 1982 and 2008, using Illumina and 454 platforms. Analyses of these genomes, together with previously published genomes, revealed a large monophyletic clade of Eurasian swine-lineage polymerase segments containing H1N1, H1N2 and H3N2 subtypes. We subsequently examined reassortments between the haemagglutinin and neuraminidase segments and estimated the reassortment rates between lineages using a recently developed evolutionary analysis method. High rates of reassortment between H1N2 and H1N1 Eurasian swine lineages were detected in European strains, with an average of one reassortment every 2-3 years. This rapid reassortment results from co-circulating lineages in swine, and in consequence we should expect further reassortments between currently circulating swine strains and the recent swine-origin H1N1v pandemic strain.
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Affiliation(s)
- S. J. Lycett
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - G. Baillie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - E. Coulter
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - S. Bhatt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - P. Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - J. W. McCauley
- Division of Virology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - J. L. N. Wood
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - I. H. Brown
- Animal Health and Veterinary Laboratories Agency – Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - O. G. Pybus
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - A. J. Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
| | - for the Combating Swine Influenza Initiative (COSI) Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
- Division of Virology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
- Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
- Animal Health and Veterinary Laboratories Agency – Weybridge, Addlestone, Surrey, KT15 3NB, UK
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72
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Therapeutics for dengue: recommendations for design and conduct of early-phase clinical trials. PLoS Negl Trop Dis 2012; 6:e1752. [PMID: 23029567 PMCID: PMC3459884 DOI: 10.1371/journal.pntd.0001752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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73
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Carneiro AR, Cruz ACR, Vallinoto M, Melo DDV, Ramos RTJ, Medeiros DBA, Silva EVPD, Vasconcelos PFDC. Molecular characterisation of dengue virus type 1 reveals lineage replacement during circulation in Brazilian territory. Mem Inst Oswaldo Cruz 2012; 107:805-12. [DOI: 10.1590/s0074-02762012000600016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/10/2012] [Indexed: 11/22/2022] Open
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74
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Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. INFECTION GENETICS AND EVOLUTION 2012; 15:77-86. [PMID: 22677620 DOI: 10.1016/j.meegid.2012.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/13/2012] [Accepted: 05/16/2012] [Indexed: 11/23/2022]
Abstract
The Dengue National Control Program was established in Cambodia in 2000 and has reported between 10,000 and 40,000 dengue cases per year with a case fatality rate ranging from 0.7 to 1.7. In this study 39 DENV-2 and 57 DENV-3 viruses isolated from patients between 2000 and 2008 were fully sequenced. Five DENV2 and four DENV3 distinct lineages with different dynamics were identified. Each lineage was characterized by the presence of specific mutations with no evidence of recombination. In both DENV-2 and DENV-3 the lineages present prior to 2003 were replaced after that date by unrelated lineages. After 2003, DENV-2 lineages D2-3 and D2-4 cocirculated until 2007 when they were almost completely replaced by a lineage D2-5 which emerged from D2-3 Conversely, all DENV-3 lineages remained, diversified and cocirculated with novel lineages emerging. Years 2006 and 2007 were marked by a high prevalence of DENV-3 and 2007 with a large dengue outbreak and a high proportion of patients with severe disease. Selective sweeps in DENV-1 and DENV-2 were linked to immunological escape to a predominately DENV-3-driven immunological response. The complex dynamic of dengue in Cambodia in the last ten years has been associated with a combination of stochastic climatic events, cocirculation, coevolution, adaptation to different vector populations, and with the human population immunological landscape.
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75
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Dugan VG, Saira K, Ghedin E. Large-scale sequencing and the natural history of model human RNA viruses. Future Virol 2012; 7:563-573. [PMID: 23682295 DOI: 10.2217/fvl.12.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA virus exploration within the field of medical virology has greatly benefited from technological developments in genomics, deepening our understanding of viral dynamics and emergence. Large-scale first-generation technology sequencing projects have expedited molecular epidemiology studies at an unprecedented scale for two pathogenic RNA viruses chosen as models: influenza A virus and dengue. Next-generation sequencing approaches are now leading to a more in-depth analysis of virus genetic diversity, which is greater for RNA than DNA viruses because of high replication rates and the absence of proofreading activity of the RNA-dependent RNA polymerase. In the field of virus discovery, technological advancements and metagenomic approaches are expanding the catalogs of novel viruses by facilitating our probing into the RNA virus world.
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Affiliation(s)
- Vivien G Dugan
- Viral Genomics, J Craig Venter Institute, Rockville, MD, USA
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76
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Revealing the microscale spatial signature of dengue transmission and immunity in an urban population. Proc Natl Acad Sci U S A 2012; 109:9535-8. [PMID: 22645364 DOI: 10.1073/pnas.1120621109] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well-known that the distribution of immunity in a population dictates the future incidence of infectious disease, but this process is generally understood at individual or macroscales. For example, herd immunity to multiple pathogens has been observed at national and city levels. However, the effects of population immunity have not previously been shown at scales smaller than the city (e.g., neighborhoods). In particular, no study has shown long-term effects of population immunity at scales consistent with the spatial scale of person-to-person transmission. Here, we use the location of dengue patients' homes in Bangkok with the serotype of the infecting pathogen to investigate the spatiotemporal distribution of disease risk at small spatial scales over a 5-y period. We find evidence for localized transmission at distances of under 1 km. We also observe patterns of spatiotemporal dependence consistent with the expected impacts of homotypic immunity, heterotypic immunity, and immune enhancement of disease at these distances. Our observations indicate that immunological memory of dengue serotypes occurs at the neighborhood level in this large urban setting. These methods have broad applications to studying the spatiotemporal structure of disease risk where pathogen serotype or genetic information is known.
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77
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WHO-VMI Dengue Vaccine Modeling Group. Assessing the potential of a candidate dengue vaccine with mathematical modeling. PLoS Negl Trop Dis 2012; 6:e1450. [PMID: 22479655 PMCID: PMC3313921 DOI: 10.1371/journal.pntd.0001450] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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78
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Liebman KA, Stoddard ST, Morrison AC, Rocha C, Minnick S, Sihuincha M, Russell KL, Olson JG, Blair PJ, Watts DM, Kochel T, Scott TW. Spatial dimensions of dengue virus transmission across interepidemic and epidemic periods in Iquitos, Peru (1999-2003). PLoS Negl Trop Dis 2012; 6:e1472. [PMID: 22363822 PMCID: PMC3283551 DOI: 10.1371/journal.pntd.0001472] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 11/29/2011] [Indexed: 11/18/2022] Open
Abstract
Background Knowledge of spatial patterns of dengue virus (DENV) infection is important for understanding transmission dynamics and guiding effective disease prevention strategies. Because movement of infected humans and mosquito vectors plays a role in the spread and persistence of virus, spatial dimensions of transmission can range from small household foci to large community clusters. Current understanding is limited because past analyses emphasized clinically apparent illness and did not account for the potentially large proportion of inapparent infections. In this study we analyzed both clinically apparent and overall infections to determine the extent of clustering among human DENV infections. Methodology/Principal Findings We conducted spatial analyses at global and local scales, using acute case and seroconversion data from a prospective longitudinal cohort in Iquitos, Peru, from 1999–2003. Our study began during a period of interepidemic DENV-1 and DENV-2 transmission and transitioned to epidemic DENV-3 transmission. Infection status was determined by seroconversion based on plaque neutralization testing of sequential blood samples taken at approximately six-month intervals, with date of infection assigned as the middate between paired samples. Each year was divided into three distinct seasonal periods of DENV transmission. Spatial heterogeneity was detected in baseline seroprevalence for DENV-1 and DENV-2. Cumulative DENV-3 seroprevalence calculated by trimester from 2001–2003 was spatially similar to preexisting DENV-1 and DENV-2 seroprevalence. Global clustering (case-control Ripley's K statistic) appeared at radii of ∼200–800 m. Local analyses (Kuldorf spatial scan statistic) identified eight DENV-1 and 15 DENV-3 clusters from 1999–2003. The number of seroconversions per cluster ranged from 3–34 with radii from zero (a single household) to 750 m; 65% of clusters had radii >100 m. No clustering was detected among clinically apparent infections. Conclusions/Significance Seroprevalence of previously circulating DENV serotypes can be a predictor of transmission risk for a different invading serotype and, thus, identify targets for strategically placed surveillance and intervention. Seroprevalence of a specific serotype is also important, but does not preclude other contributing factors, such as mosquito density, in determining where transmission of that virus will occur. Regardless of the epidemiological context or virus serotype, human movement appears to be an important factor in defining the spatial dimensions of DENV transmission and, thus, should be considered in the design and evaluation of surveillance and intervention strategies. To target prevention and control strategies for dengue fever, it is essential to understand how the virus travels through the city. We report spatial analyses of dengue infections from a study monitoring school children and adult family members for dengue infection at six-month intervals from 1999–2003, in the Amazonian city of Iquitos, Peru. At the beginning of the study, only DENV serotypes 1 and 2 were circulating. Clusters of infections of these two viruses were concentrated in the northern region of the city, where mosquito indices and previous DENV infection were both high. In 2002, DENV-3 invaded the city, replacing DENV-1 and -2 as the dominant strain. During the invasion process, the virus spread rapidly across the city, at low levels. After this initial phase, clusters of infection appeared first in the northern region of the city, where clusters of DENV-1 and DENV-2 had occurred in prior years. Most of the clusters we identified had radii >100 meters, indicating that targeted or reactive treatment of these high-risk areas might be an effective proactive intervention strategy. Our results also help explain why vector control within 100 m of a dengue case is often not successful for large-scale disease prevention.
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Affiliation(s)
- Kelly A Liebman
- Department of Entomology, University of California Davis, Davis, California, USA.
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79
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Castro-Nallar E, Pérez-Losada M, Burton GF, Crandall KA. The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol 2012; 62:777-92. [PMID: 22138161 PMCID: PMC3258026 DOI: 10.1016/j.ympev.2011.11.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 12/02/2022]
Abstract
Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
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Affiliation(s)
- Eduardo Castro-Nallar
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA.
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80
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Thai KTD, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT, Farrar J, van Doorn HR, de Jong MD, Birren BW, Holmes EC, Simmons CP. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. J Virol 2012; 86:835-43. [PMID: 22090119 PMCID: PMC3255838 DOI: 10.1128/jvi.05985-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 10/17/2011] [Indexed: 11/20/2022] Open
Abstract
Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this diversity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of sampling and/or experimental methods that do not fully account for errors generated through amplification and sequencing of viral RNAs. We investigated the extent and pattern of genetic diversity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma samples (n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from amplification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence diversities of viral populations were very low, with conservative estimates of the average levels of genetic diversity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic diversity and disease severity, immune status, or level of viremia.
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Affiliation(s)
- Khoa T D Thai
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
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81
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Faria NR, Suchard MA, Rambaut A, Lemey P. Toward a quantitative understanding of viral phylogeography. Curr Opin Virol 2011; 1:423-9. [PMID: 22440846 DOI: 10.1016/j.coviro.2011.10.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 08/22/2011] [Accepted: 10/07/2011] [Indexed: 12/11/2022]
Abstract
Phylogeographic approaches help uncover the imprint that spatial epidemiological processes leave in the genomes of fast evolving viruses. Recent Bayesian inference methods that consider phylogenetic diffusion of discretely and continuously distributed traits offer a unique opportunity to explore genotypic and phenotypic evolution in greater detail. To provide a taste of the recent advances in viral diffusion approaches, we highlight key findings arising at the intrahost, local and global epidemiological scales. We also outline future areas of research and discuss how these may contribute to a quantitative understanding of the phylodynamics of RNA viruses.
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Affiliation(s)
- Nuno Rodrigues Faria
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium
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82
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Abstract
Advances in sequencing technology and genome-wide association studies are now revealing the complex interactions between hosts and pathogen through genomic variation signatures, which arise from evolutionary co-existence.
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Affiliation(s)
- Chiea-Chuen Khor
- Infectious Diseases, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome Building, Singapore 138672
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83
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Chen R, Vasilakis N. Dengue--quo tu et quo vadis? Viruses 2011; 3:1562-608. [PMID: 21994796 PMCID: PMC3187692 DOI: 10.3390/v3091562] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/12/2011] [Accepted: 08/12/2011] [Indexed: 02/08/2023] Open
Abstract
Dengue viruses (DENV) are by far the most important arboviral pathogens in the tropics around the world, putting at risk of infection nearly a third of the global human population. DENV are members of the genus Flavivirus in the Family Flaviviridae and comprise four antigenically distinct serotypes (DENV-1-4). Although they share almost identical epidemiological features, they are genetically distinct. Phylogenetic analyses have revealed valuable insights into the origins, epidemiology and the forces that shape DENV evolution in nature. In this review, we examine the current status of DENV evolution, including but not limited to rates of evolution, selection pressures, population sizes and evolutionary constraints, and we discuss how these factors influence transmission, pathogenesis and emergence.
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Affiliation(s)
- Rubing Chen
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; E-Mail:
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; E-Mail:
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
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84
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dos Santos FB, Nogueira FB, Castro MG, Nunes PC, de Filippis AMB, Faria NR, Simões JB, Sampaio SA, Santos CR, Nogueira RMR. First report of multiple lineages of dengue viruses type 1 in Rio de Janeiro, Brazil. Virol J 2011; 8:387. [PMID: 21813012 PMCID: PMC3170301 DOI: 10.1186/1743-422x-8-387] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/03/2011] [Indexed: 01/06/2023] Open
Abstract
Background In Brazil dengue has been a major public health problem since DENV-1 introduction and spread in 1986. After a low or silent co-circulation, DENV-1 re-emerged in 2009 causing a major epidemic in the country in 2010 and 2011. In this study, the phylogeny of DENV-1 strains isolated in RJ after its first introduction in 1986 and after its emergence in 2009 and 2010 was performed in order to document possible evolutionary patterns or introductions in a re-emergent virus. Findings The analysis of the E gene sequences demonstrated that DENV-1 isolated during 2009/2010 still belong to genotype V (Americas/Africa) but grouping in a distinct clade (lineage II) of that represented by earlier DENV-1 (lineage I). However, strains isolated in 2011 grouped together forming another distinct clade (lineage III). Conclusions The monitoring of DENV is important to observe the spread of potentially virulent strains as well to evaluate its impact over the population during an outbreak. Whether explosive epidemics reported in Brazil caused mainly by DENV-1 was due to lineage replacement, or due the population susceptibility to this serotype which has not circulated for almost a decade or even due to the occurrence of secondary infections in a hyperendemic country, is not clear. This is the first report of multiple lineages of DENV-1 detected in Brazil.
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