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de Carvalho Marques B, Sacchetto L, Banho CA, Estofolete CF, Dourado FS, da Silva Cândido D, Dutra KR, da Silva Salles FC, de Jesus JG, Sabino EC, Faria NR, Nogueira ML. Genetic differences of dengue virus 2 in patients with distinct clinical outcome. Braz J Microbiol 2023; 54:1411-1419. [PMID: 37178262 PMCID: PMC10485208 DOI: 10.1007/s42770-023-01006-1] [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: 02/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the virus is essential to identify lineages responsible for an epidemic and understanding the processes of virus spread and virulence. Here, we characterize, using portable nanopore genomic sequencing, different lineages of dengue virus 2 (DENV-2) detected in 22 serum samples from patients with and without dengue warning signs attended at Hospital de Base of São José do Rio Preto (SJRP) in 2019, during a DENV-2 outbreak. Demographic, epidemiological, and clinical data were also analyzed. The phylogenetic reconstruction and the clinical data showed that two lineages belonging to the American/Asian genotype of DENV-2-BR3 and BR4 (BR4L1 and BR4L2)-were co-circulating in SJRP. Although preliminary, these results indicate no specific association between clinical form and phylogenetic clustering at the virus consensus sequence level. Studies with larger sample sizes and which explore single nucleotide variants are needed. Therefore, we showed that portable nanopore genome sequencing could generate quick and reliable sequences for genomic surveillance to monitor viral diversity and its association with disease severity as an epidemic unfolds.
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Affiliation(s)
- Beatriz de Carvalho Marques
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cecília Artico Banho
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cássia Fernanda Estofolete
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Fernanda Simões Dourado
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Karina Rocha Dutra
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Jaqueline Góes de Jesus
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil.
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA.
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Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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Milhim BHGA, da Rocha LC, Terzian ACB, Mazaro CCP, Augusto MT, Luchs A, Zini N, Sacchetto L, dos Santos BF, Garcia PHC, Rocha RS, Liso E, Brienze VMS, da Silva GCD, Vasilakis N, Estofolete CF, Nogueira ML. Arboviral Infections in Neurological Disorders in Hospitalized Patients in São José do Rio Preto, São Paulo, Brazil. Viruses 2022; 14:1488. [PMID: 35891468 PMCID: PMC9323204 DOI: 10.3390/v14071488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Arbovirus infections are increasingly important causes of disease, whose spectrum of neurological manifestations are not fully known. This study sought to retrospectively assess the incidence of arboviruses in cerebrospinal fluid samples of patients with neurological symptoms to inform diagnosis of central and peripheral nervous system disorders. A total of 255 cerebrospinal fluid (CSF) samples collected from January 2016 to December 2017 were tested for dengue virus (DENV 1-4), Zika virus (ZIKV), and Chikungunya virus (CHIKV) in addition to other neurotropic arboviruses of interest, using genetic and serologic assays. Of the 255 CSF samples analyzed, 3.53% (09/255) were positive for arboviruses presenting mainly as meningitis, encephalitis, and cerebrovascular events, of which ZIKV was detected in 2.74% (7/255), DENV in 0.78% (2/255), in addition to an identified ILHV infection that was described previously. All the cases were detected in adults aged 18 to 74 years old. Our findings highlight the scientific and clinical importance of neurological syndromes associated with arboviruses and demonstrate the relevance of specific laboratory methods to achieve accurate diagnoses as well as highlight the true dimension of these diseases to ultimately improve public health planning and medical case management.
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Affiliation(s)
- Bruno H. G. A. Milhim
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Leonardo C. da Rocha
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Ana C. B. Terzian
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
- Laboratório de Imunologia Celular e Molecular (LICM), Avenida Augusto de Lima, 1715, Centro, Belo Horizonte 30190-002, MG, Brazil
- Instituto René Rachou Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Centro, Belo Horizonte 30190-002, MG, Brazil
| | - Carolina C. P. Mazaro
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Marcos T. Augusto
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Adriana Luchs
- Enteric Disease Laboratory, Department of Virology, Adolfo Lutz Institute, Avenida Dr. Arnaldo, 355, São Paulo 01246-902, SP, Brazil;
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Livia Sacchetto
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Barbara F. dos Santos
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Pedro H. C. Garcia
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Rodrigo S. Rocha
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Elisabete Liso
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544-Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (E.L.); (V.M.S.B.)
| | - Vânia M. S. Brienze
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544-Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (E.L.); (V.M.S.B.)
| | - Gislaine C. D. da Silva
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, TX 77555-1150, USA
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Cássia F. Estofolete
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
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Temperature, traveling, slums, and housing drive dengue transmission in a non-endemic metropolis. PLoS Negl Trop Dis 2021; 15:e0009465. [PMID: 34115753 PMCID: PMC8221794 DOI: 10.1371/journal.pntd.0009465] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 06/23/2021] [Accepted: 05/10/2021] [Indexed: 11/24/2022] Open
Abstract
Dengue is steadily increasing worldwide and expanding into higher latitudes. Current non-endemic areas are prone to become endemic soon. To improve understanding of dengue transmission in these settings, we assessed the spatiotemporal dynamics of the hitherto largest outbreak in the non-endemic metropolis of Buenos Aires, Argentina, based on detailed information on the 5,104 georeferenced cases registered during summer-autumn of 2016. The highly seasonal dengue transmission in Buenos Aires was modulated by temperature and triggered by imported cases coming from regions with ongoing outbreaks. However, local transmission was made possible and consolidated heterogeneously in the city due to housing and socioeconomic characteristics of the population, with 32.8% of autochthonous cases occurring in slums, which held only 6.4% of the city population. A hierarchical spatiotemporal model accounting for imperfect detection of cases showed that, outside slums, less-affluent neighborhoods of houses (vs. apartments) favored transmission. Global and local spatiotemporal point-pattern analyses demonstrated that most transmission occurred at or close to home. Additionally, based on these results, a point-pattern analysis was assessed for early identification of transmission foci during the outbreak while accounting for population spatial distribution. Altogether, our results reveal how social, physical, and biological processes shape dengue transmission in Buenos Aires and, likely, other non-endemic cities, and suggest multiple opportunities for control interventions. Dengue fever is mainly transmitted by a mosquito species that is highly urbanized, and lays eggs and develops mostly in artificial water containers. Dengue transmission is sustained year-round in most tropical regions of the world, but in many subtropical/temperate regions it occurs only in the warmest months. To improve understanding of dengue transmission in these regions, we analyzed one of the largest outbreaks in Buenos Aires city, a subtropical metropolis. Based on information on 5,104 georeferenced cases during summer-autumn 2016, we found that most transmission occurred in or near home, that slums had the highest risk of transmission, and that, outside slums, less-affluent neighborhoods of houses (vs. apartments) favored transmission. We showed that the cumulative effects of temperature over the previous few weeks set the temporal limits for transmission to occur, and that the outbreak was sparked by infected people arriving from regions with ongoing outbreaks. Additionally, we implemented a statistical method to identify transmission foci in real-time that improves targeting control interventions. Our results deepen the understanding of dengue transmission as a result of social, physical, and biological processes, and pose multiple opportunities for improving control of dengue and other mosquito-borne viruses such as Zika, chikungunya, and yellow fever.
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Warnes CM, Santacruz-Sanmartín E, Bustos Carrillo F, Vélez ID. Surveillance and Epidemiology of Dengue in Medellín, Colombia from 2009 to 2017. Am J Trop Med Hyg 2021; 104:1719-1728. [PMID: 33755586 PMCID: PMC8103481 DOI: 10.4269/ajtmh.19-0728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/22/2021] [Indexed: 11/07/2022] Open
Abstract
Dengue is the most prevalent arthropod-borne viral disease in humans, primarily transmitted by the Aedes aegypti mosquito. We conducted a descriptive analysis of dengue cases from 2009 to 2017 in Medellín, Colombia, using data available from the Secretariat of Health. We analyzed the burden of outbreak years on the healthcare system, risk of cases exhibiting severe illness, potential disease surveillance problems, gender and age as risk factors, and spatiotemporal patterns of disease occurrence. Our data consisted of 50,083 cases, separated based on whether they were diagnostic test negative, diagnostic test positive (primarily IgM ELISA), clinically confirmed, epidemiologically linked, or probable. We used dengue incidence to analyze epidemiological trends between our study years, related to human movement patterns, between gender and age-groups, and spatiotemporally. We used risk to analyze the severity of dengue cases between the study years. We identified human movement could contributed to dengue spread, and male individuals (incidence rate: 0.86; 95% CI: 0.76-0.96) and individuals younger than 15 years (incidence rate: 1.24; 95% CI: 1.13-1.34) have higher incidence of dengue and located critical parts of the city where dengue incidence was high. Analysis was limited by participant diagnostic information, data concerning circulating strains, and a lack of phylogenetic information. Understanding the characteristics of dengue is a fundamental part of improving the health outcomes of at-risk populations. This analysis will be useful to support studies and initiatives to counteract dengue and provide context to the surveillance data collected by the health authorities in Medellín.
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Affiliation(s)
- Colin M. Warnes
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellín, Colombia
| | - Eduardo Santacruz-Sanmartín
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellín, Colombia
| | | | - Iván Darío Vélez
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellín, Colombia
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Telle O, Nikolay B, Kumar V, Benkimoun S, Pal R, Nagpal BN, Paul RE. Social and environmental risk factors for dengue in Delhi city: A retrospective study. PLoS Negl Trop Dis 2021; 15:e0009024. [PMID: 33571202 PMCID: PMC7877620 DOI: 10.1371/journal.pntd.0009024] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
Global urbanization is leading to an inexorable spread of several major diseases that need to be stemmed. Dengue is one of these major diseases spreading in cities today, with its principal mosquito vector superbly adapted to the urban environment. Current mosquito control strategies are proving inadequate, especially in the face of such urbanisation and novel, evidence-based targeted approaches are needed. Through combined epidemiological and entomological approaches, we aimed to identify a novel sanitation strategy to alleviate the burden of dengue through how the dengue virus spreads through the community. We combined surveillance case mapping, prospective serological studies, year-round mosquito surveys, socio-economic and Knowledge Attitudes and Practices surveys across Delhi. We identified lack of access to tap water (≤98%) as an important risk factor for dengue virus IgG sero-positivity (adjusted Odds Ratio 4.69, 95% C.I. 2.06–10.67) and not poverty per se. Wealthier districts had a higher dengue burden despite lower mosquito densities than the Intermediary income communities (adjusted Odds Ratio 2.92, 95% C.I. 1.26–6.72). This probably reflects dengue being introduced by people travelling from poorer areas to work in wealthier houses. These poorer, high density areas, where temperatures are also warmer, also had dengue cases during the winter. Control strategies based on improved access to a reliable supply of tap water plus focal intervention in intra-urban heat islands prior to the dengue season could not only lead to a reduction in mosquito abundance but also eliminate the reservoir of dengue virus clearly circulating at low levels in winter in socio-economically disadvantaged areas. Identifying disease hotspots and individual risk factors for dengue can enable targeted intervention strategies. We conducted combined serological, entomological and socio-economic surveys across 18 areas within Delhi, taken from the total 1280 colonies (i.e. the administrative units of reference in Delhi) for which we classified their socio-economic typology. We additionally performed a Knowledge, Attitudes, Practices survey at a household level within the most socially disadvantaged sub-districts. Finally, we mapped all the winter dengue cases to 250 m x 250 m units along with their winter mean temperatures. We found that access to tap water was an important risk factor for exposure to dengue virus (DENV) and this was confirmed even within the socially disadvantaged sub-districts. The Wealthy colonies had a high burden of DENV infection despite low mosquito densities, likely linked to their connectedness through daily human mobility. The winter burden of dengue occurred majoritarily in the socio-economically disadvantaged colonies, which also have higher mean temperatures and urban heat islands. Improved access to tap water could lead to a reduction in dengue, not only for those directly affected but for the general population. Targeted intervention through mosquito control in winter in the socially disadvantaged areas could offer a rational strategy for optimising control efforts.
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Affiliation(s)
- Olivier Telle
- Géographie-cités, Université Paris-1 Panthéon-Sorbonne, Paris, France
- Centre for Policy Research, Dharam Marg, Delhi, India
- * E-mail:
| | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases, Institut Pasteur, Centre National de la Recherche Scientifique, Paris, France
| | - Vikram Kumar
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, India
| | - Samuel Benkimoun
- Géographie-cités, Université Paris-1 Panthéon-Sorbonne, Paris, France
- Centre de Sciences Humaines, UMIFRE 20 CNRS-MAE,Delhi, India
| | - Rupali Pal
- Centre de Sciences Humaines, UMIFRE 20 CNRS-MAE,Delhi, India
| | - BN Nagpal
- National Institute of Malaria Research, Sector 8, Dwarka, Delhi, India
| | - Richard E. Paul
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Paris, France
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Fustec B, Phanitchat T, Hoq MI, Aromseree S, Pientong C, Thaewnongiew K, Ekalaksananan T, Bangs MJ, Corbel V, Alexander N, Overgaard HJ. Complex relationships between Aedes vectors, socio-economics and dengue transmission-Lessons learned from a case-control study in northeastern Thailand. PLoS Negl Trop Dis 2020; 14:e0008703. [PMID: 33001972 PMCID: PMC7553337 DOI: 10.1371/journal.pntd.0008703] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/OBJECTIVES Dengue fever is an important public health concern in most tropical and subtropical countries, and its prevention and control rest on vector surveillance and control. However, many aspects of dengue epidemiology remain unclear; in particular, the relationship between Aedes vector abundance and dengue transmission risk. This study aims to identify entomological and immunological indices capable of discriminating between dengue case and control (non-case) houses, based on the assessment of candidate indices, as well as individual and household characteristics, as potential risk factors for acquiring dengue infection. METHODS This prospective, hospital-based, case-control study was conducted in northeastern Thailand between June 2016 and August 2019. Immature and adult stage Aedes were collected at the houses of case and control patients, recruited from district hospitals, and at patients' neighboring houses. Blood samples were tested by RDT and PCR to detect dengue cases, and were processed with the Nterm-34 kDa salivary peptide to measure the human immune response to Aedes bites. Socioeconomic status, and other individual and household characteristics were analyzed as potential risk factors for dengue. RESULTS Study findings showed complex relationships between entomological indices and dengue risk. The presence of DENV-infected Aedes at the patient house was associated with 4.2-fold higher odds of dengue. On the other hand, Aedes presence (irrespective of infectious status) in the patient's house was negatively associated with dengue. In addition, the human immune response to Aedes bites, was higher in control than in case patients and Aedes adult abundance and immature indices were higher in control than in case houses at the household and the neighboring level. Multivariable analysis showed that children aged 10-14 years old and those aged 15-25 years old had respectively 4.5-fold and 2.9-fold higher odds of dengue infection than those older than 25 years. CONCLUSION DENV infection in female Aedes at the house level was positively associated with dengue infection, while adult Aedes presence in the household was negatively associated. This study highlights the potential benefit of monitoring dengue viruses in Aedes vectors. Our findings suggest that monitoring the presence of DENV-infected Aedes mosquitoes could be a better indicator of dengue risk than the traditional immature entomological indices.
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Affiliation(s)
- Benedicte Fustec
- University of Montpellier, Montpellier, France
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Institut de Recherche pour le Developpement, Montpellier, France
| | - Thipruethai Phanitchat
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mohammad Injamul Hoq
- School of Public Health, Epidemiology and Social Medicine at the Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sirinart Aromseree
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | | | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- HPV & EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Michael J. Bangs
- Public Health & Malaria Control, PT Freeport Indonesia/International SOS, Mimika, Papua, Indonesia
- Department of Entomology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Vincent Corbel
- University of Montpellier, Montpellier, France
- Institut de Recherche pour le Developpement, Montpellier, France
| | - Neal Alexander
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Milhim BHGA, Estofolete CF, da Rocha LC, Liso E, Brienze VMS, Vasilakis N, Terzian ACB, Nogueira ML. Fatal Outcome of Ilheus Virus in the Cerebrospinal Fluid of a Patient Diagnosed with Encephalitis. Viruses 2020; 12:v12090957. [PMID: 32872425 PMCID: PMC7552055 DOI: 10.3390/v12090957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023] Open
Abstract
Ilheus virus is an arbovirus with the potential for central nervous system involvement. Accurate diagnosis is a challenge due to similar clinical symptoms and serologic cross-reactivity with other flaviviruses. Here, we describe the first documented case of a fatal outcome following the identification of Ilheus virus in the cerebrospinal fluid (CSF) of a patient with cerebral encephalitis in Brazil.
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Affiliation(s)
- Bruno H. G. A. Milhim
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Cássia F. Estofolete
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Leonardo C. da Rocha
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Elisabete Liso
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, SP 15090-000 São José do Rio Preto, Brazil; (E.L.); (V.M.S.B.)
| | - Vânia M. S. Brienze
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, SP 15090-000 São José do Rio Preto, Brazil; (E.L.); (V.M.S.B.)
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Ana C. B. Terzian
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
- Correspondence: ; Tel.: +55-1798811-0550
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9
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Estofolete CF, Milhim BHGA, Zini N, Scamardi SN, Selvante JD, Vasilakis N, Nogueira ML. Flavivirus Infection Associated with Cerebrovascular Events. Viruses 2020; 12:v12060671. [PMID: 32580374 PMCID: PMC7354470 DOI: 10.3390/v12060671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
Arthropod-borne viruses (arboviruses) of the genus Flavivirus are distributed globally and cause significant human disease and mortality annually. Flavivirus infections present a spectrum of clinical manifestations, ranging from asymptomatic to severe manifestations, including hemorrhage, encephalitis and death. Herein, we describe 3 case reports of cerebrovascular involvement in patients infected by dengue and Zika viruses in Sao Jose do Rio Preto, São Paulo State, Brazil, a hyperendemic area for arbovirus circulation, including dengue, yellow fever, chikungunya and Saint Louis encephalitis viruses. Our findings highlight the potential threat that unusual clinical manifestations may pose to arbovirus disease management and recovery.
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Affiliation(s)
- Cássia F Estofolete
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Bruno H G A Milhim
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Nathalia Zini
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Samuel N Scamardi
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Joana D'Arc Selvante
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Maurício L Nogueira
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
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Evaluation of the usefulness of Aedes aegypti rapid larval surveys to anticipate seasonal dengue transmission between 2012-2015 in Fortaleza, Brazil. Acta Trop 2020; 205:105391. [PMID: 32057775 DOI: 10.1016/j.actatropica.2020.105391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/11/2022]
Abstract
Rapid larval surveys have been mandated in nearly every urban Brazilian municipality and promoted by the Pan American Health Organization. These surveys purport to classify arbovirus transmission risk as a basis to triage local surveillance and vector control operations, yet no previous analyses have determined relative risk associated with marginal changes in infestation at administrative and temporal scales relevant to vector control. We estimated associations between entomological indices from six larval surveys and daily incidence rates of confirmed dengue cases in Fortaleza, Brazil using models adjusted for rainfall, and indicators of spatial association. Poor correspondence between infestation and incidence indicates that these surveys may systematically mislead vector control activities and treatment strategies in Fortaleza and in similar cities throughout Latin America. The co-circulation of multiple arboviruses enhances the importance of determining the true informational value of these surveys, and of identifying complementary tools to discern local and inter-annual transmission risk.
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11
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Pollett S, Fauver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2020; 221:S308-S318. [PMID: 31711190 PMCID: PMC11095994 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
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Affiliation(s)
- S. Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland
- Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J. R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L. D. Gillis
- Bureau of Public Health Laboratories–Miami, Florida Department of Health
| | - M. A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R. G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N. D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
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12
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Teissier Y, Paul R, Aubry M, Rodo X, Dommar C, Salje H, Sakuntabhai A, Cazelles B, Cao-Lormeau VM. Long-term persistence of monotypic dengue transmission in small size isolated populations, French Polynesia, 1978-2014. PLoS Negl Trop Dis 2020; 14:e0008110. [PMID: 32142511 PMCID: PMC7080275 DOI: 10.1371/journal.pntd.0008110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/18/2020] [Accepted: 02/02/2020] [Indexed: 01/18/2023] Open
Abstract
Understanding the transition of epidemic to endemic dengue transmission remains a challenge in regions where serotypes co-circulate and there is extensive human mobility. French Polynesia, an isolated group of 117 islands of which 72 are inhabited, distributed among five geographically separated subdivisions, has recorded mono-serotype epidemics since 1944, with long inter-epidemic periods of circulation. Laboratory confirmed cases have been recorded since 1978, enabling exploration of dengue epidemiology under monotypic conditions in an isolated, spatially structured geographical location. A database was constructed of confirmed dengue cases, geolocated to island for a 35-year period. Statistical analyses of viral establishment, persistence and fade-out as well as synchrony among subdivisions were performed. Seven monotypic and one heterotypic dengue epidemic occurred, followed by low-level viral circulation with a recrudescent epidemic occurring on one occasion. Incidence was asynchronous among the subdivisions. Complete viral die-out occurred on several occasions with invasion of a new serotype. Competitive serotype replacement has been observed previously and seems to be characteristic of the South Pacific. Island population size had a strong impact on the establishment, persistence and fade-out of dengue cases and endemicity was estimated achievable only at a population size in excess of 175 000. Despite island remoteness and low population size, dengue cases were observed somewhere in French Polynesia almost constantly, in part due to the spatial structuration generating asynchrony among subdivisions. Long-term persistence of dengue virus in this group of island populations may be enabled by island hopping, although could equally be explained by a reservoir of sub-clinical infections on the most populated island, Tahiti. Dengue virus is the most significant arthropod-borne virus infecting man. Understanding how long dengue virus can persist in populations of varying size is key to understanding its epidemiology. This is, however, impossible to achieve in settings where dengue is endemic, because of continued human movement and is further complexified by the occurrence of several co-circulating serotypes. By contrast, French Polynesia, an isolated group of 72 inhabited islands in the South Pacific, has had intermittent majoritarily monotypic dengue epidemics since the 1940s and offers a unique opportunity to address questions of viral persistence, turnover and the importance of spatial sub-structure in determining dengue epidemiology. Collating and analyzing a database of laboratory-confirmed dengue cases from across French Polynesia over a 35 year period we were able to show that dengue virus die-out can occur with or without replacement by a new serotype, monotypic transmission of dengue viruses fails to be maintained within small island populations but can persist for years among isolated islands connected via air and sea links. This remarkable long-term persistence of dengue virus in French Polynesia could be maintained by asynchronous viral transmission among connected islands and/or by repeated seeding from a reservoir of sub-clinical infections in the most populated island, Tahiti.
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Affiliation(s)
- Yoann Teissier
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
- Université Paris Descartes, PSL University, Paris, France
| | - Richard Paul
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, UMR 2000 CNRS, Paris, France
- Pasteur Kyoto International Joint Research Unit for Integrative Vaccinomics, Kyoto, Japan
- * E-mail: (RP); (VMCL)
| | - Maite Aubry
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Xavier Rodo
- ICREA, Barcelona, Spain
- CLIMA (Climate and Health) Program, ISGlobal, Barcelona, Spain
| | - Carlos Dommar
- CLIMA (Climate and Health) Program, ISGlobal, Barcelona, Spain
| | - Henrik Salje
- Institut Pasteur, Mathematical Modelling of Infectious Diseases Unit, UMR 2000, Centre National de la Recherche Scientifique, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, UMR 2000 CNRS, Paris, France
- Pasteur Kyoto International Joint Research Unit for Integrative Vaccinomics, Kyoto, Japan
| | - Bernard Cazelles
- International Center for Mathematical and Computational Modeling of Complex Systems (UMMISCO), UMI 209, Sorbonne Université - IRD, Bondy cedex, France
- iGLOBE, UMI CNRS 3157, University of Arizona, Tucson, Arizona, United States of America
- IBENS, UMR 8197 CNRS-ENS Ecole Normale Supérieure, Paris, France
| | - Van-Mai Cao-Lormeau
- Laboratoire de recherche sur les maladies infectieuses à transmission vectorielle, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
- * E-mail: (RP); (VMCL)
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Dodero-Rojas E, Ferreira LG, Leite VBP, Onuchic JN, Contessoto VG. Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. PLoS One 2020; 15:e0222900. [PMID: 31990920 PMCID: PMC6986714 DOI: 10.1371/journal.pone.0222900] [Citation(s) in RCA: 9] [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: 09/05/2019] [Accepted: 01/02/2020] [Indexed: 12/15/2022] Open
Abstract
Mosquito-borne diseases have become a significant health issue in many regions around the world. For tropical countries, diseases such as Dengue, Zika, and Chikungunya, became epidemic in the last decades. Health surveillance reports during this period were crucial in providing scientific-based information to guide decision making and resources allocation to control outbreaks. In this work, we perform data analysis of the last Chikungunya epidemics in the city of Rio de Janeiro by applying a compartmental mathematical model. Sensitivity analyses were performed in order to describe the contribution of each parameter to the outbreak incidence. We estimate the "basic reproduction number" for those outbreaks and predict the potential epidemic outbreak of the Mayaro virus. We also simulated several scenarios with different public interventions to decrease the number of infected people. Such scenarios should provide insights about possible strategies to control future outbreaks.
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Affiliation(s)
- Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States of America
- Theoretical and Computational Physics Laboratory, University of Costa Rica, San José, Costa Rica
| | - Luiza G. Ferreira
- Department of Chemistry, Rice University, Houston, TX, United States of America
| | - Vitor B. P. Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States of America
- Department of Chemistry, Rice University, Houston, TX, United States of America
- Department of Physics & Astronomy, Rice University, Houston, TX, United States of America
- Department of Biosciences, Rice University, Houston, TX, United States of America
| | - Vinícius G. Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States of America
- Brazilian Biorenewables National Laboratory - LNBR, Brazilian Center for Research in Energy and Materials - CNPEM, Campinas, SP, Brazil
- * E-mail:
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Lizarazo E, Vincenti-Gonzalez M, Grillet ME, Bethencourt S, Diaz O, Ojeda N, Ochoa H, Rangel MA, Tami A. Spatial Dynamics of Chikungunya Virus, Venezuela, 2014. Emerg Infect Dis 2019; 25:672-680. [PMID: 30882314 PMCID: PMC6433008 DOI: 10.3201/eid2504.172121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Since chikungunya virus emerged in the Caribbean region in late 2013, ≈45 countries have experienced chikungunya outbreaks. We described and quantified the spatial and temporal events after the introduction and propagation of chikungunya into an immunologically naive population from the urban north-central region of Venezuela during 2014. The epidemic curve (n = 810 cases) unraveled within 5 months with a basic reproductive number of 3.7 and a radial spread traveled distance of 9.4 km at a mean velocity of 82.9 m/day. The highest disease diffusion speed occurred during the first 90 days, and space and space-time modeling suggest the epidemic followed a particular geographic pathway with spatiotemporal aggregation. The directionality and heterogeneity of transmission during the first introduction of chikungunya indicated existence of areas of diffusion and elevated risk for disease and highlight the importance of epidemic preparedness. This information will help in managing future threats of new or reemerging arboviruses.
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Colombo TE, Versiani AF, Dutra KR, Rubiato JGD, Galvão TM, Negri Reis AF, Nogueira ML. Performance of CDC Trioplex qPCR during a dengue outbreak in Brazil. J Clin Virol 2019; 121:104208. [PMID: 31707203 DOI: 10.1016/j.jcv.2019.104208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND In recent years real‑time reverse transcription polymerase chain reaction (real-time RT-PCR) has become a leading technique for nucleic acid detection and quantification of flaviviruses, including Dengue virus (DENV). Trioplex real-time RT-PCR has the advantages of providing the concurrent detection of Zika virus (ZIKV), DENV, and Chikungunya virus (CHIKV) RNA in human serum. OBJECTIVE This study sought to compare the sensitivity and specificity of the Trioplex real-time RT-PCR assay to those provided by CDC DENV TaqMan® RT-qPCR assay and conventional PCR when used for DENV detection in the context of a dengue epidemic. STUDY DESIGN We analyzed 1656 serum samples from symptomatic patients with acute febrile disease for 5 days less between December 2018 and May 2019. The samples were tested using the various PCR-based assays. RESULTS Of the 1656 serum samples analyzed, 713 (43%) were laboratory-confirmed as arboviruses: 99.86% (712/713) were confirmed as DENV and 0.14% (1/713) were confirmed as ZIKV. Next, 590 samples were selected, and of these, 331 samples (56.1%) were determined to be positive (Ct < 38) and 259 samples (43.9%) were determined to be negative (Ct > 38) using the Trioplex real-time RT-PCR assay. The multiplex method found that the test exhibits 95% sensitivity and 100% specificity. CONCLUSION This evaluation demonstrates the capacity of the Trioplex real-time RT-PCR assay to detect DENV at a high sensitivity and specificity in a geographic area with a current dengue outbreak and a lower co-circulation of other arboviruses - such as ZIKV and CHIKV, and the results prove it´s applicability as clinical screening test that can serve as a confirmatory test.
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Affiliation(s)
- Tatiana Elias Colombo
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil; Universidade Paulista (UNIP), São José do Rio Preto, SP, Brazil
| | - Alice Freitas Versiani
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
| | - Karina Rocha Dutra
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
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Chiaravalloti-Neto F, da Silva RA, Zini N, da Silva GCD, da Silva NS, Parra MCP, Dibo MR, Estofolete CF, Fávaro EA, Dutra KR, Mota MTO, Guimarães GF, Terzian ACB, Blangiardo M, Nogueira ML. Seroprevalence for dengue virus in a hyperendemic area and associated socioeconomic and demographic factors using a cross-sectional design and a geostatistical approach, state of São Paulo, Brazil. BMC Infect Dis 2019; 19:441. [PMID: 31109295 PMCID: PMC6528304 DOI: 10.1186/s12879-019-4074-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/09/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND São José do Rio Preto is one of the cities of the state of São Paulo, Brazil, that is hyperendemic for dengue, with the presence of the four dengue serotypes. OBJECTIVES to calculate dengue seroprevalence in a neighbourhood of São José do Rio Preto and identify if socioeconomic and demographic covariates are associated with dengue seropositivity. METHODS A cohort study to evaluate dengue seroprevalence and incidence and associated factors on people aged 10 years or older, was assembled in Vila Toninho neighbourhood, São José do Rio Preto. The participant enrolment occurred from October 2015 to March 2016 (the first wave of the cohort study), when blood samples were collected for serological test (ELISA IgG anti-DENV) and questionnaires were administrated on socio-demographic variables. We evaluated the data collected in this first wave using a cross-sectional design. We considered seropositive the participants that were positive in the serological test (seronegative otherwise). We modelled the seroprevalence with a logistic regression in a geostatistical approach. The Bayesian inference was made using integrated nested Laplace approximations (INLA) coupled with the Stochastic Partial Differential Equation method (SPDE). RESULTS We found 986 seropositive individuals for DENV in 1322 individuals surveyed in the study area in the first wave of the cohort study, corresponding to a seroprevalence of 74.6% (95%CI: 72.2-76.9). Between the population that said never had dengue fever, 68.4% (566/828) were dengue seropositive. Older people, non-white and living in a house (instead of in an apartment), were positively associated with dengue seropositivity. We adjusted for the other socioeconomic and demographic covariates, and accounted for residual spatial dependence between observations, which was found to present up to 800 m. CONCLUSIONS Only one in four people aged 10 years or older did not have contact with any of the serotypes of dengue virus in Vila Toninho neighbourhood in São José do Rio Preto. Age, race and type of house were associated with the occurrence of the disease. The use of INLA in a geostatistical approach in a Bayesian context allowed us to take into account the spatial dependence between the observations and identify the associated covariates to dengue seroprevalence.
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Affiliation(s)
- Francisco Chiaravalloti-Neto
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo (USP), Avenida Doutor Arnaldo 715, São Paulo, SP, 01246-904, Brazil.
| | - Rafael Alves da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Gislaine Celestino Dutra da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Natal Santos da Silva
- Laboratório de Modelagens Matemática e Estatística em Medicina, Faculdade de Medicina, União das Faculdades dos Grandes Lagos, Rua Doutor Eduardo Nielsen 960, São José do Rio Preto, SP, 15030-070, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Margareth Regina Dibo
- Laboratório de Entomologia, Superintendência de Controle de Endemias, Rua Cardeal Arcoverde 2878, São Paulo, SP, 05408-003, Brazil
| | - Cassia Fernanda Estofolete
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Eliane Aparecida Fávaro
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Karina Rocha Dutra
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Manlio Tasso Oliveira Mota
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Georgia Freitas Guimarães
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Ana Carolina Bernardes Terzian
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
| | - Marta Blangiardo
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Imperial College, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Mauricio Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5416, São José do Rio Preto, SP, 15090-000, Brazil
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Co-infection between Zika and different Dengue serotypes during DENV outbreak in Brazil. J Infect Public Health 2019; 12:178-181. [DOI: 10.1016/j.jiph.2018.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 08/13/2018] [Accepted: 09/20/2018] [Indexed: 11/22/2022] Open
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Parra MCP, Fávaro EA, Dibo MR, Mondini A, Eiras ÁE, Kroon EG, Teixeira MM, Nogueira ML, Chiaravalloti-Neto F. Using adult Aedes aegypti females to predict areas at risk for dengue transmission: A spatial case-control study. Acta Trop 2018; 182:43-53. [PMID: 29462598 DOI: 10.1016/j.actatropica.2018.02.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/27/2018] [Accepted: 02/13/2018] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Traditional indices for measuring dengue fever risk in a given area are based on the immature forms of the vector (larvae and pupae surveys). However, this is inefficient because only adult female mosquitoes actually transmit the virus. Based on these assumptions, our objective was to evaluate the association between an entomological index obtained from adult mosquito traps and the occurrence of dengue in a hyperendemic area. Additionally, we compared its cost to that of the Breteau Index (BI). MATERIAL AND METHODS We performed this study in São José do Rio Preto, SP, Brazil, between the epidemiological weeks of 36/2012 and 19/2013. BG-Sentinel and BG-Mosquitito traps were installed to capture adult mosquitoes. Positive and negative cases of dengue fever were computed and geocoded. We generated biweekly thematic maps of the entomological index, generated by calculating the number of adult Aedes aegypti females (NAF) per 100 households during a week by kriging, and based on the number of mosquitoes captured. The relation between the occurrence of dengue fever and the NAF was tested using a spatial case-control design and a generalized additive model and was controlled by the coordinates of the positive and negative cases of dengue fever. RESULTS Our analyses showed that increases in dengue fever cases occurred in parallel with increases in the number of Ae. aegypti females. The entomological index produced in our study correlates positively with the incidence of dengue, particularly during intervals when vector control measures were applied less intensively. The operational costs of our index were lower than those of the BI: NAF used 71.5% less human resources necessary to measure the BI. CONCLUSIONS Spatial analysis techniques and the number of adult Ae. aegypti females were used to produce an indicator of dengue risk. The index can be applied at various levels of spatial aggregation for an entire study area, as well as for sub-areas, such as city blocks. Even though the index is adequate to predict dengue risk, it should be tested and validated in various scenarios before routine use.
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Lippi CA, Stewart-Ibarra AM, Muñoz ÁG, Borbor-Cordova MJ, Mejía R, Rivero K, Castillo K, Cárdenas WB, Ryan SJ. The Social and Spatial Ecology of Dengue Presence and Burden during an Outbreak in Guayaquil, Ecuador, 2012. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040827. [PMID: 29690593 PMCID: PMC5923869 DOI: 10.3390/ijerph15040827] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 01/19/2023]
Abstract
Dengue fever, a mosquito-borne arbovirus, is a major public health concern in Ecuador. In this study, we aimed to describe the spatial distribution of dengue risk and identify local social-ecological factors associated with an outbreak of dengue fever in the city of Guayaquil, Ecuador. We examined georeferenced dengue cases (n = 4248) and block-level census data variables to identify social-ecological risk factors associated with the presence/absence and burden of dengue in Guayaquil in 2012. Local Indicators of Spatial Association (LISA), specifically Anselin’s Local Moran’s I, and Moran’s I tests were used to locate hotspots of dengue transmission, and multimodel selection was used to identify covariates associated with dengue presence and burden at the census block level. We identified significant dengue transmission hotspots near the North Central and Southern portions of Guayaquil. Significant risk factors for presence of dengue included poor housing conditions, access to paved roads, and receipt of remittances. Counterintuitive positive correlations with dengue presence were observed with several municipal services such as garbage collection and access to piped water. Risk factors for increased burden of dengue included poor housing conditions, garbage collection, receipt of remittances, and sharing a property with more than one household. Social factors such as education and household demographics were negatively correlated with increased dengue burden. These findings elucidate underlying differences with dengue presence versus burden, and suggest that vulnerability and risk maps could be developed to inform dengue prevention and control; this is information that is also relevant for emerging epidemics of chikungunya and Zika viruses.
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Affiliation(s)
- Catherine A Lippi
- Quantitative Disease Ecology and Conservation Lab, Department of Geography, University of Florida, Gainesville, FL 32611 USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA.
| | - Anna M Stewart-Ibarra
- Center for Global Health and Translational Science and Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.
| | - Ángel G Muñoz
- Atmospheric and Oceanic Sciences (AOS), Princeton University, Princeton, NJ 08540, USA.
- International Research Institute for Climate and Society (IRI), Earth Institute, Columbia University, New York, NY 10964, USA.
| | | | - Raúl Mejía
- National Institute of Meteorology and Hydrology (INAMHI), Quito 170135, Ecuador.
| | - Keytia Rivero
- National Institute of Meteorology and Hydrology (INAMHI), Quito 170135, Ecuador.
| | - Katty Castillo
- Institute of Biometrics and Epidemiology, Auf'm Hennekamp 65, 40225 Düsseldorf, Germany.
| | - Washington B Cárdenas
- Laboratorio de Biomedicina, FCV, Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil 09015863, Ecuador.
| | - Sadie J Ryan
- Quantitative Disease Ecology and Conservation Lab, Department of Geography, University of Florida, Gainesville, FL 32611 USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA.
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21
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Low socioeconomic condition and the risk of dengue fever: A direct relationship. Acta Trop 2018; 180:47-57. [PMID: 29352990 DOI: 10.1016/j.actatropica.2018.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 02/05/2023]
Abstract
This study aimed to characterize the first dengue fever epidemic in Várzea Paulista, São Paulo, Brazil, and its spatial and spatio-temporal distribution in order to assess the association of socioeconomic factors with dengue occurrence. We used autochthonous dengue cases confirmed in a 2007 epidemic, the first reported in the city, available in the Information System on Diseases of Compulsory Declaration database. These cases where geocoded by address. We identified spatial and spatio-temporal clusters of high- and low-risk dengue areas using scan statistics. To access the risk of dengue occurrence and to evaluate its relationship with socioeconomic level we used a population-based case-control design. Firstly, we fitted a generalized additive model (GAM) to dengue cases and controls without considering the non-spatial covariates to estimate the odds ratios of the occurrence of the disease. The controls were drawn considering the spatial distribution of the household of the study area and represented the source population of the dengue cases. After that, we assessed the relationship between socioeconomic variables and dengue using the GAM and obtained the effect of these covariates in the occurrence of dengue adjusted by the spatial localization of the cases and controls. Cluster analysis and GAM indicated that northeastern area of Várzea Paulista was the most affected area during the epidemic. The study showed a positive relationship between low socioeconomic condition and increased risk of dengue. We studied the first dengue epidemic in a highly susceptible population at the beginning of the outbreak and therefore it may have allowed to identify an association between low socioeconomic conditions and increased risk of dengue. These results may be useful to predict the occurrence and to identify priority areas to develop control measures for dengue, and also for Zika and Chikungunya; diseases that recently reached Latin America, especially Brazil.
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Sedda L, Vilela APP, Aguiar ERGR, Gaspar CHP, Gonçalves ANA, Olmo RP, Silva ATS, de Cássia da Silveira L, Eiras ÁE, Drumond BP, Kroon EG, Marques JT. The spatial and temporal scales of local dengue virus transmission in natural settings: a retrospective analysis. Parasit Vectors 2018; 11:79. [PMID: 29394906 PMCID: PMC5797342 DOI: 10.1186/s13071-018-2662-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/19/2018] [Indexed: 11/10/2022] Open
Abstract
Background Dengue is a vector-borne disease caused by the dengue virus (DENV). Despite the crucial role of Aedes mosquitoes in DENV transmission, pure vector indices poorly correlate with human infections. Therefore there is great need for a better understanding of the spatial and temporal scales of DENV transmission between mosquitoes and humans. Here, we have systematically monitored the circulation of DENV in individual Aedes spp. mosquitoes and human patients from Caratinga, a dengue endemic city in the state of Minas Gerais, in Southeast Brazil. From these data, we have developed a novel stochastic point process pattern algorithm to identify the spatial and temporal association between DENV infected mosquitoes and human patients. Methods The algorithm comprises of: (i) parameterization of the variogram for the incidence of each DENV serotype in mosquitoes; (ii) identification of the spatial and temporal ranges and variances of DENV incidence in mosquitoes in the proximity of humans infected with dengue; and (iii) analysis of the association between a set of environmental variables and DENV incidence in mosquitoes in the proximity of humans infected with dengue using a spatio-temporal additive, geostatistical linear model. Results DENV serotypes 1 and 3 were the most common virus serotypes detected in both mosquitoes and humans. Using the data on each virus serotype separately, our spatio-temporal analyses indicated that infected humans were located in areas with the highest DENV incidence in mosquitoes, when incidence is calculated within 2.5–3 km and 50 days (credible interval 30–70 days) before onset of symptoms in humans. These measurements are in agreement with expected distances covered by mosquitoes and humans and the time for virus incubation. Finally, DENV incidence in mosquitoes found in the vicinity of infected humans correlated well with the low wind speed, higher air temperature and northerly winds that were more likely to favor vector survival and dispersal in Caratinga. Conclusions We have proposed a new way of modeling bivariate point pattern on the transmission of arthropod-borne pathogens between vector and host when the location of infection in the latter is known. This strategy avoids some of the strong and unrealistic assumptions made by other point-process models. Regarding virus transmission in Caratinga, our model showed a strong and significant association between high DENV incidence in mosquitoes and the onset of symptoms in humans at specific spatial and temporal windows. Together, our results indicate that vector surveillance must be a priority for dengue control. Nevertheless, localized vector control at distances lower than 2.5 km around premises with infected vectors in densely populated areas are not likely to be effective. Electronic supplementary material The online version of this article (10.1186/s13071-018-2662-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luigi Sedda
- Centre for Health Information Computation and Statistics (CHICAS), Furness Building, Lancaster University, Lancaster, LA1 4YG, UK
| | - Ana Paula Pessoa Vilela
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil.,Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil.,Present Address: Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, 40110-100, Brazil
| | - Caio Henrique Pessoa Gaspar
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - André Nicolau Aquime Gonçalves
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Ana Teresa Saraiva Silva
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Lízia de Cássia da Silveira
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Álvaro Eduardo Eiras
- Department of Parasitology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Betânia Paiva Drumond
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Erna Geessien Kroon
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - João Trindade Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil.
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Ramos-Castañeda J, Barreto dos Santos F, Martínez-Vega R, Galvão de Araujo JM, Joint G, Sarti E. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends. PLoS Negl Trop Dis 2017; 11:e0005224. [PMID: 28068335 PMCID: PMC5221820 DOI: 10.1371/journal.pntd.0005224] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 12/01/2016] [Indexed: 01/02/2023] Open
Abstract
Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity. The wide distribution of the mosquito vector and the co-circulation of multiple dengue virus serotypes has led to increases in the incidence of dengue in the Americas, where it is a major public health concern. Identifying molecular epidemiological trends may help to identify the reasons for the re-emergence of dengue across Latin America and the Caribbean, and, in turn, enable disease control and management. We conducted this review using well defined methods to search for and identify relevant research according to predetermined inclusion criteria. The objective was to obtain a clearer understanding of changes occurring within dengue serotypes that have resulted in substantial genetic diversity and the emergence of endemic and epidemic strains in different parts of the region. There remain fundamental gaps in our understanding of the epidemiological and evolutionary dynamics of dengue and its relation with disease, and it is not possible to correlate accurately spatial or temporal trends in disease epidemiology, disease severity, or the genetic diversity of DENV. It is important to maintain comprehensive epidemiological surveillance throughout the region (including sequencing of viral strains) to detect new DENV lineages and to understand the regional patterns of DENV dissemination.
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Affiliation(s)
- José Ramos-Castañeda
- Instituto Nacional de Salud Publica, Centro de Investigaciones sobre Enfermedades Infecciosas, Morelos, Mexico
| | - Flavia Barreto dos Santos
- Laboratório de Imunologia Viral, Instituto Oswaldo Cruz/ Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Josélio Maria Galvão de Araujo
- Laboratório de Biologia Molecular de Doenças Infecciosas e do Câncer, Departamento de Microbiologia e Parasitologia; Instituto de Medicina Tropical do Rio Grande do Norte; Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Graham Joint
- Synercom Ltd, Macclesfield, Cheshire, United Kingdom
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Colombo TE, Vedovello D, Pacca-Mazaro CC, Mondini A, Araújo JP, Cabrera E, Lopes JC, Penha dos Santos IN, Negri Reis AF, Costa FR, Antônio Cruz LEA, Ferreira J, de Oliveira Rocha ES, Kroon EG, de Morais Bronzoni RV, Vasilakis N, Nogueira ML. Dengue virus surveillance: Detection of DENV-4 in the city of São José do Rio Preto, SP, Brazil. Acta Trop 2016; 164:84-89. [PMID: 27609639 DOI: 10.1016/j.actatropica.2016.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/14/2022]
Abstract
Dengue viruses are the most common arbovirus infection worldwide and are caused by four distinct serotypes of the dengue virus (DENV). In the present study, we assessed DENV transmission in São José do Rio Preto (SJRP) from 2010 to 2014. We analyzed blood samples from febrile patients who were attended at health care centers in SJRP. DENV detection was performed using multiplex RT-PCR, using flavivirus generic primers, based on the genes of the non-structural protein (NS5), followed by nested-PCR assay with species-specific primers. We analyzed 1549 samples, of which 1389 were positive for NS1 by rapid test. One thousand and eight-seven samples (78%) were confirmed as positive by multiplex RT-PCR: DENV-4, 48.5% (528/1087); DENV-1, 41.5% (449/1087); DENV-2, 9.5% (104/1087); and co-infection (5 DENV-1/DENV-4, 1 DENV-1/DENV-2), 0.5% (6/1087). Phylogenetic analysis of the DENV-4 grouped the isolates identified in this study with the American genotype and the showed a relationship between isolates from SJRP and isolates from the northern region of South America. Taken together, our data shows the detection and emergence of new dengue genotype in a new region and reiterate the importance of surveillance programs to detect and trace the evolution of DENV.
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Furlan NB, Tukasan C, Estofolete CF, Nogueira ML, da Silva NS. Low sensitivity of the tourniquet test for differential diagnosis of dengue: an analysis of 28,000 trials in patients. BMC Infect Dis 2016; 16:627. [PMID: 27809813 PMCID: PMC5095934 DOI: 10.1186/s12879-016-1947-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/20/2016] [Indexed: 01/15/2023] Open
Abstract
Background The aim of this study was to evaluate the utility of the tourniquet test (TT) for dengue diagnosing. To our knowledge, no previous study with such a large sample, of this duration, with as many laboratory methods referenced, or relating the results of the TT to the 2009 WHO classification of severity has been conducted thus far. Methods In this study, we analyzed the records of 119,589 suspected dengue cases in a Brazilian city, with 30,670 confirmed cases. The Cohen’s Kappa test was applied to evaluate the degree of agreement between the tests, and the sensitivity and specificity was calculated for the TT. Results Twenty-eight thousand six hundred thirty-five TT were performed. No association between the outcome of the TT and greater severity of infection, according to the 2009 guideline, was observed (P = 0.28); furthermore, relevant agreement with the final diagnosis (κ = 0.01; 95 % CI = 0.00 to 0.02) or individually with the IgM enzyme-linked immunoassay was not observed (κ = 0.05; 95 % CI = 0.04 to 0.06), and was even lower with PCR (κ = 0.27; 95 % CI = 0.06 to 0.49). Most importance of the TT was shown in relation to specificity (88.9 %; 95 % CI = 0.88 to 0.89) and negative predictive value (70.3 %; CI 95 % = 0.70 to 0.71). Conclusions TT was more effective in detecting cases that were truly negative than positive. These results suggest that the TT should not be used as diagnosis of dengue.
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Affiliation(s)
- Nathália Barbosa Furlan
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil
| | - Caroline Tukasan
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil
| | - Cássia Fernanda Estofolete
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil.,Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil
| | - Natal Santos da Silva
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil. .,Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil. .,Laboratório de Modelagens Matemática e Estatística em Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil. .,Laboratório de Modelagens Matemática e Estatística em Medicina, Faculdade de Medicina, União das Faculdades dos Grandes Lagos, Rua Dr. Eduardo Nielsem, 960 Jardim Novo Aeroporto, São Jose do Rio Preto, São Paulo, CEP 15030-070, Brazil.
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Misslin R, Telle O, Daudé E, Vaguet A, Paul RE. Urban climate versus global climate change-what makes the difference for dengue? Ann N Y Acad Sci 2016; 1382:56-72. [PMID: 27197685 DOI: 10.1111/nyas.13084] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/18/2016] [Accepted: 04/07/2016] [Indexed: 12/18/2022]
Abstract
The expansion in the geographical distribution of vector-borne diseases is a much emphasized consequence of climate change, as are the consequences of urbanization for diseases that are already endemic, which may be even more important for public health. In this paper, we focus on dengue, the most widespread urban vector-borne disease. Largely urban with a tropical/subtropical distribution and vectored by a domesticated mosquito, Aedes aegypti, dengue poses a serious public health threat. Temperature plays a determinant role in dengue epidemic potential, affecting crucial parts of the mosquito and viral life cycles. The urban predilection of the mosquito species will further exacerbate the impact of global temperature change because of the urban heat island effect. Even within a city, temperatures can vary by 10 °C according to urban land use, and diurnal temperature range (DTR) can be even greater. DTR has been shown to contribute significantly to dengue epidemic potential. Unraveling the importance of within-city temperature is as important for dengue as for the negative health consequences of high temperatures that have thus far been emphasized, for example, pollution and heat stroke. Urban and landscape planning designed to mitigate the non-infectious negative effects of temperature should additionally focus on dengue, which is currently spreading worldwide with no signs of respite.
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Affiliation(s)
- Renaud Misslin
- Centre National de la Recherche Scientifique, UMR 6266 IDEES, Rouen, France
| | - Olivier Telle
- Centre des Sciences Humaines, UMIFRE 20 CNRS-MAE, Delhi, India.,Centre National de la Recherche Scientifique, UMR 8504 Geographie-cités, Paris, France
| | - Eric Daudé
- Centre des Sciences Humaines, UMIFRE 20 CNRS-MAE, Delhi, India
| | - Alain Vaguet
- Centre National de la Recherche Scientifique, UMR 6266 IDEES, Rouen, France
| | - Richard E Paul
- Institut Pasteur, Unité de la Génétique Fonctionnelle des Maladies Infectieuses, Paris, France.,Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
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Villabona-Arenas CJ, de Oliveira JL, de Sousa-Capra C, Balarini K, Pereira da Fonseca CRT, Zanotto PMDA. Epidemiological dynamics of an urban Dengue 4 outbreak in São Paulo, Brazil. PeerJ 2016; 4:e1892. [PMID: 27069820 PMCID: PMC4824887 DOI: 10.7717/peerj.1892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
Background: Dengue studies at the urban scale are scarce and required for guiding control efforts. In Brazil, the burden of dengue is high and challenges city public health administrations with limited resources. Here we studied the dynamics of a dengue epidemic in a single city. Methods: Serum samples from dengue suspected cases were collected and tested, from December 2012 and July 2013 in Guarujá, Brazil. We use incidence series analysis to provide a detailed view of the reproduction number dynamics and a Bayesian analysis to infer the spread of the serotype using geographic and temporal data. Results: We obtained nucleotide sequences from 354 envelope genes and georeferenced 286 samples during the course of the outbreak. Serotype 4 was responsible for the epidemic. We identified at least two major lineages that overlapped in distribution. We observed high reproduction numbers and high cladogenesis prior to the escalation of clinical case notifications. Three densely populated non-adjacent neighborhoods played a pivotal role during the onset and/or course of the epidemic. Discussion: Our findings point to high dengue virus transmission with a substantial proportion of unapparent cases that led to a late recognition of an outbreak. Usually source reductions initiatives tend to be insufficient once an epidemic has been established. Nevertheless, health authorities in Guarujá prioritized vector control on specific places with clusters of georeferenced viremic patients, which appear to have diminished the epidemic impact.
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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
| | - Jessica Luana de Oliveira
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil; Department of Biomedicine, University of Mogi das Cruzes, Mogi das Cruzes, São Paulo, Brazil
| | - Carla de Sousa-Capra
- Office of Epidemiological Surveillance, Department of Health of Guarujá , Guarujá, São Paulo , Brazil
| | - Karime Balarini
- Clinical Laboratory Analysis Center, ITAPEMA , Guarujá , 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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Telle O, Vaguet A, Yadav NK, Lefebvre B, Daudé E, Paul RE, Cebeillac A, Nagpal BN. The Spread of Dengue in an Endemic Urban Milieu--The Case of Delhi, India. PLoS One 2016; 11:e0146539. [PMID: 26808518 PMCID: PMC4726601 DOI: 10.1371/journal.pone.0146539] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/18/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Dengue is a major international public health concern, one of the most important arthropod-borne diseases. More than 3.5 billion people are at risk of dengue infection and there are an estimated 390 million dengue infections annually. This prolific increase has been connected to societal changes such as population growth and increasing urbanization generating intense agglomeration leading to proliferation of synanthropic mosquito species. Quantifying the spatio-temporal epidemiology of dengue in large cities within the context of a Geographic Information System is a first step in the identification of socio-economic risk factors. METHODOLOGY/PRINCIPAL FINDINGS This Project has been approved by the ethical committee of Institut Pasteur. Data has been anonymized and de-identified prior to geolocalisation and analysis. A GIS was developed for Delhi, enabling typological characterization of the urban environment. Dengue cases identified in the Delhi surveillance system from 2008 to 2010 were collated, localised and embedded within this GIS. The spatio-temporal distribution of dengue cases and extent of clustering were analyzed. Increasing distance from the forest in Delhi reduced the risk of occurrence of a dengue case. Proximity to a hospital did not increase risk of a notified dengue case. Overall, there was high heterogeneity in incidence rate within areas with the same socio-economical profiles and substantial inter-annual variability. Dengue affected the poorest areas with high density of humans, but rich areas were also found to be infected, potentially because of their central location with respect to the daily mobility network of Delhi. Dengue cases were highly clustered in space and there was a strong relationship between the time of introduction of the virus and subsequent cluster size. At a larger scale, earlier introduction predicted the total number of cases. CONCLUSIONS/SIGNIFICANCE DENV epidemiology within Delhi has a forest fire signature. The stochastic nature of this invasion process likely smothers any detectable socio-economic risk factors. However, the significant finding that the size of the dengue case cluster depends on the timing of its emergence emphasizes the need for early case detection and implementation of effective mosquito control. A better understanding of the role of population mobility in contributing to dengue risk could also help focus control on areas at particular risk of dengue virus importation.
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Affiliation(s)
- Olivier Telle
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 8204 Géographie-cités, Paris, France
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Paris, France
- Centre de Sciences Humaines, Delhi, India
- * E-mail:
| | - Alain Vaguet
- Centre National de la Recherche Scientifique, Unité Mixte de la de Recherche 6266, IDEES, Rouen, France
| | - N. K. Yadav
- Municipal Corporation of Delhi, Delhi, India
| | - B. Lefebvre
- Centre National de la Recherche Scientifique, Unité Mixte de la de Recherche 6266, IDEES, Rouen, France
| | - Eric Daudé
- Centre National de la Recherche Scientifique, Unité Mixte de la de Recherche 6266, IDEES, Rouen, France
- Centre de Sciences Humaines, Delhi, India
| | - Richard E. Paul
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 8204 Géographie-cités, Paris, France
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Paris, France
| | - A. Cebeillac
- Centre National de la Recherche Scientifique, Unité Mixte de la de Recherche 6266, IDEES, Rouen, France
- Centre de Sciences Humaines, Delhi, India
| | - B. N. Nagpal
- National Institute of Malaria Research, Delhi, India
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Abstract
Dengue is currently the most rapidly spreading vector-borne disease, with an increasing burden over recent decades. Currently, neither a licensed vaccine nor an effective anti-viral therapy is available, and treatment largely remains supportive. Current vector control strategies to prevent and reduce dengue transmission are neither efficient nor sustainable as long-term interventions. Increased globalization and climate change have been reported to influence dengue transmission. In this article, we reviewed the non-climatic and climatic risk factors which facilitate dengue transmission. Sustainable and effective interventions to reduce the increasing threat from dengue would require the integration of these risk factors into current and future prevention strategies, including dengue vaccination, as well as the continuous support and commitment from the political and environmental stakeholders.
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Affiliation(s)
- Pang Junxiong
- Communicable Disease Center, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, IIDE, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
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Chiaravalloti-Neto F, Pereira M, Fávaro EA, Dibo MR, Mondini A, Rodrigues-Junior AL, Chierotti AP, Nogueira ML. Assessment of the relationship between entomologic indicators of Aedes aegypti and the epidemic occurrence of dengue virus 3 in a susceptible population, São José do Rio Preto, São Paulo, Brazil. Acta Trop 2015; 142:167-77. [PMID: 25484110 DOI: 10.1016/j.actatropica.2014.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/26/2022]
Abstract
The aims of this study were to describe the occurrence of dengue in space and time and to assess the relationships between dengue incidence and entomologic indicators. We selected the dengue autochthonous cases that occurred between September 2005 and August 2007 in São José do Rio Preto to calculate incidence rates by month, year and census tracts. The monthly incidence rates of the city were compared to the monthly Breteau indices (BI) of the São José do Rio Region. Between December 2006 and February 2007, an entomological survey was conducted to collect immature forms of Aedes aegypti in Jaguaré, a São José do Rio Preto neighborhood, and to obtain entomological indices. These indices were represented using statistical interpolation. To represent the occurrence of dengue in the Jaguaré neighborhood in 2006 and 2007, we used the Kernel ratio and to evaluate the relationship between dengue and the entomological indices, we used a generalized additive model in a spatial case-control design. Between September 2005 and August 2007, the occurrence of dengue in São José do Rio Preto was almost entirely caused by DENV3, and the monthly incidence rates presented high correlation coefficients with the monthly BI. In Jaguaré neighborhood, the entomological indices calculated by hectare were better predictors of the spatial distribution of dengue than the indices calculated by properties, but the pupae quantification did not show better prediction qualities than the indices based on the container positivity, in relation to the risk of dengue occurrence. The fact that the municipality's population had a high susceptibility to the serotype DENV3 before the development of this research, along with the almost total predominance of the occurrence of this serotype between 2005 and 2007, facilitated the analysis of the epidemiological situation of the disease and allowed us to connect it to the entomological indicators.
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Stewart-Ibarra AM, Muñoz ÁG, Ryan SJ, Ayala EB, Borbor-Cordova MJ, Finkelstein JL, Mejía R, Ordoñez T, Recalde-Coronel GC, Rivero K. Spatiotemporal clustering, climate periodicity, and social-ecological risk factors for dengue during an outbreak in Machala, Ecuador, in 2010. BMC Infect Dis 2014; 14:610. [PMID: 25420543 PMCID: PMC4264610 DOI: 10.1186/s12879-014-0610-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/04/2014] [Indexed: 11/18/2022] Open
Abstract
Background Dengue fever, a mosquito-borne viral disease, is a rapidly emerging public health problem in Ecuador and throughout the tropics. However, we have a limited understanding of the disease transmission dynamics in these regions. Previous studies in southern coastal Ecuador have demonstrated the potential to develop a dengue early warning system (EWS) that incorporates climate and non-climate information. The objective of this study was to characterize the spatiotemporal dynamics and climatic and social-ecological risk factors associated with the largest dengue epidemic to date in Machala, Ecuador, to inform the development of a dengue EWS. Methods The following data from Machala were included in analyses: neighborhood-level georeferenced dengue cases, national census data, and entomological surveillance data from 2010; and time series of weekly dengue cases (aggregated to the city-level) and meteorological data from 2003 to 2012. We applied LISA and Moran’s I to analyze the spatial distribution of the 2010 dengue cases, and developed multivariate logistic regression models through a multi-model selection process to identify census variables and entomological covariates associated with the presence of dengue at the neighborhood level. Using data aggregated at the city-level, we conducted a time-series (wavelet) analysis of weekly climate and dengue incidence (2003-2012) to identify significant time periods (e.g., annual, biannual) when climate co-varied with dengue, and to describe the climate conditions associated with the 2010 outbreak. Results We found significant hotspots of dengue transmission near the center of Machala. The best-fit model to predict the presence of dengue included older age and female gender of the head of the household, greater access to piped water in the home, poor housing condition, and less distance to the central hospital. Wavelet analyses revealed that dengue transmission co-varied with rainfall and minimum temperature at annual and biannual cycles, and we found that anomalously high rainfall and temperatures were associated with the 2010 outbreak. Conclusions Our findings highlight the importance of geospatial information in dengue surveillance and the potential to develop a climate-driven spatiotemporal prediction model to inform disease prevention and control interventions. This study provides an operational methodological framework that can be applied to understand the drivers of local dengue risk. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0610-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna M Stewart-Ibarra
- Department of Microbiology and Immunology, Center for Global Health and Translational Science, State University of New York Upstate Medical University, 750 East Adams St, Syracuse, NY, 13210, USA.
| | - Ángel G Muñoz
- International Research Institute for Climate and Society (IRI), Earth Institute, Columbia University, New York, NY, USA. .,Centro de Modelado Científico (CMC), Universidad del Zulia, Maracaibo, Venezuela.
| | - Sadie J Ryan
- Department of Microbiology and Immunology, Center for Global Health and Translational Science, State University of New York Upstate Medical University, 750 East Adams St, Syracuse, NY, 13210, USA. .,Department of Geography, Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. .,School of Life Sciences, College of Agriculture, Engineering, and Science, University of KwaZulu-Natal, Durban, South Africa.
| | - Efraín Beltrán Ayala
- The National Service for the Control of Vector-Borne Diseases, Ministry of Health, Machala, El Oro Province, Ecuador. .,Facultad de Medicina, Universidad Técnica de Machala, Machala, El Oro Province, Ecuador.
| | | | - Julia L Finkelstein
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA. .,Center for Geographic Analysis, Harvard University, Cambridge, MA, USA.
| | - Raúl Mejía
- National Institute of Meteorology and Hydrology, Guayaquil, Ecuador.
| | - Tania Ordoñez
- The National Service for the Control of Vector-Borne Diseases, Ministry of Health, Machala, El Oro Province, Ecuador.
| | - G Cristina Recalde-Coronel
- Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador. .,National Institute of Meteorology and Hydrology, Guayaquil, Ecuador.
| | - Keytia Rivero
- National Institute of Meteorology and Hydrology, Guayaquil, Ecuador.
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Favaro EA, Dibo MR, Pereira M, Chierotti AP, Rodrigues-Junior AL, Chiaravalloti-Neto F. Aedes aegypti entomological indices in an endemic area for dengue in Sao Paulo State, Brazil. Rev Saude Publica 2014; 47:588-97. [PMID: 24346572 DOI: 10.1590/s0034-8910.2013047004506] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 01/19/2013] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To evaluate the most productive types of properties and containers for Aedes aegypti and the spatial distribution of entomological indices. METHODS Between December 2006 and February 2007, the vector's immature forms were collected to obtain entomological indices in 9,875 properties in the Jaguare neighborhood of Sao Jose do Rio Preto, SP, Southeastern Brazil. In March and April 2007, a questionnaire about the conditions and characteristics of properties was administered. Logistic regression was used to identify variables associated with the presence of pupae at the properties. Indices calculated per block were combined with a geo-referenced map, and thematic maps of these indices were obtained using statistical interpolation. RESULTS The properties inspected had the following Ae. aegypti indices: Breteau Index = 18.9, 3.7 larvae and 0.42 pupae per property, 5.2 containers harboring Ae. aegypti per hectare, 100.0 larvae and 11.6 pupae per hectare, and 1.3 larvae and 0.15 pupae per inhabitant. The presence of yards, gardens and animals was associated with the presence of pupae. CONCLUSIONS Specific types of properties and containers that simultaneously had low frequencies among those positive for the vector and high participation in the productivity of larvae and pupae were not identified. The use of indices including larval and pupal counts does not provide further information beyond that obtained from the traditional Stegomyia indices in locations with characteristics similar to those of São José do Rio Preto. The indices calculated per area were found to be more accurate for the spatial assessment of infestation. The Ae. aegypti infestation levels exhibited extensive spatial variation, indicating that the assessment of infestation in micro areas is needed.
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Souza LS, Barata RDCB. Intra-urbandiferentials in dengue distribution, Cuiabá, 2007-2008. REVISTA BRASILEIRA DE EPIDEMIOLOGIA 2014; 15:761-70. [PMID: 23515772 DOI: 10.1590/s1415-790x2012000400008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 03/25/2012] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Cuiaba presents a huge number of cases of dengue in the endemic periods as well as in the cyclical epidemics. The aim of the study was to analyze the intra-urban differentials of the incidence in 2007 and 2008 relating them with socio-economical and environmental life conditions. METHOD study of ecological approach using secondary data. The characterization of the life conditions was gotten from the Demographic Census (IBGE, 2000) and the epidemiologic data from the Surveillance National System (SINAN). The socio-economical index was based on school level and income of the head of family and overcrowding; the socioambiental index used information about sanitation and proportion of precarious domiciles. The variables were classified in quintis and points were attributed for each one. The score for neighborhood was resultant of the addition of the points for each variable. The neighborhoods had been classified in stratus of risk from the combination of results of the two indexes. RESULTS The incidence was lesser in stratus of average and low risk and very high in the stratum of the highest risk but was bigger then expected in the stratum classified at minimum risk indicating dissociation between life conditions and occurrence of the illness. CONCLUSION Higher incidences of the dengue fever in Cuiaba in 2007 and 2008 have been observed in places with precarious conditions of sanitation and inhabited by populations with lesser level of income and education level but there is no linear correlation between life conditions and incidence.
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Socially structured human movement shapes dengue transmission despite the diffusive effect of mosquito dispersal. Epidemics 2014; 6:30-6. [PMID: 24593919 DOI: 10.1016/j.epidem.2013.12.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/08/2013] [Accepted: 12/23/2013] [Indexed: 11/24/2022] Open
Abstract
For sexually and directly transmitted infectious diseases, social connections influence transmission because they determine contact between individuals. For pathogens that are indirectly transmitted by arthropod vectors, the movement of the vectors is thought to diminish the role of social connections. Results from a recent study of mosquito-borne dengue virus (DENV), however, indicate that human movement alone can explain significant spatial variation in urban transmission rates. Because movement patterns are structured by social ties, this result suggests that social proximity may be a good predictor of infection risk for DENV and other pathogens transmitted by the mosquito Aedes aegypti. Here we investigated the effect of socially structured movement on DENV transmission using a spatially explicit, agent-based transmission model. When individual movements overlap to a high degree within social groups we were able to recreate infection patterns similar to those detected in dengue-endemic, northeastern Peru. Our results are consistent with the hypothesis that social proximity drives fine-scale heterogeneity in DENV transmission rates, a result that was robust to the influence of mosquito dispersal. This heterogeneity in transmission caused by socially structured movements appeared to be hidden by the diffusive effect of mosquito dispersal in aggregated infection dynamics, which implies this heterogeneity could be present and active in real dengue systems without being easily noticed. Accounting for socially determined, overlapping human movements could substantially improve the efficiency and efficacy of dengue surveillance and disease prevention programs as well as result in more accurate estimates of important epidemiological quantities, such as R0.
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Colombo TE, Vedovello D, Mondini A, Reis AFN, Cury AAF, Oliveira FHD, Cruz LEAA, Bronzoni RVDM, Nogueira ML. CO-INFECTION OF DENGUE VIRUS BY SEROTYPES 1 AND 4 IN PATIENT FROM MEDIUM SIZED CITY FROM BRAZIL. Rev Inst Med Trop Sao Paulo 2013. [DOI: 10.1590/s0036-46652013000400009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
SUMMARY The natural co-infection with dengue virus can occur in highly endemic areas where different serotypes have been observed for many years. We report one case of DENV-1/DENV-4 co-infection in human serum detected by molecular tests. Phylogenetic analysis of the sequences obtained indicated the presence of genotype V and II for DENV-1 and DENV-4, respectively.
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Affiliation(s)
- Tatiana Elias Colombo
- Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), Brazil; Universidade Estadual Paulista Julio de Mesquita Filho (IBILCE/UNESP), Brazil
| | | | - Adriano Mondini
- Universidade Estadual Paulista Julio de Mesquita Filho (FCFAR/UNESP), Brazil
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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: 60] [Impact Index Per Article: 5.5] [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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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: 1.1] [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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Kar P, Ghosh S. An analysis on model development for climatic factors influencing prediction of dengue incidences in urban cities. Indian J Med Res 2013; 137:811-2. [PMID: 23703353 PMCID: PMC3724266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- P.K. Kar
- National Institute of Malaria Research NIMR Unit, ICMR Complex Devanahalli, Bangalore 562 110, India
| | - S.K. Ghosh
- National Institute of Malaria Research NIMR Unit, ICMR Complex Devanahalli, Bangalore 562 110, India,For correspondence:
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Drumond BP, Mondini A, Schmidt DJ, Bronzoni RVDM, Bosch I, Nogueira ML. Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization. PLoS One 2013; 8:e59422. [PMID: 23533624 PMCID: PMC3606110 DOI: 10.1371/journal.pone.0059422] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/14/2013] [Indexed: 01/05/2023] Open
Abstract
The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80′s. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998–2000) and BR3 (2003–05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.
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Affiliation(s)
- Betânia Paiva Drumond
- Laboratório de Virologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- * E-mail: (BPD); (MLN)
| | - Adriano Mondini
- Laboratório de Saúde Pública, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, Araraquara, São Paulo, Brazil
| | - Diane J. Schmidt
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | | | - Irene Bosch
- Genome Resources in Dengue Consortium, Massachusetts Institute of Technology. Cambridge, Massachusetts, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
- * E-mail: (BPD); (MLN)
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de Carvalho LMF, Santos LBL, Faria NR, de Castro Silveira W. Phylogeography of foot-and-mouth disease virus serotype O in Ecuador. INFECTION GENETICS AND EVOLUTION 2013; 13:76-88. [DOI: 10.1016/j.meegid.2012.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/03/2012] [Accepted: 08/20/2012] [Indexed: 01/09/2023]
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Katzov-Eckert H, Botosso VF, Neto EA, Zanotto PMDA. Phylodynamics and dispersal of HRSV entails its permanence in the general population in between yearly outbreaks in children. PLoS One 2012; 7:e41953. [PMID: 23077477 PMCID: PMC3471929 DOI: 10.1371/journal.pone.0041953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/29/2012] [Indexed: 12/22/2022] Open
Abstract
Background Human respiratory syncytial virus (HRSV) is one of the major etiologic agents of respiratory tract infections among children worldwide. Methodology/Principal Findings Here through a comprehensive analysis of the two major HRSV groups A and B (n = 1983) which comprise of several genotypes, we present a complex pattern of population dynamics of HRSV over a time period of 50 years (1956–2006). Circulation pattern of HRSV revealed a series of expansions and fluctuations of co-circulating lineages with a predominance of HRSVA. Positively selected amino acid substitutions of the G glycoprotein occurred upon population growth of GB3 with a 60-nucleotide insertion (GB3 Insert), while other genotypes acquired substitutions upon both population growth and decrease, thus possibly reflecting a role for immune selected epitopes in linkage to the traced substitution sites that may have important relevance for vaccine design. Analysis evidenced the co-circulation and predominance of distinct HRSV genotypes in Brazil and suggested a year-round presence of the virus. In Brazil, GA2 and GA5 were the main culprits of HRSV outbreaks until recently, when the GB3 Insert became highly prevalent. Using Bayesian methods, we determined the dispersal patterns of genotypes through several inferred migratory routes. Conclusions/Significance Genotypes spread across continents and between neighboring areas. Crucially, genotypes also remained at any given region for extended periods, independent of seasonal outbreaks possibly maintained by re-infecting the general population.
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Affiliation(s)
- Hagit Katzov-Eckert
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICB-II, University of São Paulo, São Paulo, Brazil
| | | | - Eurico Arruda Neto
- Department of Cell Biology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil, and the VGDN Consortium
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICB-II, University of São Paulo, São Paulo, Brazil
- * E-mail:
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de Araújo JMG, Bello G, Romero H, Nogueira RMR. Origin and evolution of dengue virus type 3 in Brazil. PLoS Negl Trop Dis 2012; 6:e1784. [PMID: 22970331 PMCID: PMC3435237 DOI: 10.1371/journal.pntd.0001784] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 07/04/2012] [Indexed: 11/17/2022] Open
Abstract
The incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 (DENV-3) at the early 2000s. Despite the major public health concerns, there have been very few studies of the molecular epidemiology and time-scale of this DENV lineage in Brazil. In this study, we investigated the origin and dispersion dynamics of DENV-3 genotype III in Brazil by examining a large number (n = 107) of E gene sequences sampled between 2001 and 2009 from diverse Brazilian regions. These Brazilian sequences were combined with 457 DENV-3 genotype III E gene sequences from 29 countries around the world. Our phylogenetic analysis reveals that there have been at least four introductions of the DENV-3 genotype III in Brazil, as signified by the presence of four phylogenetically distinct lineages. Three lineages (BR-I, BR-II, and BR-III) were probably imported from the Lesser Antilles (Caribbean), while the fourth one (BR-IV) was probably introduced from Colombia or Venezuela. While lineages BR-I and BR-II succeeded in getting established and disseminated in Brazil and other countries from the Southern Cone, lineages BR-III and BR-IV were only detected in one single individual each from the North region. The phylogeographic analysis indicates that DENV-3 lineages BR-I and BR-II were most likely introduced into Brazil through the Southeast and North regions around 1999 (95% HPD: 1998–2000) and 2001 (95% HPD: 2000–2002), respectively. These findings show that importation of DENV-3 lineages from the Caribbean islands into Brazil seems to be relatively frequent. Our study further suggests that the North and Southeast Brazilian regions were the most important hubs of introduction and spread of DENV-3 lineages and deserve an intense epidemiological surveillance. Dengue is a major health problem in the tropics and the incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 (DENV-3). In this study, the authors reconstruct the spatio-temporal dispersion pattern of the DENV-3 lineage that circulates in Brazil and the Americas. The authors found that DENV-3 outbreaks occurring in the American continent since the mid-1990s are the result of a single introduction of genotype III. The Central American countries and Mexico were the hubs of genotype III spread in the Americas, while the Caribbean region acted as a staging post between Central America/Mexico and South America. The authors estimate that there have been at least four introductions of the DENV-3 genotype III in Brazil, although only two of them succeeded in getting established and disseminating through the country. The Lesser Antilles (Caribbean) were the main source of DENV-3 viruses that arrived into Brazil,and the North and Southeast country regions seem to be most important hubs of introduction and dissemination of DENV-3 lineages. These findings offer important information to perform more effective surveillance programs to detect introduction and dispersal of new DENV lineages in Brazil.
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Affiliation(s)
- Josélio Maria Galvão de Araújo
- Laboratory of Molecular Biology for Infectious Diseases and Cancer, Federal University of Rio Grande do Norte, Natal, Brazil.
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Machado DC, Mondini A, Santana VDS, Yonamine PTK, Chiaravalloti Neto F, Zanotto PMDA, Nogueira ML. First Identification of Culex flavivirus (Flaviviridae) in Brazil. Intervirology 2012; 55:475-83. [DOI: 10.1159/000337166] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 01/31/2012] [Indexed: 11/19/2022] Open
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Aldstadt J, Yoon IK, Tannitisupawong D, Jarman RG, Thomas SJ, Gibbons RV, Uppapong A, Iamsirithaworn S, Rothman AL, Scott TW, Endy T. Space-time analysis of hospitalised dengue patients in rural Thailand reveals important temporal intervals in the pattern of dengue virus transmission. Trop Med Int Health 2012; 17:1076-85. [PMID: 22808917 DOI: 10.1111/j.1365-3156.2012.03040.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To determine the temporal intervals at which spatial clustering of dengue hospitalisations occurs. METHODS Space-time analysis of 262 people hospitalised and serologically confirmed with dengue virus infections in Kamphaeng Phet, Thailand was performed. The cases were observed between 1 January 2009 and 6 May 2011. Spatial coordinates of each patient's home were captured using the Global Positioning System. A novel method based on the Knox test was used to determine the temporal intervals between cases at which spatial clustering occurred. These intervals are indicative of the length of time between successive illnesses in the chain of dengue virus transmission. RESULTS The strongest spatial clustering occurred at the 15-17-day interval. There was also significant spatial clustering over short intervals (2-5 days). The highest excess risk was observed within 200 m of a previous hospitalised case and significantly elevated risk persisted within this distance for 32-34 days. CONCLUSIONS Fifteen to seventeen days are the most likely serial interval between successive dengue illnesses. This novel method relies only on passively detected, hospitalised case data with household locations and provides a useful tool for understanding region-specific and outbreak-specific dengue virus transmission dynamics.
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Affiliation(s)
- Jared Aldstadt
- Department of Geography, University at Buffalo, Buffalo, NY 14260, USA.
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Abstract
Using sequence data to infer population dynamics is playing an increasing role in the analysis of outbreaks. The most common methods in use, based on coalescent inference, have been widely used but not extensively tested against simulated epidemics. Here, we use simulated data to test the ability of both parametric and non-parametric methods for inference of effective population size (coded in the popular BEAST package) to reconstruct epidemic dynamics. We consider a range of simulations centred on scenarios considered plausible for pandemic influenza, but our conclusions are generic for any exponentially growing epidemic. We highlight systematic biases in non-parametric effective population size estimation. The most prominent such bias leads to the false inference of slowing of epidemic spread in the recent past even when the real epidemic is growing exponentially. We suggest some sampling strategies that could reduce (but not eliminate) some of the biases. Parametric methods can correct for these biases if the infected population size is large. We also explore how some poor sampling strategies (e.g. that over-represent epidemiologically linked clusters of cases) could dramatically exacerbate bias in an uncontrolled manner. Finally, we present a simple diagnostic indicator, based on coalescent density and which can easily be applied to reconstructed phylogenies, that identifies time-periods for which effective population size estimates are less likely to be biased. We illustrate this with an application to the 2009 H1N1 pandemic.
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Affiliation(s)
- Eric de Silva
- Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, Imperial College London, London W2 1PG, UK
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Allicock OM, Lemey P, Tatem AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CVF. Phylogeography and population dynamics of dengue viruses in the Americas. Mol Biol Evol 2012; 29:1533-43. [PMID: 22319149 DOI: 10.1093/molbev/msr320] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Changes in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) gene isolates from 11 Caribbean countries, along with sequences available on GenBank, we sought to document the population genetic and spatiotemporal transmission histories of the four main invading DENV genotypes within the Americas and investigate factors that influence the rate and intensity of DENV transmission. For all genotypes, there was an initial invasion phase characterized by rapid increases in genetic diversity, which coincided with the first confirmed cases of each genotype in the region. Rapid geographic dispersal occurred upon each genotype's introduction, after which individual lineages were locally maintained, and gene flow was primarily observed among neighboring and nearby countries. There were, however, centers of viral diversity (Barbados, Puerto Rico, Colombia, Suriname, Venezuela, and Brazil) that were repeatedly involved in gene flow with more distant locations. For DENV-1 and DENV-2, we found that a "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries. However, for DENV-3 and DENV-4, the more stochastic "equal rates" model was preferred.
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Affiliation(s)
- Orchid M Allicock
- Department of Preclinical Sciences, Faculty of Medical Sciences, University of the West Indies, St Augustine, Trinidad and Tobago
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Costa RL, Voloch CM, Schrago CG. Comparative evolutionary epidemiology of dengue virus serotypes. INFECTION GENETICS AND EVOLUTION 2011; 12:309-14. [PMID: 22226705 DOI: 10.1016/j.meegid.2011.12.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 11/29/2011] [Accepted: 12/12/2011] [Indexed: 10/14/2022]
Abstract
Evolutionary studies on dengue virus have frequently focused on intra-serotype diversity or on specific epidemics. In this study, we compiled a comprehensive data set of the envelope gene of dengue virus serotypes and conducted an extensive comparative study of evolutionary molecular epidemiology. We found that substitution rates are homogeneous among dengue serotypes, although their population dynamics have differed over the past few years as inferred by Bayesian coalescent methods. On a global scale, DENV-2 is the serotype with the highest effective population size. The genealogies also showed geographical structure within the serotypes. Finally, we also explored the causes of dengue virus serotype diversification by investigating the plausibility that it was driven by adaptive changes. Our results suggest that the envelope gene is under significant purifying selection and the hypothesis that dengue virus serotype diversification was the result of stochastic events cannot be ruled out.
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Affiliation(s)
- Raquel L Costa
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
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Terzian ACB, Mondini A, de Moraes Bronzoni RV, Drumond BP, Ferro BP, Cabrera EMS, Figueiredo LTM, Chiaravalloti-Neto F, Nogueira ML. Detection of Saint Louis Encephalitis Virus in Dengue-Suspected Cases During a Dengue 3 Outbreak. Vector Borne Zoonotic Dis 2011; 11:291-300. [DOI: 10.1089/vbz.2009.0200] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ana Carolina Bernardes Terzian
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Adriano Mondini
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
- Laboratório de Vetores, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | | | | | - Bianca Piovezan Ferro
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Eliana Márcia Sotello Cabrera
- Departamento de Saúde Coletiva, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | | | - Francisco Chiaravalloti-Neto
- Laboratório de Vetores, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
- Superintendência de Controle de Endemias—SUCEN, São José do Rio Preto, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
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Vazquez-Prokopec GM, Kitron U, Montgomery B, Horne P, Ritchie SA. Quantifying the spatial dimension of dengue virus epidemic spread within a tropical urban environment. PLoS Negl Trop Dis 2010; 4:e920. [PMID: 21200419 PMCID: PMC3006131 DOI: 10.1371/journal.pntd.0000920] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 11/18/2010] [Indexed: 12/20/2022] Open
Abstract
Background Dengue infection spread in naive populations occurs in an explosive and widespread fashion primarily due to the absence of population herd immunity, the population dynamics and dispersal of Ae. aegypti, and the movement of individuals within the urban space. Knowledge on the relative contribution of such factors to the spatial dimension of dengue virus spread has been limited. In the present study we analyzed the spatio-temporal pattern of a large dengue virus-2 (DENV-2) outbreak that affected the Australian city of Cairns (north Queensland) in 2003, quantified the relationship between dengue transmission and distance to the epidemic's index case (IC), evaluated the effects of indoor residual spraying (IRS) on the odds of dengue infection, and generated recommendations for city-wide dengue surveillance and control. Methods and Findings We retrospectively analyzed data from 383 DENV-2 confirmed cases and 1,163 IRS applications performed during the 25-week epidemic period. Spatial (local k-function, angular wavelets) and space-time (Knox test) analyses quantified the intensity and directionality of clustering of dengue cases, whereas a semi-parametric Bayesian space-time regression assessed the impact of IRS and spatial autocorrelation in the odds of weekly dengue infection. About 63% of the cases clustered up to 800 m around the IC's house. Most cases were distributed in the NW-SE axis as a consequence of the spatial arrangement of blocks within the city and, possibly, the prevailing winds. Space-time analysis showed that DENV-2 infection spread rapidly, generating 18 clusters (comprising 65% of all cases), and that these clusters varied in extent as a function of their distance to the IC's residence. IRS applications had a significant protective effect in the further occurrence of dengue cases, but only when they reached coverage of 60% or more of the neighboring premises of a house. Conclusion By applying sound statistical analysis to a very detailed dataset from one of the largest outbreaks that affected the city of Cairns in recent times, we not only described the spread of dengue virus with high detail but also quantified the spatio-temporal dimension of dengue virus transmission within this complex urban environment. In areas susceptible to non-periodic dengue epidemics, effective disease prevention and control would depend on the prompt response to introduced cases. We foresee that some of the results and recommendations derived from our study may also be applicable to other areas currently affected or potentially subject to dengue epidemics. Global trends in population growth and human redistribution and movement have reshaped the map of dengue transmission risk, exposing a significant proportion of the world's population to the threat of dengue epidemics. Knowledge on the relative contribution of vector and human movement to the widespread and explosive nature of dengue epidemic spread within an urban environment is limited. By analyzing a very detailed dataset of a dengue epidemic that affected the Australian city of Cairns we performed a comprehensive quantification of the spatio-temporal dimensions of dengue virus epidemic transmission and propagation within a complex urban environment. Space and space-time analysis and models allowed derivation of detailed information on the pattern of introduction and epidemic spread of dengue infection within the urban space. We foresee that some of the results and recommendations derived from our study may also be applicable to many other areas currently affected or potentially subject to dengue epidemics.
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Romano CM, de Matos AM, Araújo ESA, Villas-Boas LS, da Silva WC, Oliveira OMNPF, Carvalho KI, de Souza ACM, Rodrigues CL, Levi JE, Kallas EG, Pannuti CS. Characterization of Dengue virus type 2: new insights on the 2010 Brazilian epidemic. PLoS One 2010; 5:e11811. [PMID: 20676363 PMCID: PMC2911371 DOI: 10.1371/journal.pone.0011811] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 07/02/2010] [Indexed: 11/18/2022] Open
Abstract
Dengue viruses (DENV) serotypes 1, 2, and 3 have been causing yearly outbreaks in Brazil. In this study, we report the re-introduction of DENV2 in the coast of São Paulo State. Partial envelope viral genes were sequenced from eighteen patients with dengue fever during the 2010 epidemic. Phylogenetic analysis showed this strain belongs to the American/Asian genotype and was closely related to the virus that circulated in Rio de Janeiro in 2007 and 2008. The phylogeny also showed no clustering by clinical presentation, suggesting that the disease severity could not be explained by distinct variants or genotypes. The time of the most recent common ancestor of American/Asian genotype and the São Paulo and Rio de Janeiro (SP/RJ) monophyletic cluster was estimated to be around 40 and 10 years, respectively. Since this virus was first identified in Brazil in 2007, we suggest that it was already circulating in the country before causing the first documented outbreak. This is the first description of the 2010 outbreak in the State of São Paulo, Brazil, and should contribute to efforts to control and monitor the spread of DENVs in endemic areas.
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Affiliation(s)
- Camila Malta Romano
- Departamento de Moléstias Infecciosas e Parasitárias-(LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.
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