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Tay M, Lee B, Ismail MH, Yam J, Maliki D, Gin KYH, Chae SR, Ho ZJM, Teoh YL, Ng LC, Wong JCC. Usefulness of aircraft and airport wastewater for monitoring multiple pathogens including SARS-CoV-2 variants. J Travel Med 2024; 31:taae074. [PMID: 38813965 DOI: 10.1093/jtm/taae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/17/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND As global travel resumed in coronavirus disease 2019 (COVID-19) endemicity, the potential of aircraft wastewater monitoring to provide early warning of disease trends for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and other infectious diseases, particularly at international air travel hubs, was recognized. We therefore assessed and compared the feasibility of testing wastewater from inbound aircraft and airport terminals for 18 pathogens including SARS-CoV-2 in Singapore, a popular travel hub in Asia. METHODS Wastewater samples collected from inbound medium- and long-haul flights and airport terminals were tested for SARS-CoV-2. Next Generation Sequencing was carried out on positive samples to identify SARS-CoV-2 variants. Airport and aircraft samples were further tested for 17 other pathogens through quantitative reverse transcription polymerase chain reaction. RESULTS The proportion of SARS-CoV-2-positive samples and the average virus load was higher for wastewater samples from aircraft as compared with airport terminals. Cross-correlation analyses indicated that viral load trends from airport wastewater led local COVID-19 case trends by 2-5 days. A total of 10 variants (44 sub-lineages) were successfully identified from aircraft wastewater and airport terminals, and four variants of interest and one variant under monitoring were detected in aircraft and airport wastewater 18-31 days prior to detection in local clinical cases. The detection of five respiratory and four enteric viruses in aircraft wastewater samples further underscores the potential to expand aircraft wastewater to monitoring pathogens beyond SARS-CoV-2. CONCLUSION Our findings demonstrate the feasibility of aircraft wastewater testing for monitoring infectious diseases threats, potentially detecting signals before clinical cases are reported. The triangulation of similar datapoints from aircraft wastewater of international travel nodes could therefore serve as a useful early warning system for global health threats.
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Affiliation(s)
- Martin Tay
- Environmental Health Institute, National Environment Agency, Singapore
| | - Benjamin Lee
- Environmental Health Institute, National Environment Agency, Singapore
| | | | - Jerald Yam
- Environmental Health Institute, National Environment Agency, Singapore
| | | | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, Singapore
- Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore
| | - Sae-Rom Chae
- Communicable Diseases Group, Ministry of Health, Singapore
- National Centre for Infectious Diseases, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | - Yee Leong Teoh
- Communicable Diseases Group, Ministry of Health, Singapore
- National Centre for Infectious Diseases, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
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2
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Koch RT, Erazo D, Folly AJ, Johnson N, Dellicour S, Grubaugh ND, Vogels CBF. Genomic epidemiology of West Nile virus in Europe. One Health 2024; 18:100664. [PMID: 38193029 PMCID: PMC10772404 DOI: 10.1016/j.onehlt.2023.100664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
West Nile virus is one of the most widespread mosquito-borne zoonotic viruses, with unique transmission dynamics in various parts of the world. Genomic surveillance has provided important insights in the global patterns of West Nile virus emergence and spread. In Europe, multiple West Nile virus lineages have been isolated, with lineage 1a and 2 being the main lineages responsible for human infections. In contrast to North America, where a single introduction of lineage 1a resulted in the virus establishing itself in a new continent, at least 13 introductions of lineages 1a and 2 have occurred into Europe, which is likely a vast underestimation of the true number of introductions. Historically, lineage 1a was the main lineage circulating in Europe, but since the emergence of lineage 2 in the early 2000s, the latter has become the predominant lineage. This shift in West Nile virus lineage prevalence has been broadly linked to the expansion of the virus into northerly temperate regions, where autochthonous cases in animals and humans have been reported in Germany and The Netherlands. Here, we discuss how genomic analysis has increased our understanding of the epidemiology of West Nile virus in Europe, and we present a global Nextstrain build consisting of publicly available West Nile virus genomes (https://nextstrain.org/community/grubaughlab/WNV-Global). Our results elucidate recent insights in West Nile virus lineage dynamics in Europe, and discuss how expanded programs can fill current genomic surveillance gaps.
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Affiliation(s)
- R Tobias Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Diana Erazo
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Arran J Folly
- Vector-Borne Diseases, Virology Department, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, UK
| | - Nicholas Johnson
- Vector-Borne Diseases, Virology Department, Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, United States of America
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
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3
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Ting R, Dickens BL, Hanley R, Cook AR, Ismail E. The epidemiologic and economic burden of dengue in Singapore: A systematic review. PLoS Negl Trop Dis 2024; 18:e0012240. [PMID: 38857260 PMCID: PMC11192419 DOI: 10.1371/journal.pntd.0012240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/21/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Despite its well-regarded vector control program, Singapore remains susceptible to dengue epidemics. To assist evaluation of dengue interventions, we aimed to synthesize current data on the epidemiologic and economic burden of dengue in Singapore. METHODOLOGY We used multiple databases (PubMed, Embase, Cochrane, international/national repositories, surveillance) to search for published and gray literature (2000-2022). We included observational and cost studies, and two interventional studies, reporting Singapore-specific data on our co-primary outcomes, dengue incidence and dengue-related costs. Quality was assessed using the Newcastle-Ottawa Scale and an adapted cost-of-illness evaluation checklist. We performed a narrative synthesis and grouped studies according to reported outcomes and available stratified analyses. FINDINGS In total, 333 reports (330 epidemiological, 3 economic) were included. Most published epidemiological studies (89%) and all economic studies were of good quality. All gray literature reports were from the Ministry of Health or National Environment Agency. Based predominantly on surveillance data, Singapore experienced multiple outbreaks in 2000-2021, attaining peak incidence rate in 2020 (621.1 cases/100,000 person-years). Stratified analyses revealed the highest incidence rates in DENV-2 and DENV-3 serotypes and the 15-44 age group. Among dengue cases, the risk of hospitalization has been highest in the ≥45-year-old age groups while the risks of dengue hemorrhagic fever and death have generally been low (both <1%) for the last decade. Our search yielded limited data on deaths by age, severity, and infection type (primary, secondary, post-secondary). Seroprevalence (dengue immunoglobulin G) increases with age but has remained <50% in the general population. Comprising 21-63% indirect costs, dengue-related total costs were higher in 2010-2020 (SGD 148 million) versus the preceding decade (SGD 58-110 million). CONCLUSION Despite abundant passive surveillance data, more stratified and up-to-date data on the epidemiologic and economic burden of dengue are warranted in Singapore to continuously assess prevention and management strategies.
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Affiliation(s)
- Rita Ting
- Takeda Malaysia Sdn Bhd, Selangor, Malaysia
| | - Borame L. Dickens
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Riona Hanley
- Takeda Pharmaceuticals International AG, Zurich, Switzerland
| | - Alex R. Cook
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
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4
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de Souza WM, Weaver SC. Effects of climate change and human activities on vector-borne diseases. Nat Rev Microbiol 2024:10.1038/s41579-024-01026-0. [PMID: 38486116 DOI: 10.1038/s41579-024-01026-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2024] [Indexed: 03/18/2024]
Abstract
Vector-borne diseases are transmitted by haematophagous arthropods (for example, mosquitoes, ticks and sandflies) to humans and wild and domestic animals, with the largest burden on global public health disproportionately affecting people in tropical and subtropical areas. Because vectors are ectothermic, climate and weather alterations (for example, temperature, rainfall and humidity) can affect their reproduction, survival, geographic distribution and, consequently, ability to transmit pathogens. However, the effects of climate change on vector-borne diseases can be multifaceted and complex, sometimes with ambiguous consequences. In this Review, we discuss the potential effects of climate change, weather and other anthropogenic factors, including land use, human mobility and behaviour, as possible contributors to the redistribution of vectors and spread of vector-borne diseases worldwide.
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Affiliation(s)
- William M de Souza
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, College of Medicine, Lexington, KY, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Global Virus Network, Baltimore, MD, USA
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Global Virus Network, Baltimore, MD, USA.
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Ospina-Aguirre C, Soriano-Paños D, Olivar-Tost G, Galindo-González CC, Gómez-Gardeñes J, Osorio G. Effects of human mobility on the spread of Dengue in the region of Caldas, Colombia. PLoS Negl Trop Dis 2023; 17:e0011087. [PMID: 38011274 PMCID: PMC10703399 DOI: 10.1371/journal.pntd.0011087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 12/07/2023] [Accepted: 09/21/2023] [Indexed: 11/29/2023] Open
Abstract
According to the World Health Organization (WHO), dengue is the most common acute arthropod-borne viral infection in the world. The spread of dengue and other infectious diseases is closely related to human activity and mobility. In this paper we analyze the effect of introducing mobility restrictions as a public health policy on the total number of dengue cases within a population. To perform the analysis, we use a complex metapopulation in which we implement a compartmental propagation model coupled with the mobility of individuals between the patches. This model is used to investigate the spread of dengue in the municipalities of Caldas (CO). Two scenarios corresponding to different types of mobility restrictions are applied. In the first scenario, the effect of restricting mobility is analyzed in three different ways: a) limiting the access to the endemic node but allowing the movement of its inhabitants, b) restricting the diaspora of the inhabitants of the endemic node but allowing the access of outsiders, and c) a total isolation of the inhabitants of the endemic node. In this scenario, the best simulation results are obtained when specific endemic nodes are isolated during a dengue outbreak, obtaining a reduction of up to 2.5% of dengue cases. Finally, the second scenario simulates a total isolation of the network, i.e., mobility between nodes is completely limited. We have found that this control measure increases the number of total dengue cases in the network by 2.36%.
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Affiliation(s)
- Carolina Ospina-Aguirre
- ABCDynamics, Facultad de ciencias exactas y naturales, Universidad Nacional de Colombia - Sede Manizales, Manizales, Colombia
- Departamento de electrónica y automatización, Universidad Autonoma de Manizales, Manizales, Colombia
| | - David Soriano-Paños
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- GOTHAM lab, Institute for Biocomputation & Physics of Complex Systems (BIFI), Zaragoza, España
| | - Gerard Olivar-Tost
- Departamento de Ciencias Naturales y Tecnología, Universidad de Aysén, Coyhaique, Chile
| | - Cristian C. Galindo-González
- Percepción y Control Inteligente (PCI), Departamento de Ingeniería Eléctrica, Electrónica y Computación, Universidad Nacional de Colombia - Sede Manizales, Manizales, Colombia
| | - Jesús Gómez-Gardeñes
- Departamento de Física de la Materia Condensada Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, España
- GOTHAM lab, Institute for Biocomputation & Physics of Complex Systems (BIFI), Zaragoza, España
| | - Gustavo Osorio
- Percepción y Control Inteligente (PCI), Departamento de Ingeniería Eléctrica, Electrónica y Computación, Universidad Nacional de Colombia - Sede Manizales, Manizales, Colombia
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Tran VT, Inward RPD, Gutierrez B, Nguyen NM, Nguyen PT, Rajendiran I, Cao TT, Duong KTH, Kraemer MUG, Yacoub S. Reemergence of Cosmopolitan Genotype Dengue Virus Serotype 2, Southern Vietnam. Emerg Infect Dis 2023; 29:2180-2182. [PMID: 37735803 PMCID: PMC10521597 DOI: 10.3201/eid2910.230529] [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] [Indexed: 09/23/2023] Open
Abstract
We performed phylogenetic analysis on dengue virus serotype 2 Cosmopolitan genotype in Ho Chi Minh City, Vietnam. We document virus emergence, probable routes of introduction, and timeline of events. Our findings highlight the need for continuous, systematic genomic surveillance to manage outbreaks and forecast future epidemics.
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Min KD, Kim SY, Cho YY, Kim S, Yeom JS. Potential applicability of the importation risk index for predicting the risk of rarely imported infectious diseases. BMC Public Health 2023; 23:1776. [PMID: 37700251 PMCID: PMC10496286 DOI: 10.1186/s12889-023-16380-6] [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: 12/27/2022] [Accepted: 07/25/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND There have been many prediction studies for imported infectious diseases, employing air-travel volume or the importation risk (IR) index, which is the product of travel-volume and disease burden in the source countries, as major predictors. However, there is a lack of studies validating the predictability of the variables especially for infectious diseases that have rarely been reported. In this study, we analyzed the prediction performance of the IR index and air-travel volume to predict disease importation. METHODS Rabies and African trypanosomiasis were used as target diseases. The list of rabies and African trypanosomiasis importation events, annual air-travel volume between two specific countries, and incidence of rabies and African trypanosomiasis in the source countries were obtained from various databases. RESULTS Logistic regression analysis showed that IR index was significantly associated with rabies importation risk (p value < 0.001), but the association with African trypanosomiasis was not significant (p value = 0.923). The univariable logistic regression models showed reasonable prediction performance for rabies (area under curve for Receiver operating characteristic [AUC] = 0.734) but poor performance for African trypanosomiasis (AUC = 0.641). CONCLUSIONS Our study found that the IR index cannot be generally applicable for predicting rare importation events. However, it showed the potential utility of the IR index by suggesting acceptable performance in rabies models. Further studies are recommended to explore the generalizability of the IR index's applicability and to propose disease-specific prediction models.
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Affiliation(s)
- Kyung-Duk Min
- College of Veterinary Medicine, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju, 28644, South Korea
| | - Sun-Young Kim
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
| | - Yoon Young Cho
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Seyoung Kim
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Joon-Sup Yeom
- Division of Infectious Disease, Department of Internal Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, South Korea.
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Colón-González FJ, Gibb R, Khan K, Watts A, Lowe R, Brady OJ. Projecting the future incidence and burden of dengue in Southeast Asia. Nat Commun 2023; 14:5439. [PMID: 37673859 PMCID: PMC10482941 DOI: 10.1038/s41467-023-41017-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/17/2023] [Indexed: 09/08/2023] Open
Abstract
The recent global expansion of dengue has been facilitated by changes in urbanisation, mobility, and climate. In this work, we project future changes in dengue incidence and case burden to 2099 under the latest climate change scenarios. We fit a statistical model to province-level monthly dengue case counts from eight countries across Southeast Asia, one of the worst affected regions. We project that dengue incidence will peak this century before declining to lower levels with large variations between and within countries. Our findings reveal that northern Thailand and Cambodia will show the biggest decreases and equatorial areas will show the biggest increases. The impact of climate change will be counterbalanced by income growth, with population growth having the biggest influence on increasing burden. These findings can be used for formulating mitigation and adaptation interventions to reduce the immediate growing impact of dengue virus in the region.
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Affiliation(s)
- Felipe J Colón-González
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Tyndall Centre for Climate Change Research, School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
- Data for Science and Health, Wellcome Trust, London, NW1 2BE, UK.
| | - Rory Gibb
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Kamran Khan
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, M5S 3H2, Canada
- BlueDot, Toronto, ON, M5J 1A7, Canada
| | - Alexander Watts
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Esri Canada, Toronto, ON, M3C 3R8, Canada
| | - Rachel Lowe
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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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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Sarkar MMH, Rahman MS, Islam MR, Rahman A, Islam MS, Banu TA, Akter S, Goswami B, Jahan I, Habib MA, Uddin MM, Mia MZ, Miah MI, Shaikh AA, Khan MS. Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh. Virol J 2023; 20:127. [PMID: 37337232 PMCID: PMC10278332 DOI: 10.1186/s12985-023-02030-1] [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: 12/28/2022] [Accepted: 04/04/2023] [Indexed: 06/21/2023] Open
Abstract
Background The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever. Methods In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools. Results The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = < 0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signaling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was a significant increase of a class of immunoregulatory proteins in dengue patients in compared to the controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signaling pathways were found in dengue patients. These TLR pathways were particularly involved for the activation of innate system coupled with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue. Conclusion This is a first report describing DENV complete genomic features and differentially expressed genes in patients in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-023-02030-1.
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Affiliation(s)
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Arafat Rahman
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Iffat Jahan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Mohammad Mohi Uddin
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Zakaria Mia
- Department of Microbiology, Jagannath University, Dhaka, Bangladesh
| | - Md Ibrahim Miah
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh.
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11
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Zaw W, Lin Z, Ko Ko J, Rotejanaprasert C, Pantanilla N, Ebener S, Maude RJ. Dengue in Myanmar: Spatiotemporal epidemiology, association with climate and short-term prediction. PLoS Negl Trop Dis 2023; 17:e0011331. [PMID: 37276226 PMCID: PMC10270578 DOI: 10.1371/journal.pntd.0011331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 06/15/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
Dengue is a major public health problem in Myanmar. The country aims to reduce morbidity by 50% and mortality by 90% by 2025 based on 2015 data. To support efforts to reach these goals it is important to have a detailed picture of the epidemiology of dengue, its relationship to meteorological factors and ideally to predict ahead of time numbers of cases to plan resource allocations and control efforts. Health facility-level data on numbers of dengue cases from 2012 to 2017 were obtained from the Vector Borne Disease Control Unit, Department of Public Health, Myanmar. A detailed analysis of routine dengue and dengue hemorrhagic fever (DHF) incidence was conducted to examine the spatial and temporal epidemiology. Incidence was compared to climate data over the same period. Dengue was found to be widespread across the country with an increase in spatial extent over time. The temporal pattern of dengue cases and fatalities was episodic with annual outbreaks and no clear longitudinal trend. There were 127,912 reported cases and 632 deaths from 2012 and 2017 with peaks in 2013, 2015 and 2017. The case fatality rate was around 0.5% throughout. The peak season of dengue cases was from May to August in the wet season but in 2014 peak dengue season continued until November. The strength of correlation of dengue incidence with different climate factors (total rainfall, maximum, mean and minimum temperature and absolute humidity) varied between different States and Regions. Monthly incidence was forecasted 1 month ahead using the Auto Regressive Integrated Moving Average (ARIMA) method at country and subnational levels. With further development and validation, this may be a simple way to quickly generate short-term predictions at subnational scales with sufficient certainty to use for intervention planning.
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Affiliation(s)
- Win Zaw
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Zaw Lin
- Vector Borne Disease Control, Department of Public Health, Ministry of Health, Nay Pyi Taw, Myanmar
| | - July Ko Ko
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chawarat Rotejanaprasert
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Neriza Pantanilla
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Steeve Ebener
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Richard James Maude
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Harvard TH Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
- The Open University, Milton Keynes, United Kingdom
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Behera SP, Bhardwaj P, Deval H, Srivastava N, Singh R, Misra BR, Agrawal A, Kavathekar A, Kant R. Co-circulation of all the four Dengue virus serotypes during 2018-2019: first report from Eastern Uttar Pradesh, India. PeerJ 2023; 11:e14504. [PMID: 36643644 PMCID: PMC9835713 DOI: 10.7717/peerj.14504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/11/2022] [Indexed: 01/17/2023] Open
Abstract
Dengue fever is an endemic disease in India, transmitted by an infected mosquito bite. In India, the number of concurrent infections and the circulation of multiple dengue virus (DENV) serotypes has increased in recent decades. Molecular surveillance among the DENV serotype is important to keep track of the circulating serotypes, evolutionary changes, and key mutations that can alter the diagnostics. The current study included patients admitted for dengue in the Eastern Uttar Pradesh (E-UP) region during 2018-2019. The genetic characterization of the circulating DENV was accomplished through partial CprM (511 bp) gene amplification via reverse transcriptase polymerase chain reaction and sequencing. Phylogenetic analysis revealed the circulation of all four DENV1-4 serotypes. DENV-2 was the most abundant serotype (44%, 27/61), followed by DENV-3 (32%, 20/61). DENV-1 had a 16% (10/61) predominance, while DENV-4 (6%, 4/61) was found to be the least abundant serotype. DENV-2 genotypes were distributed among lineages I (7.4%), II (85%) and III (7.4%) of genotype IV, DENV-3 to lineage III of genotype III, DENV-1 to genotype III; DENV-2 to lineage B (75%) and C (25%) of genotype I. This primary report on the co-circulation of DENV1-4 serotypes from the E-UP region highlights the requirement of continuous molecular surveillance for monitoring circulating DENV serotypes.
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Affiliation(s)
| | - Pooja Bhardwaj
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Hirawati Deval
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Neha Srivastava
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Brij Ranjan Misra
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Awdhesh Agrawal
- Division of Pathology, Gorakhnath Hospital, Gorakhpur, Uttar Pradesh, India
| | - Asif Kavathekar
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh, India
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Kayesh MEH, Khalil I, Kohara M, Tsukiyama-Kohara K. Increasing Dengue Burden and Severe Dengue Risk in Bangladesh: An Overview. Trop Med Infect Dis 2023; 8:tropicalmed8010032. [PMID: 36668939 PMCID: PMC9866424 DOI: 10.3390/tropicalmed8010032] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Dengue is a prevalent and rapidly spreading mosquito-borne viral disease affecting humans. The geographic range of dengue is expanding, and much like in many other tropical regions of the world, dengue has become a major public health issue in Bangladesh. Until a large epidemic dengue outbreak in 2000, sporadic outbreaks have occurred in Bangladesh since 1964. After 2000, varying intensities of dengue activity were observed each year until 2018. However, in 2019, Bangladesh experienced the largest dengue epidemic in its history, with 101,354 dengue cases and 164 dengue-related deaths. Notably, this outbreak occurred in many regions that were previously considered free of the disease. As of 10 December 2022, a total of 60,078 dengue cases and 266 dengue-related deaths were reported in Bangladesh, with the 2022 outbreak being the second largest since 2000. There is an increased genetic diversity of the dengue virus (DENV) in Bangladesh and all four DENV serotypes are prevalent and co-circulating, which increases the risk for severe dengue owing to the antibody-dependent enhancement effect. Vector control remains the mainstay of dengue outbreak prevention; however, the vector control programs adopted in Bangladesh seem inadequate, requiring improved vector control strategies. In this review, we provide an overview of the epidemiology of DENV infection and the risks for a severe dengue outbreak in Bangladesh. Additionally, we discuss different dengue vector control strategies, from which the most suitable and effective measures can be applied in the context of Bangladesh for tackling future dengue epidemics.
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Affiliation(s)
- Mohammad Enamul Hoque Kayesh
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal 8210, Bangladesh
- Correspondence: (M.E.H.K.); (K.T.-K.); Tel.: +88-025-506-1677 (M.E.H.K.); +81-99-285-3589 (K.T.-K.)
| | - Ibrahim Khalil
- Department of Livestock Services, Ministry of Fisheries & Livestock, Government of the Peoples Republic of Bangladesh, Dhaka 1215, Bangladesh
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Correspondence: (M.E.H.K.); (K.T.-K.); Tel.: +88-025-506-1677 (M.E.H.K.); +81-99-285-3589 (K.T.-K.)
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Jing F, Li Z, Qiao S, Zhang J, Olatosi B, Li X. Investigating the relationships between concentrated disadvantage, place connectivity, and COVID-19 fatality in the United States over time. BMC Public Health 2022; 22:2346. [PMID: 36517796 PMCID: PMC9748905 DOI: 10.1186/s12889-022-14779-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Concentrated disadvantaged areas have been disproportionately affected by COVID-19 outbreak in the United States (US). Meanwhile, highly connected areas may contribute to higher human movement, leading to higher COVID-19 cases and deaths. This study examined the associations between concentrated disadvantage, place connectivity, and COVID-19 fatality in the US over time. METHODS Concentrated disadvantage was assessed based on the spatial concentration of residents with low socioeconomic status. Place connectivity was defined as the normalized number of shared Twitter users between the county and all other counties in the contiguous US in a year (Y = 2019). COVID-19 fatality was measured as the cumulative COVID-19 deaths divided by the cumulative COVID-19 cases. Using county-level (N = 3,091) COVID-19 fatality over four time periods (up to October 31, 2021), we performed mixed-effect negative binomial regressions to examine the association between concentrated disadvantage, place connectivity, and COVID-19 fatality, considering potential state-level variations. The moderation effects of county-level place connectivity and concentrated disadvantage were analyzed. Spatially lagged variables of COVID-19 fatality were added to the models to control for the effect of spatial autocorrelations in COVID-19 fatality. RESULTS Concentrated disadvantage was significantly associated with an increased COVID-19 fatality in four time periods (p < 0.01). More importantly, moderation analysis suggested that place connectivity significantly exacerbated the harmful effect of concentrated disadvantage on COVID-19 fatality in three periods (p < 0.01), and this significant moderation effect increased over time. The moderation effects were also significant when using place connectivity data from the previous year. CONCLUSIONS Populations living in counties with both high concentrated disadvantage and high place connectivity may be at risk of a higher COVID-19 fatality. Greater COVID-19 fatality that occurs in concentrated disadvantaged counties may be partially due to higher human movement through place connectivity. In response to COVID-19 and other future infectious disease outbreaks, policymakers are encouraged to take advantage of historical disadvantage and place connectivity data in epidemic monitoring and surveillance of the disadvantaged areas that are highly connected, as well as targeting vulnerable populations and communities for additional intervention.
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Affiliation(s)
- Fengrui Jing
- Department of Geography, Geoinformation and Big Data Research Lab, University of South Carolina, Columbia, SC, 29208, USA.
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA.
| | - Zhenlong Li
- Department of Geography, Geoinformation and Big Data Research Lab, University of South Carolina, Columbia, SC, 29208, USA
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
| | - Shan Qiao
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Jiajia Zhang
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Bankole Olatosi
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Xiaoming Li
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
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15
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Li L, Guo X, Zhang X, Zhao L, Li L, Wang Y, Xie T, Yin Q, Jing Q, Hu T, Li Z, Wu R, Zhao W, Xin SX, Shi B, Liu J, Xia S, Peng Z, Yang Z, Zhang F, Chen XG, Zhou X. A unified global genotyping framework of dengue virus serotype-1 for a stratified coordinated surveillance strategy of dengue epidemics. Infect Dis Poverty 2022; 11:107. [PMID: 36224651 PMCID: PMC9556283 DOI: 10.1186/s40249-022-01024-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Dengue is the fastest spreading arboviral disease, posing great challenges on global public health. A reproduceable and comparable global genotyping framework for contextualizing spatiotemporal epidemiological data of dengue virus (DENV) is essential for research studies and collaborative surveillance. METHODS Targeting DENV-1 spreading prominently in recent decades, by reconciling all qualified complete E gene sequences of 5003 DENV-1 strains with epidemiological information from 78 epidemic countries/areas ranging from 1944 to 2018, we established and characterized a unified global high-resolution genotyping framework using phylogenetics, population genetics, phylogeography, and phylodynamics. RESULTS The defined framework was discriminated with three hierarchical layers of genotype, subgenotype and clade with respective mean pairwise distances 2-6%, 0.8-2%, and ≤ 0.8%. The global epidemic patterns of DENV-1 showed strong geographic constraints representing stratified spatial-genetic epidemic pairs of Continent-Genotype, Region-Subgenotype and Nation-Clade, thereby identifying 12 epidemic regions which prospectively facilitates the region-based coordination. The increasing cross-transmission trends were also demonstrated. The traditional endemic countries such as Thailand, Vietnam and Indonesia displayed as persisting dominant source centers, while the emerging epidemic countries such as China, Australia, and the USA, where dengue outbreaks were frequently triggered by importation, showed a growing trend of DENV-1 diffusion. The probably hidden epidemics were found especially in Africa and India. Then, our framework can be utilized in an accurate stratified coordinated surveillance based on the defined viral population compositions. Thereby it is prospectively valuable for further hampering the ongoing transition process of epidemic to endemic, addressing the issue of inadequate monitoring, and warning us to be concerned about the cross-national, cross-regional, and cross-continental diffusions of dengue, which can potentially trigger large epidemics. CONCLUSIONS The framework and its utilization in quantitatively assessing DENV-1 epidemics has laid a foundation and re-unveiled the urgency for establishing a stratified coordinated surveillance platform for blocking global spreading of dengue. This framework is also expected to bridge classical DENV-1 genotyping with genomic epidemiology and risk modeling. We will promote it to the public and update it periodically.
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Affiliation(s)
- Liqiang Li
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiang Guo
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqing Zhang
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Lingzhai Zhao
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, Guangdong, China
| | - Li Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yuji Wang
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Tian Xie
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qingqing Yin
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qinlong Jing
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Tian Hu
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Ziyao Li
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Rangke Wu
- School of Foreign Studies, Southern Medical University, Guangzhou, 510515, China
| | - Wei Zhao
- BSL-3 Laboratory (Guangdong), School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Sherman Xuegang Xin
- Laboratory of Biophysics, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Benyun Shi
- School of Computer Science and Technology, Nanjing Tech University, Nanjing, 211816, China
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Shang Xia
- National Institute of Parasitic Diseases at Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, Shanghai, People's Republic of China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhiqiang Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Zhicong Yang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Fuchun Zhang
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510060, Guangdong, China.
| | - Xiao-Guang Chen
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| | - Xiaohong Zhou
- Institute of Tropical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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Nova N, Athni TS, Childs ML, Mandle L, Mordecai EA. Global Change and Emerging Infectious Diseases. ANNUAL REVIEW OF RESOURCE ECONOMICS 2022; 14:333-354. [PMID: 38371741 PMCID: PMC10871673 DOI: 10.1146/annurev-resource-111820-024214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Our world is undergoing rapid planetary changes driven by human activities, often mediated by economic incentives and resource management, affecting all life on Earth. Concurrently, many infectious diseases have recently emerged or spread into new populations. Mounting evidence suggests that global change-including climate change, land-use change, urbanization, and global movement of individuals, species, and goods-may be accelerating disease emergence by reshaping ecological systems in concert with socioeconomic factors. Here, we review insights, approaches, and mechanisms by which global change drives disease emergence from a disease ecology perspective. We aim to spur more interdisciplinary collaboration with economists and identification of more effective and sustainable interventions to prevent disease emergence. While almost all infectious diseases change in response to global change, the mechanisms and directions of these effects are system specific, requiring new, integrated approaches to disease control that recognize linkages between environmental and economic sustainability and human and planetary health.
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Affiliation(s)
- Nicole Nova
- Department of Biology, Stanford University, Stanford, California, USA
| | - Tejas S Athni
- Department of Biology, Stanford University, Stanford, California, USA
| | - Marissa L Childs
- Emmett Interdisciplinary Program in Environment and Resources, Stanford University, Stanford, California, USA
| | - Lisa Mandle
- Department of Biology, Stanford University, Stanford, California, USA
- Natural Capital Project, Stanford University, Stanford, California, USA
- Woods Institute for the Environment, Stanford University, Stanford, California, USA
| | - Erin A Mordecai
- Department of Biology, Stanford University, Stanford, California, USA
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In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines. Vaccines (Basel) 2022; 10:vaccines10081259. [PMID: 36016147 PMCID: PMC9415047 DOI: 10.3390/vaccines10081259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022] Open
Abstract
Dengue is a viral mosquito-borne disease that rapidly spreads in tropical and subtropical countries, including the Philippines. One of its most distinguishing characteristics is the ability of the Dengue Virus (DENV) to easily surpass the innate responses of the body, thus activating B cells of the adaptive immunity to produce virus-specific antibodies. Moreover, Dengvaxia® is the only licensed vaccine for DENV, but recent studies showed that seronegative individuals become prone to increased disease severity and hospitalization. Owing to this limitation of the dengue vaccine, this study determined and compared consensus and unique B cell epitopes among each DENV (1–4) Philippine isolate to identify potential areas of interest for future vaccine studies and therapeutic developments. An in silico-based epitope prediction of forty (40) DENV 1–4 strains, each serotype represented by ten (10) sequences from The National Center for Biotechnology Information (NCBI), was conducted using Kolaskar and Tongaonkar antigenicity, Emini surface accessibility, and Parker hydrophilicity prediction in Immune Epitope Database (IEDB). Results showed that five (5) epitopes were consensus for DENV-1 with no detected unique epitope, one (1) consensus epitope for DENV-2 with two (2) unique epitopes, one (1) consensus epitope for DENV-3 plus two (2) unique epitopes, and two (2) consensus epitopes and one (1) unique epitope for DENV-4. The findings of this study would contribute to determining potential vaccine and diagnostic marker candidates for further research studies and immunological applications against DENV (1–4) Philippine isolates.
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Juarez JG, Carbajal E, Dickinson KL, Garcia-Luna S, Vuong N, Mutebi JP, Hemme RR, Badillo-Vargas I, Hamer GL. The unreachable doorbells of South Texas: community engagement in colonias on the US-Mexico border for mosquito control. BMC Public Health 2022; 22:1176. [PMID: 35698216 PMCID: PMC9190097 DOI: 10.1186/s12889-022-13426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Mosquitoes and the diseases they transmit continue to place millions of people at risk of infection around the world. Novel methods of vector control are being developed to provide public health officials with the necessary tools to prevent disease transmission and reduce local mosquito populations. However, these methods will require public acceptance for a sustainable approach and evaluations at local settings. We present our efforts in community engagement carried out in colonias of the Lower Rio Grande Valley in south Texas for mosquito surveillance, control, and ecological projects. Along the US-Mexico border the term colonia refers to impoverished communities that are usually inhabited by families of Hispanic heritage. The different engagements were carried out from September 2016 to February 2019; during this time, we had three distinct phases for community engagement. In Phase 1 we show the initial approach to the colonias in which we assessed security and willingness to participate; in Phase 2 we carried out the first recruitment procedure involving community meetings and house-to-house recruitment; and in Phase 3 we conducted a modified recruitment procedure based on community members' input. Our findings show that incorporating community members in the development of communication materials and following their suggestions for engagement allowed us to generate culturally sensitive recruitment materials and to better understand the social relationships and power dynamics within these communities. We were able to effectively reach a larger portion of the community and decrease the dropout rate of participants. Progress gained with building trust in the communities allowed us to convey participant risks and benefits of collaborating with our research projects. Community engagement should be viewed as a key component of any local vector control program as well as for any scientific research project related to vector control. Even in the face of budgetary constraints, small efforts in community engagement go a long way.
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Affiliation(s)
- Jose G Juarez
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Ester Carbajal
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | | | - Selene Garcia-Luna
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Nga Vuong
- Division of Vector Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - John-Paul Mutebi
- Division of Vector Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Ryan R Hemme
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Dengue Branch, San Juan, PR, USA
| | | | - Gabriel L Hamer
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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19
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Neto Z, Martinez PA, Hill SC, Jandondo D, Thézé J, Mirandela M, Aguiar RS, Xavier J, dos Santos Sebastião C, Cândido ALM, Vaz F, Castro GR, Paixão JP, Loman NJ, Lemey P, Pybus OG, Vasconcelos J, Faria NR, de Morais J. Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. PLoS Negl Trop Dis 2022; 16:e0010255. [PMID: 35584153 PMCID: PMC9166355 DOI: 10.1371/journal.pntd.0010255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/03/2022] [Accepted: 02/11/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The transmission patterns and genetic diversity of dengue virus (DENV) circulating in Africa remain poorly understood. Circulation of the DENV serotype 1 (DENV1) in Angola was detected in 2013, while DENV serotype 2 (DENV2) was detected in 2018. Here, we report results from molecular and genomic investigations conducted at the Ministry of Health national reference laboratory (INIS) in Angola on suspected dengue cases detected between January 2017 and February 2019. METHODS A total of 401 serum samples from dengue suspected cases were collected in 13 of the 18 provinces in Angola. Of those, 351 samples had complete data for demographic and epidemiological analysis, including age, gender, province, type of residence, clinical symptoms, as well as dates of onset of symptoms and sample collection. RNA was extracted from residual samples and tested for DENV-RNA using two distinct real time RT-PCR protocols. On-site whole genome nanopore sequencing was performed on RT-PCR+ samples. Bayesian coalescent models were used to estimate date and origin of outbreak emergence, as well as population growth rates. RESULTS Molecular screening showed that 66 out of 351 (19%) suspected cases were DENV-RNA positive across 5 provinces in Angola. DENV RT-PCR+ cases were detected more frequently in urban sites compared to rural sites. Of the DENV RT-PCR+ cases most were collected within 6 days of symptom onset. 93% of infections were confirmed by serotype-specific RT-PCR as DENV2 and 1 case (1.4%) was confirmed as DENV1. Six CHIKV RT-PCR+ cases were also detected during the study period, including 1 co-infection of CHIKV with DENV1. Most cases (87%) were detected in Luanda during the rainy season between April and October. Symptoms associated with severe dengue were observed in 11 patients, including 2 with a fatal outcome. On-site nanopore genome sequencing followed by genetic analysis revealed an introduction of DENV2 Cosmopolitan genotype (also known as DENV2-II genotype) possibly from India in or around October 2015, at least 1 year before its detection in the country. Coalescent models suggest relatively moderately rapid epidemic growth rates and doubling times, and a moderate expansion of DENV2 in Angola during the studied period. CONCLUSION This study describes genomic, epidemiological and demographic characteristic of predominately urban transmission of DENV2 in Angola. We also find co-circulation of DENV2 with DENV1 and CHIKV and report several RT-PCR confirmed severe dengue cases in the country. Increasing dengue awareness in healthcare professional, expanding the monitorization of arboviral epidemics across the country, identifying most common mosquito breeding sites in urban settings, implementing innovative vector control interventions and dengue vaccination campaigns could help to reduce vector presence and DENV transmission in Angola.
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Affiliation(s)
- Zoraima Neto
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Pedro A. Martinez
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Sarah C. Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Domingos Jandondo
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Julien Thézé
- Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Marinela Mirandela
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Renato Santana Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Filipa Vaz
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
- World Health Organization Angola, Luanda, Angola
| | - Gisel Reyes Castro
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Joana Paula Paixão
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jocelyne Vasconcelos
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
| | - Joana de Morais
- Instituto Nacional de Investigação em Saúde (INIS), Ministry of Health, Luanda, Angola
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20
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Finding a chink in the armor: Update, limitations, and challenges toward successful antivirals against flaviviruses. PLoS Negl Trop Dis 2022; 16:e0010291. [PMID: 35482672 PMCID: PMC9049358 DOI: 10.1371/journal.pntd.0010291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Flaviviruses have caused large epidemics and ongoing outbreaks for centuries. They are now distributed in every continent infecting up to millions of people annually and may emerge to cause future epidemics. Some of the viruses from this group cause severe illnesses ranging from hemorrhagic to neurological manifestations. Despite decades of research, there are currently no approved antiviral drugs against flaviviruses, urging for new strategies and antiviral targets. In recent years, integrated omics data-based drug repurposing paired with novel drug validation methodologies and appropriate animal models has substantially aided in the discovery of new antiviral medicines. Here, we aim to review the latest progress in the development of both new and repurposed (i) direct-acting antivirals; (ii) host-targeting antivirals; and (iii) multitarget antivirals against flaviviruses, which have been evaluated both in vitro and in vivo, with an emphasis on their targets and mechanisms. The search yielded 37 compounds that have been evaluated for their efficacy against flaviviruses in animal models; 20 of them are repurposed drugs, and the majority of them exhibit broad-spectrum antiviral activity. The review also highlighted the major limitations and challenges faced in the current in vitro and in vivo evaluations that hamper the development of successful antiviral drugs for flaviviruses. We provided an analysis of what can be learned from some of the approved antiviral drugs as well as drugs that failed clinical trials. Potent in vitro and in vivo antiviral efficacy alone does not warrant successful antiviral drugs; current gaps in studies need to be addressed to improve efficacy and safety in clinical trials.
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21
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Cui F, He F, Huang X, Tian L, Li S, Liang C, Zeng L, Lin H, Su J, Liu L, Zhao W, Sun L, Lin L, Sun J. Dengue and Dengue Virus in Guangdong, China, 1978-2017: Epidemiology, Seroprevalence, Evolution, and Policies. Front Med (Lausanne) 2022; 9:797674. [PMID: 35386910 PMCID: PMC8979027 DOI: 10.3389/fmed.2022.797674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background Guangdong is a hyperepidemic area of dengue, which has over 0.72 million cumulative cases within the last four decades, accounting for more than 90% of cases in China. The local epidemic of dengue in Guangdong is suspected to be triggered by imported cases and results in consequent seasonal transmission. However, the comprehensive epidemiological characteristics of dengue in Guangdong are still unclear. Methods The epidemiology, seroprevalence, molecular evolution of dengue virus, and the development of policies and strategies on the prevention and control of dengue were analyzed in Guangdong, China from 1978 to 2017. Findings Seasonal transmission of dengue virus in Guangdong, China was mainly sustained from July to October of each year. August to September was the highest risk period of local dengue outbreaks. Most of the dengue cases in Guangdong were young and middle-aged adults. Five hundred and three fatal cases were recorded, which declined within the last two decades (n = 10). The serological test of healthy donors' serum samples showed a positive rate of 5.77%. Dengue virus 1-4 (DENV 1-4) was detected in Guangdong from 1978 to 2017. DENV 1 was the dominant serotype of dengue outbreaks from 1978 to 2017, with an increasing tendency of DENV 2 since 2010. Local outbreaks of DENV 3 were rare. DENV 4 was only encountered in imported cases in Guangdong, China. The imported cases were the main source of outbreaks of DENV 1-2. Early detection, management of dengue cases, and precise vector control were the key strategies for local dengue prevention and control in Guangdong, China. Interpretation Dengue has not become an endemic arboviral disease in Guangdong, China. Early detection, case management, and implementation of precise control strategies are key findings for preventing local dengue transmission, which may serve for countries still struggling to combat imported dengue in the west pacific areas.
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Affiliation(s)
- Fengfu Cui
- School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Feiwu He
- School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaorong Huang
- School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lina Tian
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Saiqiang Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chumin Liang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lilian Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huifang Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Juan Su
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Liping Liu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Wei Zhao
- School of Public Health, Southern Medical University, Guangzhou, China
| | - Limei Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lifeng Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Jiufeng Sun
- School of Public Health, Southern Medical University, Guangzhou, China.,Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
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22
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Lai SC, Huang YY, Wey JJ, Tsai MH, Chen YL, Shu PY, Chang SF, Hung YJ, Hou JN, Lin CC. Development of Novel Dengue NS1 Multiplex Lateral Flow Immunoassay to Differentiate Serotypes in Serum of Acute Phase Patients and Infected Mosquitoes. Front Immunol 2022; 13:852452. [PMID: 35309328 PMCID: PMC8931297 DOI: 10.3389/fimmu.2022.852452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Dengue is among the most rapidly spreading arboviral disease in the world. A low-cost, easy to use point-of-care diagnostic tool for the detection and differentiation of dengue virus serotypes could improve clinical management, disease prevention, epidemiological surveillance, and outbreak monitoring, particularly in regions where multiple serotypes co-circulate. Despite widespread deployment, no commercial dengue antigen diagnostic test has proven effective in differentiating among dengue virus serotypes. In the current study, we first established mAb pairs and developed a multiplex lateral flow immunoassay for the simultaneous detection of the dengue viral NS1 antigen and identification of serotype. The proposed system, called Dengue serotype NS1 Multiplex LFIA, provides high sensitivity and specificity. In testing for JEV, ZIKV, YFV, WNV, and CHIKV, the multiplex LFIA gave no indication of cross- reactivity with cell culture supernatants of other flaviviruses or chikungunya virus. In analyzing 187 samples from patients suspected of dengue infection, the detection sensitivity for serotype D1 to D4 was 90.0%, 88.24%, 82.61%, and 83.33% and serotype specificity was 98.74%, 96.13%, 99.39%, and 97.04%, respectively. Our multiplex LFIA can also identify mono- and co-infection of different serotype of dengue viruses in mosquitoes. The proposed Multiplex LFIA provides a simple tool for the rapid detection of dengue serotypes and in the differential diagnosis of fever patients in regions where medical resources are limited and/or multiple DENVs co-circulate.
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Affiliation(s)
- Szu-Chia Lai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Yu-Yine Huang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Jiunn-Jye Wey
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Meng-Hung Tsai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Yi-Ling Chen
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Pei-Yun Shu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei City, Taiwan
| | - Shu-Fen Chang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei City, Taiwan
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Jiu-Nan Hou
- Diagnostic Device Group, Trison Technology Corporation, Taoyuan City, Taiwan
| | - Chang-Chi Lin
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
- Institute of Microbiology and Immunology, National Defense Medical Center, Taipei City, Taiwan
- *Correspondence: Chang-Chi Lin, ;
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23
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Russell TL, Horwood PF, Harrington H, Apairamo A, Kama NJ, Bobogare A, MacLaren D, Burkot TR. Seroprevalence of dengue, Zika, chikungunya and Ross River viruses across the Solomon Islands. PLoS Negl Trop Dis 2022; 16:e0009848. [PMID: 35143495 PMCID: PMC8865700 DOI: 10.1371/journal.pntd.0009848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/23/2022] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Across the Pacific, and including in the Solomon Islands, outbreaks of arboviruses such as dengue, chikungunya, and Zika are increasing in frequency, scale and impact. Outbreaks of mosquito-borne disease have the potential to overwhelm the health systems of small island nations. This study mapped the seroprevalence of dengue, Zika, chikungunya and Ross River viruses in 5 study sites in the Solomon Islands. Serum samples from 1,021 participants were analysed by ELISA. Overall, 56% of participants were flavivirus-seropositive for dengue (28%), Zika (1%) or both flaviviruses (27%); and 53% of participants were alphavirus-seropositive for chikungunya (3%), Ross River virus (31%) or both alphaviruses (18%). Seroprevalence for both flaviviruses and alphaviruses varied by village and age of the participant. The most prevalent arboviruses in the Solomon Islands were dengue and Ross River virus. The high seroprevalence of dengue suggests that herd immunity may be a driver of dengue outbreak dynamics in the Solomon Islands. Despite being undetected prior to this survey, serology results suggest that Ross River virus transmission is endemic. There is a real need to increase the diagnostic capacities for each of the arboviruses to support effective case management and to provide timely information to inform vector control efforts and other outbreak mitigation interventions. The occurrence of arboviruses is increasing and causing significant impacts on human health. This is of high concern in small Pacific island nations where fragile health systems are regularly overwhelmed by disease outbreaks. To effectively prevent and control disease transmission there is a need to understand which viruses have been in circulation. Therefore, we conducted a cross-sectional survey of residents from 5 study sites distributed across the Solomon Islands. The serum samples were tested for antibodies that indicate prior infection for four arboviruses. We found evidence that the residents of the Solomon Islands have been exposed to substantial transmission of dengue and Ross River viruses, with lower levels of Zika and chikungunya transmission. Two large dengue outbreaks have been recently experienced and the outbreak pattern suggests that natural herd immunity may still be a driver of dengue outbreak dynamics in the Solomon Islands. Regarding Ross River virus, transmission is endemic despite being undetected prior to this survey. There is a real need to increase the capacity to accurately diagnose each of these arboviruses to support effective case management and to provide timely information to inform vector control efforts.
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Affiliation(s)
- Tanya L. Russell
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
- * E-mail:
| | - Paul F. Horwood
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Humpress Harrington
- College of Medicine and Dentistry, James Cook University, Cairns, Australia
- Atoifi College of Nursing, Atoifi Adventist Hospital, Atoifi, Malaita, Solomon Islands
| | - Allan Apairamo
- National Vector Borne Disease Control Program, Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Nathan J. Kama
- National Vector Borne Disease Control Program, Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - Albino Bobogare
- National Vector Borne Disease Control Program, Ministry of Health and Medical Services, Honiara, Solomon Islands
| | - David MacLaren
- College of Medicine and Dentistry, James Cook University, Cairns, Australia
| | - Thomas R. Burkot
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
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24
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Sang S, Liu Q, Guo X, Wu D, Ke C, Liu-Helmersson J, Jiang J, Weng Y, Wang Y. The epidemiological characteristics of dengue in high-risk areas of China, 2013-2016. PLoS Negl Trop Dis 2021; 15:e0009970. [PMID: 34928951 PMCID: PMC8687583 DOI: 10.1371/journal.pntd.0009970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Introduction Dengue has become a more serious human health concern in China, with increased incidence and expanded outbreak regions. The knowledge of the cross-sectional and longitudinal epidemiological characteristics and the evolutionary dynamics of dengue in high-risk areas of China is limited. Methods Records of dengue cases from 2013 to 2016 were obtained from the China Notifiable Disease Surveillance System. Full envelope gene sequences of dengue viruses detected from the high-risk areas of China were collected. Maximum Likelihood tree and haplotype network analyses were conducted to explore the phylogenetic relationship of viruses from high-risk areas of China. Results A total of 56,520 cases was reported in China from 2013 to 2016. During this time, Yunnan, Guangdong and Fujian provinces were the high-risk areas. Imported cases occurred almost year-round, and were mainly introduced from Southeast Asia. The first indigenous case usually occurred in June to August, and the last one occurred before December in Yunnan and Fujian provinces but in December in Guangdong Province. Seven genotypes of DENV 1–3 were detected in the high-risk areas, with DENV 1-I the main genotype and DENV 2-Cosmopolitan the secondary one. The Maximum Likelihood trees show that almost all the indigenous viruses separated into different clusters. DENV 1-I viruses were found to be clustered in Guangdong Province, but not in Fujian and Yunnan, from 2013 to 2015. The ancestors of the Guangdong viruses in the cluster in 2013 and 2014 were most closely related to strains from Thailand or Singapore, and the Guangdong virus in 2015 was most closely related to the Guangdong virus of 2014. Based on closest phylogenetic relationships, viruses from Myanmar possibly initiated further indigenous cases in Yunnan, those from Indonesia in Fujian, while viruses from Thailand, Malaysia, Singapore and Indonesia were predominant in Guangdong Province. Conclusions Dengue is still an imported disease in China, although some genotypes continued to circulate in successive years. Viral phylogenies based on the envelope gene suggested periodic introductions of dengue strains into China, primarily from Southeast Asia, with occasional sustained, multi-year transmission in some regions of China. Dengue is the most prevalent and rapidly spreading mosquito-borne viral disease globally. Because of the multiple introductions, dengue outbreaks occurred in epidemic seasons in Southern China, supported by suitable weather conditions. Surveillance data from 2013 to 2016 in China showed that Guangdong, Yunnan and Fujian provinces were the high-risk areas, with dengue outbreaks occurring almost every year. However, knowledge has been lacking of the epidemiological characteristics and the evolution pattern of dengue virus in these high-risk areas. This study shows a variety of epidemiological characteristics and sources of imported cases among the high-risk areas in China, with likely origins primarily from countries in Southeast Asia. Seven genotypes of the DENV 1–3 variety co-circulated with DENV1-I, the main genotype, and DENV 2-Cosmopolitan, the secondary. Genetic relationships among viral strains suggest that the indigenous viruses in the high-risk areas arose from imported viruses and sometimes persisted between years into the next epidemic season, especially in Guangdong Province. Population movement has played a vital role in dengue epidemics in China. This information may be useful in dengue control, especially during epidemic seasons and in the development of an early warning system within the region, in collaboration with bordering countries.
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Affiliation(s)
- Shaowei Sang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong, People’s Republic of China
- Clinical Research Center of Shandong University, Jinan, Shandong, People’s Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong, People’s Republic of China
- * E-mail:
| | - Qiyong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People’s Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Center of Arborvirus Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan Institute of Parasitic Diseases, Pu’er, Yunnan, People’s Republic of China
| | - De Wu
- Institute of Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
| | - Changwen Ke
- Institute of Microbiology, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, People’s Republic of China
| | | | - Jinyong Jiang
- Yunnan Provincial Center of Arborvirus Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan Institute of Parasitic Diseases, Pu’er, Yunnan, People’s Republic of China
| | - Yuwei Weng
- Fujian center for disease control and prevention, Fuzhou, People’s Republic of China
| | - Yiguan Wang
- School of Biological Sciences, University of Queensland, St Lucia, Australia
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25
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Rashkov P, Kooi BW. Complexity of host-vector dynamics in a two-strain dengue model. JOURNAL OF BIOLOGICAL DYNAMICS 2021; 15:35-72. [PMID: 33357025 DOI: 10.1080/17513758.2020.1864038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
We introduce a compartmental host-vector model for dengue with two viral strains, temporary cross-immunity for the hosts, and possible secondary infections. We study the conditions on existence of endemic equilibria where one strain displaces the other or the two virus strains co-exist. Since the host and vector epidemiology follow different time scales, the model is described as a slow-fast system. We use the geometric singular perturbation technique to reduce the model dimension. We compare the behaviour of the full model with that of the model with a quasi-steady approximation for the vector dynamics. We also perform numerical bifurcation analysis with parameter values from the literature and compare the bifurcation structure to that of previous two-strain host-only models.
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Affiliation(s)
- Peter Rashkov
- Institute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Bob W Kooi
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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26
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Liu A, Kim YR, O'Connell JF. COVID-19 and the aviation industry: The interrelationship between the spread of the COVID-19 pandemic and the frequency of flights on the EU market. ANNALS OF TOURISM RESEARCH 2021; 91:103298. [PMID: 34518712 PMCID: PMC8426192 DOI: 10.1016/j.annals.2021.103298] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 05/26/2023]
Abstract
This study aims to investigate the contribution of aviation related travel restrictions to control the spread of COVID-19 in Europe by using quasi-experiment approaches including the regression discontinuity design and a two-stage spatial Durbin model with an instrumental variable. The study provides concrete evidence that the severe curtailing of flights had a spontaneous impact in controlling the spread of COVID-19. The counterfactual analysis encapsulated the spillover effects deduced that a 1% decrease in flight frequency can decrease the number of confirmed cases by 0.908%. The study also reveals that during the lockdown, the aviation industry cancelled over 795,000 flights, which resulted in averting an additional six million people being from being infected and saving 101,309 lives.
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Affiliation(s)
- Anyu Liu
- University of Surrey, United Kingdom
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Vernal S, Nahas AK, Chiaravalloti Neto F, Prete Junior CA, Cortez AL, Sabino EC, Luna EJDA. Geoclimatic, demographic and socioeconomic characteristics related to dengue outbreaks in Southeastern Brazil: an annual spatial and spatiotemporal risk model over a 12-year period. Rev Inst Med Trop Sao Paulo 2021; 63:e70. [PMID: 34586304 PMCID: PMC8494490 DOI: 10.1590/s1678-9946202163070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022] Open
Abstract
Dengue fever is re-emerging worldwide, however the reasons of this new emergence
are not fully understood. Our goal was to report the incidence of dengue in one
of the most populous States of Brazil, and to assess the high-risk areas using a
spatial and spatio-temporal annual models including geoclimatic, demographic and
socioeconomic characteristics. An ecological study with both, a spatial and a
temporal component was carried out in Sao Paulo State, Southeastern Brazil,
between January 1st, 2007 and December 31st, 2019. Crude
and Bayesian empirical rates of dengue cases following by Standardized Incidence
Ratios (SIR) were calculated considering the municipalities as the analytical
units and using the Integrated Nested Laplace Approximation in a Bayesian
context. A total of 2,027,142 cases of dengue were reported during the studied
period. The spatial model allocated the municipalities in four groups according
to the SIR values: (I) SIR<0.8; (II) SIR 0.8<1.2; (III) SIR 1.2<2.0 and
SIR>2.0 identified the municipalities with higher risk for dengue outbreaks.
“Hot spots” are shown in the thematic maps. Significant correlations between SIR
and two climate variables, two demographic variables and one socioeconomical
variable were found. No significant correlations were found in the
spatio-temporal model. The incidence of dengue exhibited an inconstant and
unpredictable variation every year. The highest rates of dengue are concentrated
in geographical clusters with lower surface pressure, rainfall and altitude, but
also in municipalities with higher degree of urbanization and better
socioeconomic conditions. Nevertheless, annual consolidated variations in
climatic features do not influence in the epidemic yearly pattern of dengue in
southeastern Brazil.
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Affiliation(s)
- Sebastian Vernal
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Andressa K Nahas
- Universidade de São Paulo, Faculdade de Saúde Pública, Departamento de Epidemiologia, São Paulo, São Paulo, Brazil
| | - Francisco Chiaravalloti Neto
- Universidade de São Paulo, Faculdade de Saúde Pública, Departamento de Epidemiologia, São Paulo, São Paulo, Brazil
| | - Carlos A Prete Junior
- Universidade de São Paulo, Escola Politécnica, Departamento de Engenharia de Sistemas Eletrônicos, São Paulo, São Paulo, Brazil
| | - André L Cortez
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Expedito José de Albuquerque Luna
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Medicina Preventiva, São Paulo, São Paulo, Brazil
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Bulterys PL, Solis D, Verghese M, Huang C, Sibai M, Costales C, Sahoo MK, Pinsky BA. Diagnosis of Dengue in a returning traveler from Pakistan suspected of COVID-19, California, USA. Diagn Microbiol Infect Dis 2021; 101:115517. [PMID: 34537475 PMCID: PMC8342863 DOI: 10.1016/j.diagmicrobio.2021.115517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/10/2021] [Accepted: 05/15/2021] [Indexed: 11/06/2022]
Abstract
Dengue and COVID-19 cocirculation presents a diagnostic conundrum for physicians evaluating patients with acute febrile illnesses, both in endemic regions and among returning travelers. We present a case of a returning traveler from Pakistan who, following repeated negative SARS-CoV-2 tests, was found to have a Dengue virus serotype 2 infection.
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Affiliation(s)
| | - Daniel Solis
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Michelle Verghese
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Chunhong Huang
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Mamdouh Sibai
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | | | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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29
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Kayesh MEH, Kohara M, Tsukiyama-Kohara K. Recent Insights Into the Molecular Mechanism of Toll-Like Receptor Response to Dengue Virus Infection. Front Microbiol 2021; 12:744233. [PMID: 34603272 PMCID: PMC8483762 DOI: 10.3389/fmicb.2021.744233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
Dengue is the most prevalent and rapidly spreading mosquito-borne viral disease caused by dengue virus (DENV). Recently, DENV has been affecting humans within an expanding geographic range due to the warming of the earth. Innate immune responses play a significant role in antiviral defense, and Toll-like receptors (TLRs) are key regulators of innate immunity. Therefore, a detailed understanding of TLR and DENV interactions is important for devising therapeutic and preventive strategies. Several studies have indicated the ability of DENV to modulate the TLR signaling pathway and host immune response. Vaccination is considered one of the most successful medical interventions for preventing viral infections. However, only a partially protective dengue vaccine, the first licensed dengue vaccine CYD-TDV, is available in some dengue-endemic countries to protect against DENV infection. Therefore, the development of a fully protective, durable, and safe DENV vaccine is a priority for global health. Here, we demonstrate the progress made in our understanding of the host response to DENV infection, with a particular focus on TLR response and how DENV avoids the response toward establishing infection. We also discuss dengue vaccine candidates in late-stage development and the issues that must be overcome to enable their success.
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Affiliation(s)
- Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal, Bangladesh
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
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Li N, Feng Y, Vrancken B, Chen Y, Dong L, Yang Q, Kraemer MU, Pybus OG, Zhang H, Brady OJ, Tian H. Assessing the impact of COVID-19 border restrictions on dengue transmission in Yunnan Province, China: an observational epidemiological and phylogenetic analysis. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 14:100259. [PMID: 34528006 PMCID: PMC8387751 DOI: 10.1016/j.lanwpc.2021.100259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND In response to the COVID-19 pandemic, China implemented strict restrictions on cross-border travel to prevent disease importation. Yunnan, a Chinese province that borders dengue-endemic countries in Southeast Asia, experienced unprecedented reduction in dengue, from 6840 recorded cases in 2019 to 260 in 2020. METHODS Using a combination of epidemiological and virus genomic data, collected from 2013 to 2020 in Yunnan and neighbouring countries, we conduct a series of analyses to characterise the role of virus importation in driving dengue dynamics in Yunnan and assess the association between recent international travel restrictions and the decline in dengue reported in Yunnan in 2020. FINDINGS We find strong evidence that dengue incidence between 2013-2019 in Yunnan was closely linked with international importation of cases. A 0-2 month lag in incidence not explained by seasonal differences, absence of local transmission in the winter, effective reproductive numbers < 1 (as estimated independently using genetic data) and diverse cosmopolitan dengue virus phylogenies all suggest dengue is non-endemic in Yunnan. Using a multivariate statistical model we show that the substantial decline in dengue incidence observed in Yunnan in 2020 but not in neighbouring countries is closely associated with the timing of international travel restrictions, even after accounting for other environmental drivers of dengue incidence. INTERPRETATION We conclude that Yunnan is a regional sink for DENV lineage movement and that border restrictions may have substantially reduced dengue burden in 2020, potentially averting thousands of cases. Targeted testing and surveillance of travelers returning from high-risk areas could help to inform public health strategies to minimise or even eliminate dengue outbreaks in non-endemic settings like southern China. FUNDING Funding for this study was provided by National Key Research and Development Program of China, Beijing Science and Technology Planning Project (Z201100005420010); Beijing Natural Science Foundation (JQ18025); Beijing Advanced Innovation Program for Land Surface Science; National Natural Science Foundation of China (82073616); Young Elite Scientist Sponsorship Program by CAST (YESS) (2018QNRC001); H.T., O.P.G. and M.U.G.K. acknowledge support from the Oxford Martin School. O.J.B was supported by a Wellcome Trust Sir Henry Wellcome Fellowship (206471/Z/17/Z). Chinese translation of the abstract (Appendix 2).
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Affiliation(s)
- Naizhe Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yun Feng
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, KU Leuven, Leuven, Belgium
| | - Yuyang Chen
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Moritz U.G. Kraemer
- Department of Zoology, University of Oxford, Oxford, UK,Harvard Medical School, Harvard University, Boston, MA, USA,Boston Children's Hospital, Boston, MA, USA
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK,Department of Pathobiology and Population Science, The Royal Veterinary College, London, UK
| | - Hailin Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, China,Corresponding author
| | - Oliver J. Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK,Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK,Corresponding author
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China,College of Life Sciences, Beijing Normal University, Beijing, China,Corresponding author
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A Cluster of Dengue Cases in Travelers: A Clinical Series from Thailand. Trop Med Infect Dis 2021; 6:tropicalmed6030152. [PMID: 34449752 PMCID: PMC8396219 DOI: 10.3390/tropicalmed6030152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
Dengue is an overlooked tropical disease for which billions of people are at risk. The disease, caused by a Flavivirus with four distinct serotypes, is transmitted primarily by urban Aedes mosquito species. The infection leads to a spectrum of clinical manifestations, with the majority being asymptomatic. Primary dengue fever and, to a greater extent, a subsequent infection with a different serotype is associated with increased severity. Increased global travel and recreational tourism expose individuals naïve to the dengue viruses, the most common arboviral infections among travelers. We describe a cluster of possible primary acute dengue infections in a group of 12 individuals who presented to Bangkok Hospital for Tropical Diseases in 2017. Infection was confirmed by dengue NS1 antigen and multiplex real-time RT-PCR. Nine individuals required hospitalization, and four developed dengue warning signs. Leukocytes, neutrophils, and platelets declined towards defervescence and were negatively correlated with day of illness. Six clinical isolates were identified as dengue serotype-1, with 100% nucleotide identity suggesting that these patients were infected with the same virus.
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Cadavid Restrepo A, Furuya-Kanamori L, Mayfield H, Nilles E, Lau CL. Implications of a travel connectivity-based approach for infectious disease transmission risks in Oceania. BMJ Open 2021; 11:e046206. [PMID: 34385235 PMCID: PMC8361703 DOI: 10.1136/bmjopen-2020-046206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION The increase in international travel brought about by globalisation has enabled the rapid spread of emerging pathogens with epidemic and pandemic potential. While travel connectivity-based assessments may help understand patterns of travel network-mediated epidemics, such approaches are rarely carried out in sufficient detail for Oceania where air travel is the dominant method of transportation between countries. DESIGN Travel data from the Australian Bureau of Statistics, Stats NZ and the United Nations World Tourism Organization websites were used to calculate travel volumes in 2018 within Oceania and between Oceania and the rest of the world. The Infectious Disease Vulnerability Index (IDVI) was incorporated into the analysis as an indicator of each country's capacity to contain an outbreak. Travel networks were developed to assess the spread of infectious diseases (1) into and from Oceania, (2) within Oceania and (3) between each of the Pacific Island Countries and Territories (PICTs) and their most connected countries. RESULTS Oceania was highly connected to countries in Asia, Europe and North America. Australia, New Zealand and several PICTs were highly connected to the USA and the UK (least vulnerable countries for outbreaks based on the IDVI), and to China (intermediate low vulnerable country). High variability was also observed between the PICTs in the geographical distribution of their international connections. The PICTs with the highest number of international connections were Fiji, French Polynesia, Guam and Papua New Guinea. CONCLUSION Travel connectivity assessments may help to accurately stratify the risk of infectious disease importation and outbreaks in countries depending on disease transmission in other parts of the world. This information is essential to track future requirements for scaling up and targeting outbreak surveillance and control strategies in Oceania.
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Affiliation(s)
- Angela Cadavid Restrepo
- School of Public Health, The University of Queensland, Faculty of Medicine, Brisbane, Queensland, Australia
- Research School of Population Health, College of Health and Medicine, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Luis Furuya-Kanamori
- Research School of Population Health, College of Health and Medicine, The Australian National University, Canberra, Australian Capital Territory, Australia
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Helen Mayfield
- School of Public Health, The University of Queensland, Faculty of Medicine, Brisbane, Queensland, Australia
- Research School of Population Health, College of Health and Medicine, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eric Nilles
- Harvard Medical Shool, Harvard University, Cambridge, Massachusetts, USA
- Harvard Humanitarian Initiative, Harvard University, Cambridge, Massachusetts, USA
| | - Colleen L Lau
- School of Public Health, The University of Queensland, Faculty of Medicine, Brisbane, Queensland, Australia
- Research School of Population Health, College of Health and Medicine, The Australian National University, Canberra, Australian Capital Territory, Australia
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Berry IM, Melendrez MC, Pollett S, Figueroa K, Buddhari D, Klungthong C, Nisalak A, Panciera M, Thaisomboonsuk B, Li T, Vallard TG, Macareo L, Yoon IK, Thomas SJ, Endy T, Jarman RG. Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand. Emerg Infect Dis 2021; 27:1637-1644. [PMID: 34013878 PMCID: PMC8153871 DOI: 10.3201/eid2706.204323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dengue control approaches are best informed by granular spatial epidemiology of these viruses, yet reconstruction of inter- and intra-household transmissions is limited when analyzing case count, serologic, or genomic consensus sequence data. To determine viral spread on a finer spatial scale, we extended phylogenomic discrete trait analyses to reconstructions of house-to-house transmissions within a prospective cluster study in Kamphaeng Phet, Thailand. For additional resolution and transmission confirmation, we mapped dengue intra-host single nucleotide variants on the taxa of these time-scaled phylogenies. This approach confirmed 19 household transmissions and revealed that dengue disperses an average of 70 m per day between households in these communities. We describe an evolutionary biology framework for the resolution of dengue transmissions that cannot be differentiated based on epidemiologic and consensus genome data alone. This framework can be used as a public health tool to inform control approaches and enable precise tracing of dengue transmissions.
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Long H, Zhang C, Chen C, Tang J, Zhang B, Wang Y, Pang J, Su W, Li K, Di B, Chen YQ, Shu Y, Du X. Assessment of the global circulation and endemicity of dengue. Transbound Emerg Dis 2021; 69:2148-2155. [PMID: 34197697 DOI: 10.1111/tbed.14211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/27/2021] [Indexed: 11/30/2022]
Abstract
Dengue is a significant public health issue, affecting hundreds of millions of people worldwide. As it is spreading from tropical and subtropical zones, some regions previously recognised as non-endemic are at risk of becoming endemic. However, the global circulation of dengue is not fully understood and quantitative measurements of endemicity levels are lacking, posing an obstacle in the precise control of dengue spread. In this study, a sequence-based pipeline was designed based on random sampling to study the transmission of dengue. The limited intercontinental transmission was identified, while regional circulation of dengue was quantified in terms of importation, local circulation and exportation. Additionally, hypo- and hyper-endemic regions were identified using a new metric, with the former characterised by low local circulation and increased importation, whereas the latter by high local circulation and reduced importation. In this study, the global circulation pattern of dengue was examined and a sequence-based endemicity measurement was proposed, which will be helpful for future surveillance and targeted control of dengue.
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Affiliation(s)
- Haoyu Long
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Chi Zhang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Cai Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Jing Tang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Bing Zhang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Yinghan Wang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Jiali Pang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Biao Di
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou, China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
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Wu T, Wu Z, Li YP. Dengue fever and dengue virus in the People's Republic of China. Rev Med Virol 2021; 32:e2245. [PMID: 34235802 DOI: 10.1002/rmv.2245] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 01/05/2023]
Abstract
Infection with dengue virus (DENV) leads to symptoms variable from dengue fever to severe dengue, which has posed a huge socioeconomic and disease burden to the world population, particularly in tropical and subtropical regions. To date, four serotypes of DENV (DENV-1 to DENV-4) have been identified to sustain the transmission cycle in humans. In the past decades, dengue incidences have become more frequent, and four serotypes and various genotypes have been identified in PR China. Several large-scale dengue outbreaks and frequent local endemics occurred in the southern and coastal provinces, and the imported dengue cases accounted primarily for the initiation of the epidemics. No antiviral drug exists for dengue, and no vaccine has been approved to use in PR China, however strategies including public awareness, national reporting system of infectious diseases and public health emergencies, vector mosquito control, personal protection, and improved environmental sanitation have greatly reduced dengue prevalence. Some new technologies in vector mosquito control are emerging and being applied for dengue control. China's territory spans tropical, subtropical, and temperate climates, hence understanding the dengue status in China will be of beneficial for the global prevention and control of dengue. Here, we review the dengue status in PR China for the past decades and the strategies emerging for dengue control.
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Affiliation(s)
- Tiantian Wu
- Institute of Human Virology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yet-sen University, Guangzhou, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yet-sen University, Guangzhou, China
| | - Yi-Ping Li
- Institute of Human Virology, Zhongshan School of Medicine, Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yet-sen University, Guangzhou, China
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36
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Knerer G, Currie CSM, Brailsford SC. Reducing dengue fever cases at the lowest budget: a constrained optimization approach applied to Thailand. BMC Public Health 2021; 21:807. [PMID: 33906628 PMCID: PMC8080389 DOI: 10.1186/s12889-021-10747-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background With the challenges that dengue fever (DF) presents to healthcare systems and societies, public health officials must determine where best to allocate scarce resources and restricted budgets. Constrained optimization (CO) helps to address some of the acknowledged limitations of conventional health economic analyses and has typically been used to identify the optimal allocation of resources across interventions subject to a variety of constraints. Methods A dynamic transmission model was developed to predict the number of dengue cases in Thailand at steady state. A CO was then applied to identify the optimal combination of interventions (release of Wolbachia-infected mosquitoes and paediatric vaccination) within the constraints of a fixed budget, set no higher than cost estimates of the current vector control programme, to minimize the number of dengue cases and disability-adjusted life years (DALYs) lost. Epidemiological, cost, and effectiveness data were informed by national data and the research literature. The time horizon was 10 years. Scenario analyses examined different disease management and intervention costs, budget constraints, vaccine efficacy, and optimization time horizon. Results Under base-case budget constraints, the optimal coverage of the two interventions to minimize dengue incidence was predicted to be nearly equal (Wolbachia 50%; paediatric vaccination 49%) with corresponding coverages under lower bound (Wolbachia 54%; paediatric vaccination 10%) and upper bound (Wolbachia 67%; paediatric vaccination 100%) budget ceilings. Scenario analyses indicated that the most impactful situations related to the costs of Wolbachia and paediatric vaccination with decreases/ increases in costs of interventions demonstrating a direct correlation with coverage (increases/ decreases) of the respective control strategies under examination. Conclusions Determining the best investment strategy for dengue control requires the identification of the optimal mix of interventions to implement in order to maximize public health outcomes, often under fixed budget constraints. A CO model was developed with the objective of minimizing dengue cases (and DALYs lost) over a 10-year time horizon, within the constraints of the estimated budgets for vector control in the absence of vaccination and Wolbachia. The model provides a tool for developing estimates of optimal coverage of combined dengue control strategies that minimize dengue burden at the lowest budget. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-021-10747-3.
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Affiliation(s)
- Gerhart Knerer
- Mathematical Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - Christine S M Currie
- Mathematical Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Sally C Brailsford
- Southampton Business School, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
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Johansen IC, Castro MCD, Alves LC, Carmo RLD. Population mobility, demographic, and environmental characteristics of dengue fever epidemics in a major city in Southeastern Brazil, 2007-2015. CAD SAUDE PUBLICA 2021; 37:e00079620. [PMID: 33886707 DOI: 10.1590/0102-311x00079620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/31/2020] [Indexed: 11/22/2022] Open
Abstract
Around 14% of world dengue virus (DENV) cases occur in the Americas, most of them in Brazil. While socioeconomic, environmental, and behavioral correlates have been analyzed thoroughly, the role played by population mobility on DENV epidemics, especially at the local level, remains scarce. This study assesses whether the daily pattern of population mobility is associated with DENV incidence in Campinas, a Brazilian major city with over 1.2 million inhabitants in São Paulo State. DENV notifications from 2007 to 2015 were geocoded at street level (n = 114,884) and combined with sociodemographic and environmental data from the 2010 population census. Population mobility was extracted from the Origin-Destination Survey (ODS), carried out in 2011, and daily precipitation was obtained from satellite imagery. Multivariate zero-inflated negative binomial regression models were applied. High population mobility presented a relevant positive effect on higher risk for DENV incidence. High income and residence in apartments were found to be protective characteristics against the disease, while unpaved streets, number of strategic points (such as scrapyards and tire repair shops), and precipitation were consistently risk factors.
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Cracknell Daniels B, Gaythorpe K, Imai N, Dorigatti I. Yellow fever in Asia-a risk analysis. J Travel Med 2021; 28:taab015. [PMID: 33506250 PMCID: PMC8045179 DOI: 10.1093/jtm/taab015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND There is concern about the risk of yellow fever (YF) establishment in Asia, owing to rising numbers of urban outbreaks in endemic countries and globalisation. Following an outbreak in Angola in 2016, YF cases were introduced into China. Prior to this, YF had never been recorded in Asia, despite climatic suitability and the presence of mosquitoes. An outbreak in Asia could result in widespread fatalities and huge economic impact. Therefore, quantifying the potential risk of YF outbreaks in Asia is a public health priority. METHODS Using international flight data and YF incidence estimates from 2016, we quantified the risk of YF introduction via air travel into Asia. In locations with evidence of a competent mosquito population, the potential for autochthonous YF transmission was estimated using a temperature-dependent model of the reproduction number and a branching process model assuming a negative binomial distribution. RESULTS In total, 25 cities across Asia were estimated to be at risk of receiving at least one YF viraemic traveller during 2016. At their average temperatures, we estimated the probability of autochthonous transmission to be <50% in all cities, which was primarily due to the limited number of estimated introductions that year. CONCLUSION Despite the rise in air travel, we found low support for travel patterns between YF endemic countries and Asia resulting in autochthonous transmission during 2016. This supports the historic absence of YF in Asia and suggests it could be due to a limited number of introductions in previous years. Future increases in travel volumes or YF incidence can increase the number of introductions and the risk of autochthonous transmission. Given the high proportion of asymptomatic or mild infections and the challenges of YF surveillance, our model can be used to estimate the introduction and outbreak risk and can provide useful information to surveillance systems.
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Affiliation(s)
- Bethan Cracknell Daniels
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London
| | - Katy Gaythorpe
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London
| | - Natsuko Imai
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis; and the Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London
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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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Allicock OM, Sahadeo N, Lemey P, Auguste AJ, Suchard MA, Rambaut A, Carrington CVF. Determinants of dengue virus dispersal in the Americas. Virus Evol 2021; 6:veaa074. [PMID: 33408877 PMCID: PMC7772473 DOI: 10.1093/ve/veaa074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we utilized a statistical framework that allows for the integration of ecological, socioeconomic, and air transport mobility data as predictors of viral diffusion while inferring the phylogeographic history. Predictors describing spatial diffusion based on several covariates were compared using a generalized linear model approach, where the support for each scenario and its contribution is estimated simultaneously from the data set. Although different predictors were identified for different serotypes, our analysis suggests that overall diffusion of DENV-1, -2, and -3 in the Americas was associated with airline traffic. The other significant predictors included human population size, the geographical distance between countries and between urban centers and the density of people living in urban environments.
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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
| | - Nikita Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Philippe Lemey
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Albert J Auguste
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The Kings Buildings, Edinburgh, EH9 3FL, UK
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
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Abstract
PURPOSE OF REVIEW Societal lockdowns in response to the COVID-19 pandemic have led to unprecedented disruption to daily life across the globe. A collateral effect of these lockdowns may be a change to transmission dynamics of a wide range of infectious diseases that are all highly dependent on rates of contact between humans. With timing, duration and intensity of lockdowns varying country-to-country, the wave of lockdowns in 2020 present a unique opportunity to observe how changes in human contact rates, disease control and surveillance affect dengue virus transmission in a global natural experiment. We explore the theoretical basis for the impact of lockdowns on dengue transmission and surveillance then summarise the current evidence base from country reports. RECENT FINDINGS We find considerable variation in the intensity of dengue epidemics reported so far in 2020 with some countries experiencing historic low levels of transmission while others are seeing record outbreaks. Despite many studies warning of the risks of lockdown for dengue transmission, few empirically quantify the impact and issues such as the specific timing of the lockdowns and multi-annual cycles of dengue are not accounted for. In the few studies where such issues have been accounted for, the impact of lockdowns on dengue appears to be limited. SUMMARY Studying the impact of lockdowns on dengue transmission is important both in how we deal with the immediate COVID-19 and dengue crisis, but also over the coming years in the post-pandemic recovery period. It is clear lockdowns have had very different impacts in different settings. Further analyses might ultimately allow this unique natural experiment to provide insights into how to better control dengue that will ultimately lead to better long-term control.
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Affiliation(s)
- Oliver Brady
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Annelies Wilder-Smith
- Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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Lim JT, Han Y, Dickens BSL, Choo ELW, Chew LZX, Cook AR. Revealing two dynamic dengue epidemic clusters in Thailand. BMC Infect Dis 2020; 20:927. [PMID: 33276742 PMCID: PMC7718674 DOI: 10.1186/s12879-020-05666-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/25/2020] [Indexed: 01/14/2023] Open
Abstract
Background Thailand is home to around 69 million individuals. Dengue is hyper-endemic and all 4 serotypes are in active circulation in the country. Dengue outbreaks occur almost annually within Thailand in at least one province but the spatio-temporal and environmental interface of these outbreaks has not been studied. Methods We develop Bayesian regime switching (BRS) models to characterize outbreaks, their persistence and infer their likelihood of occurrence across time for each administrative province where dengue case counts are collected. BRS was compared against two other classification tools and their agreement is assessed. We further examine how these spatio-temporal clusters of outbreak clusters arise by comparing reported dengue case counts, urban population, urban land cover, climate and flight volumes on the province level. Results Two dynamic dengue epidemic clusters were found nationally. One cluster consists of 47 provinces and is highly outbreak prone. Provinces with a large number of case counts, urban population, urban land cover and incoming flight passengers are associated to the epidemic prone cluster of dengue. Climate has an effect on determining the probability of outbreaks over time within provinces, but have less influence on whether provinces belong to the epidemic prone cluster. BRS found high agreement with other classification tools. Conclusions Importation and urbanization drives the risk of outbreaks across regions strongly. In provinces estimated to have high epidemic persistence, more resource allocation to vector control should be applied to those localities as heightened transmission counts are likely to occur over a longer period of time. Clustering of epidemic and non-epidemic prone areas also highlights the need for prioritization of resource allocation for disease mitigation over provinces in Thailand. Supplementary Information Supplementary information accompanies this paper at 10.1186/s12879-020-05666-4.
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Affiliation(s)
- Jue Tao Lim
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore.
| | - Yiting Han
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore.,School of Pharmacy, Fudan University, Shanghai, China
| | - Borame Sue Lee Dickens
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore
| | - Esther Li Wen Choo
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Lawrence Zheng Xiong Chew
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore.,Department of Geography, Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University Health Systems, National University of Singapore, Singapore, Singapore
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Sokadjo YM, Atchadé MN. The influence of passenger air traffic on the spread of COVID-19 in the world. TRANSPORTATION RESEARCH INTERDISCIPLINARY PERSPECTIVES 2020; 8:100213. [PMID: 34173471 PMCID: PMC7833922 DOI: 10.1016/j.trip.2020.100213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 05/05/2023]
Abstract
Countries in the world are suffering from COVID-19 and would like to control it. Thus, some authorities voted for new policies and even stopped passenger air traffic. Those decisions were not uniform, and this study focuses on how passenger air traffic might influence the spread of COVID-19 in the world. We used data sets of cases from the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University and air transport (passengers carried) from the World Bank. Besides, we computed Poisson, QuasiPoisson, Negative binomial, zero-inflated Poisson, and zero-inflated negative binomial models with cross-validation to make sure that our findings are robust. Actually, when passenger air traffic increases by one unit, the number of cases increases by one new infection.
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Affiliation(s)
- Yves Morel Sokadjo
- Université d'Abomey-Calavi/International Chair in Mathematical Physics and Applications (ICMPA: UNESCO-Chair), 072 BP 50 Cotonou, Benin
| | - Mintodê Nicodème Atchadé
- National Higher School of Mathematics Genius and Modelization, National University of Sciences, Technologies, Engineering and Mathematics, Abomey, Benin
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Friedler A. Sociocultural, behavioural and political factors shaping the COVID-19 pandemic: the need for a biocultural approach to understanding pandemics and (re)emerging pathogens. Glob Public Health 2020; 16:17-35. [PMID: 33019889 DOI: 10.1080/17441692.2020.1828982] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although there has been increasing focus in recent years on interdisciplinary approaches to health and disease, and in particular the dimension of social inequalities in epidemics, infectious diseases have been much less focused on. This is especially true in the area of cultural dynamics and their effects on pathogen behaviours, although there is evidence to suggest that this relationship is central to shaping our interactions with infectious disease agents on a variety of levels. This paper makes a case for a biocultural approach to pandemics such as COVID-19. It then uses this biocultural framework to examine the anthropogenic dynamics that influenced and continue to shape the COVID-19 pandemic, both during its initial phase and during critical intersections of the pandemic. Through this understanding of biocultural interactions between people, animals and pathogens, a broader societal and political dimension is drawn as a function of population level and international cultures, to reflect on the culturally mediated differential burden of the pandemic. Ultimately, it is argued that a biocultural perspective on infectious disease pandemics will allow for critical reflection on how culture shapes our behaviours at all levels, and how the effects of these behaviours are ultimately foundational to pathogen ecology and evolution.
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Affiliation(s)
- Anna Friedler
- Département des sciences humaines et sociales, École des Hautes Études en Santé Publique - Campus de Paris, Saint-Denis, France.,l'Unité des Virus Emergents, Aix-Marseille Université, Marseille, France
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Sim S, Ng LC, Lindsay SW, Wilson AL. A greener vision for vector control: The example of the Singapore dengue control programme. PLoS Negl Trop Dis 2020; 14:e0008428. [PMID: 32853197 PMCID: PMC7451545 DOI: 10.1371/journal.pntd.0008428] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Vector-borne diseases are a major cause of morbidity and mortality worldwide. Aedes-borne diseases, in particular, including dengue, chikungunya, yellow fever, and Zika, are increasing at an alarming rate due to urbanisation, population movement, weak vector control programmes, and climate change. The World Health Organization calls for strengthening of vector control programmes in line with the Global Vector Control Response (GVCR) strategy, and many vector control programmes are transitioning to this new approach. The Singapore dengue control programme, situated within the country’s larger vision of a clean, green, and sustainable environment for the health and well-being of its citizens, provides an excellent example of the GVCR approach in action. Since establishing vector control operations in the 1960s, the Singapore dengue control programme succeeded in reducing the dengue force of infection 10-fold by the 1990s and has maintained it at low levels ever since. Key to this success is consideration of dengue as an environmental disease, with a strong focus on source reduction and other environmental management methods as the dominant vector control strategy. The programme collaborates closely with other government ministries, as well as town councils, communities, the private sector, and academic and research institutions. Community engagement programmes encourage source reduction, and house-to-house inspections accompanied by a strong legislative framework with monetary penalties help to support compliance. Strong vector and epidemiological surveillance means that routine control activities can be heightened to specifically target dengue clusters. Despite its success, the programme continues to innovate to tackle challenges such as climate change, low herd immunity, and manpower constraints. Initiatives include development of novel vector controls such as Wolbachia-infected males and spatiotemporal models for dengue risk assessment. Lessons learnt from the Singapore programme can be applied to other settings, even those less well-resourced than Singapore, for more effective vector control. Infections due to dengue and other viruses transmitted by Aedes mosquitoes are on the rise worldwide as a result of urbanisation, trade, population movement, and climate change. Contemporary vector control programmes have struggled to control Aedes-borne diseases, but the Singapore dengue control programme provides a success story. Key to the success is consideration of dengue as an environmental disease, with a corresponding focus on removal of water containers from in and around homes, solid waste management, and limited use of insecticides. The programme relies on close collaboration with other government and nongovernment actors including communities. Community engagement campaigns to ensure high awareness are supported by house-to-house inspections for mosquito habitats and a legislative framework including penalties for noncompliance. The Singapore dengue control programme provides important lessons that can be applied to other Aedes control programmes and vector control programmes more widely.
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Affiliation(s)
- Shuzhen Sim
- Environmental Health Institute, National Environment Agency, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, Singapore
| | - Steve W. Lindsay
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Anne L. Wilson
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
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Coelho MTP, Rodrigues JFM, Medina AM, Scalco P, Terribile LC, Vilela B, Diniz-Filho JAF, Dobrovolski R. Global expansion of COVID-19 pandemic is driven by population size and airport connections. PeerJ 2020. [DOI: 10.7717/peerj.9708] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport, on the rate of daily increase of COVID-19 on its exponential phase. We found that population size and global connections, represented by countries’ importance in the global air transportation network, are the main explanations for the early growth rate of COVID-19 in different countries. Climate and socioeconomics had no significant effect in this big picture analysis. Our results indicate that the current claims that the growth rate of COVID-19 may be lower in warmer and humid countries should be taken very carefully, risking to disturb well-established and effective policy of social isolation that may help to avoid higher mortality rates due to the collapse of national health systems.
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Affiliation(s)
| | | | | | - Paulo Scalco
- Faculdade de Administração, Economia, Ciências Contábeis (FACE), Universidade Federal de Goiás, Goiânia, GO, Brazil
| | | | - Bruno Vilela
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, BA, Brazil
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Shabbir W, Pilz J, Naeem A. A spatial-temporal study for the spread of dengue depending on climate factors in Pakistan (2006-2017). BMC Public Health 2020; 20:995. [PMID: 32586294 PMCID: PMC7318413 DOI: 10.1186/s12889-020-08846-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Pakistan, dengue fever has become a major concerning factor, given that it is a relatively new disease compared to malaria. The number of people affected by dengue fever has increased at least 10-fold in the last 15 years in specific areas of Pakistan. Therefore, it is necessary to analyse this disease to reduce or prevent the effects of dengue fever in the region. METHODS Geographical information system (GIS) maps are used to identify the intensity of the spread according to the count of affected people in our study area. Generalised linear modelling (GLM) is used to study the significance of factors associated with dengue fever. RESULTS The dengue virus is present throughout the year in specific areas of Pakistan. Karachi and Lahore are most significantly affected with cases in these two most populous cities of Pakistan reported every year. In the study period (2006-2017), 2011 was the most devastating year for Pakistan. Lahore recorded more than 17,000 confirmed cases with 290 deaths in a single year. The GLM analysis shows rainfall, the average maximum temperature, and hospitals to be significant factors in the prevalence of dengue fever. CONCLUSION This study finds that Sindh and Khyber Pakhtunkhwa are two of the primarily vulnerable provinces for the spread of dengue fever. Punjab has observed sporadic increases in dengue fever cases. In Pakistan, dengue cases increase in the rainfall season, especially during monsoon season. Lack of proper hospitals and clinics are another major factor, and mobile hospitals are needed in remote hotspot regions often affected by dengue fever. Finally, improved sanitation systems in metropoles would facilitate reducing breeding grounds for Aedes Aegypti larvae.
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Affiliation(s)
- Waqas Shabbir
- Institute of Statistics, Alpen Adria University of Klagenfurt, University Street 65-67, Klagenfurt, 9020, Carinthia, Austria.
| | - Juergen Pilz
- Institute of Statistics, Alpen Adria University of Klagenfurt, University Street 65-67, Klagenfurt, 9020, Carinthia, Austria
| | - Amna Naeem
- Quaid-i-Azam University, Islamabad, 45000, Pakistan
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Salami D, Sousa CA, Martins MDRO, Capinha C. Predicting dengue importation into Europe, using machine learning and model-agnostic methods. Sci Rep 2020; 10:9689. [PMID: 32546771 PMCID: PMC7298036 DOI: 10.1038/s41598-020-66650-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/21/2020] [Indexed: 01/28/2023] Open
Abstract
The geographical spread of dengue is a global public health concern. This is largely mediated by the importation of dengue from endemic to non-endemic areas via the increasing connectivity of the global air transport network. The dynamic nature and intrinsic heterogeneity of the air transport network make it challenging to predict dengue importation. Here, we explore the capabilities of state-of-the-art machine learning algorithms to predict dengue importation. We trained four machine learning classifiers algorithms, using a 6-year historical dengue importation data for 21 countries in Europe and connectivity indices mediating importation and air transport network centrality measures. Predictive performance for the classifiers was evaluated using the area under the receiving operating characteristic curve, sensitivity, and specificity measures. Finally, we applied practical model-agnostic methods, to provide an in-depth explanation of our optimal model's predictions on a global and local scale. Our best performing model achieved high predictive accuracy, with an area under the receiver operating characteristic score of 0.94 and a maximized sensitivity score of 0.88. The predictor variables identified as most important were the source country's dengue incidence rate, population size, and volume of air passengers. Network centrality measures, describing the positioning of European countries within the air travel network, were also influential to the predictions. We demonstrated the high predictive performance of a machine learning model in predicting dengue importation and the utility of the model-agnostic methods to offer a comprehensive understanding of the reasons behind the predictions. Similar approaches can be utilized in the development of an operational early warning surveillance system for dengue importation.
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Affiliation(s)
- Donald Salami
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Global Health and Tropical Medicine, Lisbon, 1349-008, Portugal.
| | - Carla Alexandra Sousa
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Global Health and Tropical Medicine, Lisbon, 1349-008, Portugal.
| | - Maria do Rosário Oliveira Martins
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Global Health and Tropical Medicine, Lisbon, 1349-008, Portugal
| | - César Capinha
- Centro de Estudos Geográficos, Instituto de Geografia e Ordenamento do Território - IGOT, Universidade de Lisboa, 1600-276, Lisboa, Portugal.
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de Jesus JG, Dutra KR, Sales FCDS, Claro IM, Terzian AC, Candido DDS, Hill SC, Thézé J, Torres C, D'Agostini TL, Felix AC, Reis AFN, Alcantara LCJ, de Abreu AL, Croda JH, de Oliveira WK, de Filipis AMB, Camis MDCRDS, Romano CM. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019. Mem Inst Oswaldo Cruz 2020; 115:e190423. [PMID: 32428189 PMCID: PMC7227788 DOI: 10.1590/0074-02760190423] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 04/06/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Despite efforts to mitigate the impact of dengue virus (DENV) epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo State in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES To understand the origin and dynamics of the 2019 DENV outbreak. METHODS Here using portable nanopore sequencing we generated20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of São Paulo State, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.
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Affiliation(s)
| | - Karina Rocha Dutra
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | | | - Ingra Morales Claro
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Carolina Terzian
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | | | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Celeste Torres
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Tatiana Lang D'Agostini
- Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica Professor Alexandre Vranjac, Secretaria de Estado da Saúde, São Paulo, SP, Brasil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - André L de Abreu
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Júlio Hr Croda
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Wanderson K de Oliveira
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Ana Maria Bispo de Filipis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Camila Malta Romano
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
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Darcy AW, Kanda S, Dalipanda T, Joshua C, Shimono T, Lamaningao P, Mishima N, Nishiyama T. Multiple arboviral infections during a DENV-2 outbreak in Solomon Islands. Trop Med Health 2020; 48:33. [PMID: 32435149 PMCID: PMC7225641 DOI: 10.1186/s41182-020-00217-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022] Open
Abstract
Background Solomon Islands, a country made up of tropical islands, has suffered cyclic dengue fever (DF) outbreaks in the past three decades. An outbreak of dengue-like illness (DLI) that occurred in April 2016 prompted this study, which aimed to determine the population’s immunity status and identify the arboviruses circulating in the country. Methods A household survey, involving 188 participants in two urban areas (Honiara and Gizo), and a parallel hospital-based clinical survey were conducted in April 2016. The latter was repeated in December after a surge in DLI cases. Arbovirus IgG ELISA were performed on the household blood samples to determine the prevalence of arboviruses in the community, while qPCR testing of the clinical samples was used to identify the circulating arboviruses. Dengue virus (DENV)-positive samples were further characterized by amplifying and sequencing the envelope gene. Results The overall prevalence rates of DENV, Zika virus, and chikungunya virus were 83.4%, 7.6%, and 0.9%, respectively. The qPCR positivity rates of the clinical samples collected in April 2016 were as follows: DENV 39.6%, Zika virus 16.7%, and chikungunya virus 6.3%, which increased to 74%, 48%, and 20% respectively in December 2016. The displacement of the circulating serotype-3, genotype-1, with DENV serotype 2, genotype cosmopolitan was responsible for the outbreak in 2016. Conclusions A DENV outbreak in Solomon Islands was caused by the introduction of a single serotype. The high prevalence of DENV provided transient cross-protection, which prevented the introduction of a new serotype from the hyperendemic region for at least 3 years. The severe outcomes seen in the recent outbreak probably resulted from changes in the causative viruses and the effects of population immunity and changes in the outbreak pattern. Solomon Islands needs to step up surveillance to include molecular tools, increase regional communication, and perform timely interventions.
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