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Pereira SB, Dos Reis Gomes A, Morais MHF, Bohm BC, Waller SB, de Faria RO, Bruhn NCP, Bruhn FRP. Profile and temporal dynamics of the feline sporotrichosis epidemic in southern Brazil: A forecasting analysis. Vet Parasitol Reg Stud Reports 2024; 54:101091. [PMID: 39237234 DOI: 10.1016/j.vprsr.2024.101091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 09/07/2024]
Abstract
A detailed clinical-epidemiological analysis of feline sporotrichosis was conducted, and 288 cases reported between the years 2007 and 2018 were analyzed. The studied cases primarily involved mongrel cats (240/260), males (212/282), and adults (121/200). The main objectives were to identify the risk factors, calculate the monthly incidence rates, and establish a predictive model using the seasonal autoregressive integrated moving average (SARIMA) approach. The statistical analysis revealed significant associations (p < 0.05) between prolonged lesion evolution times and factors such as respiratory signs, prior treatments, and lesion contact. Empirical treatment was identified as a significant risk factor for disease progression. Moreover, the number of cases demonstrated an increasing trend over the study period, with annual peaks noted in disease incidence. The SARIMA model proved to be an effective tool for forecasting the incidence of sporotrichosis, offering robust support for epidemiological surveillance and facilitating targeted public health interventions in endemic regions. The predictive accuracy of the developed model underscored its utility in enhancing disease monitoring and supporting proactive health measures for the effective management of sporotrichosis.
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Affiliation(s)
- Sergiane Baes Pereira
- Preventive Veterinary Department, Zoonoses Control Center (UFPel), Federal University of Pelotas, Pelotas, Brazil
| | - Angelita Dos Reis Gomes
- Center of Diagnostic and Research of Veterinary Mycology, Universidade Federal de Pelotas, Pelotas/RS, Brazil
| | | | - Bianca Conrad Bohm
- Preventive Veterinary Department, Zoonoses Control Center (UFPel), Federal University of Pelotas, Pelotas, Brazil.
| | - Stefanie Bressan Waller
- Center of Diagnostic and Research of Veterinary Mycology, Universidade Federal de Pelotas, Pelotas/RS, Brazil
| | - Renata Osório de Faria
- Preventive Veterinary Department, Zoonoses Control Center (UFPel), Federal University of Pelotas, Pelotas, Brazil
| | | | - Fabio Raphael Pascoti Bruhn
- Preventive Veterinary Department, Zoonoses Control Center (UFPel), Federal University of Pelotas, Pelotas, Brazil
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2
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Martínez D, Gómez M, Hernández C, Campo-Palacio S, González-Robayo M, Montilla M, Pavas-Escobar N, Tovar-Acero C, Geovo-Arias L, Valencia-Urrutia E, Córdoba-Renteria N, Carrillo-Hernandez MY, Ruiz-Saenz J, Martinez-Gutierrez M, Paniz-Mondolfi A, Patiño LH, Muñoz M, Ramírez JD. Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia. Virus Evol 2024; 10:veae068. [PMID: 39347444 PMCID: PMC11429525 DOI: 10.1093/ve/veae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/03/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024] Open
Abstract
Dengue fever remains as a public health challenge in Colombia, standing as the most prevalent infectious disease in the country. The cyclic nature of dengue epidemics, occurring approximately every 3 years, is intricately linked to meteorological events like El Niño Southern Oscillation (ENSO). Therefore, the Colombian system faces challenges in genomic surveillance. This study aimed to evaluate local dengue virus (DENV) transmission and genetic diversity in four Colombian departments with heterogeneous incidence patterns (department is first-level territorial units in Colombia). For this study, we processed 266 serum samples to identify DENV. Subsequently, we obtained 118 genome sequences by sequencing DENV genomes from serum samples of 134 patients infected with DENV-1 and DENV-2 serotypes. The predominant serotype was DENV-2 (108/143), with the Asian-American (AA) genotype (91/118) being the most prevalent one. Phylogenetic analysis revealed concurrent circulation of two lineages of both DENV-2 AA and DENV-1 V, suggesting ongoing genetic exchange with sequences from Venezuela and Cuba. The continuous migration of Venezuelan citizens into Colombia can contribute to this exchange, emphasizing the need for strengthened prevention measures in border areas. Notably, the time to most recent common ancestor analysis identified cryptic transmission of DENV-2 AA since approximately 2015, leading to the recent epidemic. This challenges the notion that major outbreaks are solely triggered by recent virus introductions, emphasizing the importance of active genomic surveillance. The study also highlighted the contrasting selection pressures on DENV-1 V and DENV-2 AA, with the latter experiencing positive selection, possibly influencing its transmissibility. The presence of a cosmopolitan genotype in Colombia, previously reported in Brazil and Peru, raises concerns about transmission routes, emphasizing the necessity for thorough DENV evolution studies. Despite limitations, the study underscores genomic epidemiology's crucial role in early detection and comprehension of DENV genotypes, recommending the use of advanced sequencing techniques as an early warning system to help prevent and control dengue outbreaks in Colombia and worldwide.
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Affiliation(s)
- David Martínez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Carolina Hernández
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sandra Campo-Palacio
- Laboratorio de Salud Pública, Secretaría de Salud Departamental Meta, Villavicencio, Colombia
| | - Marina González-Robayo
- Laboratorio de Salud Pública, Secretaría de Salud Departamental Meta, Villavicencio, Colombia
| | - Marcela Montilla
- Laboratorio de Salud Pública, Secretaría de Salud Departamental Meta, Villavicencio, Colombia
- Universidad Cooperativa de Colombia, Villavicencio, Colombia
| | - Norma Pavas-Escobar
- Laboratorio de Salud Pública, Secretaría de Salud Departamental Meta, Villavicencio, Colombia
- Universidad Cooperativa de Colombia, Villavicencio, Colombia
| | - Catalina Tovar-Acero
- Grupo de Enfermedades Tropicales y Resistencia Bacteriana, Universidad del Sinú, Montería, Córdoba, Colombia
| | - Lillys Geovo-Arias
- Secretaria de Salud departamental Chocó-Laboratorio de Salud Pública, Chocó, Colombia
| | | | | | - Marlen Y Carrillo-Hernandez
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, Colombia
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
| | - Marlen Martinez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Instituto de Biotecnología-UN (IBUN), Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Lagrave A, Enfissi A, Tirera S, Demar MP, Jaonasoa J, Carod JF, Ramavoson T, Succo T, Carvalho L, Devos S, Dorleans F, Leon L, Berlioz-Arthaud A, Musso D, Lavergne A, Rousset D. Re-Emergence of DENV-3 in French Guiana: Retrospective Analysis of Cases That Circulated in the French Territories of the Americas from the 2000s to the 2023-2024 Outbreak. Viruses 2024; 16:1298. [PMID: 39205272 PMCID: PMC11360160 DOI: 10.3390/v16081298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/04/2024] Open
Abstract
French Guiana experienced an unprecedented dengue epidemic during 2023-2024. Prior to the 2023-2024 outbreak in French Guiana, DENV-3 had not circulated in an epidemic manner since 2005. We therefore studied retrospectively the strains circulating in the French Territories of the Americas (FTA)-French Guiana, Guadeloupe, and Martinique-from the 2000s to the current epidemic. To this end, DENV-3 samples from the collection of the National Reference Center for Arboviruses in French Guiana (NRCA-FG) were selected and sequenced using next-generation sequencing (NGS) based on Oxford Nanopore Technologies, ONT. Phylogenetic analysis showed that (i) the 97 FTA sequences obtained all belonged to genotype III (GIII); (ii) between the 2000s and 2013, the regional circulation of the GIII American-I lineage was the source of the FTA cases through local extinctions and re-introductions; (iii) multiple introductions of lineages of Asian origin appear to be the source of the 2019-2021 epidemic in Martinique and the 2023-2024 epidemic in French Guiana. Genomic surveillance is a key factor in identifying circulating DENV genotypes, monitoring strain evolution, and identifying import events.
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Affiliation(s)
- Alisé Lagrave
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Antoine Enfissi
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Sourakhata Tirera
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Magalie Pierre Demar
- Laboratoire Centre Hospitalier de Cayenne, Cayenne 97300, French Guiana; (M.P.D.); (J.J.)
| | - Jean Jaonasoa
- Laboratoire Centre Hospitalier de Cayenne, Cayenne 97300, French Guiana; (M.P.D.); (J.J.)
| | - Jean-François Carod
- Department of Biology, West French Guiana Hospital Center, Saint-Laurent-du-Maroni 97320, French Guiana; (J.-F.C.); (T.R.)
| | - Tsiriniaina Ramavoson
- Department of Biology, West French Guiana Hospital Center, Saint-Laurent-du-Maroni 97320, French Guiana; (J.-F.C.); (T.R.)
| | - Tiphanie Succo
- Santé Publique France, Cellule Guyane, Cayenne 97300, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Luisiane Carvalho
- Santé Publique France, Cellule Guyane, Cayenne 97300, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Sophie Devos
- Santé Publique France, Cellule Guyane, Cayenne 97300, French Guiana; (T.S.); (L.C.); (S.D.)
| | - Frédérique Dorleans
- Santé Publique France, Cellule Antilles, French Caribbean Islands; (F.D.); (L.L.)
| | - Lucie Leon
- Santé Publique France, Cellule Antilles, French Caribbean Islands; (F.D.); (L.L.)
| | | | - Didier Musso
- Laboratoires Eurofins Guyane, French Guiana; (A.B.-A.); (D.M.)
| | - Anne Lavergne
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
| | - Dominique Rousset
- Arbovirus National Reference Center, Virology Unit, Institut Pasteur de la Guyane, Cayenne 97300, French Guiana; (A.L.); (A.E.); (S.T.); (A.L.)
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4
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Phadungsombat J, Nakayama EE, Shioda T. Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses 2024; 16:1046. [PMID: 39066210 PMCID: PMC11281397 DOI: 10.3390/v16071046] [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: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics.
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Affiliation(s)
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (J.P.); (E.E.N.)
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5
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Ou G, Liu J, Zou R, Gu Y, Niu S, Yin J, Yuan J, Qu Z, Yang Y, Liu Y. The dynamic molecular characteristics of neutrophils are associated with disease progression in dengue patients. J Med Virol 2024; 96:e29729. [PMID: 38860590 DOI: 10.1002/jmv.29729] [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: 03/26/2024] [Revised: 05/26/2024] [Accepted: 06/01/2024] [Indexed: 06/12/2024]
Abstract
Dengue, the most prevalent mosquito-borne disease worldwide, poses a significant health burden. This study integrates clinical data and transcriptomic datasets from different phases of dengue to investigate distinctive and shared cellular and molecular features. Clinical data from 29 dengue patients were collected and analyzed alongside a public transcriptomic data set (GSE28405) to perform differential gene expression analysis, functional enrichment, immune landscape assessment, and development of machine learning model. Neutropenia was observed in 54.79% of dengue patients, particularly during the defervescence phase (65.79%) in clinical cohorts. Bioinformatics analyses corroborated a significant reduction in neutrophil immune infiltration in dengue patients. Receiver operating characteristic curve analysis demonstrated that dynamic changes in neutrophil infiltration levels could predict disease progression, especially during the defervescence phase, with the area under the curve of 0.96. Three neutrophil-associated biomarkers-DHRS12, Transforming growth factor alpha, and ZDHHC19-were identified as promising for diagnosing and predicting dengue progression. In addition, the activation of neutrophil extracellular traps was significantly enhanced and linked to FcγR-mediated signaling pathways and Toll-like receptor signaling pathways. Neutrophil activation and depletion play a critical role in dengue's immune response. The identified biomarkers and their associated pathways offer potential for improved diagnosis and understanding of dengue pathogenesis and progression.
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Affiliation(s)
- Guanyong Ou
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jiexiang Liu
- Shenzhen Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Rongrong Zou
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Yuchen Gu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Shiyu Niu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Juzhen Yin
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Zhijun Qu
- Longgang Central Hospital of Shenzhen, Guangdong, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
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6
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Fraenkel S, Nabeshima T, Xayavong D, Nguyen TTN, Xu Q, Kapandji M, Yamao K, Balingit JC, Pandey BD, Morita K, Hasebe F, Ngwe Tun MM, Takamatsu Y. The Development of New Primer Sets for the Amplification and Sequencing of the Envelope Gene of All Dengue Virus Serotypes. Microorganisms 2024; 12:1092. [PMID: 38930474 PMCID: PMC11205395 DOI: 10.3390/microorganisms12061092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Dengue virus (DENV) poses a significant threat to global health, infecting approximately 390 million people annually. This virus comprises four serotypes capable of causing severe disease. Genetic analyses are crucial for understanding the epidemiology, evolution, and spread of DENV. Although previous studies have focused on the envelope protein-coding (E) gene, only a few primers can efficiently detect and amplify the viral genes from multiple endemic countries simultaneously. In this study, we designed degenerate primer pairs for each DENV serotype to amplify and sequence the entire E gene, using globally representative sequences for each serotype. These primers were validated using DENV isolates from various Asian countries and demonstrated broad-spectrum detection capabilities and high-quality sequences. The primers provide effective tools for genetic analysis in the regions affected by dengue, aiding strain identification and epidemiological studies during outbreaks.
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Affiliation(s)
- Stefania Fraenkel
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- School of Tropical Medicine and Global Health (TMGH), Nagasaki University, Nagasaki 852-8523, Japan
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Kenya Research Station, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan
| | - Dalouny Xayavong
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Thi Thanh Ngan Nguyen
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Qiang Xu
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Merveille Kapandji
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Kano Yamao
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Dental School, Nagasaki University, Nagasaki 852-8588, Japan
| | - Jean Claude Balingit
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
| | - Basu Dev Pandey
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
- Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 690-8504, Japan
| | - Futoshi Hasebe
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Vietnam Research Station, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan
| | - Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
- Center for Vaccines and Therapeutic Antibodies for Emerging Infectious Diseases, Shimane University, Izumo 690-8504, Japan
| | - Yuki Takamatsu
- Department of Virology, Institute of Tropical Medicine (ITM-NU), Nagasaki University, Nagasaki 852-8523, Japan; (S.F.); (T.N.); (D.X.); (T.T.N.N.); (Q.X.); (M.K.); (K.Y.); (J.C.B.); (B.D.P.); (K.M.); (F.H.); (M.M.N.T.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- DEJIMA Infectious Disease Research Alliance, Nagasaki University, Nagasaki 852-8523, Japan
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da Consolação Magalhães Cunha M, Conrad Bohm B, Morais MHF, Dias Campos NB, Schultes OL, Pereira Campos Bruhn N, Pascoti Bruhn FR, Caiaffa WT. Temporal trends of dengue cases and deaths from 2007 to 2020 in Belo Horizonte, Brazil. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:2248-2263. [PMID: 37485862 DOI: 10.1080/09603123.2023.2237420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
Dengue, a disease with multifactorial determinants, is linked to population susceptibility to circulating viruses and the extent of vector infestation. This study aimed to analyze the temporal trends of dengue cases and deaths in Belo Horizonte, Minas Gerais, Brazil, from 2007 to 2020. Data from the Notifiable Diseases Information System (Sinan) were utilized for the investigation. To assess the disease's progression over the study period and predict its future incidence, time series analyses were conducted using a generalized additive model (GAM) and a seasonal autoregressive integrated moving average (SARIMA) model. Over the study period, a total of 463,566 dengue cases and 125 deaths were reported. Notably, there was an increase in severe cases and deaths, marking hyperendemics characterized by simultaneous virus circulation (79.17% in 2016-50% in 2019). The generalized additive model revealed a non-linear pattern with epidemic peaks in 2010, 2013, 2016, and 2019, indicating an explosive pattern of dengue incidence. The SARIMA (3,1,1) (0,0,0)12 model was validated for each year (2015 to 2019). Comparing the actual and predicted numbers of dengue cases, the model demonstrated its effectiveness for predicting cases in the municipality. The rising number of dengue cases emphasizes the importance of vector surveillance and control. Enhanced models and predictions by local health services will aid in anticipating necessary control measures to combat future epidemics.
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Affiliation(s)
| | - Bianca Conrad Bohm
- Veterinary Epidemiology Laboratory, Preventive Veterinary Department, Federal University of Pelotas (UFPel), Pelotas, Brazil
| | | | - Natalia Bruna Dias Campos
- Urban Health Observatory - Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Olivia Lang Schultes
- Urban Health Observatory - Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Fabio Raphael Pascoti Bruhn
- Veterinary Epidemiology Laboratory, Preventive Veterinary Department, Federal University of Pelotas (UFPel), Pelotas, Brazil
| | - Waleska Teixeira Caiaffa
- Urban Health Observatory - Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
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8
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Frumence E, Wilkinson DA, Klitting R, Vincent M, Mnemosyme N, Grard G, Traversier N, Li-Pat-Yuen G, Heaugwane D, Souply L, Giry C, Paty MC, Collet L, Gérardin P, Thouillot F, De Lamballerie X, Jaffar-Bandjee MC. Dynamics of emergence and genetic diversity of dengue virus in Reunion Island from 2012 to 2022. PLoS Negl Trop Dis 2024; 18:e0012184. [PMID: 38768248 PMCID: PMC11142707 DOI: 10.1371/journal.pntd.0012184] [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: 11/13/2023] [Revised: 05/31/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Dengue is a major public health concern in Reunion Island, marked by recurrent epidemics, including successive outbreaks of dengue virus serotypes 1 and 2 (DENV1 and DENV2) with over 70,000 cases confirmed since 2017. METHODOLOGY/PRINCIPAL FINDINGS In this study, we used Oxford Nanopore NGS technology for sequencing virologically-confirmed samples and clinical isolates collected between 2012 and 2022 to investigate the molecular epidemiology and evolution of DENV in Reunion Island. Here, we generated and analyzed a total of 499 DENV1, 360 DENV2, and 18 DENV3 sequences. By phylogenetic analysis, we show that different genotypes and variants of DENV have circulated in the past decade that likely originated from Seychelles, Mayotte and Southeast Asia and highly affected areas in Asia and Africa. CONCLUSIONS/SIGNIFICANCE DENV sequences from Reunion Island exhibit a high genetic diversity which suggests regular introductions of new viral lineages from various Indian Ocean islands. The insights from our phylogenetic analysis may inform local health authorities about the endemicity of DENV variants circulating in Reunion Island and may improve dengue management and surveillance. This work emphasizes the importance of strong local coordination and collaboration to inform public health stakeholders in Reunion Island, neighboring areas, and mainland France.
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Affiliation(s)
- Etienne Frumence
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - David A. Wilkinson
- UMR ASTRE, CIRAD, INRAE, Université de Montpellier, Plateforme technologique CYROI, Sainte-Clotilde, Réunion, France
| | - Raphaelle Klitting
- Unité des Virus Émergents (UVE), Aix-Marseille Univ, IRD 190, INSERM 1207, Marseille, France
- CNR des Arbovirus, Marseille, France
| | | | - Nicolas Mnemosyme
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | | | - Nicolas Traversier
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Ghislaine Li-Pat-Yuen
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Diana Heaugwane
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Laurent Souply
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | - Claude Giry
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
| | | | | | | | - Patrick Gérardin
- INSERM CIC 1410, CHU de la Réunion, Saint-Pierre, Réunion, France
| | | | - Xavier De Lamballerie
- Unité des Virus Émergents (UVE), Aix-Marseille Univ, IRD 190, INSERM 1207, Marseille, France
- CNR des Arbovirus, Marseille, France
| | - Marie-Christine Jaffar-Bandjee
- Centre National de Référence Arbovirus Associé, CHU de la Réunion Site Nord, Saint-Denis, Réunion, France
- Laboratoire de microbiologie, CHU de la Réunion-Site Nord, Saint-Denis, Réunion, France
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9
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Rojas A, Shen J, Cardozo F, Bernal C, Caballero O, Ping S, Key A, Haider A, de Guillén Y, Langjahr P, Acosta ME, Aria L, Mendoza L, Páez M, Von-Horoch M, Luraschi P, Cabral S, Sánchez MC, Torres A, Pinsky BA, Piantadosi A, Waggoner JJ. Characterization of Dengue Virus 4 Cases in Paraguay, 2019-2020. Viruses 2024; 16:181. [PMID: 38399957 PMCID: PMC10892180 DOI: 10.3390/v16020181] [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: 10/26/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
In 2019-2020, dengue virus (DENV) type 4 emerged to cause the largest DENV outbreak in Paraguay's history. This study sought to characterize dengue relative to other acute illness cases and use phylogenetic analysis to understand the outbreak's origin. Individuals with an acute illness (≤7 days) were enrolled and tested for DENV nonstructural protein 1 (NS1) and viral RNA by real-time RT-PCR. Near-complete genome sequences were obtained from 62 DENV-4 positive samples. From January 2019 to March 2020, 799 participants were enrolled: 253 dengue (14 severe dengue, 5.5%) and 546 other acute illness cases. DENV-4 was detected in 238 dengue cases (94.1%). NS1 detection by rapid test was 52.5% sensitive (53/101) and 96.5% specific (387/401) for dengue compared to rRT-PCR. DENV-4 sequences were grouped into two clades within genotype II. No clustering was observed based on dengue severity, location, or date. Sequences obtained here were most closely related to 2018 DENV-4 sequences from Paraguay, followed by a 2013 sequence from southern Brazil. DENV-4 can result in large outbreaks, including severe cases, and is poorly detected with available rapid diagnostics. Outbreak strains seem to have been circulating in Paraguay and Brazil prior to 2018, highlighting the importance of sustained DENV genomic surveillance.
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Affiliation(s)
- Alejandra Rojas
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - John Shen
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - Fátima Cardozo
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
- Departamento de Laboratorio de Análisis Clínicos, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.C.S.); (A.T.)
| | - Cynthia Bernal
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Oliver Caballero
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Sara Ping
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
| | - Autum Key
- Department of Pathology, Emory University, Atlanta, GA 30322, USA;
| | - Ali Haider
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
| | - Yvalena de Guillén
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Patricia Langjahr
- Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo 111421, Paraguay;
| | - Maria Eugenia Acosta
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Laura Aria
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Laura Mendoza
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Malvina Páez
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Marta Von-Horoch
- Departamento de Epidemiología, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.V.-H.); (P.L.); (S.C.)
| | - Patricia Luraschi
- Departamento de Epidemiología, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.V.-H.); (P.L.); (S.C.)
| | - Sandra Cabral
- Departamento de Epidemiología, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.V.-H.); (P.L.); (S.C.)
| | - María Cecilia Sánchez
- Departamento de Laboratorio de Análisis Clínicos, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.C.S.); (A.T.)
| | - Aurelia Torres
- Departamento de Laboratorio de Análisis Clínicos, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.C.S.); (A.T.)
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anne Piantadosi
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
- Department of Pathology, Emory University, Atlanta, GA 30322, USA;
| | - Jesse J. Waggoner
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
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10
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Martínez D, Gómez M, Hernández C, Muñoz M, Campo-Palacio S, González-Robayo M, Montilla M, Pavas-Escobar N, Ramírez JD. Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Colombia. Emerg Infect Dis 2024; 30:189-192. [PMID: 38086397 PMCID: PMC10756373 DOI: 10.3201/eid3001.230972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Using Oxford Nanopore technologies and phylogenetic analyses, we sequenced and identified the cosmopolitan genotype of dengue virus serotype 2 isolated from 2 patients in the city of Villavicencio, Meta department, Colombia. This identification suggests the emergence of this genotype in the country, which warrants further surveillance to identify its epidemic potential.
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11
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Nii-Trebi NI, Mughogho TS, Abdulai A, Tetteh F, Ofosu PM, Osei MM, Yalley AK. Dynamics of viral disease outbreaks: A hundred years (1918/19-2019/20) in retrospect - Loses, lessons and emerging issues. Rev Med Virol 2023; 33:e2475. [PMID: 37602770 DOI: 10.1002/rmv.2475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
Infectious diseases continue to be the leading cause of morbidity and mortality, and a formidable obstacle to the development and well-being of people worldwide. Viruses account for more than half of infectious disease outbreaks that have plagued the world. The past century (1918/19-2019/20) has witnessed some of the worst viral disease outbreaks the world has recorded, with overwhelming impact especially in low- and middle-income countries (LMIC). The frequency of viral disease outbreak appears to be increasing. Generally, although infectious diseases have afflicted the world for centuries and humankind has had opportunities to examine the nature of their emergence and mode of spread, almost every new outbreak poses a formidable challenge to humankind, beating the existing pandemic preparedness systems, if any, and causing significant losses. These underscore inadequacy in our understanding of the dynamics and preparedness against viral disease outbreaks that lead to epidemics and pandemics. Despite these challenges, the past 100 years of increasing frequencies of viral disease outbreaks have engendered significant improvements in response to epidemics and pandemics, and offered lessons to inform preparedness. Hence, the increasing frequency of emergence of viral outbreaks and the challenges these outbreaks pose to humankind, call for the continued search for effective ways to tackle viral disease outbreaks in real time. Through a PRISMA-based approach, this systematic review examines the outbreak of viral diseases in retrospect to decipher the outbreak patterns, losses inflicted on humanity and highlights lessons these offer for meaningful preparation against future viral disease outbreaks and pandemics.
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Affiliation(s)
- Nicholas I Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | | | - Anisa Abdulai
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Francis Tetteh
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Priscilla M Ofosu
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Mary-Magdalene Osei
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | - Akua K Yalley
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
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12
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Phadungsombat J, Vu HTT, Nguyen QT, Nguyen HTV, Nguyen HTN, Dang BT, Nakayama EE, Ishizaki A, Ichimura H, Shioda T, Pham TN. Molecular Characterization of Dengue Virus Strains from the 2019-2020 Epidemic in Hanoi, Vietnam. Microorganisms 2023; 11:1267. [PMID: 37317240 DOI: 10.3390/microorganisms11051267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Dengue virus (DENV), which has circulated in Vietnam for several decades, has multiple serotypes and genotypes. A 2019 dengue outbreak resulted in a larger number of cases than any other outbreak. We conducted a molecular characterization using samples collected in 2019-2020 from dengue patients in Hanoi and nearby cities located in northern Vietnam. The circulating serotypes were DENV-1 (25%, n = 22) and DENV-2 (73%, n = 64). Phylogenetic analyses revealed that all DENV-1 (n = 13) were genotype I and clustered to local strains circulating during the previous outbreak in the 2017, whereas DENV-2 consisted of two genotypes: Asian-I (n = 5), related to local strains from 2006-2022, and cosmopolitan (n = 18), the predominant genotype in this epidemic. The current cosmopolitan virus was identified as having an Asian-Pacific lineage. The virus was closely related to strains in other recent outbreaks in Southeast Asian countries and China. Multiple introductions occurred in 2016-2017, which were possibly from maritime Southeast Asia (Indonesia, Singapore, and Malaysia), mainland Southeast Asia (Cambodia and Thailand), or China, rather than from an expansion of localized Vietnamese cosmopolitan strains that were previously detected in the 2000s. We also analyzed the genetic relationship between Vietnam's cosmopolitan strain and recent global strains reported from Asia, Oceania, Africa, and South America. This analysis revealed that viruses of Asian-Pacific lineage are not restricted to Asia but have spread to Peru and Brazil in South America.
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Affiliation(s)
- Juthamas Phadungsombat
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | | | - Quynh Thi Nguyen
- Department of Viral infection and International Health, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
| | | | | | - Bich Thi Dang
- National Hospital for Tropical Disease, Hanoi 100000, Vietnam
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Azumi Ishizaki
- Department of Viral infection and International Health, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
| | - Hiroshi Ichimura
- Department of Viral infection and International Health, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8640, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Thach Ngoc Pham
- National Hospital for Tropical Disease, Hanoi 100000, Vietnam
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13
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Association of Dengue Virus Serotypes 1&2 with Severe Dengue Having Deletions in Their 3′Untranslated Regions (3′UTRs). Microorganisms 2023; 11:microorganisms11030666. [PMID: 36985238 PMCID: PMC10057630 DOI: 10.3390/microorganisms11030666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
Dengue virus infections are recorded as hyper-endemic in many countries, including India. Research pertaining to the reasons for frequent outbreaks and severe dengue is ongoing. Hyderabad city, India, has been recorded as a ‘hotspot’ for dengue virus infections. Dengue virus strains circulating over the past few years in Hyderabad city have been characterized at the molecular level to analyze the serotype/genotypes; 3′UTRs were further amplified and sequenced. The disease severity in patients infected with dengue virus strains with complete and 3′UTR deletion mutants was analyzed. Genotype I of the serotype 1 replaced genotype III, which has been circulating over the past few years in this region. Coincidentally, the number of dengue virus infections significantly increased in this region during the study period. Nucleotide sequence analysis suggested twenty-two and eight nucleotide deletions in the 3′UTR of DENV-1. The eight nucleotide deletions observed in the case of DENV-1 3′UTR were the first reported in this instance. A 50 nucleotide deletion was identified in the case of the serotype DENV-2. Importantly, these deletion mutants were found to cause severe dengue, even though they were found to be replication incompetent. This study emphasized the role of dengue virus 3′UTRs on severe dengue and emerging outbreaks.
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14
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Zhu X, Jiang Y, Zhang H, Li C, Xing D, Guo X, Zhao T. An alternating transmission model between mice and mosquitoes for genetic study of dengue virus. Acta Trop 2023; 239:106834. [PMID: 36646237 DOI: 10.1016/j.actatropica.2023.106834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023]
Abstract
Rapidly increased incidence and prevalence of dengue virus serotype 2 (DENV-2) in recent decades highlight the need for better understanding of the selective pressures that drive genetic and phenotypic changes in this virus. We simulated the transfer of DENV-2 between human hosts and mosquito vectors by horizontally transmitting the virus between suckling mice and Aedes aegypti (Linnaeus, Diptera: Culicidae). A total of 3 cycles of alternating transmission were performed and 3 passages of virus population were harvested from the infected sucking mice. The viral titer in mice brain and infectivity to mosquitoes of theses viral populations were tested. The genome of the viruses was also sequenced. Results showed that viral titer were similar and infection rate in the mosquitoes were not significantly different among those 3 passages. This in vivo model could be utilized to explore virus evolution and genetic variance in alternating transmission.
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Affiliation(s)
- Xiaojuan Zhu
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China; NHC Key laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Yuting Jiang
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Hengduan Zhang
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Chunxiao Li
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Dan Xing
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China
| | - Xiaoxia Guo
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China.
| | - Tongyan Zhao
- Department of Vector Biology and Control, State Key Laboratory of Pathogen and Biosecurity, Beijing Key Laboratory of Vector Borne and Natural Focus Infectious Diseases, Institute of Microbiology and Epidemiology, Beijing Key Laboratory, Beijing 100071, China.
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15
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Ashall J, Shah S, Biggs JR, Chang JNR, Jafari Y, Brady OJ, Mai HK, Lien LT, Do Thai H, Nguyen HAT, Anh DD, Iwasaki C, Kitamura N, Van Loock M, Herrera-Taracena G, Rasschaert F, Van Wesenbeeck L, Yoshida LM, Hafalla JCR, Hue S, Hibberd ML. A phylogenetic study of dengue virus in urban Vietnam shows long-term persistence of endemic strains. Virus Evol 2023; 9:vead012. [PMID: 36926448 PMCID: PMC10013730 DOI: 10.1093/ve/vead012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 10/31/2022] [Accepted: 02/15/2023] [Indexed: 02/17/2023] Open
Abstract
Dengue virus (DENV) causes repeated outbreaks of disease in endemic areas, with patterns of local transmission strongly influenced by seasonality, importation via human movement, immunity, and vector control efforts. An understanding of how each of these interacts to enable endemic transmission (continual circulation of local virus strains) is largely unknown. There are times of the year when no cases are reported, often for extended periods of time, perhaps wrongly implying the successful eradication of a local strain from that area. Individuals who presented at a clinic or hospital in four communes in Nha Trang, Vietnam, were initially tested for DENV antigen presence. Enrolled positive individuals then had their corresponding household members invited to participate, and those who enrolled were tested for DENV. The presence of viral nucleic acid in all samples was confirmed using quantitative polymerase chain reaction, and positive samples were then whole-genome sequenced using an amplicon and target enrichment library preparation techniques and Illumina MiSeq sequencing technology. Generated consensus genome sequences were then analysed using phylogenetic tree reconstruction to categorise sequences into clades with a common ancestor, enabling investigations of both viral clade persistence and introductions. Hypothetical introduction dates were additionally assessed using a molecular clock model that calculated the time to the most recent common ancestor (TMRCA). We obtained 511 DENV whole-genome sequences covering four serotypes and more than ten distinct viral clades. For five of these clades, we had sufficient data to show that the same viral lineage persisted for at least several months. We noted that some clades persisted longer than others during the sampling time, and by comparison with other published sequences from elsewhere in Vietnam and around the world, we saw that at least two different viral lineages were introduced into the population during the study period (April 2017-2019). Next, by inferring the TMRCA from the construction of molecular clock phylogenies, we predicted that two of the viral lineages had been present in the study population for over a decade. We observed five viral lineages co-circulating in Nha Trang from three DENV serotypes, with two likely to have remained as uninterrupted transmission chains for a decade. This suggests clade cryptic persistence in the area, even during periods of low reported incidence.
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Affiliation(s)
- James Ashall
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Sonal Shah
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Joseph R Biggs
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jui-Ning R Chang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Yalda Jafari
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Huynh Kim Mai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Le Thuy Lien
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hung Do Thai
- Department of Microbiology and Immunology, Pasteur Institute of Nha Trang, Xương Huân, Nha Trang, 650000, Vietnam
| | - Hien Anh Thi Nguyen
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, 1 P. Yec Xanh, Phạm Đình Hổ, Hai Bà Trưng, Hà Nội, 100000, Vietnam
| | - Chihiro Iwasaki
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Noriko Kitamura
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Marnix Van Loock
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Guillermo Herrera-Taracena
- Janssen Global Public Health, Janssen Research & Development, LLC, 800 Ridgeview Drive, Horsham, PA 19044, USA
| | - Freya Rasschaert
- Janssen R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, Beerse B-2340, Belgium
| | | | - Lay-Myint Yoshida
- Paediatric Infectious Diseases Department, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Julius Clemence R Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Stephane Hue
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
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16
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Rahimi-Ardabili H, Magrabi F, Coiera E. Digital health for climate change mitigation and response: a scoping review. J Am Med Inform Assoc 2022; 29:2140-2152. [PMID: 35960171 PMCID: PMC9667157 DOI: 10.1093/jamia/ocac134] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/23/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Climate change poses a major threat to the operation of global health systems, triggering large scale health events, and disrupting normal system operation. Digital health may have a role in the management of such challenges and in greenhouse gas emission reduction. This scoping review explores recent work on digital health responses and mitigation approaches to climate change. MATERIALS AND METHODS We searched Medline up to February 11, 2022, using terms for digital health and climate change. Included articles were categorized into 3 application domains (mitigation, infectious disease, or environmental health risk management), and 6 technical tasks (data sensing, monitoring, electronic data capture, modeling, decision support, and communication). The review was PRISMA-ScR compliant. RESULTS The 142 included publications reported a wide variety of research designs. Publication numbers have grown substantially in recent years, but few come from low- and middle-income countries. Digital health has the potential to reduce health system greenhouse gas emissions, for example by shifting to virtual services. It can assist in managing changing patterns of infectious diseases as well as environmental health events by timely detection, reducing exposure to risk factors, and facilitating the delivery of care to under-resourced areas. DISCUSSION While digital health has real potential to help in managing climate change, research remains preliminary with little real-world evaluation. CONCLUSION Significant acceleration in the quality and quantity of digital health climate change research is urgently needed, given the enormity of the global challenge.
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Affiliation(s)
- Hania Rahimi-Ardabili
- Centre for Health Informatics, Australian Institute of Health Innovation, Macquarie University, Macquarie Park, NSW, Australia
| | - Farah Magrabi
- Centre for Health Informatics, Australian Institute of Health Innovation, Macquarie University, Macquarie Park, NSW, Australia
| | - Enrico Coiera
- Centre for Health Informatics, Australian Institute of Health Innovation, Macquarie University, Macquarie Park, NSW, Australia
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17
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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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Rodríguez-Aguilar ED, Martínez-Barnetche J, Rodríguez MH. Three highly variable genome regions of the four dengue virus serotypes can accurately recapitulate the CDS phylogeny. MethodsX 2022; 9:101859. [PMID: 36187156 PMCID: PMC9516459 DOI: 10.1016/j.mex.2022.101859] [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: 07/12/2022] [Accepted: 09/10/2022] [Indexed: 11/18/2022] Open
Abstract
The circulation of the four-dengue virus (DENV) serotypes has significantly increased in recent years, accompanied by an increase in viral genetic diversity. In order to conduct disease surveillance and understand DENV evolution and its effects on virus transmission and disease, efficient and accurate methods for phylogenetic classification are required. Phylogenetic analysis of different viral genes sequences is the most used method, the envelope gene (E) being the most frequently selected target. We explored the genetic variability of the four DENV serotypes throughout their complete coding sequence (CDS) of sequences available in GenBank and used genomic regions of different variability rate to recapitulate the phylogeny obtained with the DENV CDS. Our results indicate that the use of high or low variable regions accurately recapitulate the phylogeny obtained with CDS of sequences from different DENV genotypes. However, when analyzing the phylogeny of a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny. The use of three concatenated highly variable regions was not statistically different in distance branch length and support to that obtained in CDS phylogeny.•This study demonstrated the ability of highly variable regions of the DENV genome to recapitulate the phylogeny obtained with the full coding sequence (CDS).•The use of genomic regions of high or low variability did not affect the performance in recapitulating the phylogeny obtained with CDS from different genotypes. However, when phylogeny was analyzed for sequences from a single genotype, highly variable regions performed better in recapitulating the distance branch length, topology, and support of the CDS phylogeny.•The use of concatenated highly variable genome regions represent a useful option for recapitulating genome-wide phylogenies in analyses of sequences belonging to the same DENV genotype.
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19
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Gómez M, Martínez D, Hernández C, Luna N, Patiño LH, Bohórquez Melo R, Suarez LA, Palma-Cuero M, Murcia LM, González Páez L, Estrada Bustos L, Medina MA, Ariza Campo K, Padilla HD, Zamora Flórez A, De las Salas JL, Muñoz M, Ramírez JD. Arbovirus infection in Aedes aegypti from different departments of Colombia. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The lack of precise and timely knowledge about the molecular epidemiology of arboviruses of public health importance, particularly in the vector, has limited the comprehensive control of arboviruses. In Colombia and the Americas, entomovirological studies are scarce. Therefore, this study aimed to describe the frequency of natural infection and/or co-infection by Dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) in Aedes spp. circulating in different departments of Colombia (Amazonas, Boyacá, Magdalena, and Vichada) and identifying vector species by barcoding. Aedes mosquitoes were collected in departments with reported prevalence or incidence of arbovirus cases during 2020–2021, located in different biogeographic zones of the country: Amazonas, Boyacá, Magdalena, and Vichada. The insects were processed individually for RNA extraction, cDNA synthesis, and subsequent detection of DENV (serotypes DENV1-4 by multiplex PCR), CHIKV, and ZIKV (qRT-PCR). The positive mosquitoes for arboviruses were sequenced (Sanger method) using the subunit I of the cytochrome oxidase (COI) gene for species-level identification. In total, 558 Aedes mosquitoes were captured, 28.1% (n = 157) predominantly infected by DENV in all departments. The serotypes with the highest frequency of infection were DENV-1 and DENV-2 with 10.7% (n = 58) and 14.5% (n = 81), respectively. Coinfections between serotypes represented 3.9% (n = 22). CHIKV infection was detected in one individual (0.2%), and ZIKV infections were not detected. All infected samples were identified as A. aegypti (100%). From the COI dataset (593 bp), high levels of haplotype diversity (H = 0.948 ± 0.012) and moderate nucleotide diversity (π = 0.0225 ± 0.003) were identified, suggesting recent population expansions. Constructed phylogenetic analyses showed our COI sequences’ association with lineage I, which was reported widespread and related to a West African conspecific. We conclude that natural infection in A. aegypti by arbovirus might reflect the country’s epidemiological behavior, with a higher incidence of serotypes DENV-1 and DENV-2, which may be associated with high seroprevalence and asymptomatic infections in humans. This study demonstrates the high susceptibility of this species to arbovirus infection and confirms that A. aegypti is the main vector in Colombia. The importance of including entomovirological surveillance strategy within public health systems to understand transmission dynamics and the potential risk to the population is highlighted herein.
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Gómez M, Martinez D, Muñoz M, Ramírez JD. Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission? Parasit Vectors 2022; 15:287. [PMID: 35945559 PMCID: PMC9364528 DOI: 10.1186/s13071-022-05401-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023] Open
Abstract
Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.
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Affiliation(s)
- Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - David Martinez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia. .,Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Arguni E, Indriani C, Rahayu A, Supriyati E, Yohan B, Hayati RF, Wardana S, Tantowijoyo W, Anshari MR, Rahayu E, Ahmad RA, Utarini A, Simmons CP, Sasmono RT. Dengue virus population genetics in Yogyakarta, Indonesia prior to city-wide Wolbachia deployment. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105308. [PMID: 35644356 DOI: 10.1016/j.meegid.2022.105308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/29/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Dengue has been endemic in Yogyakarta, Indonesia for decades. Here, we report the dengue epidemiology, entomology, and virology in Yogyakarta in 2016-2017, prior to the commencement of the Applying Wolbachia to Eliminate Dengue (AWED) randomized trial. Dengue epidemiological data were compiled and blood samples from dengue-suspected patients were tested for dengue virus (DENV). Ae. aegypti mosquito samples were caught from the field using BG-Sentinel traps and tested for the presence of DENV infection. Sequencing of the DENV E gene was used to determine the phylogeny and genotypes of circulating DENV. Within the last decade, the 2016-2017 dengue incidence was considered very high. Among the 649 plasma samples collected between March 2016-February 2017; and 36,910 mosquito samples collected between December 2016-May 2017, a total of 197 and 38 samples were DENV-positive by qRT-PCR, respectively. All four DENV serotypes were detected, with DENV-3 (n = 88; 44.67%) and DENV-1 (n = 87; 44.16%) as the predominant serotype, followed by DENV-4 (n = 12; 6.09%) and DENV-2 (n = 10; 5.08%). The Yogyakarta DENV-1 isolates were classified into Genotype I and IV, while DENV-2, DENV-3, and DENV-4 isolates were classified into the Cosmopolitan genotype, Genotype I, and Genotype II, respectively. Yogyakarta DENV isolates were closely related to Indonesian strains from neighboring Javanese cities, consistent with the endemic circulation of DENV on this highly populous island. Our study provides comprehensive baseline information on the DENV population genetic characteristics in Yogyakarta, which are useful as baseline data for the AWED trial and the future DENV surveillance in the city in the presence of a Wolbachia-infected Ae. aegypti population.
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Affiliation(s)
- Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Citra Indriani
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ayu Rahayu
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Satrio Wardana
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Warsito Tantowijoyo
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Muhammad Ridwan Anshari
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endang Rahayu
- Disease Control Department, Yogyakarta District Health Office, Yogyakarta, Indonesia
| | - Riris Andono Ahmad
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Biostatistics, Epidemiology and Population Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Adi Utarini
- World Mosquito Program Yogyakarta, Centre of Tropical Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Department of Health Policy and Management, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Cameron P Simmons
- World Mosquito Program, Institute of Vector Borne Disease, Monash University, Clayton, Victoria 3800, Australia
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
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Castro-Jiménez TK, Gómez-Legorreta LC, López-Campa LA, Martínez-Torres V, Alvarado-Silva M, Posadas-Mondragón A, Díaz-Lima N, Angulo-Mendez HA, Mejía-Domínguez NR, Vaca-Paniagua F, Ávila-Moreno F, García-Cordero J, Cedillo-Barrón L, Aguilar-Ruíz SR, Bustos-Arriaga J. Variability in Susceptibility to Type I Interferon Response and Subgenomic RNA Accumulation Between Clinical Isolates of Dengue and Zika Virus From Oaxaca Mexico Correlate With Replication Efficiency in Human Cells and Disease Severity. Front Cell Infect Microbiol 2022; 12:890750. [PMID: 35800385 PMCID: PMC9254156 DOI: 10.3389/fcimb.2022.890750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Dengue and Zika viruses cocirculate annually in endemic areas of Mexico, causing outbreaks of different magnitude and severity every year, suggesting a continuous selection of Flavivirus variants with variable phenotypes of transmissibility and virulence. To evaluate if Flavivirus variants with different phenotypes cocirculate during outbreaks, we isolated dengue and Zika viruses from blood samples of febrile patients from Oaxaca City during the 2016 and 2019 epidemic years. We compared their replication kinetics in human cells, susceptibility to type I interferon antiviral response, and the accumulation of subgenomic RNA on infected cells. We observed correlations between type I interferon susceptibility and subgenomic RNA accumulation, with high hematocrit percentage and thrombocytopenia. Our results suggest that Flaviviruses that cocirculate in Oaxaca, Mexico, have variable sensitivity to the antiviral activity of type I interferons, and this phenotypic trait correlates with the severity of the disease.
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Affiliation(s)
- Tannya Karen Castro-Jiménez
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Laura Cristina Gómez-Legorreta
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Laura Alejandra López-Campa
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Valeria Martínez-Torres
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Marcos Alvarado-Silva
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Araceli Posadas-Mondragón
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | | | | | - Nancy R. Mejía-Domínguez
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Felipe Vaca-Paniagua
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Federico Ávila-Moreno
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Julio García-Cordero
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Leticia Cedillo-Barrón
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Sergio Roberto Aguilar-Ruíz
- Departamento de Biomedicina Experimental, Facultad de Medicina y Cirugía de la Universidad Autónoma ‘Benito Juárez’ de Oaxaca, Oaxaca, Mexico
| | - José Bustos-Arriaga
- Laboratorio de Biología Molecular e Inmunología de arbovirus, Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- *Correspondence: José Bustos-Arriaga,
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Letizia AG, Pratt CB, Wiley MR, Fox AT, Mosore M, Agbodzi B, Yeboah C, Kumordjie S, Di Paola N, Assana KC, Coulidiaty D, Ouedraogo C, Bonney JHK, Ampofo W, Tarnagda Z, Sangaré L. Retrospective Genomic Characterization of a 2017 Dengue Virus Outbreak, Burkina Faso. Emerg Infect Dis 2022; 28:1198-1210. [PMID: 35608626 PMCID: PMC9155902 DOI: 10.3201/eid2806.212491] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Knowledge of contemporary genetic composition of dengue virus (DENV) in Africa is lacking. By using next-generation sequencing of samples from the 2017 DENV outbreak in Burkina Faso, we isolated 29 DENV genomes (5 serotype 1, 16 serotype 2 [DENV-2], and 8 serotype 3). Phylogenetic analysis demonstrated the endemic nature of DENV-2 in Burkina Faso. We noted discordant diagnostic results, probably related to genetic divergence between these genomes and the Trioplex PCR. Forward and reverse1 primers had a single mismatch when mapped to the DENV-2 genomes, probably explaining the insensitivity of the molecular test. Although we observed considerable homogeneity between the Dengvaxia and TetraVax-DV-TV003 vaccine strains as well as B cell epitopes compared with these genomes, we noted unique divergence. Continual surveillance of dengue virus in Africa is needed to clarify the ongoing novel evolutionary dynamics of circulating virus populations and support the development of effective diagnostic, therapeutic, and preventive countermeasures.
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24
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Stica CJ, Barrero RA, Murray RZ, Devine GJ, Phillips MJ, Frentiu FD. Global Evolutionary History and Dynamics of Dengue Viruses Inferred from Whole Genome Sequences. Viruses 2022; 14:v14040703. [PMID: 35458433 PMCID: PMC9030598 DOI: 10.3390/v14040703] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 12/20/2022] Open
Abstract
Dengue is an arboviral disease caused by dengue virus (DENV), leading to approximately 25,000 deaths/year and with over 40% of the world’s population at risk. Increased international travel and trade, poorly regulated urban expansion, and warming global temperatures have expanded the geographic range and incidence of the virus in recent decades. This study used phylogenetic and selection pressure analyses to investigate trends in DENV evolution, using whole genome coding sequences from publicly available databases alongside newly sequenced isolates collected between 1963–1997 from Southeast Asia and the Pacific. Results revealed very similar phylogenetic relationships when using the envelope gene and the whole genome coding sequences. Although DENV evolution is predominantly driven by negative selection, a number of amino acid sites undergoing positive selection were found across the genome, with the majority located in the envelope and NS5 genes. Some genotypes appear to be diversifying faster than others within each serotype. The results from this research improve our understanding of DENV evolution, with implications for disease control efforts such as Wolbachia-based biocontrol and vaccine design.
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Affiliation(s)
- Caleb J. Stica
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, 300 Herston Road, Herston, QLD 4006, Australia;
| | - Roberto A. Barrero
- eResearch Office, Division of Research and Innovation, Queensland University of Technology, P Block, 2 George Street, Brisbane, QLD 4000, Australia;
| | - Rachael Z. Murray
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, KG-Q Block, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD 4059, Australia;
| | - Gregor J. Devine
- Mosquito Control Lab, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia;
| | - Matthew J. Phillips
- School of Biology and Environmental Science, Queensland University of Technology, R Block, 2 George Street, Brisbane, QLD 4000, Australia;
| | - Francesca D. Frentiu
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, 300 Herston Road, Herston, QLD 4006, Australia;
- Correspondence:
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25
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Tsai JF, Chu TL, Cuevas Brun EH, Lin MH. Solving Patient Allocation Problem during an Epidemic Dengue Fever Outbreak by Mathematical Modelling. Healthcare (Basel) 2022; 10:163. [PMID: 35052326 PMCID: PMC8775972 DOI: 10.3390/healthcare10010163] [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: 12/08/2021] [Revised: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
Dengue fever is a mosquito-borne disease that has rapidly spread throughout the last few decades. Most preventive mechanisms to deal with the disease focus on the eradication of the vector mosquito and vaccination campaigns. However, appropriate mechanisms of response are indispensable to face the consequent events when an outbreak takes place. This study applied single and multiple objective linear programming models to optimize the allocation of patients and additional resources during an epidemic dengue fever outbreak, minimizing the summation of the distance travelled by all patients. An empirical study was set in Ciudad del Este, Paraguay. Data provided by a privately run health insurance cooperative was used to verify the applicability of the models in this study. The results can be used by analysts and decision makers to solve patient allocation problems for providing essential medical care during an epidemic dengue fever outbreak.
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Affiliation(s)
- Jung-Fa Tsai
- Department of Business Management, National Taipei University of Technology, Taipei 10608, Taiwan; (J.-F.T.); (T.-L.C.); (E.H.C.B.)
| | - Tai-Lin Chu
- Department of Business Management, National Taipei University of Technology, Taipei 10608, Taiwan; (J.-F.T.); (T.-L.C.); (E.H.C.B.)
| | - Edgar Hernan Cuevas Brun
- Department of Business Management, National Taipei University of Technology, Taipei 10608, Taiwan; (J.-F.T.); (T.-L.C.); (E.H.C.B.)
| | - Ming-Hua Lin
- Department of Urban Industrial Management and Marketing, University of Taipei, Taipei 11153, Taiwan
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26
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Paradkar PN, Sahasrabudhe PR, Ghag Sawant M, Mukherjee S, Blasdell KR. Towards Integrated Management of Dengue in Mumbai. Viruses 2021; 13:2436. [PMID: 34960705 PMCID: PMC8703503 DOI: 10.3390/v13122436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/15/2022] Open
Abstract
With increasing urbanisation, the dengue disease burden is on the rise in India, especially in large cities such as Mumbai. Current dengue surveillance in Mumbai includes municipal corporation carrying out specific activities to reduce mosquito breeding sites and the use of insecticides to suppress the adult mosquito populations. Clinical cases remain either underreported or misreported due to the restriction to government clinics, missing the large private health care sector. There is a need for an integrated approach to manage dengue outbreaks in Mumbai. There are various novel strategies available for use that can be utilised to improve disease detection, mosquito surveillance, and control of mosquito-borne diseases. These novel technologies are discussed in this manuscript. Given the complex ecosystem of mosquito-borne diseases in Mumbai, integrating data obtained from these technologies would support the ongoing mosquito control measures in Mumbai.
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Affiliation(s)
- Prasad N. Paradkar
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong 3220, Australia;
| | | | - Mrunal Ghag Sawant
- Department of Zoonosis, Haffkine Institute for Training Research and Testing, Parel, Mumbai 400012, India;
| | - Sandeepan Mukherjee
- Department of Virology, Haffkine Institute for Training Research and Testing, Parel, Mumbai 400012, India;
| | - Kim R. Blasdell
- CSIRO Health & Biosecurity, Australian Centre for Disease Preparedness, 5 Portarlington Road, Geelong 3220, Australia;
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27
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Chen RE, Smith BK, Errico JM, Gordon DN, Winkler ES, VanBlargan LA, Desai C, Handley SA, Dowd KA, Amaro-Carambot E, Cardosa MJ, Sariol CA, Kallas EG, Sékaly RP, Vasilakis N, Fremont DH, Whitehead SS, Pierson TC, Diamond MS. Implications of a highly divergent dengue virus strain for cross-neutralization, protection, and vaccine immunity. Cell Host Microbe 2021; 29:1634-1648.e5. [PMID: 34610295 PMCID: PMC8595868 DOI: 10.1016/j.chom.2021.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/15/2021] [Accepted: 09/10/2021] [Indexed: 01/29/2023]
Abstract
Although divergent dengue viruses (DENVs) have been isolated in insects, nonhuman primates, and humans, their relationships to the four canonical serotypes (DENV 1-4) are poorly understood. One virus isolated from a dengue patient, DKE-121, falls between genotype and serotype levels of sequence divergence to DENV-4. To examine its antigenic relationship to DENV-4, we assessed serum neutralizing and protective activity. Whereas DENV-4-immune mouse sera neutralize DKE-121 infection, DKE-121-immune sera inhibit DENV-4 less efficiently. Passive transfer of DENV-4 or DKE-121-immune sera protects mice against homologous, but not heterologous, DENV-4 or DKE-121 challenge. Antigenic cartography suggests that DENV-4 and DKE-121 are related but antigenically distinct. However, DENV-4 vaccination confers protection against DKE-121 in nonhuman primates, and serum from humans immunized with a tetravalent vaccine neutralize DENV-4 and DKE-121 infection equivalently. As divergent DENV strains, such as DKE-121, may meet criteria for serotype distinction, monitoring their capacity to impact dengue disease and vaccine efficacy appears warranted.
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Affiliation(s)
- Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Brittany K Smith
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - David N Gordon
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Emma S Winkler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Chandni Desai
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Scott A Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Kimberly A Dowd
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Emerito Amaro-Carambot
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - M Jane Cardosa
- Institute of Health and Community Medicine, Universiti Sarawak Malaysia (UNIMAS), Kota Samarahan, Sarawak 94300, Malaysia; Integrated Research Associates, San Rafael, CA 94903, USA
| | - Carlos A Sariol
- Unit of Comparative Medicine, Caribbean Primate Research Center, University of Puerto Rico-Medical Sciences Campus, San Juan, PR 00936-5067, USA
| | - Esper G Kallas
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
| | - Rafick-Pierre Sékaly
- Department of Microbiology and Immunology, Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; The Andrew M. Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110-1010, USA
| | - Stephen S Whitehead
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Theodore C Pierson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-9806, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; The Andrew M. Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110-1010, USA; Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, Saint Louis, MO 63110-1010, USA.
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28
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Hayati RF, Denis D, Tallo KT, Sirait T, Tukan J, Santoso MS, Yohan B, Haryanto S, Frost SDW, Stubbs SCB, Sasmono RT. Molecular epidemiology of dengue in a setting of low reported endemicity: Kupang, East Nusa Tenggara province, Indonesia. Trans R Soc Trop Med Hyg 2021; 115:1304-1316. [PMID: 34528099 DOI: 10.1093/trstmh/trab138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/17/2021] [Accepted: 08/23/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Most regions in Indonesia experience annual dengue epidemics. However, the province of East Nusa Tenggara has consistently reported low incidence. We conducted a dengue molecular epidemiology study in Kupang, the capital of the province. METHODS Dengue patients were recruited from May 2016 to September 2017. Dengue virus (DENV) screening was performed using NS1 and immunoglobulin G (IgG)/IgM detection. Serotype was determined using reverse transcription polymerase chain reaction and the envelope genes were sequenced to infer the genetic identity and phylogeny. RESULTS From 119 patients, dengue was confirmed in 62 (52%). Compared with official data, underreporting of dengue incidence was observed. The majority (36%) of patients were children <10 y of age. Most patients (80%) experienced mild fever. All serotypes were detected, with DENV-3 as the predominant (57%). Kupang DENV-1 isolate was classified as genotype IV, an old and endemic strain, DENV-2 as cosmopolitan, DENV-3 as genotype I and DENV-4 as genotype II. Most isolates showed relatively low evolutionary rates and are closely related with strains from Bali and Timor Leste. CONCLUSIONS The low dengue incidence was most likely caused by sustained local circulation of endemic viruses. This study provides information on the epidemiology of dengue in a low-endemicity setting that should help future mitigation and disease management.
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Affiliation(s)
- Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Tuppak Sirait
- SK Lerik Regional Public Hospital, Kupang, Indonesia
| | - Joanita Tukan
- SK Lerik Regional Public Hospital, Kupang, Indonesia
| | | | | | | | - Simon D W Frost
- London School of Hygiene and Tropical Medicine, London, UK.,Microsoft Research, Redmond, WA, USA
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29
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Simo Tchetgna H, Sado Yousseu F, Kamgang B, Tedjou A, McCall PJ, Wondji CS. Concurrent circulation of dengue serotype 1, 2 and 3 among acute febrile patients in Cameroon. PLoS Negl Trop Dis 2021; 15:e0009860. [PMID: 34695135 PMCID: PMC8568189 DOI: 10.1371/journal.pntd.0009860] [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: 05/17/2021] [Revised: 11/04/2021] [Accepted: 09/28/2021] [Indexed: 11/21/2022] Open
Abstract
Acute febrile patients presenting at hospitals in Douala, Cameroon between July and December 2020, were screened for dengue infections using real time RT-PCR on fragments of the 5’ and 3’ UTR genomic regions. In total, 12.8% (41/320) of cases examined were positive for dengue. Dengue virus 3 (DENV-3) was the most common serotype found (68.3%), followed by DENV-2 (19.5%) and DENV-1 (4.9%). Co-infections of DENV-3 and DENV-2 were found in 3 cases. Jaundice and headache were the most frequent clinical signs associated with infection and 56% (23/41) of the cases were co-infections with malaria. Phylogenetic analysis of the envelope gene identified DENV-1 as belonging to genotype V, DENV-2 to genotype II and DENV-3 to genotype III. The simultaneous occurrence of three serotypes in Douala reveals dengue as a serious public health threat for Cameroon and highlights the need for further epidemiological studies in the major cities of this region. Acute febrile patients presenting at hospitals in Douala, Cameroon between July and December 2020, were screened for dengue infections by Polymerase chain reaction. In total, 12.8% (41/320) of cases examined were infected by dengue virus. Dengue virus 3 (DENV-3) was the most common serotype found (68.3%), followed by DENV-2 (19.5%) and DENV-1 (4.9%). Co-infections of DENV-3 and DENV-2 were found in 3 cases. Jaundice and headache were the most frequent clinical signs associated with infection and 56% (23/41) of the cases were co-infections with malaria. The simultaneous occurrence of three serotypes in Douala reveals dengue as a serious public health threat for Cameroon and highlights the need for further epidemiological studies in the major cities of this region.
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Affiliation(s)
| | - Francine Sado Yousseu
- Centre for Research in Infectious Diseases, Yaoundé, Cameroon
- University of Buéa, Buéa, Cameroon
| | - Basile Kamgang
- Centre for Research in Infectious Diseases, Yaoundé, Cameroon
| | - Armel Tedjou
- Centre for Research in Infectious Diseases, Yaoundé, Cameroon
- University of Yaoundé I, Yaoundé, Cameroon
| | - Philip J. McCall
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Charles S. Wondji
- Centre for Research in Infectious Diseases, Yaoundé, Cameroon
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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30
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Navero-Castillejos J, Benitez R, Torner N, Muñoz J, Camprubí-Ferrer D, Peiró-Mestres A, Sulleiro E, Silgado A, Gonzalo V, Falgueras T, Alejo-Cancho I, Roldán M, Plasencia V, Albarracin R, Perez J, Navarro A, Calderón A, Rubio R, Navarro M, Micó M, Llaberia J, Navarro M, Barrachina J, Vilamala A, Martí C, Pulido MÁ, Sanchez-Seco MP, Vazquez A, Martínez A, Jané M, Martínez MJ. Molecular Characterization of Imported and Autochthonous Dengue in Northeastern Spain. Viruses 2021; 13:1910. [PMID: 34696340 PMCID: PMC8539074 DOI: 10.3390/v13101910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022] Open
Abstract
Dengue is the most significant arbovirus worldwide and a public health threat to non-endemic areas in which Aedes vectors are present. Autochthonous dengue transmission has been reported in several European countries in the last decade. Infected travelers from endemic regions arriving to areas colonized by Aedes albopictus in Europe need to be monitored in surveillance and control programs. We aimed to perform molecular characterization of RT-PCR-positive dengue cases detected in Catalonia, northeastern Spain, from 2013 to 2018. The basic demographic information and the geographical regions of importation were also analyzed. One-hundred four dengue cases were studied (103 imported infections and the first autochthonous case in our region). The dengue virus strains detected were serotyped and genotyped using molecular methods, and phylogenetic analyses were conducted. All four dengue serotypes were detected in travelers, including up to 10 different genotypes, reflecting the global circulation of dengue in endemic areas. The primary travel-related case of the 2018 autochthonous transmission was not identified, but the molecular analysis revealed dengue serotype 1, genotype I of Asian origin. Our results highlight the diversity of imported dengue virus strains and the role of molecular epidemiology in supporting arbovirus surveillance programs.
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Affiliation(s)
- Jessica Navero-Castillejos
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, 08036 Barcelona, Spain; (J.M.); (D.C.-F.); (M.R.)
| | - Rosa Benitez
- North Metropolitan International Health Unit PROSICS, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain;
| | - Nuria Torner
- CIBER Epidemiology and Public Health CIBERESP, University of Barcelona, 08036 Barcelona, Spain;
| | - José Muñoz
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, 08036 Barcelona, Spain; (J.M.); (D.C.-F.); (M.R.)
| | - Daniel Camprubí-Ferrer
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, 08036 Barcelona, Spain; (J.M.); (D.C.-F.); (M.R.)
| | - Aida Peiró-Mestres
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
| | - Elena Sulleiro
- Department of Microbiology, Vall d’Hebron University Hospital, PROSICS, 08035 Barcelona, Spain; (E.S.); (A.S.)
| | - Aroa Silgado
- Department of Microbiology, Vall d’Hebron University Hospital, PROSICS, 08035 Barcelona, Spain; (E.S.); (A.S.)
| | - Verónica Gonzalo
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
| | - Teresa Falgueras
- Hospital Municipal de Badalona, Badalona Serveis Assistencials, 08911 Badalona, Spain; (T.F.); (A.C.)
| | - Izaskun Alejo-Cancho
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
| | - Montserrat Roldán
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, 08036 Barcelona, Spain; (J.M.); (D.C.-F.); (M.R.)
| | - Virginia Plasencia
- Microbiology Laboratory, Catlab, 08232 Viladecavalls, Spain; (V.P.); (J.P.); (R.R.)
| | - Rosa Albarracin
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
| | - Josefa Perez
- Microbiology Laboratory, Catlab, 08232 Viladecavalls, Spain; (V.P.); (J.P.); (R.R.)
| | - Alexander Navarro
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
| | - Ana Calderón
- Hospital Municipal de Badalona, Badalona Serveis Assistencials, 08911 Badalona, Spain; (T.F.); (A.C.)
| | - Rosa Rubio
- Microbiology Laboratory, Catlab, 08232 Viladecavalls, Spain; (V.P.); (J.P.); (R.R.)
| | - Mireia Navarro
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, 08036 Barcelona, Spain; (J.M.); (D.C.-F.); (M.R.)
| | - Miguel Micó
- Microbiology Department, Xarxa Assistencial Universitària de Manresa, 08243 Manresa, Spain;
| | - Jaume Llaberia
- Hospital de Barcelona, Societat Cooperativa d’Instal·lacions Assistencials Sanitàries (SCIAS), 08034 Barcelona, Spain;
| | - María Navarro
- Microbiology Department, Hospital Universitari de Vic, 08500 Barcelona, Spain; (M.N.); (A.V.)
| | - Josep Barrachina
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
| | - Anna Vilamala
- Microbiology Department, Hospital Universitari de Vic, 08500 Barcelona, Spain; (M.N.); (A.V.)
| | - Carmina Martí
- Hospital General de Granollers, 08402 Granollers, Spain; (C.M.); (M.Á.P.)
| | | | - María Paz Sanchez-Seco
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28222 Madrid, Spain; (M.P.S.-S.); (A.V.)
| | - Ana Vazquez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28222 Madrid, Spain; (M.P.S.-S.); (A.V.)
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Ana Martínez
- Public Health Agency of Catalonia, Generalitat of Catalonia, 08005 Barcelona, Spain; (A.M.); (M.J.)
| | - Mireia Jané
- Public Health Agency of Catalonia, Generalitat of Catalonia, 08005 Barcelona, Spain; (A.M.); (M.J.)
| | - Miguel Julián Martínez
- Department of Clinical Microbiology, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (J.N.-C.); (A.P.-M.); (V.G.); (I.A.-C.); (R.A.); (A.N.); (M.N.); (J.B.)
- Barcelona Institute for Global Health (ISGlobal), Hospital Clinic de Barcelona, Universitat de Barcelona, 08036 Barcelona, Spain; (J.M.); (D.C.-F.); (M.R.)
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31
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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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Abstract
Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle - that underlying the Biological Species Concept (BSC) - to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
| | - Angela C O'Donnell
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, TX 78712, USA
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33
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Fung CK, Li T, Pollett S, Alera MT, Yoon IK, Hang J, Macareo L, Srikiatkhachorn A, Ellison D, Rothman AL, Fernandez S, Jarman RG, Maljkovic Berry I. Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies. J Gen Virol 2021; 102:001553. [PMID: 33591246 PMCID: PMC8515859 DOI: 10.1099/jgv.0.001553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T. splendens inoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 500×, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNVs with frequencies ≥5 % were often preserved between the samples, and that the number of iSNV positions, and sample diversity, at this frequency cutoff did not differ significantly between the sample pairs (clinical sample and isolate) in either DENV1 or DENV2 data. Our results show that low-passage DENV isolate consensus genomes are largely representative of their direct sample parental viruses, and that low-passage isolates often mirror high frequency within-host variants from direct samples.
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Affiliation(s)
| | - Tao Li
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Simon Pollett
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - In-Kyu Yoon
- Coalition for Epidemic Preparedness Innovations, Washington, DC, USA
| | - Jun Hang
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Louis Macareo
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anon Srikiatkhachorn
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- University of Rhode Island, Kingston, RI, USA
| | - Damon Ellison
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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34
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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35
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Thornton J, Gomes B, Ayres C, Reimer L. Insecticide resistance selection and reversal in two strains of Aedes aegypti. Wellcome Open Res 2020; 5:183. [PMID: 33521329 PMCID: PMC7814284 DOI: 10.12688/wellcomeopenres.15974.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2020] [Indexed: 01/12/2023] Open
Abstract
Background: Laboratory reared mosquito colonies are essential tools to understand insecticide action. However, they differ considerably from wild populations and from each other depending on their origin and rearing conditions, which makes studying the effects of specific resistance mechanisms difficult. This paper describes our methods for establishing multiple resistant strains of Aedes aegypti from two colonies as a new resource for further research on metabolic and target site resistance. Methods: Two resistant colonies of Ae. aegypti, from Cayman and Recife, were selected through 10 generations of exposure to insecticides including permethrin, malathion and temephos, to yield eight strains with different profiles of resistance due to either target site or metabolic resistance. Resistance ratios for each insecticide were calculated for the selected and unselected strains. The frequency of kdr alleles (F1534C and V1016I) in the Cayman strains was determined using TaqMan assays. A comparative gene expression analysis among Recife strains was conducted using qPCR in larvae (CCae3A, CYP6N12, CYP6F3, CYP9M9) and adults (CCae3A, CYP6N12, CYP6BB2, CYP9J28a). Results: In the selected strain of Cayman, mortality against permethrin reduced almost to 0% and kdr became fixated by 5 generations. A similar phenotype was seen in the unselected homozygous resistant colony, whilst mortality in the susceptible homozygous colony rose to 82.9%. The Recife strains showed different responses between exposure to adulticide and larvicide, with detoxification genes in the temephos selected strain staying similar to the baseline, but a reduction in detoxification genes displayed in the other strains. Conclusions: These selected strains, with a range of insecticide resistance phenotypes and genotypes, will support further research on the effects of target-site and/or metabolic resistance mechanisms on various life-history traits, behaviours and vector competence of this important arbovirus vector.
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Affiliation(s)
- Jonathan Thornton
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | - Bruno Gomes
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
- Laboratório de Bioquímica e Fisiologia de Insetos, Oswaldo Cruz Institute (IOC-FIOCRUZ), Rio de Janeiro, 21040-360, Brazil
| | - Constância Ayres
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation (IAM-FIOCRUZ), Recife, Brazil
| | - Lisa Reimer
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
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Kuno G. The Absence of Yellow Fever in Asia: History, Hypotheses, Vector Dispersal, Possibility of YF in Asia, and Other Enigmas. Viruses 2020; 12:E1349. [PMID: 33255615 PMCID: PMC7759908 DOI: 10.3390/v12121349] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 01/11/2023] Open
Abstract
Since the recent epidemics of yellow fever in Angola and Brazil as well as the importation of cases to China in 2016, there has been an increased interest in the century-old enigma, absence of yellow fever in Asia. Although this topic has been repeatedly reviewed before, the history of human intervention has never been considered a critical factor. A two-stage literature search online for this review, however, yielded a rich history indispensable for the debate over this medical enigma. As we combat the pandemic of COVID-19 coronavirus worldwide today, we can learn invaluable lessons from the historical events in Asia. In this review, I explore the history first and then critically examine in depth major hypotheses proposed in light of accumulated data, global dispersal of the principal vector, patterns of YF transmission, persistence of urban transmission, and the possibility of YF in Asia. Through this process of re-examination of the current knowledge, the subjects for research that should be conducted are identified. This review also reveals the importance of holistic approach incorporating ecological and human factors for many unresolved subjects, such as the enigma of YF absence in Asia, vector competence, vector dispersal, spillback, viral persistence and transmission mechanisms.
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Affiliation(s)
- Goro Kuno
- Centers for Disease Control and Prevention, Formerly Division of Vector-Borne Infectious Diseases, Fort Collins, CO 80521, USA
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37
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Pollett S, Gathii K, Figueroa K, Rutvisuttinunt W, Srikanth A, Nyataya J, Mutai BK, Awinda G, Jarman RG, Berry IM, Waitumbi JN. The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications. INFECTION GENETICS AND EVOLUTION 2020; 90:104617. [PMID: 33161179 DOI: 10.1016/j.meegid.2020.104617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 11/01/2020] [Indexed: 01/17/2023]
Abstract
Kenya experiences a substantial burden of dengue, yet there are very few DENV-2 sequence data available from this country and indeed the entire continent of Africa. We therefore undertook whole genome sequencing and evolutionary analysis of fourteen dengue virus (DENV)-2 strains sampled from Malindi sub-County Hospital during the 2017 DENV-2 outbreak in the Kenyan coast. We further performed an extended East African phylogenetic analysis, which leveraged 26 complete African env genes. Maximum likelihood analysis showed that the 2017 outbreak was due to the Cosmopolitan genotype, indicating that this has been the only confirmed human DENV-2 genotype circulating in Africa to date. Phylogeographic analyses indicated transmission of DENV-2 viruses between East Africa and South/South-West Asia. Time-scaled genealogies show that DENV-2 viruses shows spatial structure at the country level in Kenya, with a time-to-most-common-recent ancestor analysis indicating that these DENV-2 strains were circulating for up to 5.38 years in Kenya before detection in the 2017 Malindi outbreak. Selection pressure analyses indicated sampled Kenyan DENV strains uniquely being under positive selection at 6 sites, predominantly across the non-structural genes, and epitope prediction analyses showed that one of these sites corresponds to a putative predicted MHC-I CD8+ DENV-2 Cosmopolitan virus epitope only evident in a sampled Kenyan virus. Taken together, our findings indicate that the 2017 Malindi DENV-2 outbreak arose from a strain which had circulated for several years in Kenya before recent detection, has experienced diversifying selection pressure, and may contain new putative immunogens relevant to vaccine design. These findings prompt further genomic epidemiology studies in this and other Kenyan locations to further elucidate the transmission dynamics of DENV in this region.
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Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Kimita Gathii
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Katherine Figueroa
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Abhi Srikanth
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Josphat Nyataya
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Beth K Mutai
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - George Awinda
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
| | - J N Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
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38
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Thornton J, Gomes B, Ayres C, Reimer L. Insecticide resistance selection and reversal in two strains of Aedes aegypti. Wellcome Open Res 2020; 5:183. [PMID: 33521329 PMCID: PMC7814284 DOI: 10.12688/wellcomeopenres.15974.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Laboratory reared mosquito colonies are essential tools to understand insecticide action. However, they differ considerably from wild populations and from each other depending on their origin and rearing conditions, which makes studying the effects of specific resistance mechanisms difficult. This paper describes our methods for establishing multiple resistant strains of Aedes aegypti from two colonies as a new resource for further research on metabolic and target site resistance. Methods: Two resistant colonies of Ae. aegypti, from Cayman and Recife, were selected through 10 generations of exposure to insecticides including permethrin, malathion and temephos, to yield eight strains with different profiles of resistance due to either target site or metabolic resistance. Resistance ratios for each insecticide were calculated for the selected and unselected strains. The frequency of kdr alleles in the Cayman strains was determined using TaqMan assays. A comparative gene expression analysis among Recife strains was conducted using qPCR in larvae (CCae3A, CYP6N12, CYP6F3, CYP9M9) and adults (CCae3A, CYP6N12, CYP6BB2, CYP9J28a). Results: In the selected strain of Cayman, mortality against permethrin reduced almost to 0% and kdr became fixated by 5 generations. A similar phenotype was seen in the unselected homozygous resistant colony, whilst mortality in the susceptible homozygous colony rose to 82.9%. The Recife strains showed different responses between exposure to adulticide and larvicide, with detoxification genes in the temephos selected strain staying similar to the baseline, but a reduction in detoxification genes displayed in the other strains. Conclusions: These selected strains, with a range of insecticide resistance phenotypes and genotypes, will support further research on the effects of target-site and/or metabolic resistance mechanisms on various life-history traits, behaviours and vector competence of this important arbovirus vector.
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Affiliation(s)
- Jonathan Thornton
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
| | - Bruno Gomes
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
- Laboratório de Bioquímica e Fisiologia de Insetos, Oswaldo Cruz Institute (IOC-FIOCRUZ), Rio de Janeiro, 21040-360, Brazil
| | - Constância Ayres
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation (IAM-FIOCRUZ), Recife, Brazil
| | - Lisa Reimer
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L35QA, UK
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Molecular epidemiology of dengue fever outbreaks in Bhutan, 2016-2017. PLoS Negl Trop Dis 2020; 14:e0008165. [PMID: 32320397 PMCID: PMC7176082 DOI: 10.1371/journal.pntd.0008165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/23/2020] [Indexed: 12/30/2022] Open
Abstract
Dengue continues to pose a significant public health problem in tropical and subtropical countries. In Bhutan, first outbreak of dengue fever (DF) was reported in 2004 in a southern border town, followed by sporadic cases over the years. In this study, we analysed DF outbreaks that occurred in 3 different places during the years 2016 and 2017. A total of 533 cases in 2016 and 163 in 2017 were suspected of having of DF, where young adults were mostly affected. A total of 240 acute serum specimens collected and analyzed for serotype by nested RT-PCR revealed predominance of serotypes 1 and 2 (DENV-1 and 2). Phylogenetic analysis using envelope gene for both the serotypes demonstrated cosmopolitan genotype which were closely related to strains from India, indicating that they were probably imported from the neighboring country over the past few years. Endemicity of DENV in some places of southern Bhutan has been established previously. In this study, we analysed outbreaks of DF that occurred in 3 places over a period of 2 years, 1 of which was previously not known to be endemic to DENV. Serum specimens collected from patients suspected of having DF were analyzed in the Royal Centre for Disease Control (RCDC) in Bhutan and in Armed Forces Research Institute of Medical Sciences (AFRIMS), Thailand. DENV-1 and 2 were established as the causes of the outbreaks, also indicating that serotypes of DENV circulating in the country over the past years have remained the same. Our analyses reveal that the current DENV-1and DENV-2 in Bhutan probably originated from India, Bhutan’s closest neighboring country.
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40
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Pollett S, Fauver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2020; 221:S308-S318. [PMID: 31711190 PMCID: PMC11095994 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
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Affiliation(s)
- S. Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland
- Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J. R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L. D. Gillis
- Bureau of Public Health Laboratories–Miami, Florida Department of Health
| | - M. A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R. G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N. D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
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41
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Stubbs SCB, Blacklaws BA, Yohan B, Yudhaputri FA, Hayati RF, Schwem B, Salvaña EM, Destura RV, Lester JS, Myint KS, Sasmono RT, Frost SDW. Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia. Virol J 2020; 17:24. [PMID: 32054488 PMCID: PMC7020346 DOI: 10.1186/s12985-020-1294-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome. Methods We evaluated a method designed to address this challenge, using the ‘Primal Scheme’ multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and by phylogenetic analysis. Results The multiplex approach proved capable of producing near complete coding-region coverage from all samples tested (\documentclass[12pt]{minimal}
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\begin{document}$$ \overline{x} $$\end{document}x¯ = 99.96%, n = 18), 61% of which could not be fully amplified using the current, long-amplicon PCR, approach. Nanopore-generated consensus sequences were found to be between 99.17–99.92% identical to those produced by high-coverage Illumina sequencing. Consensus accuracy could be improved by masking regions below 20X coverage depth (99.69–99.92%). However, coding-region coverage was reduced at this depth (\documentclass[12pt]{minimal}
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\begin{document}$$ \overline{x} $$\end{document}x¯ = 93.48%). Nanopore and Illumina consensus sequences generated from the same samples formed monophyletic clades on phylogenetic analysis, and Indonesian consensus sequences accurately clustered by geographical origin. Conclusion The multiplex, short-amplicon approach proved superior for amplifying DENV genomes from clinical samples, particularly when the virus was present at low concentrations. The accuracy of Nanopore-generated consensus sequences from these amplicons was sufficient for identifying the geographic origin of the samples, demonstrating that the approach can be a useful tool for identifying and monitoring DENV clades circulating in low-resource settings across Indonesia. However, the inaccuracies in Nanopore-generated consensus sequences mean that the approach may not be appropriate for higher resolution transmission studies, particularly when more accurate sequencing technologies are available.
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Affiliation(s)
- Samuel C B Stubbs
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.
| | - Barbara A Blacklaws
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | | | | | - Rahma F Hayati
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Brian Schwem
- University of Philippines Manila, Manila, Philippines
| | | | | | - James S Lester
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK
| | - Khin S Myint
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK.,The Alan Turing Institution, London, UK.,Present address: London School of Hygiene and Tropical Medicine, London, UK.,Microsoft Healthcare, Redmond, USA
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Serotype‐specific differences in the laboratory parameters among hospitalized children with dengue and genetic diversity of dengue viruses circulating in Tamil Nadu, India during 2017. J Med Virol 2019; 92:1013-1022. [DOI: 10.1002/jmv.25639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022]
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Kobres PY, Chretien JP, Johansson MA, Morgan JJ, Whung PY, Mukundan H, Del Valle SY, Forshey BM, Quandelacy TM, Biggerstaff M, Viboud C, Pollett S. A systematic review and evaluation of Zika virus forecasting and prediction research during a public health emergency of international concern. PLoS Negl Trop Dis 2019; 13:e0007451. [PMID: 31584946 PMCID: PMC6805005 DOI: 10.1371/journal.pntd.0007451] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/22/2019] [Accepted: 08/27/2019] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Epidemic forecasting and prediction tools have the potential to provide actionable information in the midst of emerging epidemics. While numerous predictive studies were published during the 2016-2017 Zika Virus (ZIKV) pandemic, it remains unknown how timely, reproducible, and actionable the information produced by these studies was. METHODS To improve the functional use of mathematical modeling in support of future infectious disease outbreaks, we conducted a systematic review of all ZIKV prediction studies published during the recent ZIKV pandemic using the PRISMA guidelines. Using MEDLINE, EMBASE, and grey literature review, we identified studies that forecasted, predicted, or simulated ecological or epidemiological phenomena related to the Zika pandemic that were published as of March 01, 2017. Eligible studies underwent evaluation of objectives, data sources, methods, timeliness, reproducibility, accessibility, and clarity by independent reviewers. RESULTS 2034 studies were identified, of which n = 73 met the eligibility criteria. Spatial spread, R0 (basic reproductive number), and epidemic dynamics were most commonly predicted, with few studies predicting Guillain-Barré Syndrome burden (4%), sexual transmission risk (4%), and intervention impact (4%). Most studies specifically examined populations in the Americas (52%), with few African-specific studies (4%). Case count (67%), vector (41%), and demographic data (37%) were the most common data sources. Real-time internet data and pathogen genomic information were used in 7% and 0% of studies, respectively, and social science and behavioral data were typically absent in modeling efforts. Deterministic models were favored over stochastic approaches. Forty percent of studies made model data entirely available, 29% provided all relevant model code, 43% presented uncertainty in all predictions, and 54% provided sufficient methodological detail to allow complete reproducibility. Fifty-one percent of predictions were published after the epidemic peak in the Americas. While the use of preprints improved the accessibility of ZIKV predictions by a median of 119 days sooner than journal publication dates, they were used in only 30% of studies. CONCLUSIONS Many ZIKV predictions were published during the 2016-2017 pandemic. The accessibility, reproducibility, timeliness, and incorporation of uncertainty in these published predictions varied and indicates there is substantial room for improvement. To enhance the utility of analytical tools for outbreak response it is essential to improve the sharing of model data, code, and preprints for future outbreaks, epidemics, and pandemics.
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Affiliation(s)
- Pei-Ying Kobres
- School of Public Health, George Washington University, Washington, DC, United States of America
| | | | - Michael A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, Atlanta, Georgia, United States of America
| | - Jeffrey J. Morgan
- Joint Research and Development Inc, Stafford, Virginia, United States of America
| | - Pai-Yei Whung
- Office of Research & Development, US Environmental Protection Agency, Washington, DC, United States of America
| | - Harshini Mukundan
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Sara Y. Del Valle
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brett M. Forshey
- Armed Forces Health Surveillance Branch, Silver Spring, Maryland, United States of America
| | - Talia M. Quandelacy
- Division of Vector-Borne Diseases, Centers for Disease Control & Prevention, Atlanta, Georgia, United States of America
- Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Matthew Biggerstaff
- Influenza Division, Centers for Disease Control & Prevention, Atlanta, Georgia, United States of America
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Department of Preventive Medicine & Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Marie Bashir Institute, University of Sydney, Sydney, New South Wales, Australia
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Yuzon MK, Kim JH, Kim S. A Novel Paper-plastic Microfluidic Hybrid Chip Integrated with a Lateral Flow Immunoassay for Dengue Nonstructural Protein 1 Antigen Detection. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3305-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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45
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Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ. Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. PLoS Comput Biol 2019; 15:e1007189. [PMID: 31386651 PMCID: PMC6684064 DOI: 10.1371/journal.pcbi.1007189] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 06/17/2019] [Indexed: 11/25/2022] Open
Abstract
Model-based phylodynamic approaches recently employed generalized linear models (GLMs) to uncover potential predictors of viral spread. Very recently some of these models have allowed both the predictors and their coefficients to be time-dependent. However, these studies mainly focused on predictors that are assumed to be constant through time. Here we inferred the phylodynamics of avian influenza A virus H9N2 isolated in 12 Asian countries and regions under both discrete trait analysis (DTA) and structured coalescent (MASCOT) approaches. Using MASCOT we applied a new time-dependent GLM to uncover the underlying factors behind H9N2 spread. We curated a rich set of time-series predictors including annual international live poultry trade and national poultry production figures. This time-dependent phylodynamic prediction model was compared to commonly employed time-independent alternatives. Additionally the time-dependent MASCOT model allowed for the estimation of viral effective sub-population sizes and their changes through time, and these effective population dynamics within each country were predicted by a GLM. International annual poultry trade is a strongly supported predictor of virus migration rates. There was also strong support for geographic proximity as a predictor of migration rate in all GLMs investigated. In time-dependent MASCOT models, national poultry production was also identified as a predictor of virus genetic diversity through time and this signal was obvious in mainland China. Our application of a recently introduced time-dependent GLM predictors integrated rich time-series data in Bayesian phylodynamic prediction. We demonstrated the contribution of poultry trade and geographic proximity (potentially unheralded wild bird movements) to avian influenza spread in Asia. To gain a better understanding of the drivers of H9N2 spread, we suggest increased surveillance of the H9N2 virus in countries that are currently under-sampled as well as in wild bird populations in the most affected countries.
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Affiliation(s)
- Jing Yang
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
- School of Computer Science, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
| | - Nicola F. Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Remco Bouckaert
- School of Computer Science, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Bing Xu
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
- Department of Earth System Science, Tsinghua University, Beijing, China
| | - Alexei J. Drummond
- School of Computer Science, University of Auckland, Auckland, New Zealand
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
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Abstract
This is a selective review of recent publications on dengue clinical features, epidemiology, pathogenesis, and vaccine development placed in a context of observations made over the past half century. Four dengue viruses (DENVs) are transmitted by urban cycle mosquitoes causing diseases whose nature and severity are influenced by interacting factors such as virus, age, immune status of the host, and human genetic variability. A phenomenon that controls the kinetics of DENV infection, antibody-dependent enhancement, best explains the correlation of the vascular permeability syndrome with second heterotypic DENV infections and infection in the presence of passively acquired antibodies. Based on growing evidence in vivo and in vitro, the tissue-damaging DENV non-structural protein 1 (NS1) is responsible for most of the pathophysiological features of severe dengue. This review considers the contribution of hemophagocytic histiocytosis syndrome to cases of severe dengue, the role of movement of humans in dengue epidemiology, and modeling and planning control programs and describes a country-wide survey for dengue infections in Bangladesh and efforts to learn what controls the clinical outcome of dengue infections. Progress and problems with three tetravalent live-attenuated vaccines are reviewed. Several research mysteries remain: why is the risk of severe disease during second heterotypic DENV infection so low, why is the onset of vascular permeability correlated with defervescence, and what are the crucial components of protective immunity?
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Affiliation(s)
- Scott Halstead
- Emeritus Professor, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
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Masel J, McCracken MK, Gleeson T, Morrison B, Rutherford G, Imrie A, Jarman RG, Koren M, Pollett S. Does prior dengue virus exposure worsen clinical outcomes of Zika virus infection? A systematic review, pooled analysis and lessons learned. PLoS Negl Trop Dis 2019; 13:e0007060. [PMID: 30682026 PMCID: PMC6370234 DOI: 10.1371/journal.pntd.0007060] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 02/11/2019] [Accepted: 12/06/2018] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV) recently caused a pandemic complicated by Guillain-Barre syndrome (GBS) and birth defects. ZIKV is structurally similar to the dengue viruses (DENV) and in vitro studies suggest antibody dependent enhancement occurs in ZIKV infections preceded by DENV; however, the clinical significance of this remains unclear. We undertook a PRISMA-adherent systematic review of all current human and non-human primate (NHP) data to determine if prior infection with DENV, compared to DENV-naïve hosts, is associated with a greater risk of ZIKV clinical complications or greater ZIKV peak viremia in vivo. We identified 1146 studies in MEDLINE, EMBASE and the grey literature, of which five studies were eligible. One human study indicated no increase in the risk of GBS in ZIKV infections with prior DENV exposure. Two additional human studies showed a small increase in ZIKV viremia in those with prior DENV exposure; however, this was not statistically significant nor was it associated with an increase in clinical severity or adverse pregnancy outcomes. While no meta-analysis was possible using human data, a pooled analysis of the two NHP studies leveraging extended data provided only weak evidence of a 0.39 log10 GE/mL rise in ZIKV viremia in DENV experienced rhesus macaques compared to those with no DENV exposure (p = 0.22). Using a customized quality grading criteria, we further show that no existing published human studies have offered high quality measurement of both acute ZIKV and antecedent DENV infections. In conclusion, limited human and NHP studies indicate a small and non-statistically significant increase in ZIKV viremia in DENV-experienced versus DENV-naïve hosts; however, there is no evidence that even a possible small increase in ZIKV viremia would correlate with a change in ZIKV clinical phenotype. More data derived from larger sample sizes and improved sero-assays are needed to resolve this question, which has major relevance for clinical prognosis and vaccine design. Zika virus (ZIKV) is a mosquito borne virus that recently caused a large epidemic with some cases complicated by ascending paralysis (Guillain-Barre syndrome) and birth defects. One major concern is that such complications may be more common in those who have had previous infection with the closely related mosquito-borne dengue virus (DENV) which also circulates in the tropics. Here, we undertook a thorough, structured review of all human and high-order animal literature to synthesize the current evidence about whether ZIKV outcomes are worse in those with previous DENV exposure. We further undertook a pooled analysis across the two major non-human primate studies to improve statistical power. We summarize that, in humans and in non-human primates, prior DENV exposure may lead to a small increase in ZIKV viral load during infection. However, we do not show that any possible increase in ZIKV viral replication is associated with a higher rate of Zika complications or Zika clinical severity. We further graded the quality of these published literature and indicate that substantial improvements in the immunological measurement of ZIKV and DENV exposure in humans are needed to answer these and other pertinent questions about these two epidemic pathogens.
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Affiliation(s)
- Jennifer Masel
- Department of Medicine, USUHS, Bethesda, MD, United States of America
| | - Michael K. McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Todd Gleeson
- Department of Medicine, USUHS, Bethesda, MD, United States of America
| | - Brian Morrison
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - George Rutherford
- Institute for Global Health Sciences, University of California, San Francisco, CA, United States of America
| | - Allison Imrie
- University of Western Australia, Perth, WA, Australia
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Michael Koren
- Department of Medicine, USUHS, Bethesda, MD, United States of America
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Department of Preventive Medicine & Biostatistics, USUHS, Bethesda, MD, United States of America
- Marie Bashir Institute for Infectious Diseases, University of Sydney, Camperdown, NSW, Australia
- * E-mail:
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Should travellers be offered vaccination against the dengue virus? Travel Med Infect Dis 2019; 27:2-4. [DOI: 10.1016/j.tmaid.2018.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 11/24/2022]
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Phadungsombat J, Lin MYC, Srimark N, Yamanaka A, Nakayama EE, Moolasart V, Suttha P, Shioda T, Uttayamakul S. Emergence of genotype Cosmopolitan of dengue virus type 2 and genotype III of dengue virus type 3 in Thailand. PLoS One 2018; 13:e0207220. [PMID: 30419004 PMCID: PMC6231660 DOI: 10.1371/journal.pone.0207220] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/26/2018] [Indexed: 01/27/2023] Open
Abstract
Dengue is a mosquito-borne disease that has spread to over 100 countries. Dengue fever is caused by dengue virus (DENV), which belongs to the Flavivirus genus of the family Flaviviridae. DENV comprises 4 serotypes (DENV-1 to DENV-4), and each serotype is divided into distinct genotypes. Thailand is an endemic area where all 4 serotypes of DENV co-circulate. To understand the current genotype distribution of DENVs in Thailand, we enrolled 100 cases of fever with dengue-like symptoms at the Bamrasnaradura Infectious Diseases Institute during 2016–2017. Among them, 37 cases were shown to be dengue-positive by real-time PCR. We were able to isolate DENVs from 21 cases, including 1 DENV-1, 8 DENV-2, 4 DENV-3, and 8 DENV-4. To investigate the divergence of the viruses, RNA was extracted from isolated DENVs and viral near-whole genome sequences were determined. Phylogenetic analysis of the obtained viral sequences revealed that DENV-2 genotype Cosmopolitan was co-circulating with DENV-2 genotype Asian-I, the previously predominating genotype in Thailand. Furthermore, DENV-3 genotype III was found instead of DENV-3 genotype II. The DENV-2 Cosmopolitan and DENV-3 genotype III found in Thailand were closely related to the respective strains found in nearby countries. These results indicated that DENVs in Thailand have increased in genotypic diversity, and suggested that the DENV genotypic shift observed in other Asian countries also might be taking place in Thailand.
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Affiliation(s)
- Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Narinee Srimark
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Atsushi Yamanaka
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Visal Moolasart
- Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand
| | - Patama Suttha
- Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- * E-mail:
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