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de Souza CS, Caleiro GS, Claro IM, de Jesus JG, Coletti TM, da Silva CAM, Costa ÂA, Inenami M, Ribeiro AC, Felix AC, de Paula AV, Figueiredo WM, de Albuquerque Luna EJ, Sabino EC, Romano CM. Phylogenetics, Epidemiology and Temporal Patterns of Dengue Virus in Araraquara, São Paulo State. Viruses 2024; 16:274. [PMID: 38400049 PMCID: PMC10892747 DOI: 10.3390/v16020274] [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: 11/23/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
Dengue virus (DENV) is a prominent arbovirus with global spread, causing approximately 390 million infections each year. In Brazil, yearly epidemics follow a well-documented pattern of serotype replacement every three to four years on average. Araraquara, located in the state of São Paulo, has faced significant impacts from DENV epidemics since the emergence of DENV-1 in 2010. The municipality then transitioned from low to moderate endemicity in less than 10 years. Yet, there remains an insufficient understanding of virus circulation dynamics, particularly concerning DENV-1, in the region, as well as the genetic characteristics of the virus. To address this, we sequenced 37 complete or partial DENV-1 genomes sampled from 2015 to 2022 in Araraquara. Then, using also Brazilian and worldwide DENV-1 sequences we reconstructed the evolutionary history of DENV-1 in Araraquara and estimated the time to the most recent common ancestor (tMRCA) for serotype 1, for genotype V and its main lineages. Within the last ten years, there have been at least three introductions of genotype V in Araraquara, distributed in two main lineages (L Ia and L Ib, and L II). The tMRCA for the first sampled lineage (2015/2016 epidemics) was approximately 15 years ago (in 2008). Crucially, our analysis challenges existing assumptions regarding the emergence time of the DENV-1 genotypes, suggesting that genotype V might have diverged more recently than previously described. The presence of the two lineages of genotype V in the municipality might have contributed to the extended persistence of DENV-1 in the region.
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Affiliation(s)
- Caio Santos de Souza
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
| | - Giovana Santos Caleiro
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil
| | - Ingra Morales Claro
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
- MRC Center for Global Infectious Disease Analysis, Imperial College London, London SW7 2AZ, UK
| | - Jaqueline Goes de Jesus
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
- Instituto Oswaldo Cruz, Salvador 21040-900, BA, Brazil
| | - Thaís Moura Coletti
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
| | - Camila Alves Maia da Silva
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
| | - Ângela Aparecida Costa
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Marta Inenami
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Andreia C. Ribeiro
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Alvina Clara Felix
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
| | - Anderson Vicente de Paula
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
| | - Walter M. Figueiredo
- Serviço Especial de Saúde de Araraquara-SESA, Faculdade de Saúde Pública da USP, São Paulo 01246-904, SP, Brazil; (Â.A.C.); (M.I.); (A.C.R.); (W.M.F.)
| | - Expedito José de Albuquerque Luna
- Departamento de Medicina Preventiva/Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil;
| | - Ester C. Sabino
- Laboratório de Parasitologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (I.M.C.); (J.G.d.J.); (T.M.C.); (C.A.M.d.S.); (E.C.S.)
| | - Camila M. Romano
- Laboratório de Virologia, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (C.S.d.S.); (G.S.C.); (A.C.F.); (A.V.d.P.)
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HCFMUSP), São Paulo 05403-010, SP, Brazil
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Thongsripong P, Edgerton SV, Bos S, Saborío S, Kuan G, Balmaseda A, Harris E, Bennett SN. Phylodynamics of dengue virus 2 in Nicaragua leading up to the 2019 epidemic reveals a role for lineage turnover. BMC Ecol Evol 2023; 23:58. [PMID: 37770825 PMCID: PMC10537812 DOI: 10.1186/s12862-023-02156-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Dengue is a mosquito-borne viral disease posing a significant threat to public health. Dengue virus (DENV) evolution is often characterized by lineage turnover, which, along with ecological and immunological factors, has been linked to changes in dengue phenotype affecting epidemic dynamics. Utilizing epidemiologic and virologic data from long-term population-based studies (the Nicaraguan Pediatric Dengue Cohort Study and Nicaraguan Dengue Hospital-based Study), we describe a lineage turnover of DENV serotype 2 (DENV-2) prior to a large dengue epidemic in 2019. Prior to this epidemic, Nicaragua had experienced relatively low levels of DENV transmission from 2014 to 2019, a period dominated by chikungunya in 2014/15 and Zika in 2016. RESULTS Our phylogenetic analyses confirmed that all Nicaraguan DENV-2 isolates from 2018 to 2019 formed their own clade within the Nicaraguan lineage of the Asian/American genotype. The emergence of the new DENV-2 lineage reflects a replacement of the formerly dominant clade presiding from 2005 to 2009, a lineage turnover marked by several shared derived amino acid substitutions throughout the genome. To elucidate evolutionary drivers of lineage turnover, we performed selection pressure analysis and reconstructed the demographic history of DENV-2. We found evidence of adaptive evolution by natural selection at the codon level as well as in branch formation. CONCLUSIONS The timing of its emergence, along with a statistical signal of adaptive evolution and distinctive amino acid substitutions, the latest in the NS5 gene, suggest that this lineage may have increased fitness relative to the prior dominant DENV-2 strains. This may have contributed to the intensity of the 2019 DENV-2 epidemic, in addition to previously identified immunological factors associated with pre-existing Zika virus immunity.
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Affiliation(s)
- Panpim Thongsripong
- Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, FL, USA
| | - Sean V Edgerton
- Interdisciplinary Studies Graduate Program, The University of British Columbia, Vancouver, BC, Canada
| | - Sandra Bos
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Saira Saborío
- Centro Nacional de Diagnóstico y Referencia, Laboraorio Nacional de Virología, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Angel Balmaseda
- Centro Nacional de Diagnóstico y Referencia, Laboraorio Nacional de Virología, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Shannon N Bennett
- Department of Microbiology, California Academy of Sciences, San Francisco, CA, USA.
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Chen L, Zhang X, Guo X, Peng W, Zhu Y, Wang Z, Yu X, Shi H, Li Y, Zhang L, Wang L, Wang P, Cheng G. Neighboring mutation-mediated enhancement of dengue virus infectivity and spread. EMBO Rep 2022; 23:e55671. [PMID: 36197120 PMCID: PMC9638853 DOI: 10.15252/embr.202255671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 10/07/2023] Open
Abstract
Frequent turnover of dengue virus (DENV) clades is one of the major forces driving DENV persistence and prevalence. In this study, we assess the fitness advantage of nine stable substitutions within the envelope (E) protein of DENV serotypes. Two tandem neighboring substitutions, threonine to lysine at the 226th (T226K) and glycine to glutamic acid at the 228th (G228E) residues in the DENV2 Asian I genotype, enhance virus infectivity in either mosquitoes or mammalian hosts, thereby promoting clades turnover and dengue epidemics. Mechanistic studies indicate that the substitution-mediated polarity changes in these two residues increase the binding affinity of E for host C-type lectins. Accordingly, we predict that a G228E substitution could potentially result in a forthcoming epidemic of the DENV2 Cosmopolitan genotype. Investigations into the substitutions associated with DENV fitness in hosts may offer mechanistic insights into dengue prevalence, thus providing a warning of potential epidemics in the future.
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Affiliation(s)
- Lu Chen
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Xianwen Zhang
- Institute of Infectious DiseasesShenzhen Bay LaboratoryShenzhenChina
| | - Xuan Guo
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Wenyu Peng
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Yibin Zhu
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Zhaoyang Wang
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Xi Yu
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Huicheng Shi
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Yuhan Li
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Liming Zhang
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
| | - Lei Wang
- Institute of Infectious DiseasesShenzhen Bay LaboratoryShenzhenChina
| | - Penghua Wang
- Department of Immunology, School of Medicinethe University of Connecticut Health CenterFarmingtonCTUSA
| | - Gong Cheng
- Tsinghua‐Peking Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Institute of Infectious DiseasesShenzhen Bay LaboratoryShenzhenChina
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4
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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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5
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Inizan C, Minier M, Prot M, O’Connor O, Forfait C, Laumond S, Marois I, Biron A, Gourinat AC, Goujart MA, Descloux E, Sakuntabhai A, Tarantola A, Simon-Lorière E, Dupont-Rouzeyrol M. Viral evolution sustains a dengue outbreak of enhanced severity. Emerg Microbes Infect 2021; 10:536-544. [PMID: 33686914 PMCID: PMC8011692 DOI: 10.1080/22221751.2021.1899057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/18/2021] [Accepted: 03/01/2021] [Indexed: 01/21/2023]
Abstract
Compared to the previous 2013-2014 outbreak, dengue 2016-2017 outbreak in New Caledonia was characterized by an increased number of severe forms associated with hepatic presentations. In this study, we assessed the virological factors associated with this enhanced severity. Whole-genome sequences were retrieved from dengue virus (DENV)-1 strains collected in 2013-2014 and from severe and non-severe patients in 2016-2017. Fitness, hepatic tropism and cytopathogenicity of DENV 2016-2017 strains were compared to those of 2013-2014 strains using replication kinetics in the human hepatic cell line HuH7. Whole-genome sequencing identified four amino acid substitutions specific to 2016-2017 strains and absent from 2013-2014 strains. Three of these mutations occurred in predicted T cell epitopes, among which one was also a B cell epitope. Strains retrieved from severe forms did not exhibit specific genetic features. DENV strains from 2016-2017 exhibited a trend towards reduced replicative fitness and cytopathogenicity in vitro compared to strains from 2013-2014. Overall, the 2016-2017 dengue outbreak in New Caledonia was associated with a viral genetic evolution which had limited impact on DENV hepatic tropism and cytopathogenicity. These mutations, however, may have modified DENV strains antigenicity, altering the anti-DENV immune response in some patients, in turn favoring the development of severe forms.Trial registration: ClinicalTrials.gov identifier: NCT04615364.
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Affiliation(s)
- Catherine Inizan
- URE Dengue and Arboviruses, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Nouméa, New Caledonia
| | - Marine Minier
- URE Dengue and Arboviruses, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Nouméa, New Caledonia
| | - Matthieu Prot
- Evolutionary genomics of RNA viruses, Institut Pasteur, Paris, France
| | - Olivia O’Connor
- URE Dengue and Arboviruses, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Nouméa, New Caledonia
| | | | | | - Ingrid Marois
- Internal medicine and infectious diseases department, Territorial Hospital Center (CHT), Dumbéa, New Caledonia
| | - Antoine Biron
- Microbiology laboratory, Territorial Hospital Center (CHT), Dumbéa, New Caledonia
| | - Ann-Claire Gourinat
- Microbiology laboratory, Territorial Hospital Center (CHT), Dumbéa, New Caledonia
| | - Marie-Amélie Goujart
- Microbiology laboratory, Territorial Hospital Center (CHT), Dumbéa, New Caledonia
| | - Elodie Descloux
- Internal medicine and infectious diseases department, Territorial Hospital Center (CHT), Dumbéa, New Caledonia
| | - Anavaj Sakuntabhai
- Functional genetics of infectious diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique évolutive, modélisation et santé (GEMS), Paris, France
| | - Arnaud Tarantola
- URE Epidemiology, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Nouméa, New Caledonia
| | | | - Myrielle Dupont-Rouzeyrol
- URE Dengue and Arboviruses, Institut Pasteur in New Caledonia, Institut Pasteur International Network, Nouméa, New Caledonia
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Molecular epidemiology of dengue in North Kalimantan, a province with the highest incidence rates in Indonesia in 2019. INFECTION GENETICS AND EVOLUTION 2021; 95:105036. [PMID: 34411743 DOI: 10.1016/j.meegid.2021.105036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Dengue is endemic to Indonesia, a country that has largely varied geographical and demographic conditions across different regions. In 2019, dengue epidemic occurred in North Kalimantan province and recorded as the highest incidence rate in Indonesia. This study aims to investigate the molecular epidemiology of dengue during outbreak in the province and compare the epidemiological characteristics between two cities/towns in North Kalimantan, namely Malinau, an inland town surrounded by a dense rainforest, and Tarakan, an island city. METHODS A cross sectional study was conducted between September 2018 and July 2019. Dengue-like illness patients were recruited in hospitals and tested for dengue NS1 and IgG/IgM. Serological prevalence was measured using IgG ELISA, dengue virus (DENV) serotyping was conducted using RT-PCR and Envelope gene sequencing was performed to infer the virus origins and phylogeny. Clinical, demographical, and diagnostics data were also recorded and analyzed. RESULTS We recruited 523 patients, 261 from Malinau and 262 from Tarakan. Among them, 349 patients were confirmed dengue. Cases in Malinau had a higher proportion of confirmed dengue (82.0%) compared to those in Tarakan (51.5%). Cases in Malinau were more likely to be dengue hemorrhagic fever with more severe hematological features compared to those in Tarakan. All four DENV serotypes were detected in both cities, the most prevalent serotype being DENV-2. The genetic characteristics of the viruses in the two towns was similar except for DENV-3. No sylvatic DENV was detected as well as alphaviruses and non-dengue flaviviruses during the outbreak. CONCLUSIONS The molecular epidemiology of dengue in North Kalimantan revealed the similar virological characteristics but different clinical and demographic aspects in Malinau and Tarakan. The distinct dengue dynamics between different regions of Indonesia is prominent and this knowledge will be important for understanding future patterns of DENV transmission in the region.
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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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O'Connor O, Ou TP, Aubry F, Dabo S, Russet S, Girault D, In S, Minier M, Lequime S, Hoem T, Boyer S, Dussart P, Pocquet N, Burtet-Sarramegna V, Lambrechts L, Duong V, Dupont-Rouzeyrol M. Potential role of vector-mediated natural selection in dengue virus genotype/lineage replacements in two epidemiologically contrasted settings. Emerg Microbes Infect 2021; 10:1346-1357. [PMID: 34139961 PMCID: PMC8259877 DOI: 10.1080/22221751.2021.1944789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dengue virus (DENV) evolutionary dynamics are characterized by frequent DENV genotype/lineage replacements, potentially associated with changes in disease severity and human immunity. New Caledonia (NC) and Cambodia, two contrasted epidemiological settings, respectively experienced a DENV-1 genotype IV to I replacement in 2012 and a DENV-1 genotype I lineage 3–4 replacement in 2005–2007, both followed by a massive dengue outbreak. However, their underlying evolutionary drivers have not been elucidated. Here, we tested the hypothesis that these genotype/lineage switches reflected a higher transmission fitness of the replacing DENV genotype/lineage in the mosquito vector using in vivo competition experiments. For this purpose, field-derived Aedes aegypti from NC and Cambodia were orally challenged with epidemiologically relevant pairs of four DENV-1 genotype I and IV strains from NC or four DENV-1 genotype I lineage 3 and 4 strains from Cambodia, respectively. The relative transmission fitness of each DENV-1 genotype/lineage was measured by quantitative RT–PCR for infection, dissemination, and transmission rates. Results showed a clear transmission fitness advantage of the replacing DENV-1 genotype I from NC within the vector. A similar but more subtle pattern was observed for the DENV-1 lineage 4 replacement in Cambodia. Our results support the hypothesis that vector-driven selection contributed to the DENV-1 genotype/lineage replacements in these two contrasted epidemiological settings, and reinforce the idea that natural selection taking place within the mosquito vector plays an important role in DENV short-term evolutionary dynamics.
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Affiliation(s)
- Olivia O'Connor
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Tey Putita Ou
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sylvie Russet
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Dominique Girault
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Saraden In
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Marine Minier
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Sebastian Lequime
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Thavry Hoem
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Sébastien Boyer
- Medical Entomology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Nicolas Pocquet
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Valérie Burtet-Sarramegna
- Institute For Exact and Applied Sciences, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Veasna Duong
- Medical Entomology Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
| | - Myrielle Dupont-Rouzeyrol
- Dengue and Arboviruses Research and Expertise Unit, Institut Pasteur de Nouvelle-Calédonie, Institut Pasteur International Network, Noumea, New Caledonia
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9
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Ngwe Tun MM, Kyaw AK, Nabeshima T, Soe AM, Nwe KM, Htet KKK, Aung TH, Htwe TT, Aung T, Myaing SS, Mar TT, Lwin EP, Thu HM, Thant KZ, Morita K. Detection of genotype-1 of dengue virus serotype 3 for the first time and complete genome analysis of dengue viruses during the 2018 epidemic in Mandalay, Upper Myanmar. PLoS One 2021; 16:e0251314. [PMID: 34086703 PMCID: PMC8177515 DOI: 10.1371/journal.pone.0251314] [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: 02/01/2021] [Accepted: 04/24/2021] [Indexed: 11/24/2022] Open
Abstract
Background Dengue (DEN) is a neglected tropical disease, and surveillance of dengue virus (DENV) serotypes and genotypes is critical for the early detection of outbreaks. Risk factors for outbreaks include the emergence of new genotypes and serotype shifting. Methodology and principal findings To understand the genomic and viral characteristics of DENV-infected patients, we conducted a cross-sectional descriptive study among pediatric patients admitted at the 550-bedded Mandalay Children Hospital during the 2018 DEN endemic season. We conducted virus isolation, serological tests, viremia level measurement, and whole-genome sequencing. Among the 202 serum samples, we detected 85 samples with DENV (46 DENV-1, 10 DENV-3, 26 DENV-4 and three multiple serotype co-infections) via reverse transcription quantitative/real-time PCR (RT-qPCR), and we obtained 49 DENV isolates (31 DENV-1, 10 DENV-3 and 8 DEN-4). We did not detect DENV-2 in this study. The viral genome levels in serum did not differ significantly among virus serotypes, infection status (primary versus secondary) and disease severity. Based on the phylogenetic analysis, we identified DENV-1 genotype-1, DENV-4 genotype-1 and DENV-3 genotype-3 and genotype-1 which was detected for the first time. Next-generation sequencing analysis revealed greater frequencies of nonsynonymous and synonymous mutations per gene in the nonstructural genes. Moreover, mutation rates were also higher among DENV-1. Conclusion/Significance In conclusion, there was an increasing trend of DENV-3 cases during DENV endemic season in 2018 with the first detection of the genotype 1. However, DENV-1 has remained the predominant serotype in this study area since 2013, and we identified stop codon mutations in the DENV-1 genome. This report is the first to feature a complete genome analysis of the strains of DENV-3 and DENV-4 circulating among pediatric patients in Myanmar. This study highlighted the importance of annual surveillance for a better understanding of the molecular epidemiology of DENVs.
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Affiliation(s)
- Mya Myat Ngwe Tun
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- * E-mail: (MMNT); (KM)
| | - Aung Kyaw Kyaw
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Aung Min Soe
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Khine Mya Nwe
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Kyaw Ko Ko Htet
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Thet Htoo Aung
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Thein Thein Htwe
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Thidar Aung
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Su Su Myaing
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Tu Tu Mar
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Ei Phyu Lwin
- Department of Medical Services, 550 Bedded Children Hospital (Mandalay), Ministry of Health and Sports, Mandalay, Myanmar
| | - Hlaing Myat Thu
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | | | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- * E-mail: (MMNT); (KM)
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10
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Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka. Viruses 2021; 13:v13030421. [PMID: 33807922 PMCID: PMC8001906 DOI: 10.3390/v13030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Genetic variations in dengue virus (DENV) play a distinct role in epidemic emergence. The DENV 3′ UTR has become a recent interest in research. The objective of the study was to examine the genetic variation in the domain II, 3′ UTR region of human and mosquito-derived DENV. DENV-infected human sera were orally infected to laboratory reared Aedes aegypti mosquitoes. The domain II, 3′ UTR of each human- and mosquito-derived sample was amplified. The nucleotide sequence variation, phylogenetic and secondary structure analysis was carried out incorporating respective regions of so far recorded Sri Lankan and the reference genotype strains of the DENV3 and DENV1 serotypes. The human- and mosquito-derived domain II, 3′ UTR were identical in nucleotide sequences within the serotypes isolated, indicating the conserved nature of the region during host switch. The sequence analysis revealed distinct variations in study isolates compared to so far recorded Sri Lankan isolates. However, despite single nucleotide variations, the maintenance of structural integrity was evident in related strains within the serotypes in the secondary structure analysis. The phylogenetic analysis revealed distinct clade segregation of the study sequences from so far reported Sri Lankan isolates and illustrated the phylogenetic relations of the study sequences to the available global isolates of respective serotypes.
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11
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Ma M, Wu S, He Z, Yuan L, Bai Z, Jiang L, Marshall J, Lu J, Yang Z, Jing Q. New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China. Parasit Vectors 2021; 14:126. [PMID: 33639996 PMCID: PMC7910771 DOI: 10.1186/s13071-021-04631-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/06/2021] [Indexed: 11/26/2022] Open
Abstract
Background Dengue fever is a mosquito-borne infectious disease that has caused major health problems. Variations in dengue virus (DENV) genes are important features of epidemic outbreaks. However, the associations of DENV genes with epidemic potential have not been extensively examined. Here, we assessed new genotype invasion of DENV-1 isolated from Guangzhou in China to evaluate associations with epidemic outbreaks. Methodology/principal findings We used DENV-1 strains isolated from sera of dengue cases from 2002 to 2016 in Guangzhou for complete genome sequencing. A neighbor-joining phylogenetic tree was constructed to elucidate the genotype characteristics and determine if new genotype invasion was correlated with major outbreaks. In our study, a new genotype invasion event was observed during each significant outbreak period in 2002–2003, 2006–2007, and 2013–2014. Genotype II was the main epidemic genotype in 2003 and before. Invasion of genotype I in 2006 caused an unusual outbreak with 765 cases (relative risk [RR] = 16.24, 95% confidence interval [CI] 12.41–21.25). At the middle and late stages of the 2013 outbreak, genotype III was introduced to Guangzhou as a new genotype invasion responsible for 37,340 cases with RR 541.73 (95% CI 417.78–702.45), after which genotypes I and III began co-circulating. Base mutations occurred after new genotype invasion, and the gene sequence of NS3 protein had the lowest average similarity ratio (99.82%), followed by the gene sequence of E protein (99.86%), as compared to the 2013 strain. Conclusions/significance Genotype replacement and co-circulation of multiple DENV-1 genotypes were observed. New genotype invasion was highly correlated with local unusual outbreaks. In addition to DENV-1 genotype I in the unprecedented outbreak in 2014, new genotype invasion by DENV-1 genotype III occurred in Guangzhou.![]()
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Affiliation(s)
- Mengmeng Ma
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - Sean Wu
- Department of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Zhenjian He
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Lihong Yuan
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong, People's Republic of China
| | - Zhijun Bai
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - Liyun Jiang
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - John Marshall
- Department of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Jiahai Lu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Zhicong Yang
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China
| | - Qinlong Jing
- Department of Infectious Diseases, Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, People's Republic of China.
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12
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Punpapong V, Sittivicharpinyo T, Wonnapinij P, Surat W. Phylogenetic and recombinant analyses of complete coding sequences of DENV-1 from field-caught mosquitoes in Thailand. Virus Res 2020; 286:198041. [PMID: 32497574 DOI: 10.1016/j.virusres.2020.198041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 11/26/2022]
Abstract
Dengue diseases are a group of infectious diseases that have been widespread throughout the world for several decades. Dengue outbreaks have occurred in many parts of the world, including Southeast Asia. The outbreak and the severity of the diseases depend on many factors including dengue genotype. Data on the genetic variation of dengue virus is highly informative for dengue protection plans and vaccine development. In this study, we focused on the analyses of genetic variation and amino acid changes of the whole coding sequences in two dengue strains isolated from Aedes mosquitoes in Bangkok, Thailand, an endemic area. The strains were identified as belonging to dengue virus serotype 1 (DENV-1) genotype I, and have unique nucleotide sequences. In the recombinant analysis, these strains were identified as recombinants derived from Chinese counterparts for both the major (DENV-1 genotype I) and the minor (DENV-1 genotype IV) parental strains. The recombination event occurred within the prM and E genes. This corresponded with the result of multiple alignments where several amino acid residues between the recombination breakpoints in the strains were identical to those in DENV-1 genotype IV. Several of the amino acid substitutions also have changed the amino acid properties, which might affect viral infection and antigenicity. These results provide insight into the genetic variation of DENV in this endemic area, which might have been involved in the dengue outbreak and high numbers of dengue haemorrhagic fever and dengue shock syndrome cases in Thailand in 2015.
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Affiliation(s)
- Vitara Punpapong
- Department of Statistics, Faculty of Commerce and Accountancy, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Thikhumporn Sittivicharpinyo
- Evolutionary Genetics and Computer Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Lat Yao District, Chatuchak, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Evolutionary Genetics and Computer Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Lat Yao District, Chatuchak, Bangkok 10900, Thailand; Centre for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand), 50 Ngam Wong Wan Road, Lat Yao District, Chatuchak, Bangkok 10900, Thailand
| | - Wunrada Surat
- Evolutionary Genetics and Computer Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Lat Yao District, Chatuchak, Bangkok 10900, Thailand; Centre for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU, Thailand), 50 Ngam Wong Wan Road, Lat Yao District, Chatuchak, Bangkok 10900, Thailand.
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13
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Finol E, Ooi EE. Evolution of Subgenomic RNA Shapes Dengue Virus Adaptation and Epidemiological Fitness. iScience 2019; 16:94-105. [PMID: 31154208 PMCID: PMC6545344 DOI: 10.1016/j.isci.2019.05.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 02/02/2019] [Accepted: 05/13/2019] [Indexed: 01/07/2023] Open
Abstract
Changes in dengue virus (DENV) genome affect viral fitness both clinically and epidemiologically. Even in the 3′ untranslated region (3′ UTR), mutations could affect subgenomic flaviviral RNA (sfRNA) production and its affinity for host proteins, which are necessary for successful viral replication. Indeed, we recently showed that mutations in DENV2 3′ UTR of epidemic strains increased sfRNA ability to bind host proteins and reduce interferon expression. However, whether 3′ UTR differences shape the overall DENV evolution remains incompletely understood. Herein, we combined RNA phylogeny with phylogenetics to gain insights on sfRNA evolution. We found that sfRNA structures are under purifying selection and highly conserved despite sequence divergence. Only the second flaviviral nuclease-resistant RNA (fNR2) structure of DENV2 sfRNA has undergone strong positive selection. Epidemiological reports suggest that substitutions in fNR2 may drive DENV2 epidemiological fitness, possibly through sfRNA-protein interactions. Collectively, our findings indicate that 3′ UTRs are important determinants of DENV fitness in human-mosquito cycles. Dengue viruses (DENVs) preserve RNA elements in their 3′ untranslated region (UTR). Quantification of natural selection revealed positive selection on DENV2 sfRNA Flaviviral nuclease-resistant RNAs (fNR) in the 3′ UTRs contribute to DENV speciation A highly evolving fNR structure appears to increase DENV2 epidemiological fitness
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Affiliation(s)
- Esteban Finol
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Swiss Tropical and Public Health Institute, University of Basel, Basel 4051, Switzerland; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore.
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore.
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14
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Salvo MA, Aliota MT, Moncla LH, Velez ID, Trujillo AI, Friedrich TC, Osorio JE. Tracking dengue virus type 1 genetic diversity during lineage replacement in an hyperendemic area in Colombia. PLoS One 2019; 14:e0212947. [PMID: 30845200 PMCID: PMC6405123 DOI: 10.1371/journal.pone.0212947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/12/2019] [Indexed: 12/16/2022] Open
Abstract
Dengue virus (DENV) is a flavivirus responsible for the most common and burdensome arthropod-borne viral disease of humans[1]. DENV evolution has been extensively studied on broad geographic and time scales, using sequences from a single gene[2,3]. It is believed that DENV evolution in humans is dominated primarily by purifying selection due to the constraint of maintaining fitness in both humans and mosquitoes[4,5]. Few studies have explored DENV evolutionary dynamics using whole genome sequences, nor have they explored changes in viral diversity that occur during intra-epidemic periods. We used deep sequencing of the viral coding region to characterize DENV-1 evolution in a Colombian population sampled during two high-prevalence dengue seasons in which serotype dominance shifted. Our data demonstrate patterns of strain extinction and replacement within DENV-1 as its prevalence waned and DENV-3 became established. A comparison of whole-genome versus single-gene-based phylogenetic analyses highlights an important difference in evolutionary patterns. We report a trend of higher nonsynonymous to synonymous diversity ratios among non-structural (NS) genes, and statistically significantly higher values among these ratios in the NS1 gene after DENV-1 strain replacement. These results suggest that positive selection could be driving DENV evolution within individual communities. Signals of positive selection coming from distinct samples may be drowned out when combining multiple regions with differing patterns of endemic transmission as commonly done by large-scale geo-temporal assessments. Here, we frame our findings within a small, local transmission history which aids significance. Moreover, these data suggest that the NS1 gene, rather than the E gene, may be a target of positive selection, although not mutually exclusive, and potentially useful sentinel of adaptive changes at the population level.
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Affiliation(s)
- Mauricio A. Salvo
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Matthew T. Aliota
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Louise H. Moncla
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Ivan D. Velez
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellin, Colombia
| | - Andrea I. Trujillo
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Universidad de Antioquia, Medellin, Colombia
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jorge E. Osorio
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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15
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Ahamed SF, Rosario V, Britto C, Dias M, Nayak K, Chandele A, Kaja MK, Shet A. Emergence of new genotypes and lineages of dengue viruses during the 2012-15 epidemics in southern India. Int J Infect Dis 2019; 84S:S34-S43. [PMID: 30639622 DOI: 10.1016/j.ijid.2019.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012-13/2014-15 outbreaks in southern India. METHODS Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n=612), a representative selection of DENV isolates (n=99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. RESULTS In 2012-13 (n=113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014-15 (n=499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012-13 and 2014-15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012-13, ceding to GI predominance (80.8%) in 2014-15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, 'GIVc'. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. CONCLUSIONS New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.
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Affiliation(s)
- Syed Fazil Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore, 560064, Karnataka, India.
| | - Vivek Rosario
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Carl Britto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK.
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; Department of Microbiology, St. John's Medical College Hospital, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Murali-Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Pediatrics, Emory University, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
| | - Anita Shet
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, 415 N Washington St, Baltimore 21231, USA.
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16
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Nikin-Beers R, Blackwood JC, Childs LM, Ciupe SM. Unraveling within-host signatures of dengue infection at the population level. J Theor Biol 2018. [DOI: 10.1016/j.jtbi.2018.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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17
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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18
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Lourenço J, Tennant W, Faria NR, Walker A, Gupta S, Recker M. Challenges in dengue research: A computational perspective. Evol Appl 2018; 11:516-533. [PMID: 29636803 PMCID: PMC5891037 DOI: 10.1111/eva.12554] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/08/2017] [Indexed: 01/12/2023] Open
Abstract
The dengue virus is now the most widespread arbovirus affecting human populations, causing significant economic and social impact in South America and South-East Asia. Increasing urbanization and globalization, coupled with insufficient resources for control, misguided policies or lack of political will, and expansion of its mosquito vectors are some of the reasons why interventions have so far failed to curb this major public health problem. Computational approaches have elucidated on dengue's population dynamics with the aim to provide not only a better understanding of the evolution and epidemiology of the virus but also robust intervention strategies. It is clear, however, that these have been insufficient to address key aspects of dengue's biology, many of which will play a crucial role for the success of future control programmes, including vaccination. Within a multiscale perspective on this biological system, with the aim of linking evolutionary, ecological and epidemiological thinking, as well as to expand on classic modelling assumptions, we here propose, discuss and exemplify a few major computational avenues-real-time computational analysis of genetic data, phylodynamic modelling frameworks, within-host model frameworks and GPU-accelerated computing. We argue that these emerging approaches should offer valuable research opportunities over the coming years, as previously applied and demonstrated in the context of other pathogens.
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Affiliation(s)
| | - Warren Tennant
- Centre for Mathematics and the EnvironmentUniversity of ExeterPenrynUK
| | | | | | | | - Mario Recker
- Centre for Mathematics and the EnvironmentUniversity of ExeterPenrynUK
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19
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Pham Thi KL, Briant L, Gavotte L, Labbe P, Perriat-Sanguinet M, Cornillot E, Vu TD, Nguyen TY, Tran VP, Nguyen VS, Devaux C, Afelt A, Tran CC, Phan TN, Tran ND, Frutos R. Incidence of dengue and chikungunya viruses in mosquitoes and human patients in border provinces of Vietnam. Parasit Vectors 2017; 10:556. [PMID: 29121985 PMCID: PMC5680899 DOI: 10.1186/s13071-017-2422-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/03/2017] [Indexed: 11/22/2022] Open
Abstract
Background Dengue virus remains a major threat in Vietnam, while chikungunya virus is expected to become one. Surveillance was conducted from 2012 to 2014 in Vietnam to assess the presence of dengue and chikungunya viruses in patients hospitalized with acute fever in five Vietnam provinces neighboring Lao PDR and Cambodia. Surveillance was extended to mosquitoes present in the vicinity of the patients’ households. Results A total 558 human serum samples were collected along with 1104 adult mosquitoes and 12,041 larvae from 2250 households. Dengue virus was found in 17 (3%) human serum samples and in 9 (0.8%) adult mosquitoes. Chikungunya virus was detected in 2 adult mosquitoes (0.18%) while no chikungunya virus was detected in humans. Differing densities of mosquito populations were found, with the highest in the Long An Province border with Cambodia. Long An Province also displayed the lowest rate of infection, despite a very high Breteau Index, high human population density and presence of the main cross border road system. The highest incidence was found in Dac Nong Province, where the Breteau and Container indices were the second lowest. Dengue virus was detected in five Aedes albopictus, three Aedes aegypti and one Culex vishnui. Chikungunya virus was detected in two Ae. aegypti. All infected mosquitoes belonged to haplotypes described in other parts of the world and a number of novel haplotypes were found among uninfected mosquitoes. Conclusions Dengue is considered to be regularly introduced to Vietnam from Cambodia, mostly through human movement. The data reported here provides a complementary picture. Due to intensive international trade, long-distance transportation of mosquito populations may play a role in the regular importation of dengue in Vietnam through Ho Chi Minh City. It is important to decipher the movement of mosquitoes in Vietnam, not only at the Lao PDR and Cambodia borders but also through international trade routes. Mosquito surveillance programs should address and follow mosquito populations instead of mosquito species. Electronic supplementary material The online version of this article (10.1186/s13071-017-2422-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim Lien Pham Thi
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam. .,IRIM, University of Montpellier, CNRS, Montpellier, France. .,Cirad, Intertryp, UMR 17, TA-A17/G, Campus International de Baillarguet, 34398 Cedex 5, Montpellier, France.
| | | | - Laurent Gavotte
- ISEM, University of Montpellier, CNRS, EPHE IRD, Montpellier, France
| | - Pierrick Labbe
- ISEM, University of Montpellier, CNRS, EPHE IRD, Montpellier, France
| | | | - Emmanuel Cornillot
- Institut de Biologie Computationnelle (IBC), Montpellier, France.,IRCM, University of Montpellier, INSERM, ICM,, Montpellier, France
| | - Trong Duoc Vu
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Thi Yen Nguyen
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Vu Phong Tran
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Van Soai Nguyen
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Christian Devaux
- Aix Marseille Université, CNRS, IRD, INSERM, AP-HM, URMITE, IHU-Méditerranée infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Aneta Afelt
- University of Warsaw, Interdisciplinary Center for Mathematical and Computational Modelling, University of Warsaw, Prosta 69, 00-838, Warsaw, Poland
| | - Chi Cuong Tran
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Thi Nga Phan
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, 1 Yersin Street, Hanoi, 10000, Vietnam
| | - Roger Frutos
- Cirad, Intertryp, UMR 17, TA-A17/G, Campus International de Baillarguet, 34398 Cedex 5, Montpellier, France. .,IES, University of Montpellier, CNRS, Montpellier, France.
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20
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Mayer SV, Tesh RB, Vasilakis N. The emergence of arthropod-borne viral diseases: A global prospective on dengue, chikungunya and zika fevers. Acta Trop 2017; 166:155-163. [PMID: 27876643 PMCID: PMC5203945 DOI: 10.1016/j.actatropica.2016.11.020] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/02/2023]
Abstract
Arthropod-borne viruses (arboviruses) present a substantial threat to human and animal health worldwide. Arboviruses can cause a variety of clinical presentations that range from mild to life threatening symptoms. Many arboviruses are present in nature through two distinct cycles, the urban and sylvatic cycle that are maintained in complex biological cycles. In this review we briefly discuss the factors driving the emergence of arboviruses, such as the anthropogenic aspects of unrestrained human population growth, economic expansion and globalization. Also the important aspects of viruses and vectors in the occurrence of arboviruses epidemics. The focus of this review will be on dengue, zika and chikungunya viruses, particularly because these viruses are currently causing a negative impact on public health and economic damage around the world.
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Affiliation(s)
- Sandra V Mayer
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555-0609, USA
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555-0609, USA; Center for Biodefense and Emerging Infectious Diseases, UTMB, Galveston, USA; Center for Tropical Diseases, UTMB, Galveston, TX 77555-0609, USA; Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555-0610, USA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555-0609, USA; Center for Biodefense and Emerging Infectious Diseases, UTMB, Galveston, USA; Center for Tropical Diseases, UTMB, Galveston, TX 77555-0609, USA; Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555-0610, USA.
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21
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Molecular characterization and genotype shift of dengue virus strains between 2001 and 2014 in Guangzhou. Epidemiol Infect 2016; 145:760-765. [PMID: 27919298 PMCID: PMC5426331 DOI: 10.1017/s0950268816002429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We studied the evolution, genotypes, and the molecular clock of dengue virus serotype 1 (DENV-1), between 2001 and 2014 in Guangzhou, China. The analysis of the envelope (E) gene sequences of 67 DENV-1 strains isolated in Guangzhou, together with 58 representative sequences downloaded from NCBI, have shown shifts in viral genotypes. The genotype changed several times, from genotype I to IV in 2002, from IV to I in 2005, and from I to V in 2014. These genotype shifts may be the cause of DENV outbreaks. The diversity of genotypes and clades demonstrates a high risk of future outbreaks in Guangzhou. The mean rate of virus nucleotide substitution in Guangzhou was determined to be 7·77 × 10−4 per site per year, which represents a medium substitution rate compared to two other countries. Our research can point to different ancestors of the isolated strains, which may further reveal the different origins and transmission of DENV-1 strains in Guangzhou.
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22
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Andrade CC, Young KI, Johnson WL, Villa ME, Buraczyk CA, Messer WB, Hanley KA. Rise and fall of vector infectivity during sequential strain displacements by mosquito-borne dengue virus. J Evol Biol 2016; 29:2205-2218. [PMID: 27500505 DOI: 10.1111/jeb.12939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 12/31/2022]
Abstract
Each of the four serotypes of mosquito-borne dengue virus (DENV-1-4) comprises multiple, genetically distinct strains. Competitive displacement between strains within a serotype is a common feature of DENV epidemiology and can trigger outbreaks of dengue disease. We investigated the mechanisms underlying two sequential displacements by DENV-3 strains in Sri Lanka that each coincided with abrupt increases in dengue haemorrhagic fever (DHF) incidence. First, the post-DHF strain displaced the pre-DHF strain in the 1980s. We have previously shown that post-DHF is more infectious than pre-DHF for the major DENV vector, Aedes aegypti. Then, the ultra-DHF strain evolved in situ from post-DHF and displaced its ancestor in the 2000s. We predicted that ultra-DHF would be more infectious for Ae. aegypti than post-DHF but found that ultra-DHF infected a significantly lower percentage of mosquitoes than post-DHF. We therefore hypothesized that ultra-DHF had effected displacement by disseminating in Ae. aegypti more rapidly than post-DHF, but this was not borne out by a time course of mosquito infection. To elucidate the mechanisms that shape these virus-vector interactions, we tested the impact of RNA interference (RNAi), the principal mosquito defence against DENV, on replication of each of the three DENV strains. Replication of all strains was similar in mosquito cells with dysfunctional RNAi, but in cells with functional RNAi, replication of pre-DHF was significantly suppressed relative to the other two strains. Thus, differences in susceptibility to RNAi may account for the differences in mosquito infectivity between pre-DHF and post-DHF, but other mechanisms underlie the difference between post-DHF and ultra-DHF.
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Affiliation(s)
- C C Andrade
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - K I Young
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - W L Johnson
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - M E Villa
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - C A Buraczyk
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - W B Messer
- Department of Molecular Microbiology and Immunology, Oregon Health and Sciences University, Portland, OR, USA.,Division of Infectious Diseases, Department of Medicine, Oregon Health and Sciences University, Portland, OR, USA
| | - K A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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23
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Vazeille M, Gaborit P, Mousson L, Girod R, Failloux AB. Competitive advantage of a dengue 4 virus when co-infecting the mosquito Aedes aegypti with a dengue 1 virus. BMC Infect Dis 2016; 16:318. [PMID: 27390932 PMCID: PMC4939008 DOI: 10.1186/s12879-016-1666-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/14/2016] [Indexed: 01/30/2023] Open
Abstract
Background Dengue viruses (DENV) are comprised in four related serotypes (DENV-1 to 4) and are critically important arboviral pathogens affecting human populations in the tropics. South American countries have seen the reemergence of DENV since the 1970’s associated with the progressive re-infestation by the mosquito vector, Aedes aegypti. In French Guiana, DENV is now endemic with the co-circulation of different serotypes resulting in viral epidemics. Between 2009 and 2010, a predominant serotype change occurred from DENV-1 to DENV-4 suggesting a competitive displacement. The aim of the present study was to evaluate the potential role of the mosquito in the selection of the new epidemic serotype. Methods To test this hypothesis of competitive displacement of one serotype by another in the mosquito vector, we performed mono- and co-infections of local Ae. aegypti collected during the inter-epidemic period with both viral autochthonous epidemic serotypes and compared infection, dissemination and transmission rates. We performed oral artificial infections of F1 populations in BSL-3 conditions and analyzed infection, dissemination and transmission rates. Results When two populations of Ae. aegypti from French Guiana were infected with either serotype, no significant differences in dissemination and transmission were observed between DENV-1 and DENV-4. However, in co-infection experiments, a strong competitive advantage for DENV-4 was seen at the midgut level leading to a much higher dissemination of this serotype. Furthermore only DENV-4 was present in Ae. aegypti saliva and therefore able to be transmitted. Conclusions In an endemic context, mosquito vectors may be infected by several DENV serotypes. Our results suggest a possible competition between serotypes at the midgut level in co-infected mosquitoes leading to a drastically different transmission potential and, in this case, favoring the competitive displacement of DENV-1 by DENV-4. This phenomenon was observed despite a similar replicative fitness in mono-infections conditions.
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Affiliation(s)
- Marie Vazeille
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Pascal Gaborit
- Medical Entomology Unit, Institut Pasteur of French Guiana, Cayenne, French Guiana
| | - Laurence Mousson
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur of French Guiana, Cayenne, French Guiana
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France.
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24
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Haryanto S, Hayati RF, Yohan B, Sijabat L, Sihite IF, Fahri S, Meutiawati F, Halim JAN, Halim SN, Soebandrio A, Sasmono RT. The molecular and clinical features of dengue during outbreak in Jambi, Indonesia in 2015. Pathog Glob Health 2016; 110:119-29. [PMID: 27215933 DOI: 10.1080/20477724.2016.1184864] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dengue is hyperendemic in Indonesia. In 2015, reported cases of dengue fever doubled those of 2014 in the Jambi municipality of Sumatra. We examined viral aetiology and its relationship with disease outcome in Jambi. Dengue-suspected patients' sera were collected and NS1 detection and IgM/IgG serology were performed. Dengue virus (DENV) serotyping was performed using real-time RT-PCR. Envelope genes were sequenced to determine the genotypes of DENV. Clinical, haematologic, and demographic data were recorded. Of 210 dengue-suspected patients, 107 were confirmed. The disease manifested as Dengue Fever (62%), Dengue Haemorrhagic Fever (36%), and Dengue Shock Syndrome (2%). The serotypes of 94 DENV were determined. All DENV serotypes were detected with DENV-1 as the predominant serotype (66%). Genotypically, the DENV-1 viruses belong to Genotype I, DENV-2 was of Cosmopolitan genotype, DENV-3 as Genotype I, and DENV-4 belonged to Genotype II. Comparison with historical data revealed serotype predominance switched from DENV-3 to DENV-1, and the replacement of Genotype IV of DENV-1 with Genotype I. In summary, DENV-1 predominated during the 2015 dengue outbreak in Jambi. The full spectrum of dengue disease occurred and was characterized by a switch in predominant serotypes.
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Affiliation(s)
- Sotianingsih Haryanto
- a Siloam Hospital , Jambi , Indonesia.,d Faculty of Medicine , Jambi University , Jambi , Indonesia
| | - Rahma F Hayati
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| | | | | | | | - Sukmal Fahri
- c Health Polytechnic , Jambi Provincial Health Office , Jambi , Indonesia
| | | | | | - Stefanie N Halim
- e Faculty of Medicine , Diponegoro University , Semarang , Indonesia
| | - Amin Soebandrio
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
| | - R Tedjo Sasmono
- b Eijkman Institute for Molecular Biology , Jakarta , Indonesia
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25
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Hapuarachchi HC, Koo C, Kek R, Xu H, Lai YL, Liu L, Kok SY, Shi Y, Chuen RLT, Lee KS, Maurer-Stroh S, Ng LC. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission. Sci Rep 2016; 6:22592. [PMID: 26940650 PMCID: PMC4778070 DOI: 10.1038/srep22592] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/17/2016] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013–2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.
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Affiliation(s)
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Relus Kek
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Helen Xu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Lilac Liu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Suet Yheng Kok
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yuan Shi
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Raphael Lee Tze Chuen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671
| | - Kim-Sung Lee
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Block 83, #04-00, 535 Clementi Road, Singapore 599489
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551.,National Public Health Laboratory (NPHL), Ministry of Health (MOH), 3 Biopolis Drive, #05-14 to 16, Synapse, Singapore 138623
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
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26
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Afreen N, Naqvi IH, Broor S, Ahmed A, Kazim SN, Dohare R, Kumar M, Parveen S. Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India. PLoS Negl Trop Dis 2016; 10:e0004511. [PMID: 26977703 PMCID: PMC4792444 DOI: 10.1371/journal.pntd.0004511] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/12/2016] [Indexed: 11/19/2022] Open
Abstract
Dengue fever is the most important arboviral disease in the tropical and sub-tropical countries of the world. Delhi, the metropolitan capital state of India, has reported many dengue outbreaks, with the last outbreak occurring in 2013. We have recently reported predominance of dengue virus serotype 2 during 2011-2014 in Delhi. In the present study, we report molecular characterization and evolutionary analysis of dengue serotype 2 viruses which were detected in 2011-2014 in Delhi. Envelope genes of 42 DENV-2 strains were sequenced in the study. All DENV-2 strains grouped within the Cosmopolitan genotype and further clustered into three lineages; Lineage I, II and III. Lineage III replaced lineage I during dengue fever outbreak of 2013. Further, a novel mutation Thr404Ile was detected in the stem region of the envelope protein of a single DENV-2 strain in 2014. Nucleotide substitution rate and time to the most recent common ancestor were determined by molecular clock analysis using Bayesian methods. A change in effective population size of Indian DENV-2 viruses was investigated through Bayesian skyline plot. The study will be a vital road map for investigation of epidemiology and evolutionary pattern of dengue viruses in India.
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Affiliation(s)
- Nazia Afreen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Irshad H. Naqvi
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Shobha Broor
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anwar Ahmed
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Syed Naqui Kazim
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Manoj Kumar
- Centre for Culture, Media & Governance, Jamia Millia Islamia, New Delhi, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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27
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Breyta R, McKenney D, Tesfaye T, Ono K, Kurath G. Increasing virulence, but not infectivity, associated with serially emergent virus strains of a fish rhabdovirus. Virus Evol 2016; 2:vev018. [PMID: 27774291 PMCID: PMC4989874 DOI: 10.1093/ve/vev018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Surveillance and genetic typing of field isolates of a fish rhabdovirus, infectious hematopoietic necrosis virus (IHNV), has identified four dominant viral genotypes that were involved in serial viral emergence and displacement events in steelhead trout (Oncorhynchus mykiss) in western North America. To investigate drivers of these landscape-scale events, IHNV isolates designated 007, 111, 110, and 139, representing the four relevant genotypes, were compared for virulence and infectivity in controlled laboratory challenge studies in five relevant steelhead trout populations. Viral virulence was assessed as mortality using lethal dose estimates (LD50), survival kinetics, and proportional hazards analysis. A pattern of increasing virulence for isolates 007, 111, and 110 was consistent in all five host populations tested, and correlated with serial emergence and displacements in the virus-endemic lower Columbia River source region during 1980-2013. The fourth isolate, 139, did not have higher virulence than the previous isolate 110. However, the mG139M genotype displayed a conditional displacement phenotype in that it displaced type mG110M in coastal Washington, but not in the lower Columbia River region, indicating that factors other than evolution of higher viral virulence were involved in some displacement events. Viral infectivity, measured as infectious dose (ID50), did not correlate consistently with virulence or with viral emergence, and showed a narrow range of variation relative to the variation observed in virulence. Comparison among the five steelhead trout populations confirmed variation in resistance to IHNV, but correlations with previous history of virus exposure or with sites of viral emergence varied between IHNV source and sink regions. Overall, this study indicated increasing viral virulence over time as a potential driver for emergence and displacement events in the endemic Lower Columbia River source region where these IHNV genotypes originated, but not in adjacent sink regions.
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Affiliation(s)
- Rachel Breyta
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115 and; School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St., Seattle, WA 98105, USA
| | - Doug McKenney
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115 and
| | - Tarin Tesfaye
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115 and
| | - Kotaro Ono
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St., Seattle, WA 98105, USA
| | - Gael Kurath
- US Geological Survey, Western Fisheries Research Center, 6505 NE 65th St., Seattle, WA 98115 and
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28
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Choudhury MA, Lott WB, Banu S, Cheng AY, Teo YY, Ong RTH, Aaskov J. Nature and Extent of Genetic Diversity of Dengue Viruses Determined by 454 Pyrosequencing. PLoS One 2015; 10:e0142473. [PMID: 26566128 PMCID: PMC4643897 DOI: 10.1371/journal.pone.0142473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 10/22/2015] [Indexed: 12/23/2022] Open
Abstract
Dengue virus (DENV) populations are characteristically highly diverse. Regular lineage extinction and replacement is an important dynamic DENV feature, and most DENV lineage turnover events are associated with increased incidence of disease. The role of genetic diversity in DENV lineage extinctions is not understood. We investigated the nature and extent of genetic diversity in the envelope (E) gene of DENV serotype 1 representing different lineages histories. A region of the DENV genome spanning the E gene was amplified and sequenced by Roche/454 pyrosequencing. The pyrosequencing results identified distinct sub-populations (haplotypes) for each DENV-1 E gene. A phylogenetic tree was constructed with the consensus DENV-1 E gene nucleotide sequences, and the sequences of each constructed haplotype showed that the haplotypes segregated with the Sanger consensus sequence of the population from which they were drawn. Haplotypes determined through pyrosequencing identified a recombinant DENV genome that could not be identified through Sanger sequencing. Nucleotide level sequence diversities of DENV-1 populations determined from SNP analysis were very low, estimated from 0.009–0.01. There were also no stop codon, frameshift or non-frameshift mutations observed in the E genes of any lineage. No significant correlations between the accumulation of deleterious mutations or increasing genetic diversity and lineage extinction were observed (p>0.5). Although our hypothesis that accumulation of deleterious mutations over time led to the extinction and replacement of DENV lineages was ultimately not supported by the data, our data does highlight the significant technical issues that must be resolved in the way in which population diversity is measured for DENV and other viruses. The results provide an insight into the within-population genetic structure and diversity of DENV-1 populations.
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Affiliation(s)
- Md Abu Choudhury
- Menzies Health Institute Queensland, Griffith University, Brisbane, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- * E-mail:
| | - William B Lott
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
- School of Chemistry, Physics, and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Shahera Banu
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Anthony Youzhi Cheng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - John Aaskov
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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Kotaki T, Yamanaka A, Mulyatno KC, Churrotin S, Sucipto TH, Labiqah A, Ahwanah NLF, Soegijanto S, Kameoka M, Konishi E. Divergence of the dengue virus type 2 Cosmopolitan genotype associated with two predominant serotype shifts between 1 and 2 in Surabaya, Indonesia, 2008-2014. INFECTION GENETICS AND EVOLUTION 2015; 37:88-93. [PMID: 26553170 DOI: 10.1016/j.meegid.2015.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 12/30/2022]
Abstract
Indonesia is one of the biggest dengue endemic countries, and, thus, is an important place to investigate the evolution of dengue virus (DENV). We have continuously isolated DENV in Surabaya, the second biggest city in Indonesia, since 2008. We previously reported sequential changes in the predominant serotype from DENV type 2 (DENV-2) to DENV type 1 (DENV-1) in November 2008 and from DENV-1 to DENV-2 in July 2013. The predominance of DENV-2 continued in 2014, but not in 2015. We herein phylogenetically investigated DENV-2 transitions in Surabaya between 2008 and 2014 to analyze the divergence and evolution of DENV-2 concomitant with serotype shifts. All DENV-2 isolated in Surabaya were classified into the Cosmopolitan genotype, and further divided into 6 clusters. Clusters 1-3, dominated by Surabaya strains, were defined as the "Surabaya lineage". Clusters 4-6, dominated by strains from Singapore, Malaysia, and many parts of Indonesia, were the "South East Asian lineage". The most recent common ancestor of these strains existed in 1988, coinciding with the time that an Indonesian dengue outbreak took place. Cluster 1 appeared to be unique because no other DENV-2 isolate was included in this cluster. The predominance of DENV-2 in 2008 and 2013-14 were caused by cluster 1, whereas clusters 2 and 3 sporadically emerged in 2011 and 2012. The characteristic amino acids of cluster 1, E-170V and E-282Y, may be responsible for its prevalence in Surabaya. No amino acid difference was observed in the envelope region between strains in 2008 and 2013-14, suggesting that the re-emergence of DENV-2 in Surabaya was due to the loss or decrease of herd immunity in the 5-year period when DENV-2 subsided. The South East Asian lineage primarily emerged in Surabaya in 2014, probably imported from other parts of Indonesia or foreign countries.
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Affiliation(s)
- Tomohiro Kotaki
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia; Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan; Department of International Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan.
| | - Atsushi Yamanaka
- BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan(1)
| | - Kris Cahyo Mulyatno
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia
| | - Siti Churrotin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia
| | - Teguh Hari Sucipto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia
| | - Amaliah Labiqah
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia
| | - Nur Laila Fitriati Ahwanah
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia
| | - Soegeng Soegijanto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Jl, Mulyorejo, Surabaya 60115, Indonesia
| | - Masanori Kameoka
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan; Department of International Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan
| | - Eiji Konishi
- BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan(1)
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de Bruycker-Nogueira F, Nogueira RMR, Faria NRDC, Simões JBS, Nunes PCG, de Filippis AMB, dos Santos FB. Insights of the genetic diversity of DENV-1 detected in Brazil in 25 years: Analysis of the envelope domain III allows lineages characterization. INFECTION GENETICS AND EVOLUTION 2015; 34:126-36. [PMID: 26160541 DOI: 10.1016/j.meegid.2015.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 07/03/2015] [Accepted: 07/04/2015] [Indexed: 01/03/2023]
Abstract
Dengue virus type 1 (DENV-1) was first isolated in Brazil in 1986 in the state of Rio de Janeiro (RJ) and during 25years, this serotype emerged and re-emerged causing explosive epidemics in the country. Here, we aimed to present the phylogeny and molecular characterization based on the envelope gene (E) of DENV-1 (n=48) isolated during epidemics occurred from 1986 to 2011. Six full coding region genomes of DENV-1 were fully sequenced and possible genomic recombination events were analyzed. The results showed that the Brazilian DENV-1 isolates analyzed belong to genotype V (Americas/Africa), but grouping into distinct clades. Three groups were identified, one dating from 1986 to 2002 (lineage 1a), a second group isolated from 2009 to 2011 and a representative strain isolated in 2002 (lineage 2), and a group of strains isolated from 2010 to 2011 (lineage 1b). The lineages 1a and 1b were more closely related to the American strains, while lineage 2 to the Asian strains. Amino acids (aa) substitutions were observed in the domains I and III of the E protein and were associated to the lineages segregation. A substitution on E297 differentiated the lineage 1a from the lineages 1b and 2. Substitutions on E338, E394 (domain III), E428 and E436 (stem region) differentiated lineages 1a, 1b and 2. With the exception of the C gene, all the others genes analyzed allowed the DENV-1 classification into the distinct genotypes. Interestingly, the E gene's domain III and stem regions alone were able to characterize the distinct lineages, as observed by the analysis of the entire E gene and the complete coding region. No recombinant events were detected, but a strain belonging to lineage 1a was closely related to a known recombinant strain (AF513110/BR/2001).
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Affiliation(s)
| | - Rita Maria Ribeiro Nogueira
- Laboratory of Flavivirus, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
| | | | | | | | - Ana Maria Bispo de Filippis
- Laboratory of Flavivirus, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil
| | - Flávia Barreto dos Santos
- Laboratory of Flavivirus, Oswaldo Cruz Institute-FIOCRUZ, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brazil.
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Huang YJS, Higgs S, Horne KM, Vanlandingham DL. Flavivirus-mosquito interactions. Viruses 2014; 6:4703-30. [PMID: 25421894 PMCID: PMC4246245 DOI: 10.3390/v6114703] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/17/2014] [Accepted: 11/20/2014] [Indexed: 12/20/2022] Open
Abstract
The Flavivirus genus is in the family Flaviviridae and is comprised of more than 70 viruses. These viruses have a broad geographic range, circulating on every continent except Antarctica. Mosquito-borne flaviviruses, such as yellow fever virus, dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus are responsible for significant human morbidity and mortality in affected regions. This review focuses on what is known about flavivirus-mosquito interactions and presents key data collected from the field and laboratory-based molecular and ultrastructural evaluations.
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Affiliation(s)
- Yan-Jang S Huang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Stephen Higgs
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Kate McElroy Horne
- Biosecurity Research Institute, Kansas State University, Manhattan, KS 66506, USA.
| | - Dana L Vanlandingham
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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Choudhury MA, Lott WB, Aaskov J. Distribution of fitness in populations of dengue viruses. PLoS One 2014; 9:e107264. [PMID: 25222471 PMCID: PMC4164612 DOI: 10.1371/journal.pone.0107264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 08/11/2014] [Indexed: 11/22/2022] Open
Abstract
Genetically diverse RNA viruses like dengue viruses (DENVs) segregate into multiple, genetically distinct, lineages that temporally arise and disappear on a regular basis. Lineage turnover may occur through multiple processes such as, stochastic or due to variations in fitness. To determine the variation of fitness, we measured the distribution of fitness within DENV populations and correlated it with lineage extinction and replacement. The fitness of most members within a population proved lower than the aggregate fitness of populations from which they were drawn, but lineage replacement events were not associated with changes in the distribution of fitness. These data provide insights into variations in fitness of DENV populations, extending our understanding of the complexity between members of individual populations.
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Affiliation(s)
- Md Abu Choudhury
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - William B Lott
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia; School of Chemistry, Physics, and Mechanical Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, Queensland, Australia
| | - John Aaskov
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
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Kotaki T, Yamanaka A, Mulyatno KC, Churrotin S, Labiqah A, Sucipto TH, Soegijanto S, Kameoka M, Konishi E. Continuous dengue type 1 virus genotype shifts followed by co-circulation, clade shifts and subsequent disappearance in Surabaya, Indonesia, 2008-2013. INFECTION GENETICS AND EVOLUTION 2014; 28:48-54. [PMID: 25219342 DOI: 10.1016/j.meegid.2014.09.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/07/2014] [Accepted: 09/01/2014] [Indexed: 12/30/2022]
Abstract
Four serotypes of dengue virus (DENV-1 to DENV-4) and their genotypes are distributed in tropical and subtropical regions. Indonesia has been recently suggested as the origin of some dengue virus genotypes. In Surabaya, the second biggest city of Indonesia, we previously reported a shift of the predominantly circulating serotype from DENV-2 to DENV-1 in November 2008, followed by a genotype shift of DENV-1 from genotype IV (GIV) to genotype I (GI) in September 2009, based on nucleotide sequences in the envelope protein coding region. Since then, GI strains had predominantly circulated until December 2010. In this report, we investigated further DENV-1 transitions in Surabaya during 2011-2013 in order to comprehend dengue dynamics during 2008-2013 in more detail. From January 2011 through December 2011, only GIV strains were isolated, indicating that a genotype shift again took place from GI to GIV. In January 2012, GI and GIV strains started co-circulating, which continued until June 2013. To further investigate this phenomenon, analysis was performed at a clade level. GI and GIV strains isolated in Surabaya formed four and three distinct clades, respectively. Concomitant with co-circulation, new clade strains appeared in both genotypes. In contrast, some previously circulating clades were not isolated during co-circulation, indicating clade shifts. Among our Surabaya isolates, nucleotide and amino acid differences in the E region were, respectively, 1.0-2.3% and 0.2-1.0% for GI isolates and 2.0-6.3% and 0.0-1.8% for GIV isolates. Several characteristic amino acid substitutions in the envelope ectodomain were observed in some clades. After July 2013, DENV-1 strains were not isolated and were replaced with DENV-2. This study showed that continuous shifts of more than one genotype resulted in their co-circulation and subsequent disappearance and suggested the relevance of clade replacement to genotype co-circulation and disappearance in Surabaya.
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Affiliation(s)
- Tomohiro Kotaki
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia; Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan.
| | - Atsushi Yamanaka
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia; BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan(1).
| | - Kris Cahyo Mulyatno
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia.
| | - Siti Churrotin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia.
| | - Amaliah Labiqah
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia.
| | - Teguh Hari Sucipto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia.
| | - Soegeng Soegijanto
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, JI, Mulyorejo, Surabaya 60115, Indonesia.
| | - Masanori Kameoka
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan; Department of International Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo 654-0142, Japan.
| | - Eiji Konishi
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan; BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan(1).
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Dash PK, Sharma S, Soni M, Agarwal A, Sahni AK, Parida M. Complete genome sequencing and evolutionary phylogeography analysis of Indian isolates of Dengue virus type 1. Virus Res 2014; 195:124-34. [PMID: 25197040 DOI: 10.1016/j.virusres.2014.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/22/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022]
Abstract
Dengue is now hyper-endemic in most parts of south and southeast Asia including India. The northern India particularly national capital New Delhi witnessed major Dengue outbreaks with Dengue virus type 1 (DENV-1) as the dominant serotype since last five years. This study was initiated to decipher the complete genome information of recently circulating DENV-1 (2009-2011) along with the prototype Indian DENV-1, isolated in 1956. Further extensive ML phylogenetic and Bayesian phylogeography analysis was carried out to investigate the evolution of this virus and understand its spatiotemporal diffusion across the globe. The complete genome analysis revealed deletion of a unique 21-nucleotide stretch in the 3' un-translated region of recent Indian DENV-1. The north Indian DENV-1 revealed up to 5.2% nucleotide sequence difference compared to recent isolates from southern India. Selection pressure analysis revealed positive selection in few amino acid sites of both structural and non-structural proteins. The molecular phylogeny classified the Indian DENV-1 into genotype III, which is also known as cosmopolitan genotype. The northern and southern Indian DENV-1 were grouped into distinct clades. The molecular clock analysis estimated a mean evolutionary rate of 7.08×10(-4) substitutions/site/year for cosmopolitan genotype. The phylogeography analysis revealed that the cosmopolitan genotype DENV-1 originated ∼1938 in India and subsequently spread globally. The diffusion of virus from India to Caribbean and South America was confirmed through SPREAD analysis. This study also confirmed the temporal displacement of different clades of DENV-1 in India over last five decades.
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Affiliation(s)
- Paban Kumar Dash
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India.
| | - Shashi Sharma
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Manisha Soni
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Ankita Agarwal
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
| | - Ajay Kumar Sahni
- Department of Microbiology & Pathology, Army Research & Referral (R&R) Hospital, Delhi Cantt, Delhi, India
| | - Manmohan Parida
- Division of Virology, Defence R&D Establishment (DRDE), Jhansi Road, Gwalior 474002, MP, India
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Kell AM, Wargo AR, Kurath G. Viral fitness does not correlate with three genotype displacement events involving infectious hematopoietic necrosis virus. Virology 2014; 464-465:146-155. [PMID: 25068402 DOI: 10.1016/j.virol.2014.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 01/11/2023]
Abstract
Viral genotype displacement events are characterized by the replacement of a previously dominant virus genotype by a novel genotype of the same virus species in a given geographic region. We examine here the fitness of three pairs of infectious hematopoietic necrosis virus (IHNV) genotypes involved in three major genotype displacement events in Washington state over the last 30 years to determine whether increased virus fitness correlates with displacement. Fitness was assessed using in vivo assays to measure viral replication in single infection, simultaneous co-infection, and sequential superinfection in the natural host, steelhead trout. In addition, virion stability of each genotype was measured in freshwater and seawater environments at various temperatures. By these methods, we found no correlation between increased viral fitness and displacement in the field. These results suggest that other pressures likely exist in the field with important consequences for IHNV evolution.
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Affiliation(s)
- Alison M Kell
- University of Washington, Seattle, WA, USA; U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA, USA.
| | - Andrew R Wargo
- University of Washington, Seattle, WA, USA; U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Gael Kurath
- University of Washington, Seattle, WA, USA; U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
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Aghaie A, Aaskov J, Chinikar S, Niedrig M, Banazadeh S, Mohammadpour HK. Frequency of dengue virus infection in blood donors in Sistan and Baluchestan province in Iran. Transfus Apher Sci 2013; 50:59-62. [PMID: 24332363 DOI: 10.1016/j.transci.2013.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/17/2013] [Accepted: 07/05/2013] [Indexed: 11/29/2022]
Abstract
Risk of dengue virus in the blood supply has been demonstrated in recent studies. In this paper, Chabahar in Sistan and Baluchestan province, south east of Iran, was selected for studying dengue infection because of its climatic and geographical situation in the middle of the transit way between East Asia and other countries. The blood samples were taken from volunteer healthy donors who were referred to the Chabahar Blood Center for blood donation. The presence of dengue virus (DENV) was studied by detecting IgG to DENV by enzyme linked immune sorbent assay (ELISA). Reactive ELISA results were confirmed by an immune flouorescence assay (IFA). According to the results, some of the healthy donors were infected by DENV, which could not been recognized in donor selection. Therefore, special attention should be paid to the criteria of donor selection and additional screening tests are recommended.
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Affiliation(s)
- Afsaneh Aghaie
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran.
| | - John Aaskov
- Queensland University of Technology, Brisbane, Australia.
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Teoh BT, Sam SS, Tan KK, Johari J, Shu MH, Danlami MB, Abd-Jamil J, MatRahim N, Mahadi NM, AbuBakar S. Dengue virus type 1 clade replacement in recurring homotypic outbreaks. BMC Evol Biol 2013; 13:213. [PMID: 24073945 PMCID: PMC3850903 DOI: 10.1186/1471-2148-13-213] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/25/2013] [Indexed: 11/23/2022] Open
Abstract
Background Recurring dengue outbreaks occur in cyclical pattern in most endemic countries. The recurrences of dengue virus (DENV) infection predispose the population to increased risk of contracting the severe forms of dengue. Understanding the DENV evolutionary mechanism underlying the recurring dengue outbreaks has important implications for epidemic prediction and disease control. Results We used a set of viral envelope (E) gene to reconstruct the phylogeny of DENV-1 isolated between the periods of 1987–2011 in Malaysia. Phylogenetic analysis of DENV-1 E gene revealed that genotype I virus clade replacements were associated with the cyclical pattern of major DENV-1 outbreaks in Malaysia. A total of 9 non-conservative amino acid substitutions in the DENV-1 E gene consensus were identified; 4 in domain I, 3 in domain II and 2 in domain III. Selection pressure analyses did not reveal any positively selected codon site within the full length E gene sequences (1485 nt, 495 codons). A total of 183 (mean dN/dS = 0.0413) negatively selected sites were found within the Malaysian isolates; neither positive nor negative selection was noted for the remaining 312 codons. All the viruses were cross-neutralized by the respective patient sera suggesting no strong support for immunological advantage of any of the amino acid substitutions. Conclusion DENV-1 clade replacement is associated with recurrences of major DENV-1 outbreaks in Malaysia. Our findings are consistent with those of other studies that the DENV-1 clade replacement is a stochastic event independent of positive selection.
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Affiliation(s)
- Boon-Teong Teoh
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
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Rodriguez-Roche R, Gould EA. Understanding the dengue viruses and progress towards their control. BIOMED RESEARCH INTERNATIONAL 2013; 2013:690835. [PMID: 23936833 PMCID: PMC3722981 DOI: 10.1155/2013/690835] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/08/2013] [Indexed: 01/12/2023]
Abstract
Traditionally, the four dengue virus serotypes have been associated with fever, rash, and the more severe forms, haemorrhagic fever and shock syndrome. As our knowledge as well as understanding of these viruses increases, we now recognise not only that they are causing increasing numbers of human infections but also that they may cause neurological and other clinical complications, with sequelae or fatal consequences. In this review we attempt to highlight some of these features in the context of dengue virus pathogenesis. We also examine some of the efforts currently underway to control this "scourge" of the tropical and subtropical world.
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Affiliation(s)
- Rosmari Rodriguez-Roche
- Pedro Kouri Tropical Medicine Institute, WHO/PAHO Collaborating Centre for the Study of Dengue and Its Vector, Havana, Cuba.
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Sun Y, Meng S. Evolutionary history and spatiotemporal dynamics of dengue virus type 1 in Asia. INFECTION GENETICS AND EVOLUTION 2013; 16:19-26. [PMID: 23395769 DOI: 10.1016/j.meegid.2013.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 01/07/2013] [Accepted: 01/12/2013] [Indexed: 12/27/2022]
Abstract
Previous studies showed that DENV-1 transmitted from monkeys to humans approximately 125 years ago. However, there is no comprehensive analysis about phylogeography and population dynamics of Asian DENV-1. Here, we adopt a Bayesian phylogeographic approach to investigate the evolutionary history and phylogeography of Asian DENV-1 using envelope (E) protein gene sequences of 450 viruses isolated from 1954 to 2010 throughout 18 Asian countries and regions. Bayesian phylogeographic analyses indicate that the high rates of viral migration possibly follows long-distance travel for humans in Southeast Asia. Our study highlights that Southeast Asian countries have acted as the main viral sources of the dengue epidemics in East Asia. The results reveal that the time to the most recent common ancestor (TMRCA) of Asian DENV-1 is 1906 (95% HPD, years 1897-1915). We show that the spatial dissemination of virus is the major source of DENV-1 outbreaks in the different localities and leads to subsequent establishment and expansion of the virus in these areas.
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Affiliation(s)
- Yan Sun
- Department of Immunology, Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China.
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Chakravarti A, Chauhan MS, Kumar S, Ashraf A. Genotypic characterization of dengue virus strains circulating during 2007-2009 in New Delhi. Arch Virol 2012; 158:571-81. [DOI: 10.1007/s00705-012-1522-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 09/21/2012] [Indexed: 11/29/2022]
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Fan YC, Chen JM, Chiu HC, Chen YY, Lin JW, Shih CC, Chen CM, Chang CC, Chang GJJ, Chiou SS. Partially neutralizing potency against emerging genotype I virus among children received formalin-inactivated Japanese encephalitis virus vaccine. PLoS Negl Trop Dis 2012; 6:e1834. [PMID: 23029592 PMCID: PMC3459827 DOI: 10.1371/journal.pntd.0001834] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/13/2012] [Indexed: 11/23/2022] Open
Abstract
Background Genotype I (GI) Japanese encephalitis virus (JEV) that replaced GIII virus has become the dominant circulating virus in Asia. Currently, all registered live and inactivated JEV vaccines are derived from genotype III viruses. In Taiwan, the compulsory JEV vaccination policy recommends that children receives four doses of formalin-inactivated Nakayama (GIII) JEV vaccine. Methodology/Principal Findings To evaluate the influence of genotype replacement on the post-vaccination viral neutralizing ability by GIII and GI viruses, the small panel of vaccinated-children serum specimens was assembled, and the reciprocal 50% plaque-reduction neutralizing antibody titers (PRNT50) were measured against Nakayama vaccine strain, CJN GIII human brain isolate and TC2009-1 GI mosquito isolate. The seropositivity rate (PRNT50≥1∶10) and geometric mean titers (GMT) against the TC2009-1 virus were the lowest among the three viruses. The protective threshold against the CJN and TC2009-1 viruses could only be achieved when the GMT against Nakayama virus was ≥1∶20 or ≥1∶80, respectively. Using undiluted vaccinees' sera, the enhancement of JEV infection in K562 cells was observed in some low or non-neutralizing serum specimens. Conclusions/Significance Our preliminary study has shown that neutralizing antibodies, elicited by the mouse brain-derived and formalin-inactivated JEV Nakayama vaccine among a limited number of vaccinees, have reduced neutralizing capacity against circulating GI virus, but more detailed studies are needed to address the potential impact on the future vaccine policy. Genotype I (GI) Japanese encephalitis virus (JEV) that replaced GIII virus has become the dominant circulating virus in Asia; however, all available JEV vaccines are derived from genotype III viruses, and no study has been conducted on the cross-neutralization and protection elicited by GIII JEV vaccines against GI viruses using vaccinated children’s serum specimens collected from the general population. Genotype I virus was first detected in Taiwan in 2008, and became the dominant circulating JEV, and was island-wide within a year. In the present study, the small panel of GIII virus vaccinated-children serum specimens were not only showed lower strain-specific neutralization against GI virus as compared to the GIII vaccine and human isolates but also observed the enhancement of GI virus infection in K562 cells in some low or non-neutralizing serum specimens. These preliminary results indicated the reduced neutralization potency due to genotype replacement should be closely monitored in the JE epidemic/endemic regions in the future.
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MESH Headings
- Adolescent
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- Asia
- Child
- Child, Preschool
- Encephalitis Virus, Japanese/classification
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/virology
- Genotype
- Humans
- Infant
- Japanese Encephalitis Vaccines/administration & dosage
- Japanese Encephalitis Vaccines/immunology
- Mice
- Neutralization Tests
- Taiwan
- Vaccines, Inactivated/administration & dosage
- Vaccines, Inactivated/immunology
- Viral Plaque Assay
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Affiliation(s)
- Yi-Chin Fan
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jo-Mei Chen
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Hsien-Chung Chiu
- Department of Periodontology, School of Dentistry, National Defense Medical Center and Tri-Service General Hospital, Taipei, Taiwan
| | - Yi-Ying Chen
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Jen-Wei Lin
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chen-Chang Shih
- Department of Neurology, Mennonite Christian Hospital, Hualien, Taiwan
| | - Chih-Ming Chen
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
- Division of Infectious Disease, Department of Internal Medicine, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Chao-Chin Chang
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Gwong-Jen J. Chang
- Arboviral Diseases Branch, Center for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Shyan-Song Chiou
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
- * E-mail:
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Santiago GA, McElroy-Horne K, Lennon NJ, Santiago LM, Birren BW, Henn MR, Muñoz-Jordán JL. Reemergence and decline of dengue virus serotype 3 in Puerto Rico. J Infect Dis 2012; 206:893-901. [PMID: 22740715 DOI: 10.1093/infdis/jis426] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The dengue virus serotype 3 (DENV-3) Indian subcontinent strain emerged in Puerto Rico in 1998 after a 21-year absence. The rapid expansion of DENV-3 on the island correlated with the withdrawal of the other serotypes for 7 years. The DENV-3 prevalence declined in 2008 and remains undetected. METHODS We sequenced complete genomes of 92 DENV-3 clinical isolates to characterize the molecular evolution and phylogeography throughout 10 years of continued sampling (1998–2007). RESULTS We documented 8 distinct lineages that emerged simultaneously and evolved independently. Two of the 8 lineages were highly associated with transient introductions of foreign viruses, and 2 of the 3 endemic lineages covered the entire study period. We found evidence of temporal-geographical clustering only within the 3 endemic lineages. The phylogeography analysis combined with serotype-specific incidence data showed that transmission of a DENV serotype in a given location and time is usually correlated with the absence of the other serotype. CONCLUSIONS Our study shows the cotransmission of DENV-3 lineages through a complex dissemination pattern dissimilar to the evolutionary dynamics of the other serotypes in the island. High virus genetic diversity and a large naive population were underlying factors in the expansion and collapse of DENV-3 in Puerto Rico.
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Affiliation(s)
- Gilberto A Santiago
- Division of Vector-borne Infectious Diseases, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico
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Complex dynamic of dengue virus serotypes 2 and 3 in Cambodia following series of climate disasters. INFECTION GENETICS AND EVOLUTION 2012; 15:77-86. [PMID: 22677620 DOI: 10.1016/j.meegid.2012.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/13/2012] [Accepted: 05/16/2012] [Indexed: 11/23/2022]
Abstract
The Dengue National Control Program was established in Cambodia in 2000 and has reported between 10,000 and 40,000 dengue cases per year with a case fatality rate ranging from 0.7 to 1.7. In this study 39 DENV-2 and 57 DENV-3 viruses isolated from patients between 2000 and 2008 were fully sequenced. Five DENV2 and four DENV3 distinct lineages with different dynamics were identified. Each lineage was characterized by the presence of specific mutations with no evidence of recombination. In both DENV-2 and DENV-3 the lineages present prior to 2003 were replaced after that date by unrelated lineages. After 2003, DENV-2 lineages D2-3 and D2-4 cocirculated until 2007 when they were almost completely replaced by a lineage D2-5 which emerged from D2-3 Conversely, all DENV-3 lineages remained, diversified and cocirculated with novel lineages emerging. Years 2006 and 2007 were marked by a high prevalence of DENV-3 and 2007 with a large dengue outbreak and a high proportion of patients with severe disease. Selective sweeps in DENV-1 and DENV-2 were linked to immunological escape to a predominately DENV-3-driven immunological response. The complex dynamic of dengue in Cambodia in the last ten years has been associated with a combination of stochastic climatic events, cocirculation, coevolution, adaptation to different vector populations, and with the human population immunological landscape.
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Uzcátegui NY, Sironen T, Golovljova I, Jääskeläinen AE, Välimaa H, Lundkvist Å, Plyusnin A, Vaheri A, Vapalahti O. Rate of evolution and molecular epidemiology of tick-borne encephalitis virus in Europe, including two isolations from the same focus 44 years apart. J Gen Virol 2012; 93:786-796. [DOI: 10.1099/vir.0.035766-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a member of the family Flaviviridae. It is transmitted by Ixodes spp. ticks in a cycle involving rodents and small mammals. TBEV has three subtypes: European, Siberian and Far Eastern. The virus causes thousands of cases of meningoencephalitis in Europe annually, with an increasing trend. The increase may be attributed to a complex network of elements, including climatic, environmental and socio-economic factors. In an attempt to understand the evolutionary history and dispersal of TBEV, to existing genetic data we add two novel complete ORF sequences of TBEV strains from northern Europe and the completion of the genome of four others. Moreover, we provide a unique measure for the natural rate of evolution of TBEV by studying two isolations from the same forest on an island in Åland archipelago 44 years apart. For all isolates, we analysed the phylogeny, rate of evolution and probable time of radiation of the different TBEV strains. The results show that the two lineages of TBEV in different Ixodes species have evolved independently for approximately 3300 years. Notably, rapid radiation of TBEV-Eur occurred approximately 300 years ago, without the large-scale geographical clustering observed previously for the Siberian subtype. The measurements from the natural rate of evolution correlated with the estimates done by phylogenetic programs, demonstrating their robustness.
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Affiliation(s)
- Nathalie Y. Uzcátegui
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
| | - Irina Golovljova
- Department of Virology, National Institute for Health Development, EE-11619 Tallinn, Estonia
- Center for Microbiological Preparedness, Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
| | - Anu E. Jääskeläinen
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
| | - Hannamari Välimaa
- Department of Virology, Helsinki University Hospital Laboratory (HUSLAB), PO Box 400, FI-00029 HUS, Helsinki, Finland
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
| | - Åke Lundkvist
- Center for Microbiological Preparedness, Swedish Institute for Infectious Disease Control, SE-17182 Solna, Sweden
| | - Alexander Plyusnin
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
| | - Antti Vaheri
- Department of Virology, Helsinki University Hospital Laboratory (HUSLAB), PO Box 400, FI-00029 HUS, Helsinki, Finland
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, PO Box 66, FI-00014 University of Helsinki, Helsinki, Finland
- Department of Virology, Helsinki University Hospital Laboratory (HUSLAB), PO Box 400, FI-00029 HUS, Helsinki, Finland
- Infection Biology Research Program, Department of Virology, Haartman Institute, PO Box 21, FI-00014 University of Helsinki, Helsinki, Finland
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Méndez JA, Usme-Ciro JA, Domingo C, Rey GJ, Sánchez JA, Tenorio A, Gallego-Gomez JC. Phylogenetic reconstruction of dengue virus type 2 in Colombia. Virol J 2012; 9:64. [PMID: 22405440 PMCID: PMC3349600 DOI: 10.1186/1743-422x-9-64] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 03/09/2012] [Indexed: 12/31/2022] Open
Abstract
Background Dengue fever is perhaps the most important viral re-emergent disease especially in tropical and sub-tropical countries, affecting about 50 million people around the world yearly. In Colombia, dengue virus was first detected in 1971 and still remains as a major public health issue. Although four viral serotypes have been recurrently identified, dengue virus type 2 (DENV-2) has been involved in the most important outbreaks during the last 20 years, including 2010 when the fatality rate highly increased. As there are no major studies reviewing virus origin and genotype distribution in this country, the present study attempts to reconstruct the phylogenetic history of DENV-2 using a sequence analysis from a 224 bp PCR-amplified product corresponding to the carboxyl terminus of the envelope (E) gene from 48 Colombian isolates. Results As expected, the oldest isolates belonged to the American genotype (subtype V), but the strains collected since 1990 represent the American/Asian genotype (subtype IIIb) as previously reported in different American countries. Interestingly, the introduction of this genotype coincides with the first report of dengue hemorrhagic fever in Colombia at the end of 1989 and the increase of cases during the next years. Conclusion After replacement of the American genotype, several lineages of American/Asian subtype have rapidly spread all over the country evolving in new clades. Nevertheless, the direct association of these new variants in the raise of lethality rate observed during the last outbreak has to be demonstrated.
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Affiliation(s)
- Jairo A Méndez
- Laboratorio de Virología, Instituto Nacional de Salud, Avenida/Calle 26 No, 51-20, Bogotá, D.C.,Colombia.
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Abstract
PURPOSE OF REVIEW Dengue is currently an expanding global health problem. Development of an effective tetravalent dengue vaccine is considered a high public health priority. The uniqueness of the dengue viruses (DENVs) and the spectrum of disease resulting from infection has made dengue vaccine development difficult. This review focuses on the current critical issues in dengue vaccine development. RECENT FINDINGS DENVs are arboviral flaviviruses transmitted by Aedes mosquitoes causing a spectrum of clinical disease. DENV infections are a significant global health problem; the WHO estimates that more than 120 countries have endemic DENV transmission resulting in 70-500 million infections, 2.1 million clinically severe cases, and 21 000 deaths annually. There are currently no licensed antivirals or vaccines to treat or prevent dengue. The DENV-host interaction of infection is unique with severe disease a consequence of sequential dengue infection, viral immune evasion, host antibody enhancement, host immune activation, and genetic predisposition. This unique pathogen-host interaction complicates dengue vaccine development and creates provocative questions in vaccine development such as identifying markers of protective immunogenicity, the potential role of antibody in vaccine failures, and the possible impact of large-scale vaccination on the evolution of wild-type DENV. SUMMARY Dengue is a unique and complex disease; developing a dengue vaccine has proven equally complex. In this review, the authors discuss issues that will prove to be critical to the success or failure of the dengue vaccine development effort.
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Dengue-1 virus clade replacement in Thailand associated with enhanced mosquito transmission. J Virol 2011; 86:1853-61. [PMID: 22130539 DOI: 10.1128/jvi.06458-11] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dengue viruses (DENV) are characterized by extensive genetic diversity and can be organized in multiple, genetically distinct lineages that arise and die out on a regular basis in regions where dengue is endemic. A fundamental question for understanding DENV evolution is the relative extent to which stochastic processes (genetic drift) and natural selection acting on fitness differences among lineages contribute to lineage diversity and turnover. Here, we used a set of recently collected and archived low-passage DENV-1 isolates from Thailand to examine the role of mosquito vector-virus interactions in DENV evolution. By comparing the ability of 23 viruses isolated on different dates between 1985 and 2009 to be transmitted by a present-day Aedes aegypti population from Thailand, we found that a major clade replacement event in the mid-1990s was associated with virus isolates exhibiting increased titers in the vector's hemocoel, which is predicted to result in a higher probability of transmission. This finding is consistent with the hypothesis that selection for enhanced transmission by mosquitoes is a possible mechanism underlying major DENV clade replacement events. There was significant variation in transmission potential among isolates within each clade, indicating that in addition to vector-driven selection, other evolutionary forces act to maintain viral genetic diversity. We conclude that occasional adaptive processes involving the mosquito vector can drive major DENV lineage replacement events.
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Chen R, Vasilakis N. Dengue--quo tu et quo vadis? Viruses 2011; 3:1562-608. [PMID: 21994796 PMCID: PMC3187692 DOI: 10.3390/v3091562] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/12/2011] [Accepted: 08/12/2011] [Indexed: 02/08/2023] Open
Abstract
Dengue viruses (DENV) are by far the most important arboviral pathogens in the tropics around the world, putting at risk of infection nearly a third of the global human population. DENV are members of the genus Flavivirus in the Family Flaviviridae and comprise four antigenically distinct serotypes (DENV-1-4). Although they share almost identical epidemiological features, they are genetically distinct. Phylogenetic analyses have revealed valuable insights into the origins, epidemiology and the forces that shape DENV evolution in nature. In this review, we examine the current status of DENV evolution, including but not limited to rates of evolution, selection pressures, population sizes and evolutionary constraints, and we discuss how these factors influence transmission, pathogenesis and emergence.
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Affiliation(s)
- Rubing Chen
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; E-Mail:
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; E-Mail:
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
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Abstract
Dengue fever (DF) and dengue hemorrhagic fever (DHF) are mosquito-transmitted diseases of global importance. Despite significant research efforts, no approved vaccines or antiviral drugs against these diseases are currently available. This brief article reviews the status of dengue vaccine development, with particular emphasis on the vaccine strategies in more advanced stages of evaluation; these include traditional attenuation, chimerization and engineered attenuation. Several aspects of these vaccine design strategies, including concerns about vaccine candidates inducing infection-enhancing antibodies, are also presented.
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Affiliation(s)
- Eiji Konishi
- Division of Infectious Diseases, Department of International Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe 654-0412, Japan
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dos Santos FB, Nogueira FB, Castro MG, Nunes PC, de Filippis AMB, Faria NR, Simões JB, Sampaio SA, Santos CR, Nogueira RMR. First report of multiple lineages of dengue viruses type 1 in Rio de Janeiro, Brazil. Virol J 2011; 8:387. [PMID: 21813012 PMCID: PMC3170301 DOI: 10.1186/1743-422x-8-387] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/03/2011] [Indexed: 01/06/2023] Open
Abstract
Background In Brazil dengue has been a major public health problem since DENV-1 introduction and spread in 1986. After a low or silent co-circulation, DENV-1 re-emerged in 2009 causing a major epidemic in the country in 2010 and 2011. In this study, the phylogeny of DENV-1 strains isolated in RJ after its first introduction in 1986 and after its emergence in 2009 and 2010 was performed in order to document possible evolutionary patterns or introductions in a re-emergent virus. Findings The analysis of the E gene sequences demonstrated that DENV-1 isolated during 2009/2010 still belong to genotype V (Americas/Africa) but grouping in a distinct clade (lineage II) of that represented by earlier DENV-1 (lineage I). However, strains isolated in 2011 grouped together forming another distinct clade (lineage III). Conclusions The monitoring of DENV is important to observe the spread of potentially virulent strains as well to evaluate its impact over the population during an outbreak. Whether explosive epidemics reported in Brazil caused mainly by DENV-1 was due to lineage replacement, or due the population susceptibility to this serotype which has not circulated for almost a decade or even due to the occurrence of secondary infections in a hyperendemic country, is not clear. This is the first report of multiple lineages of DENV-1 detected in Brazil.
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