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Su W, Jiang L, Lu W, Xie H, Cao Y, Di B, Li Y, Nie K, Wang H, Zhang Z, Xu S. A Serotype-Specific and Multiplex PCR Method for Whole-Genome Sequencing of Dengue Virus Directly from Clinical Samples. Microbiol Spectr 2022; 10:e0121022. [PMID: 36094197 PMCID: PMC9602986 DOI: 10.1128/spectrum.01210-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/16/2022] [Indexed: 12/30/2022] Open
Abstract
Dengue virus (DENV) is the most globally prevalent member of the genus Flavivirus in the family Flaviviridae, which can be classified into four serotypes. Historically, molecular epidemiological studies of DENV depended on E gene sequencing. The development of next-generation sequencing (NGS) allowed its application to viral whole-genome sequencing (WGS). In this study, we report the improvement of the existing WGS process for DENV by optimizing the primer design procedure, designing serotype-specific primer panels and reducing the sizes of amplicons. A total of 31 DENV-positive serum samples belonging to 4 serotypes and 9 genotypes of DENV were involved in the validation of the primer panels. The threshold cycle (CT) values of these samples ranged from 23.91 to 35.11. The validation results showed that the length of consensus sequences generated at a coverage depth of 20× or more ranged from 10,370 to 10,672 bp, with 100.00% coverage of the open reading frames and 97.34% to 99.52% coverage of the DENV genome. The amplification efficiency varied across amplicons, genotypes, and serotypes of DENVs. These results indicate that the serotype-specific primer panels allow users to obtain the whole genome of DENV directly from clinical samples, providing a universal, rapid, and effective tool for the integration of genomics with dengue surveillance. IMPORTANCE Dengue virus (DENV) is becoming the most globally prevalent arbovirus. The number of people living under the threat of DENV is increasing year by year. With the development of next-generation sequencing (NGS) technology, whole-genome sequencing (WGS) has been more and more widely used in infectious disease surveillance and molecular epidemiological studies. DENV population sequencing by NGS can increase our understanding of the changing epidemiology and evolution of the DENV genome at the molecular level, which demands universal primer panels and combination with NGS platforms. Multiplex PCR with a short-amplicon approach proved superior for amplifying viral genomes from clinical samples, particularly when the viral RNA was present at low concentrations. Additionally, DENV are known for their genetic diversity within serotype groups and geographical regions, so the primer panels we designed focused on universality, which would be useful in future local DENV outbreaks.
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Affiliation(s)
- Wenzhe Su
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Liyun Jiang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Weizhi Lu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Huaping Xie
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Yimin Cao
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Biao Di
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Yan Li
- Shandong Center for Disease Control and Prevention, Jinan, China
| | - Kai Nie
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Disease Control and Prevention, Beijing, China
| | - Huanyu Wang
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Disease Control and Prevention, Beijing, China
| | - Zhoubin Zhang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
- Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Songtao Xu
- Department of Arboviruses, NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Beijing, China
- State Key Laboratory for Infectious Disease Control and Prevention, Beijing, China
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Gaber M, Ahmad AA, El-Kady AM, Tolba M, Suzuki Y, Mohammed SM, Elossily NA. Dengue fever as a reemerging disease in upper Egypt: Diagnosis, vector surveillance and genetic diversity using RT-LAMP assay. PLoS One 2022; 17:e0265760. [PMID: 35499983 PMCID: PMC9060354 DOI: 10.1371/journal.pone.0265760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 03/07/2022] [Indexed: 11/18/2022] Open
Abstract
Background
The recent increase in dengue virus (DENV) outbreaks and the absence of an effective vaccine have highlighted the importance of developing rapid and effective diagnostic surveillance tests and mosquito-based screening programs. To establish effective control measures for preventing future DENV transmission, the present study was established to identify the main mosquito vector involved in the dengue fever (DF) outbreak in Upper Egypt in 2016 and detect the diversity of dengue virus serotypes circulating in both humans and vectors.
Methods
We investigated the prevalence of DENV infection and circulating serotypes in the sera of 51 humans clinically suspected of DF and 1800 field-collected Aedes aegypti adult female mosquitoes grouped into 36 pooled samples. Both DENV non-structural protein (NS1) immunochromatographic strip assay and loop-mediated isothermal amplification (LAMP) were used for screening.
Results
Overall, the rate of DENV infection in both human sera and pooled mosquito homogenate was 33.3%, as revealed by rapid dipstick immunochromatographic analysis. However, higher detection rates were observed with RT-LAMP assay of 60.8% and 44.4% for humans and vector mosquitoes, respectively. DENV-1 was the most prevalent serotype in both populations. A combination of two, three, or even four circulating serotypes was found in 87.5% of total positive pooled mosquito samples and 83.87% of DENV-positive human sera.
Conclusion
The study reinforces the evidence of the reemergence of Aedes aegypti in Upper Egypt, inducing an outbreak of DENV. Mosquito-based surveillance of DENV infection is important to elucidate the viral activity rate and define serotype diversity to understand the virus dynamics in the reinfested area. Up to our knowledge, this is the first report of serotyping of DENV infection in an outbreak in Egypt using RT-LAMP assay.
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Affiliation(s)
- Mona Gaber
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Asmaa M. El-Kady
- Department of Parasitology, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Mohammed Tolba
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Shereen M. Mohammed
- Department of Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Nahed Ahmed Elossily
- Department of Parasitology, Faculty of Medicine, Assiut University, Assiut, Egypt
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Rojas A, Moreira Soares A, Mendoza LP, Acosta ME, Aria L, Páez M, Herebia L, Vallejos MA, de Guillén Y, Aquino VH. Revisiting the dengue epidemic of 2011 in Paraguay: molecular epidemiology of dengue virus in the Asuncion metropolitan area. BMC Infect Dis 2021; 21:769. [PMID: 34364380 PMCID: PMC8349040 DOI: 10.1186/s12879-021-06487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 07/28/2021] [Indexed: 11/23/2022] Open
Abstract
Background Dengue is one of the most important re-emerging viral diseases and the most common human arthropod-borne viral infection worldwide. Any of the four Dengue virus serotypes (DENV-1 to 4) can cause asymptomatic infections or clinical manifestations that range in severity from a mild, self-limited illness, to a severe disease characterized by a shock syndrome that can lead to death. Paraguay suffers periodic epidemic outbreaks of dengue since 1988 when the DENV-1 was introduced in the country. Epidemics caused by all four serotypes have been reported and the country. Although dengue is endemic in Paraguay, few studies have described the molecular epidemiology of DENV in the country, which is important to understand the local and global spread, as well as the evolution of this pathogen. Methods This was a cross-sectional study of a convenience sample. Suspected dengue patients of any age were recruited from the Emergency Laboratory of the Central Hospital of the Institute of Social Welfare, Asuncion, Paraguay, from February to June of 2011. A DENV antigen test was used to confirm the infection. The protein E gene sequences of isolated viruses were sequenced for phylogenetic analysis. Results Dengue was confirmed in 55.1% of the participants (n = 98/178). The most frequent clinical findings were fever, headache, and myalgia. Identity analyses of the protein E gene sequence of 56 viruses isolated showed the circulation of DENV-1 (n = 45) and DENV-2 (n = 11) in the Asuncion metropolitan area in 2011. Molecular epidemiology analyses suggest that DENV-1 was introduced into Paraguay from Argentina, while the DENV-2 from Brazil, replacing previous virus lineages. Conclusions We have analyzed the molecular epidemiology of DENV-1 and DENV-2 isolated in Paraguay in 2011. We found strong evidence that DENV-1 was introduced into Paraguay from Argentina, while the DENV-2 from Brazil, replacing previous virus lineages. Molecular epidemiology studies are of great interest to analyze the dynamic of DENV spread, which are useful for early implementation of containment measures to reduce the risk of explosive epidemics caused by this virus. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06487-9.
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Affiliation(s)
- Alejandra Rojas
- Department of Production, Health Sciences Research Institute, National University of Asuncion, San Lorenzo, Paraguay
| | - Adriana Moreira Soares
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Laura Patricia Mendoza
- Department of Public Health, Health Sciences Research Institute, National University of Asuncion, San Lorenzo, Paraguay
| | - María Eugenia Acosta
- Department of Production, Health Sciences Research Institute, National University of Asuncion, San Lorenzo, Paraguay
| | - Laura Aria
- Department of Production, Health Sciences Research Institute, National University of Asuncion, San Lorenzo, Paraguay
| | - Malvina Páez
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Lilian Herebia
- Emergency Department, Central Hospital of the Institute of Social Welfare, Asunción, Paraguay
| | - María Asunción Vallejos
- Emergency Department, Central Hospital of the Institute of Social Welfare, Asunción, Paraguay
| | - Yvalena de Guillén
- Department of Production, Health Sciences Research Institute, National University of Asuncion, San Lorenzo, Paraguay
| | - Victor Hugo Aquino
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil.
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Full-genome sequencing and analysis of DENV-3 serotype isolated from Yemen. J Infect Public Health 2021; 14:803-810. [PMID: 34044250 DOI: 10.1016/j.jiph.2021.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/24/2021] [Accepted: 03/28/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Dengue virus causes the dengue fever as well as hemorrhagic fever in tropical and sub-tropical countries. It is now endemic in most parts of the South East Asia. Full-genome information of dengue virus 3 is not available from Yemen. METHODS In this study, the dengue virus 3 was detected by diagnostic tools like serology and RT-PCR in the samples isolated from a patient in Yemen. The full-genome was sequenced, and the identity, phylogenetic relationship and recombination analysis was performed by using BioEdit, MEGA X and RDP4 softwares. RESULTS The full-genome of the Yemen isolate was found to be 10,643 nt long with 3390 amino acids. The Yemen dengue virus 3 isolate showed the sequence similarity (98.5-92.4%) with dengue virus 3 isolates from China, Pakistan, India and Bangladesh respectively. The significant non-synonymous substitutions of amino acid in Yemen isolate were observed with selected isolates. The phylogenetic tree of Yemen isolate formed a unique clade within genotype III and sub-clade into lineage III. The Dengue virus isolate from Jeddah formed separated cluster with lineage IV. CONCLUSIONS This reveals the unique genetic variability among DENV-3 serotypes from Jeddah and earlier reported isolates from other regions.
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Genetic diversity and evolutionary dynamics of dengue isolates from India. Virusdisease 2019; 30:354-359. [PMID: 31803801 DOI: 10.1007/s13337-019-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
Dengue virus (DENV) is the mosquito borne virus which causes Dengue Haemorrhagic Fever and Dengue Shock Syndrome. It consists of four distinct serotypes (DENV 1-4). DENV 1, 3 and 4 were classified into five genotypes (GI-GV), where as DENV-2 belongs to American and Cosmopolitan genotypes. Dengue virus is most prevalent in south and Southeast Asia including India. This study was initiated to study the genetic diversity and evolution among the Dengue isolates in India. Pairwise comparison of amino acid sequences among the serotypes has shown that DENV-3 is having less sequence diversity compared to other serotypes having differences in their amino acid numbers. We have analyzed the 50 Indian strains and 19 of those strains have been identified as recombinant strains by using RDP4 package, which are then excluded for future selection. Episodic positive selection of DENV was obtained using MEME with P value is ≤ 5. Positive selection on several codons was used to correlate the genetic diversity between serotypes. This study clearly established that diversity of amino acids and inter genotypic recombination of strains are the major cause for antigenicity variation and evolution of DENV within India.
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Patil JA, Alagarasu K, Kakade MB, More AM, Gadekar KA, Jadhav SM, Parashar D, Shah PS. Emergence of dengue virus type 1 and type 3 as dominant serotypes during 2017 in Pune and Nashik regions of Maharashtra, Western India. INFECTION GENETICS AND EVOLUTION 2018; 66:272-283. [PMID: 30366083 DOI: 10.1016/j.meegid.2018.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/05/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
Abstract
India witnessed dengue outbreaks during 2017 in different parts with more than 180000 cases. There is no data on the serotypes/genotypes of dengue virus (DENV) associated with the 2017 outbreak season. The present study investigated DENV circulating in Pune and Nashik regions of Maharashtra, Western India at molecular level. IgM negative samples that were collected before 6th post onset days of illness were tested for DENV RNA and serotyped by real time RT-PCR based methods. Representative samples of each serotype were processed for virus isolation and envelope (E) gene sequencing. Among the 472 samples tested for DENV serotypes from Nashik, DENV-1 was observed in 36.2%, DENV-2 in 12.9%, DENV-3 in 35.4%, DENV-4 in 8.0%, and multiple serotypes in 7.4% of the samples respectively. In Pune region, among the 109 samples tested for DENV serotypes, DENV-1 was observed in 27.5%, DENV-2 in 11.0%, DENV-3 in 52.3%, DENV-4 in 4.6%, and multiple serotypes in 4.6% of the samples respectively. Comparison of serotype distribution from 2009 to 2017 from the Pune region revealed the emergence of DENV-3 as the dominant serotype followed by DENV-1 in 2017. In the Nashik region, both DENV-1 and DENV-3 were predominant in 2017. Phylogenetic analyses revealed co-circulation of American African (AM/AF) and Asian genotypes of DENV-1. DENV-1 Asian genotype was detected for the first time in the region. No genotype changes were observed for DENV-2 (cosmopolitan genotype), DENV-3 (genotype III) and DENV-4 (genotype I). For DENV-3, a unique amino acid substitution (I380T) was observed in the domain III of E protein of 2017 isolates and was not observed in earlier DENV-3 genotype III isolates. To conclude, the results suggest the emergence of DENV-1 with circulation of both Asian and AM/AF genotypes and DENV-3 with unique amino acid substitutions in Pune and Nashik regions. The study underscores the need for continuous molecular monitoring at a large scale to detect the changes in DENV serotypes/genotypes that might have implications for earlier prediction of dengue outbreaks and designing dengue vaccines and predicting its efficacy.
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Affiliation(s)
- J A Patil
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
| | - K Alagarasu
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India.
| | - M B Kakade
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
| | - A M More
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
| | - K A Gadekar
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
| | - S M Jadhav
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
| | - D Parashar
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
| | - P S Shah
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India
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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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Slavov SN, Hespanhol MR, Ferreira AR, Rodrigues ES, Covas DT, Kashima S. Silent dengue virus circulation among asymptomatic blood donors from a hyperendemic Brazilian region. Transfus Med 2018. [DOI: 10.1111/tme.12521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- S. N. Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Rbeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
- Department of Internal Medicine, Faculty of Medicine of Ribeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
| | - M. R. Hespanhol
- Blood Center of Ribeirão Preto, Faculty of Medicine of Rbeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
| | - A. R. Ferreira
- Blood Center of Ribeirão Preto, Faculty of Medicine of Rbeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
| | - E. S. Rodrigues
- Blood Center of Ribeirão Preto, Faculty of Medicine of Rbeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
| | - D. T. Covas
- Blood Center of Ribeirão Preto, Faculty of Medicine of Rbeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
- Department of Internal Medicine, Faculty of Medicine of Ribeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
| | - S. Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Rbeirão PretoUniversity of São Paulo Ribeirão Preto São Paulo Brazil
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Sittivicharpinyo T, Wonnapinij P, Surat W. Phylogenetic analyses of DENV-3 isolated from field-caught mosquitoes in Thailand. Virus Res 2017; 244:27-35. [PMID: 29126872 DOI: 10.1016/j.virusres.2017.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 12/28/2022]
Abstract
Dengue virus serotype 3 (DENV-3) can cause all forms of dengue diseases and is a predominant serotype in many countries. This serotype is classified into five genotypes: I-V. Genotypes I-III have widely spread throughout the world, whereas genotypes IV and V are rare. Despite the impact on the spread of dengue diseases, only a few studies have reported the characteristics of DENV present in mosquito vectors. Hence, this study aimed to identify DENV-3 genotypes and reveal genetic variation of this virus presented in field-caught mosquitoes collected from endemic areas in Thailand during 2011-2015. First, we examined the effectiveness of the E gene sequence on DENV-3 genotyping, with results supporting the use of this gene for genotype identification. Then, we sequenced this gene in ten DENV-3 strains isolated from mosquitoes. The results showed that eight and two samples were genotypes III and V, respectively, and that they are closely related to DENV-3 isolated from Southeast and East Asian samples. The translated E gene sequences showed 25 unique amino acid (AA) residues located at 23 positions. Eight out of 25 residues have different chemical properties compared to the conserved AAs that are distributed across the three domains functioning in virus-host interaction. Hence, our study reports the first DENV-3 genotype V in Thailand, with these viruses potentially influencing both the disease severity and epidemic potential of DENV-3.
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Affiliation(s)
- Thikhumporn Sittivicharpinyo
- Evolutionary Genetics and Computational Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, Thailand
| | - Passorn Wonnapinij
- Evolutionary Genetics and Computational Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, Thailand; Centre for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU), Thailand
| | - Wunrada Surat
- Evolutionary Genetics and Computational Biology Research Unit, Department of Genetics, Faculty of Science, Kasetsart University, Thailand; Centre for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University (CASTNAR, NRU-KU), Thailand.
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10
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Tambunan USF, Nasution MAF, Azhima F, Parikesit AA, Toepak EP, Idrus S, Kerami D. Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation. Drug Target Insights 2017; 11:1177392817701726. [PMID: 28469408 PMCID: PMC5404899 DOI: 10.1177/1177392817701726] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/01/2017] [Indexed: 01/01/2023] Open
Abstract
Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world's population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2'OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | | | - Fauziah Azhima
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Arli Aditya Parikesit
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Erwin Prasetya Toepak
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Syarifuddin Idrus
- Industrial Standardization Laboratory, Ministry of Industrial Affair, Ambon, Indonesia
| | - Djati Kerami
- Mathematics Computation Research Group, Department of Mathematics, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
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Waman VP, Kale MM, Kulkarni-Kale U. Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study. INFECTION GENETICS AND EVOLUTION 2017; 49:234-240. [PMID: 28126562 DOI: 10.1016/j.meegid.2017.01.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/14/2017] [Accepted: 01/21/2017] [Indexed: 11/29/2022]
Abstract
Dengue virus serotype 3 (DENV-3), one of the four serotypes of Dengue viruses, is geographically diverse. There are five distinct genotypes (I-V) of DENV-3. Emerging strains and lineages of DENV-3 are increasingly being reported. Availability of genomic data for DENV-3 strains provides opportunity to study its population structure. Complete genome sequences are available for 860 strains of four genotypes (I, II, III and V) isolated worldwide and were analyzed using population genetics and evolutionary approaches to map landscape of genomic diversity. DENV-3 population is observed to be stratified into five major subpopulations. Genotype I and II formed independent subpopulations while genotype III is subdivided into three subpopulations (GIII-a, GIII-b and GIII-c) and is therefore heterogeneous. Genotypes I, II and GIII-a subpopulations comprise of Asian strains whereas GIII-c comprises of American strains. GIII-b subpopulation includes mainly of American strains along with a few strains from Sri Lanka. Genetic admixture is predominantly observed in Sri Lankan strains of genotype III and all strains of genotype V. Inter-genotype recombination was observed to occur in non-structural region of several Asian strains whereas extent of recombination was limited in American strains. Significant positive selection was found to be operational on all genes and observed to be the main driving force of genetic diversity. Positive selection was strongly operational on the branches leading to Asian genotypes and helped to delineate the genetic differences between Asian and American lineages. Thus, inter-genotype recombination, migration and adaptive evolution are the major determinants of evolution of DENV-3.
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Affiliation(s)
- Vaishali P Waman
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India
| | - Mohan M Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India.
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Cunha MDP, Guimarães VN, Souza M, de Paula Cardoso DDD, de Almeida TNV, de Oliveira TS, Fiaccadori FS. Phylodynamics of DENV-1 reveals the spatiotemporal co-circulation of two distinct lineages in 2013 and multiple introductions of dengue virus in Goiás, Brazil. INFECTION GENETICS AND EVOLUTION 2016; 43:130-4. [PMID: 27223633 DOI: 10.1016/j.meegid.2016.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/02/2023]
Abstract
Dengue virus type 1 (DENV-1) was the first serotype introduced in Brazil, during in the 1980s. Since then, this virus has spread in the Brazilian territory, causing several outbreaks. In 2013 the highest number of dengue cases was notified, when compared to the previous years in Brazil, and the state of Goiás reported over 160 thousand cases. In this study, we aimed to present the Phylodynamics of DENV-1 isolates from the state of Goiás, Brazil, during 2013 outbreak, based on the envelope gene (E) sequences. Phylogenetic analysis revealed that Brazilian DENV-1 isolates are grouped together with viruses from genotype V in two distinct lineages (lineage I and lineage II) reflecting co-circulation. Phylogeographic analyses showed that these lineages were introduced in different moments in Goiás, Brazil, using distinct routes, likely originated from the Caribbean. Lineage I was first introduced coming from Rio de Janeiro (2007-2012), followed by the introduction from Argentina (2010-2013). Lineage II was introduced in a single moment from Rio de Janeiro and this clade has existed since 2007-2010. The different viral introduction events demonstrate the viral dispersion process with neighboring regions, which is essential for the maintenance of outbreaks and introduction of new emerging viruses. In conclusion, obtained data reveals the importance of continuous molecular surveillance of this virus in different regions, providing a better understanding of DENV-1 circulation, considering the evolutionary and virus spread patterns.
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Affiliation(s)
| | | | - Menira Souza
- Federal University of Goiás, Goiânia, Goiás, Brazil
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13
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Poloni TR, Dornas FP, Dos Santos NN, Soares AM, Amarilla AA, Alfonso HL, Trigueiro S, Lavrador MAS, Yamamoto AY, Aquino VH. High prevalence of clinically unsuspected dengue disease among children in Ribeirao Preto city, Brazil. J Med Virol 2016; 88:1711-9. [PMID: 27004990 DOI: 10.1002/jmv.24533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2016] [Indexed: 11/12/2022]
Abstract
The aim of this study was to analyze the characteristics of Dengue virus (DENV)-infected children and the accuracy of dengue diagnosis based on clinical presentations. The inclusion criteria were children ≥1-year-old presenting febrile illness with 1-7 days of onset. Children (n = 110) aged 2-15 years were included in this study. DENV infection was confirmed with virological tests using serum, salvia, and/or urine samples. The attending pediatricians classified 56/110 (50.91%) of the children as suspected dengue cases. The DENV infection was confirmed by specific laboratory tests in 52/56 (92.9%) of the suspected dengue cases but also in 44/54 (81.5%) of the unsuspected dengue cases; total of 96/110 (87.27%) confirmed dengue cases. The clinical diagnosis gave an overall sensitivity of 54.2% (52/96) and a specificity of 71.4% (10/14). The positive predictive value of the clinical diagnosis was 92.8% and negative predictive value was 18.5%. After the third day of onset of symptoms, the DENV genome detection rate was similar in serum and saliva samples, suggesting that saliva samples represent an alternative to blood samples for early dengue diagnosis. Vaccination against Yellow fever virus did not influence the antibody response against DENV-1, DENV-2, and DENV-3, which circulated during the study period. Although the signs and symptoms were compatible with dengue, the attending pediatricians did not suspect the disease in several children. Therefore, the inclusion of virological tests for early diagnosis in the protocols for dengue surveillance would help in the implementation of prompt treatment of patients and epidemic containment strategies. J. Med. Virol. 88:1711-1719, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Telma Regina Poloni
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Fabio Pio Dornas
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Nilton Nascimento Dos Santos
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Adriana Moreira Soares
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Alberto Anastacio Amarilla
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Helda Liz Alfonso
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Sabrina Trigueiro
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marco Aurélio Sicchiroli Lavrador
- Laboratory of Bioinformatics and Biostatistics, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Aparecida Yulie Yamamoto
- Department of Pediatrics, School of Medicine of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Victor Hugo Aquino
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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14
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Ji GH, Deng YQ, Yu XJ, Jiang T, Wang HJ, Shi X, Zhang DP, Li XF, Zhu SY, Zhao H, Dai JX, Qin CF, Guo YJ. Characterization of a Novel Dengue Serotype 4 Virus-Specific Neutralizing Epitope on the Envelope Protein Domain III. PLoS One 2015; 10:e0139741. [PMID: 26430770 PMCID: PMC4592203 DOI: 10.1371/journal.pone.0139741] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/15/2015] [Indexed: 12/04/2022] Open
Abstract
The dengue virus (DENV) envelope protein domain III (ED3) has been suggested to contain receptor recognition sites and the critical neutralizing epitopes. Up to date, relatively little work has been done on fine mapping of neutralizing epitopes on ED3 for DENV4. In this study, a novel mouse type-specific neutralizing antibody 1G6 against DENV4 was obtained with both prophylactic and therapeutic effects. The epitope was mapped to residues 387-390 of DENV4 envelope protein. Furthermore, site-directed mutagenesis assay identified two critical residues (T388 and H390). The epitope is variable among different DENV serotypes but is highly conserved among four DENV4 genotypes. Affinity measurement showed that naturally occurring variations in ED3 outside the epitope region did not alter the binding of mAb 1G6. These findings expand our understanding of the interactions between neutralizing antibodies and the DENV4 and may be valuable for rational design of DENV vaccines and antiviral drugs.
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Affiliation(s)
- Guang-Hui Ji
- Department of Traditional Chinese Medicine, Navy General Hospital, Beijing, China
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Yong-Qiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao-Jie Yu
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Tao Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hua-Jing Wang
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Xin Shi
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Da-Peng Zhang
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Xiao-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shun-Ya Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jian-Xin Dai
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ya-Jun Guo
- International Joint Cancer Institute, Second Military Medical University, Shanghai, China
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Barcelos Figueiredo L, Sakamoto T, Leomil Coelho LF, de Oliveira Rocha ES, Gomes Cota MM, Ferreira GP, de Oliveira JG, Kroon EG. Dengue virus 2 American-Asian genotype identified during the 2006/2007 outbreak in Piauí, Brazil reveals a Caribbean route of introduction and dissemination of dengue virus in Brazil. PLoS One 2014; 9:e104516. [PMID: 25127366 PMCID: PMC4134198 DOI: 10.1371/journal.pone.0104516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is the most widespread arthropod-borne virus, and the number and severity of outbreaks has increased worldwide in recent decades. Dengue is caused by DENV-1, DENV- 2, DENV-3 and DENV-4 which are genetically distant. The species has been subdivided into genotypes based on phylogenetic studies. DENV-2, which was isolated from dengue fever patients during an outbreak in Piaui, Brazil in 2006/2007 was analyzed by sequencing the envelope (E) gene. The results indicated a high similarity among the isolated viruses, as well as to other DENV-2 from Brazil, Central America and South America. A phylogenetic and phylogeographic analysis based on DENV-2E gene sequences revealed that these viruses are grouped together with viruses of the American-Asian genotype in two distinct lineages. Our results demonstrate the co-circulation of two American-Asian genotype lineages in northeast Brazil. Moreover, we reveal that DENV-2 lineage 2 was detected in Piauí before it disseminated to other Brazilian states and South American countries, indicating the existence of a new dissemination route that has not been previously described.
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Affiliation(s)
| | - Tetsu Sakamoto
- Laboratório de Biodados, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | | | - Erna Geessien Kroon
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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16
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Manakkadan A, Joseph I, Prasanna RR, Kunju RI, Kailas L, Sreekumar E. Lineage shift in Indian strains of Dengue virus serotype-3 (Genotype III), evidenced by detection of lineage IV strains in clinical cases from Kerala. Virol J 2013; 10:37. [PMID: 23360780 PMCID: PMC3598737 DOI: 10.1186/1743-422x-10-37] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/25/2013] [Indexed: 11/23/2022] Open
Abstract
Background Local epidemiology of Dengue is defined by the genetic diversity of the circulating Dengue virus (DENV) strains. This important information is not available for the virus strains from most parts of the Indian subcontinent. The present study focused on the genetic diversity of the serotype 3 DENV strains (DENV-3) from India. Results A total of 22 DENV-3 strains identified by reverse-transcription PCR analysis of serum samples from 709 patients were studied. These samples were collected over a period of 4 years (2008–2011) from dengue fever suspected patients from Kerala, a dengue endemic state in South India. Comparison of a 1740bp nucleotide sequence of the viral Capsid-Pre-membrane-Envelope coding region of our strains and previously reported DENV-3 strains from India, South Asia and South America revealed non-synonymous substitutions that were genotype III-specific as well as sporadic. Evidence of positive selection was detected in the I81 amino acid residue of the envelope protein. Out of the 22 samples, three had I81A and 18 had I81V substitutions. In the phylogenetic analysis by maximum likelihood method the strains from Kerala clustered in two different lineages (lineage III and IV) within genotype III clade of DENV-3 strains. The ten strains that belonged to lineage IV had a signature amino acid substitution T219A in the envelope protein. Interestingly, all these strains were found to be closely related to a Singapore strain GU370053 isolated in 2007. Conclusions Our study identifies for the first time the presence of lineage IV strains in the Indian subcontinent. Results indicate the possibility of a recent exotic introduction and also a shift from the existing lineage III strains to lineage IV. Lineage shifts in DENV-3 strains have been attributed to dramatic increase in disease severity in many parts of the world. Hence the present observation could be significant in terms of the clinical severity of future dengue cases in the region.
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Affiliation(s)
- Anoop Manakkadan
- Viral Disease Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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17
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de Castro MG, de Nogueira FB, Nogueira RMR, Lourenço-de-Oliveira R, dos Santos FB. Genetic variation in the 3' untranslated region of dengue virus serotype 3 strains isolated from mosquitoes and humans in Brazil. Virol J 2013; 10:3. [PMID: 23282086 PMCID: PMC3547765 DOI: 10.1186/1743-422x-10-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 12/27/2012] [Indexed: 11/17/2022] Open
Abstract
Summary
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18
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de Araújo JMG, Bello G, Romero H, Nogueira RMR. Origin and evolution of dengue virus type 3 in Brazil. PLoS Negl Trop Dis 2012; 6:e1784. [PMID: 22970331 PMCID: PMC3435237 DOI: 10.1371/journal.pntd.0001784] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 07/04/2012] [Indexed: 11/17/2022] Open
Abstract
The incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 (DENV-3) at the early 2000s. Despite the major public health concerns, there have been very few studies of the molecular epidemiology and time-scale of this DENV lineage in Brazil. In this study, we investigated the origin and dispersion dynamics of DENV-3 genotype III in Brazil by examining a large number (n = 107) of E gene sequences sampled between 2001 and 2009 from diverse Brazilian regions. These Brazilian sequences were combined with 457 DENV-3 genotype III E gene sequences from 29 countries around the world. Our phylogenetic analysis reveals that there have been at least four introductions of the DENV-3 genotype III in Brazil, as signified by the presence of four phylogenetically distinct lineages. Three lineages (BR-I, BR-II, and BR-III) were probably imported from the Lesser Antilles (Caribbean), while the fourth one (BR-IV) was probably introduced from Colombia or Venezuela. While lineages BR-I and BR-II succeeded in getting established and disseminated in Brazil and other countries from the Southern Cone, lineages BR-III and BR-IV were only detected in one single individual each from the North region. The phylogeographic analysis indicates that DENV-3 lineages BR-I and BR-II were most likely introduced into Brazil through the Southeast and North regions around 1999 (95% HPD: 1998–2000) and 2001 (95% HPD: 2000–2002), respectively. These findings show that importation of DENV-3 lineages from the Caribbean islands into Brazil seems to be relatively frequent. Our study further suggests that the North and Southeast Brazilian regions were the most important hubs of introduction and spread of DENV-3 lineages and deserve an intense epidemiological surveillance. Dengue is a major health problem in the tropics and the incidence of dengue fever and dengue hemorrhagic fever in Brazil experienced a significant increase since the emergence of dengue virus type-3 (DENV-3). In this study, the authors reconstruct the spatio-temporal dispersion pattern of the DENV-3 lineage that circulates in Brazil and the Americas. The authors found that DENV-3 outbreaks occurring in the American continent since the mid-1990s are the result of a single introduction of genotype III. The Central American countries and Mexico were the hubs of genotype III spread in the Americas, while the Caribbean region acted as a staging post between Central America/Mexico and South America. The authors estimate that there have been at least four introductions of the DENV-3 genotype III in Brazil, although only two of them succeeded in getting established and disseminating through the country. The Lesser Antilles (Caribbean) were the main source of DENV-3 viruses that arrived into Brazil,and the North and Southeast country regions seem to be most important hubs of introduction and dissemination of DENV-3 lineages. These findings offer important information to perform more effective surveillance programs to detect introduction and dispersal of new DENV lineages in Brazil.
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Affiliation(s)
- Josélio Maria Galvão de Araújo
- Laboratory of Molecular Biology for Infectious Diseases and Cancer, Federal University of Rio Grande do Norte, Natal, Brazil.
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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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20
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Alfonso HL, Amarilla AA, Gonçalves PF, Barros MT, de Almeida FT, Silva TR, da Silva EV, Nunes MT, Vasconcelos PFC, Vieira DS, Batista WC, Bobadilla ML, Vazquez C, Moran M, Figueiredo LTM, Aquino VH. Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics. Virol J 2012; 9:124. [PMID: 22716071 PMCID: PMC3494512 DOI: 10.1186/1743-422x-9-124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 05/31/2012] [Indexed: 11/10/2022] Open
Abstract
Background Dengue is the most important mosquito-borne viral disease worldwide. Dengue virus comprises four antigenically related viruses named dengue virus type 1 to 4 (DENV1-4). DENV-3 was re-introduced into the Americas in 1994 causing outbreaks in Nicaragua and Panama. DENV-3 was introduced in Brazil in 2000 and then spread to most of the Brazilian States, reaching the neighboring country, Paraguay in 2002. In this study, we have analyzed the phylogenetic relationship of DENV-3 isolated in Brazil and Paraguay with viruses isolated worldwide. We have also analyzed the evolutionary divergence dynamics of DENV-3 viruses. Results The entire open reading frame (ORF) of thirteen DENV-3 isolated in Brazil (n = 9) and Paraguay (n = 4) were sequenced for phylogenetic analysis. DENV-3 grouped into three main genotypes (I, II and III). Several internal clades were found within each genotype that we called lineage and sub-lineage. Viruses included in this study belong to genotype III and grouped together with viruses isolated in the Americas within the lineage III. The Brazilian viruses were further segregated into two different sub-lineage, A and B, and the Paraguayan into the sub-lineage B. All three genotypes showed internal grouping. The nucleotide divergence was in average 6.7% for genotypes, 2.7% for lineages and 1.5% for sub-lineages. Phylogenetic trees constructed with any of the protein gene sequences showed the same segregation of the DENV-3 in three genotypes. Conclusion Our results showed that two groups of DENV-3 genotypes III circulated in Brazil during 2002–2009, suggesting different events of introduction of the virus through different regions of the country. In Paraguay, only one group DENV-3 genotype III is circulating that is very closely related to the Brazilian viruses of sub-lineage B. Different degree of grouping can be observed for DENV-3 and each group showed a characteristic evolutionary divergence. Finally, we have observed that any protein gene sequence can be used to identify the virus genotype.
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Affiliation(s)
- Helda Liz Alfonso
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Universidade de São Paulo, Av, do Café s/n., 14040-903, Ribeirão Preto, São Paulo, Brazil
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21
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Detection of dengue virus genome in urine by real-time reverse transcriptase PCR: a laboratory diagnostic method useful after disappearance of the genome in serum. J Clin Microbiol 2012; 50:2047-52. [PMID: 22442323 DOI: 10.1128/jcm.06557-11] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reemergence of dengue virus (DENV) infection has created a requirement for improved laboratory diagnostic procedures. In this study, DENV genome detection in urine was evaluated as a diagnostic method. The DENV genome was detected by real-time reverse transcriptase PCR (RT-PCR) in urine and serum of dengue patients. The detection rate of DENV genome in urine was 25% (2/8) on disease days 0 to 3 and 32% (7/22) on days 4 to 5. The rate was 50% or higher on days 6 to 16, 52% (11/21) on days 6 to 7, 78% (7/9) on days 8 to 9, 80% (4/5) on days 10 to 11, 50% (2/4) on days 12 to 13, and 60% (3/5) on days 14 to 16. The last positive urine sample was on day 16. The detection rates in serum were highest on days 0 to 3 and were greater than 50% on days 0 to 7. Detection rates decreased thereafter, and the last positive detection was on day 11. These results indicate that the time frames for positive detection differ between urine and serum samples, whereby detection rates of 50% or higher are evident between days 6 to 16 for urine samples and days 0 to 7 for serum samples. Nucleotide sequences of PCR products were identical between urine and serum samples. The detection of DENV genome in urine samples by real-time RT-PCR is useful to confirm DENV infection, particularly after viremia disappears.
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22
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Messer WB, Yount B, Hacker KE, Donaldson EF, Huynh JP, de Silva AM, Baric RS. Development and characterization of a reverse genetic system for studying dengue virus serotype 3 strain variation and neutralization. PLoS Negl Trop Dis 2012; 6:e1486. [PMID: 22389731 PMCID: PMC3289595 DOI: 10.1371/journal.pntd.0001486] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/07/2011] [Indexed: 12/15/2022] Open
Abstract
Dengue viruses (DENV) are enveloped single-stranded positive-sense RNA viruses transmitted by Aedes spp. mosquitoes. There are four genetically distinct serotypes designated DENV-1 through DENV-4, each further subdivided into distinct genotypes. The dengue scientific community has long contended that infection with one serotype confers lifelong protection against subsequent infection with the same serotype, irrespective of virus genotype. However this hypothesis is under increased scrutiny and the role of DENV genotypic variation in protection from repeated infection is less certain. As dengue vaccine trials move increasingly into field-testing, there is an urgent need to develop tools to better define the role of genotypic variation in DENV infection and immunity. To better understand genotypic variation in DENV-3 neutralization and protection, we designed and constructed a panel of isogenic, recombinant DENV-3 infectious clones, each expressing an envelope glycoprotein from a different DENV-3 genotype; Philippines 1982 (genotype I), Thailand 1995 (genotype II), Sri Lanka 1989 and Cuba 2002 (genotype III) and Puerto Rico 1977 (genotype IV). We used the panel to explore how natural envelope variation influences DENV-polyclonal serum interactions. When the recombinant viruses were tested in neutralization assays using immune sera from primary DENV infections, neutralization titers varied by as much as ∼19-fold, depending on the expressed envelope glycoprotein. The observed variability in neutralization titers suggests that relatively few residue changes in the E glycoprotein may have significant effects on DENV specific humoral immunity and influence antibody mediated protection or disease enhancement in the setting of both natural infection and vaccination. These genotypic differences are also likely to be important in temporal and spatial microevolution of DENV-3 in the background of heterotypic neutralization. The recombinant and synthetic tools described here are valuable for testing hypotheses on genetic determinants of DENV-3 immunopathogenesis.
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Affiliation(s)
- William B. Messer
- Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Boyd Yount
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kari E. Hacker
- Department of Microbiology and Immunology, and Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Eric F. Donaldson
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeremy P. Huynh
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, and Southeast Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ralph S. Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Schmidt DJ, Pickett BE, Camacho D, Comach G, Xhaja K, Lennon NJ, Rizzolo K, de Bosch N, Becerra A, Nogueira ML, Mondini A, da Silva EV, Vasconcelos PF, Muñoz-Jordán JL, Santiago GA, Ocazionez R, Gehrke L, Lefkowitz EJ, Birren BW, Henn MR, Bosch I. A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2011; 11:2011-9. [PMID: 21964598 PMCID: PMC3565618 DOI: 10.1016/j.meegid.2011.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/05/2011] [Accepted: 09/08/2011] [Indexed: 11/24/2022]
Abstract
Dengue virus currently causes 50-100 million infections annually. Comprehensive knowledge about the evolution of Dengue in response to selection pressure is currently unavailable, but would greatly enhance vaccine design efforts. In the current study, we sequenced 187 new dengue virus serotype 3 (DENV-3) genotype III whole genomes isolated from Asia and the Americas. We analyzed them together with previously-sequenced isolates to gain a more detailed understanding of the evolutionary adaptations existing in this prevalent American serotype. In order to analyze the phylogenetic dynamics of DENV-3 during outbreak periods; we incorporated datasets of 48 and 11 sequences spanning two major outbreaks in Venezuela during 2001 and 2007-2008, respectively. Our phylogenetic analysis of newly sequenced viruses shows that subsets of genomes cluster primarily by geographic location, and secondarily by time of virus isolation. DENV-3 genotype III sequences from Asia are significantly divergent from those from the Americas due to their geographical separation and subsequent speciation. We measured amino acid variation for the E protein by calculating the Shannon entropy at each position between Asian and American genomes. We found a cluster of seven amino acid substitutions having high variability within E protein domain III, which has previously been implicated in serotype-specific neutralization escape mutants. No novel mutations were found in the E protein of sequences isolated during either Venezuelan outbreak. Shannon entropy analysis of the NS5 polymerase mature protein revealed that a G374E mutation, in a region that contributes to interferon resistance in other flaviviruses by interfering with JAK-STAT signaling was present in both the Asian and American sequences from the 2007-2008 Venezuelan outbreak, but was absent in the sequences from the 2001 Venezuelan outbreak. In addition to E, several NS5 amino acid changes were unique to the 2007-2008 epidemic in Venezuela and may give additional insight into the adaptive response of DENV-3 at the population level.
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Affiliation(s)
- DJ Schmidt
- University of Massachusetts Medical School, Worcester, MA, US. Current address DJS: Tuft University Veternary School, North Grafton, MA
| | - BE Pickett
- University of Alabama at Birmingham, Birmingham, AL. Current address BEP: University of Texas Southwestern Medical Center, Dallas, TX, US
| | - D Camacho
- Biomed, Universidad de Carabobo, Maracay, Venezuela
| | - G Comach
- Biomed, Universidad de Carabobo, Maracay, Venezuela
| | - K Xhaja
- University of Massachusetts Medical School, Worcester, MA, US. Current address DJS: Tuft University Veternary School, North Grafton, MA
| | | | - K Rizzolo
- University of Massachusetts Medical School, Worcester, MA, US. Current address DJS: Tuft University Veternary School, North Grafton, MA
- Broad Institute. Cambridge, MA, US
| | - N de Bosch
- Banco Metropolitano de Caracas, Universidad Central de Venezuela, Caracas, Venezuela
| | - A Becerra
- University of Massachusetts Medical School, Worcester, MA, US. Current address DJS: Tuft University Veternary School, North Grafton, MA
- Banco Metropolitano de Caracas, Universidad Central de Venezuela, Caracas, Venezuela
| | - ML Nogueira
- Faculdade de Medicina de São José do Rio Preto, Laboratório de Pesquisas em Virologia, Departamento de Doenças Infecciosas e Parasitárias, São José do Rio Preto, SP, Brazil
| | - A Mondini
- Faculdade de Medicina de São José do Rio Preto, Laboratório de Pesquisas em Virologia, Departamento de Doenças Infecciosas e Parasitárias, São José do Rio Preto, SP, Brazil
| | - EV da Silva
- Instituto Nacional de Ciência e Tecnologia em Dengue, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Bioquímica e Imunologia, Belo Horizonte and Instituto Nacional de Ciência e Tecnologia para Febres Hemorrágicas Virais (INCT-FHV), Instituto Evandro Chagas, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - PF Vasconcelos
- Instituto Nacional de Ciência e Tecnologia em Dengue, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Bioquímica e Imunologia, Belo Horizonte and Instituto Nacional de Ciência e Tecnologia para Febres Hemorrágicas Virais (INCT-FHV), Instituto Evandro Chagas, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - JL Muñoz-Jordán
- Centers for Disease Control and Prevention, San Juan, Puerto Rico, US
| | - GA Santiago
- Centers for Disease Control and Prevention, San Juan, Puerto Rico, US
| | - R Ocazionez
- Universidad Industrial de Santander, Santander, Colombia
| | - L Gehrke
- Massachusetts Institute of Technology. Division of Heath Science and Technology. Cambridge, MA, US
| | - EJ Lefkowitz
- University of Alabama at Birmingham, Birmingham, AL. Current address BEP: University of Texas Southwestern Medical Center, Dallas, TX, US
| | | | - MR Henn
- Broad Institute. Cambridge, MA, US
| | - I Bosch
- University of Massachusetts Medical School, Worcester, MA, US. Current address DJS: Tuft University Veternary School, North Grafton, MA
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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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25
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de Figueiredo MLG, de C Gomes A, Amarilla AA, de S Leandro A, de S Orrico A, de Araujo RF, do S M Castro J, Durigon EL, Aquino VH, Figueiredo LTM. Mosquitoes infected with dengue viruses in Brazil. Virol J 2010; 7:152. [PMID: 20624314 PMCID: PMC2913956 DOI: 10.1186/1743-422x-7-152] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 07/12/2010] [Indexed: 12/02/2022] Open
Abstract
Dengue epidemics have been reported in Brazil since 1985. The scenery has worsened in the last decade because several serotypes are circulating and producing a hyper-endemic situation, with an increase of DHF/DSS cases as well as the number of fatalities. Herein, we report dengue virus surveillance in mosquitoes using a Flavivirus genus-specific RT-Hemi-Nested-PCR assay. The mosquitoes (Culicidae, n = 1700) collected in the Northeast, Southeast and South of Brazil, between 1999 and 2005, were grouped into 154 pools. Putative genomes of DENV-1, -2 and -3 were detected in 6 mosquito pools (3.8%). One amplicon of putative DENV-1 was detected in a pool of Haemagogus leucocelaenus suggesting that this virus could be involved in a sylvatic cycle. DENV-3 was found infecting 3 pools of larvae of Aedes albopictus and the nucleotide sequence of one of these viruses was identified as DENV-3 of genotype III, phylogenetically related to other DENV-3 isolated in Brazil. This is the first report of a nucleotide sequence of DENV-3 from larvae of Aedes albopictus.
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26
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Poloni TR, Oliveira AS, Alfonso HL, Galvão LR, Amarilla AA, Poloni DF, Figueiredo LT, Aquino VH. Detection of dengue virus in saliva and urine by real time RT-PCR. Virol J 2010; 7:22. [PMID: 20105295 PMCID: PMC2835670 DOI: 10.1186/1743-422x-7-22] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 01/27/2010] [Indexed: 11/27/2022] Open
Abstract
Early diagnosis of dengue virus (DENV) infection is important for patient management and control of dengue outbreaks. The objective of this study was to analyze the usefulness of urine and saliva samples for early diagnosis of DENV infection by real time RT-PCR. Two febrile patients, who have been attended at the General Hospital of the School of Medicine of Ribeirao Preto, Sao Paulo University were included in the study. Serum, urine and saliva samples collected from both patients were subjected to real time RT-PCR for DENV detection and quantification. Dengue RNA was detected in serum, urine and saliva samples of both patients. Patient 1 was infected with DENV-2 and patient 2 with DENV-3. Data presented in this study suggest that urine and saliva could be used as alternative samples for early diagnosis of dengue virus infection when blood samples are difficult to obtain, e.g., in newborns and patients with hemorrhagic syndromes.
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Affiliation(s)
- Telma R Poloni
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto14040-903, São Paulo, Brasil
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