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Rauniyar R, Prajapati S, Manandhar B, Bastola A, Chalise BS, Shrestha S, Khanal C, Thapa M, Napit R, Bajracharya AM, Shrestha S, Adhikari A, Das Manandhar K. Dengue virus infection during window period of consecutive outbreaks in Nepal and assessment of clinical parameters. Sci Rep 2023; 13:9262. [PMID: 37286625 DOI: 10.1038/s41598-023-35928-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023] Open
Abstract
Nepal is an endemic country for dengue infection with rolling of every 3 year's clear cyclic outbreaks with exponential growth since 2019 outbreak and the virus gearing towards the non-foci temperate hill regions. However, the information regarding circulating serotype and genotype is not frequent. This research discusses on the clinical features, diagnosis, epidemiology, circulating serotype and genotype among 61 dengue suspected cases from different hospitals of Nepal during the window period 2017-2018 between the two outbreaks of 2016 and 2019. E-gene sequences from PCR positive samples were subjected to phylogenetic analysis under time to most recent common ancestor tree using Markov Chain Monte Carlo (MCMC) and BEAST v2.5.1. Both evolution and genotypes were determined based on the phylogenetic tree. Serotyping by Real-time PCR and Nested PCR showed the co-circulation of all the 3 serotypes of dengue in the year 2017 and only DENV-2 in 2018. Genotype V for DENV-1 and Cosmopolitan Genotype IVa for DENV-2 were detected. The detected Genotype V of DENV-1 in Terai was found close to Indian genotype while Cosmopolitan IVa of DENV-2 found spreading to geographically safe hilly region (now gripped to 9 districts) was close to South-East Asia. The genetic drift of DENV-2 is probably due to climate change and rapid viral evolution which could be a representative model for high altitude shift of the infection. Further, the increased primary infection indicates dengue venturing to new populations. Platelets count together with Aspartate transaminase and Aalanine transaminase could serve as important clinical markers to support clinical diagnosis. The study will support future dengue virology and epidemiology in Nepal.
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Affiliation(s)
- Ramanuj Rauniyar
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sabita Prajapati
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Binod Manandhar
- Department of Mathematical Sciences, Clark Atlanta University, Atlanta, USA
| | - Anup Bastola
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital (STIDH), Teku, Kathmandu, Nepal
| | - Bimal Sharma Chalise
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital (STIDH), Teku, Kathmandu, Nepal
| | - Srijan Shrestha
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Chetana Khanal
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Machchhendra Thapa
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rajindra Napit
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Molecular Biology and Virology, Centre for Molecular Dynamics Nepal (CMDN), Thapathali, Kathmandu, Nepal
| | | | - Shova Shrestha
- Microbiology Department, Trichandra Multiple Campus, Kathmandu, Nepal
| | - Anurag Adhikari
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences (KRIBS), Lalitpur, Nepal
| | - Krishna Das Manandhar
- Central Department of Biotechnology (CDBT), Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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Molecular surveillance of arboviruses circulation and co-infection during a large chikungunya virus outbreak in Thailand, October 2018 to February 2020. Sci Rep 2022; 12:22323. [PMID: 36566236 PMCID: PMC9789961 DOI: 10.1038/s41598-022-27028-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022] Open
Abstract
A large national outbreak of chikungunya virus (CHIKV) was recently reported in Thailand. While dengue virus (DENV) infection tends to occur year-round with an upsurge in the rainy season, Zika virus (ZIKV) also circulates in the country. The overlap in the distribution of these viruses increased the probability of co-infections during the heightened CHIKV activity. By examining 1806 patient serum samples submitted for CHIKV diagnostics from October 2018-February 2020 (511 CHIKV-negatives and 1295 CHIKV-positives), we used real-time reverse transcription-polymerase chain reaction to identify DENV and ZIKV individually. A total of 29 ZIKV and 36 DENV single-infections were identified. Interestingly, 13 co-infection cases were observed, of which 8 were CHIKV/DENV, 3 were CHIKV/ZIKV, and 2 were DENV/ZIKV. There were six DENV genotypes (13 DENV-1 genotype I, 10 DENV-2 Asian I, 10 DENV-2 Cosmopolitan, 6 DENV-3 genotype I, 2 DENV-3 genotype III, and 5 DENV-4 genotype I). Additionally, ZIKV strains identified in this study either clustered with strains previously circulating in Thailand and Singapore, or with strains previously reported in China, French Polynesia, and the Americas. Our findings reveal the co-infection and genetic diversity patterns of mosquito-borne viruses circulating in Thailand.
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Poltep K, Phadungsombat J, Nakayama EE, Kosoltanapiwat N, Hanboonkunupakarn B, Wiriyarat W, Shioda T, Leaungwutiwong P. Genetic Diversity of Dengue Virus in Clinical Specimens from Bangkok, Thailand, during 2018-2020: Co-Circulation of All Four Serotypes with Multiple Genotypes and/or Clades. Trop Med Infect Dis 2021; 6:tropicalmed6030162. [PMID: 34564546 PMCID: PMC8482112 DOI: 10.3390/tropicalmed6030162] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Dengue is an arboviral disease highly endemic in Bangkok, Thailand. To characterize the current genetic diversity of dengue virus (DENV), we recruited patients with suspected DENV infection at the Hospital for Tropical Diseases, Bangkok, during 2018-2020. We determined complete nucleotide sequences of the DENV envelope region for 111 of 276 participant serum samples. All four DENV serotypes were detected, with the highest proportion being DENV-1. Although all DENV-1 sequences were genotype I, our DENV-1 sequences were divided into four distinct clades with different distributions in Asian countries. Two genotypes of DENV-2 were identified, Asian I and Cosmopolitan, which were further divided into two and three distinct clades, respectively. In DENV-3, in addition to the previously dominant genotype III, a cluster of 6 genotype I viruses only rarely reported in Thailand was also observed. All of the DENV-4 viruses belonged to genotype I, but they were separated into three distinct clades. These results indicated that all four serotypes of DENV with multiple genotypes and/or clades co-circulate in Bangkok. Continuous investigation of DENV is warranted to further determine the relationship between DENV within Thailand and neighboring countries in Southeast Asia and Asia.
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Affiliation(s)
- Kanaporn Poltep
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.P.); (N.K.)
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.P.); (N.K.)
| | - Borimas Hanboonkunupakarn
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Witthawat Wiriyarat
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.P.); (E.E.N.)
- Department of Viral Infections, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
- Correspondence: (T.S.); (P.L.)
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.P.); (N.K.)
- Correspondence: (T.S.); (P.L.)
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Prajapati S, Napit R, Bastola A, Rauniyar R, Shrestha S, Lamsal M, Adhikari A, Bhandari P, Yadav SR, Manandhar KD. Molecular phylogeny and distribution of dengue virus serotypes circulating in Nepal in 2017. PLoS One 2020; 15:e0234929. [PMID: 32634137 PMCID: PMC7340289 DOI: 10.1371/journal.pone.0234929] [Citation(s) in RCA: 3] [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: 02/17/2020] [Accepted: 06/04/2020] [Indexed: 11/23/2022] Open
Abstract
Dengue virus (DENV) infection is endemic in Nepal. Although infection rates are reported annually, little information is available about the circulating viral serotypes and genotypes. Here, we report the results of a multicentre cross-sectional study of DENV serotypes and genotypes sampled from individuals with suspected DENV infection in Nepal in 2017. Of the 50 patients sampled, 40 were serologically positive for DENV NS1, 29 for anti-DENV IgM, 21 for anti-DENV IgG and 14 were positive by qRT-PCR. The three serotypes DENV-1, 2 and 3 were detected and there was no DENV-4. Positive samples from serotyping were subjected to PCR amplification by envelope (E) gene specific primer and subsequent bidirectional sequencing of 5 samples. A time to most recent common ancestor phylogenetic tree was constructed from the new sequences obtained here together with historical DENV-1 and DENV-2 E gene sequences. The DENV-1 isolates (n = 2) from Nepalese individuals were closely related to Indian genotype V, whereas DENV-2 isolates (n = 3) belonged to Cosmopolitan genotype IVa, which is closely related to Indonesian isolates. Historical DENV isolates obtained between 2004 and 2013 clustered with Cosmopolitan IVb, Cosmopolitan IVa, and Asian II genotypes. All Nepalese isolates had different lineages with distinct ancestries. With the exception of isolates obtained in 2004, all other previously published isolates had ancestry to geographically distant part of the world. Molecular analysis revealed dengue epidemics to be comprised of different genotypes of serotype 1 and 2 raising concerns on potential role of different genotypes causing Dengue hemorrhagic fever. Also, our result indicated spread of DENV-2 in non-endemic area such as hilly region of Nepal which was considered to be free of dengue due to high altitude and cold weather.
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Affiliation(s)
- Sabita Prajapati
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rajindra Napit
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Molecular Biology and Virology, Centre for Molecular Dynamics Nepal, Thapathali, Kathmandu, Nepal
| | - Anup Bastola
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | - Ramanuj Rauniyar
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Srijan Shrestha
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Mahesh Lamsal
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Anurag Adhikari
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Infection and Immunology, Kathmandu Research Institute for Biological Sciences, Lalitpur, Nepal
| | - Parmananda Bhandari
- Department of Tropical and Infectious Disease, Sukraraj Tropical and Infectious Disease Hospital, Teku, Kathmandu, Nepal
| | - Sanjay Ray Yadav
- Department of Haematology and Biochemistry, Chitwan Medical College and Teaching Hospital, Chitwan, Bharatpur, Nepal
| | - Krishna Das Manandhar
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- * E-mail:
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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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Gutiérrez-Barbosa H, Castañeda NY, Castellanos JE. Differential replicative fitness of the four dengue virus serotypes circulating in Colombia in human liver Huh7 cells. Braz J Infect Dis 2019; 24:13-24. [PMID: 31843340 PMCID: PMC9392035 DOI: 10.1016/j.bjid.2019.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/12/2019] [Accepted: 11/24/2019] [Indexed: 12/20/2022] Open
Abstract
Dengue has been a significant public health problem in Colombia since the simultaneous circulation of the four dengue virus serotypes. The replicative fitness of dengue is a biological feature important for virus evolution and contributes to elucidating the behavior of virus populations and viral pathogenesis. However, it has not yet been studied in Colombian isolates. This study aimed to compare the replicative fitness of the four dengue virus serotypes and understand the association between the serotypes, their in vitro infection ability, and their replication in target cells. We used three isolates of each DENV serotype to infect Huh-7 cells at an MOI of 0.5. The percentage of infected cells was evaluated by flow cytometry, cell viability was evaluated by MTT assay, and the pathogenicity index was calculated as a ratio of both parameters. The replicative fitness was measured by the number of viral genome copies produced using quantitative PCR and the production of infectious viral progeny was measured by plaque assay. We showed that Huh-7 cells were susceptible to infection with all the different strain isolates. Nevertheless, the biological characteristics, such as infectious ability and cell viability, were strain-dependent. We also found different degrees of pathogenicity between strains of the four serotypes, representative of the heterogeneity displayed in the circulating population. When we analyzed the replicative fitness using the mean values obtained from RT-qPCR and plaque assay for the different strains, we found serotype-dependent behavior. The highest mean values of replicative fitness were obtained for DENV-1 (log 4.9 PFU/ml) and DENV-4 (log 5.28 PFU/ml), followed by DENV-2 (log 3.9 PFU/ml) and DENV-3 (log 4.31 PFU/ml). The internal heterogeneity of the replicative fitness within each serotype could explain the simultaneous circulation of the four DENV serotypes in Colombia.
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Ortiz-Baez AS, Cunha MDP, Vedovello D, Colombo TE, Nogueira ML, Villabona-Arenas CJ, Zanotto PMDA. Origin, tempo, and mode of the spread of DENV-4 Genotype IIB across the state of São Paulo, Brazil during the 2012-2013 outbreak. Mem Inst Oswaldo Cruz 2019; 114:e180251. [PMID: 30624458 PMCID: PMC6333047 DOI: 10.1590/0074-02760180251] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/27/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Dengue virus type 4 (DENV-4) was first reported in Brazil in 1982 and since then no more cases were detected again in Brazil until 2010, when the virus was reintroduced. Over the following years, the virus spread to several Brazilian states and resulted in about 1,400,000 dengue cases, in 2013. The largest number of cases were documented in the Southeast macro-region. OBJECTIVES To determine the phylogeography of DENV-4 Genotype IIB strains isolated during the epidemics in 2012-2013 in São Paulo, Brazil, we aimed to contextualise the contribution of viruses sampled in different localities across the overall movement of DENV-4 in Brazil. METHODS Based on the envelope gene sequences retrieved from GenBank, we employed a Bayesian phylogeographic approach to assess the spatiotemporal dynamics of DENV-4 Genotype IIB in São Paulo, Brazil. FINDINGS The dispersal dynamics of DENV-4 Genotype IIB in Brazil indicated Rio de Janeiro and Mato Grosso states as the most likely routes toward São Paulo before the 2012-2013 outbreak. Likewise, Guarujá and São José do Rio Preto facilitated viral spread and transmission to other localities in the South and Southeast macro-regions in Brazil. CONCLUSIONS The spread pattern of DENV-4 Genotype IIB strains across the country supports two independent introductions of the virus in São Paulo in a short period of time. Furthermore, São Paulo appears to have played a pivotal role in the dissemination of DENV-4 to other locations in Brazil.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática,
São Paulo, SP, Brasil
| | - Marielton dos Passos Cunha
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática,
São Paulo, SP, Brasil
| | - Danila Vedovello
- Faculdade de Medicina de Jundiaí, Departamento de Pediatria,
Laboratório de Infectologia Pediátrica, Jundiaí, SP, Brasil
| | | | | | - Christian Julián Villabona-Arenas
- Université de Montpellier, Institut de Recherche pour le
Développement, Montpellier, France
- Université de Montpellier, Institut de Biologie Computationnelle,
Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier,
Montpellier, France
| | - Paolo Marinho de Andrade Zanotto
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, Laboratório de Evolução Molecular e Bioinformática,
São Paulo, SP, Brasil
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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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Yamashita A, Sakamoto T, Sekizuka T, Kato K, Takasaki T, Kuroda M. DGV: Dengue Genographic Viewer. Front Microbiol 2016; 7:875. [PMID: 27375595 PMCID: PMC4894901 DOI: 10.3389/fmicb.2016.00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 05/24/2016] [Indexed: 01/23/2023] Open
Abstract
Dengue viruses (DENVs) and their vectors are widely distributed throughout the tropical and subtropical regions of the world. An autochthonous case of DENV was reported in Tokyo, Japan, in 2014, for the first time in 70 years. A comprehensive database of DENV sequences containing both serotype and genotype data and epidemiological data is crucial to trace DENV outbreak isolates and promptly respond to outbreaks. We constructed a DENV database containing the serotype, genotype, year and country/region of collection by collecting all publically available DENV sequence information from the National Center for Biotechnology Information (NCBI) and assigning genotype information. We also implemented the web service Dengue Genographic Viewer (DGV), which shows the geographical distribution of each DENV genotype in a user-specified time span. DGV also assigns the serotype and genotype to a user-specified sequence by performing a homology search against the curated DENV database, and shows its homologous sequences with the geographical position and year of collection. DGV also shows the distribution of DENV-infected entrants to Japan by plotting epidemiological data from the Infectious Agents Surveillance Report (IASR), Japan. This overview of the DENV genotype distribution may aid in planning for the control of DENV infections. DGV is freely available online at: (https://gph.niid.go.jp/geograph/dengue/content/genomemap).
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Affiliation(s)
- Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Tetsuya Sakamoto
- Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan; Remote Operations Services Department, CTC System Management CorporationTokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Kengo Kato
- Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Tomohiko Takasaki
- Department of Virology I, National Institute of Infectious Diseases Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
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Ali A, Ali I. The Complete Genome Phylogeny of Geographically Distinct Dengue Virus Serotype 2 Isolates (1944-2013) Supports Further Groupings within the Cosmopolitan Genotype. PLoS One 2015; 10:e0138900. [PMID: 26414178 PMCID: PMC4587552 DOI: 10.1371/journal.pone.0138900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 09/04/2015] [Indexed: 11/19/2022] Open
Abstract
Dengue virus serotype 2 (DENV-2) isolates have been implicated in deadly outbreaks of dengue fever (DF) and dengue hemorrhagic fever (DHF) in several regions of the world. Phylogenetic analysis of DENV-2 isolates collected from particular countries has been performed using partial or individual genes but only a few studies have examined complete whole-genome sequences collected worldwide. Herein, 50 complete genome sequences of DENV-2 isolates, reported over the past 70 years from 19 different countries, were downloaded from GenBank. Phylogenetic analysis was conducted and evolutionary distances of the 50 DENV-2 isolates were determined using maximum likelihood (ML) trees or Bayesian phylogenetic analysis created from complete genome nucleotide (nt) and amino acid (aa) sequences or individual gene sequences. The results showed that all DENV-2 isolates fell into seven main groups containing five previously defined genotypes. A Cosmopolitan genotype showed further division into three groups (C-I, C-II, and C-III) with the C-I group containing two subgroups (C-IA and C-IB). Comparison of the aa sequences showed specific mutations among the various groups of DENV-2 isolates. A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes. Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes. Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world.
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Affiliation(s)
- Akhtar Ali
- Department of Biological Science, The University of Tulsa, Tulsa Oklahoma, 74104, United States of America
- * E-mail:
| | - Ijaz Ali
- Department of Biological Science, The University of Tulsa, Tulsa Oklahoma, 74104, United States of America
| |
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