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Mishra B, Aduri R. The RNA Secondary Structure Analysis Reveals Potential for Emergence of Pathogenic Flaviviruses. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:10-29. [PMID: 34694573 DOI: 10.1007/s12560-021-09502-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
The Flavivirus genus is divided into four groups: Mosquito-borne flaviviruses, Tick-borne flaviviruses, no-known vector flaviviruses, and Insect specific flaviviruses. Millions of people are affected worldwide every year due to the flaviviral infections. The 5' UTR of the RNA genome plays a critical role in the biology of flaviviruses. To explore any correlation between the topology of the 5' UTR and pathogenesis, a global scale study of the RNA secondary structure of different groups of flaviviruses has been conducted. We found that most of the pathogenic flaviviruses, irrespective of their mode of transmission, tend to form a Y shaped topology in the Stem loop A of the 5' UTR. Some of the current non-pathogenic flaviviruses were also observed to form Y shaped structure. Based on this study, it has been proposed that the flaviviruses having the Y shaped topology in their 5' UTR regions may have the potential to become pathogenic.
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Affiliation(s)
- Bibhudutta Mishra
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa campus, Zuarinagar, South Goa, 403726, India
- Department of Zoology, Centurion University of Technology and Management, Bhubaneswar Campus, Khurda, Jatni, 752050, Odisha, India
| | - Raviprasad Aduri
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa campus, Zuarinagar, South Goa, 403726, India.
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2
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Verma M, Bhatnagar S, Kumari K, Mittal N, Sukhralia S, Gopirajan At S, Dhanaraj PS, Lal R. Highly conserved epitopes of DENV structural and non-structural proteins: Candidates for universal vaccine targets. Gene 2019; 695:18-25. [PMID: 30738967 PMCID: PMC7125761 DOI: 10.1016/j.gene.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/22/2019] [Accepted: 02/01/2019] [Indexed: 12/11/2022]
Abstract
Dengue is a severe emerging arthropod borne viral disease occurring globally. Around two fifths of the world's population, or up to 3.9 billion people, are at a risk of dengue infection. Infection induces a life-long protective immunity to the homologous serotype but confers only partial and transient protection against subsequent infection caused by other serotypes. Thus, there is a need for a vaccine which is capable of providing a life- long protection against all the serotypes of dengue virus. In our study, comparative genomics of Dengue virus (DENV) was conducted to explore potential candidates for novel vaccine targets. From our analysis we successfully found 100% conserved epitopes in Envelope protein (RCPTQGE); NS3 (SAAQRRGR, PGTSGSPI); NS4A (QRTPQDNQL); NS4B (LQAKATREAQKRA) and NS5 proteins (QRGSGQV) in all DENV serotypes. Some serotype specific conserved motifs were also found in NS1, NS5, Capsid, PrM and Envelope proteins. Using comparative genomics and immunoinformatics approach, we could find conserved epitopes which can be explored as peptide vaccine candidates to combat dengue worldwide. Serotype specific epitopes can also be exploited for rapid diagnostics. All ten proteins are explored to find the conserved epitopes in DENV serotypes, thus making it the most extensively studied viral genome so far.
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Affiliation(s)
- Mansi Verma
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India; Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
| | - Shradha Bhatnagar
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India
| | - Kavita Kumari
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India
| | - Nidhi Mittal
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India
| | - Shivani Sukhralia
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India
| | - Shruthi Gopirajan At
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India
| | - P S Dhanaraj
- Sri Venkateswara College, South Campus, University of Delhi, New Delhi 110021, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
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3
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Lew RJ, Tsai WY, Wang WK. Dengue outbreaks in Hawai'i After WWII - A Review of Public Health Response and Scientific Literature. HAWAI'I JOURNAL OF MEDICINE & PUBLIC HEALTH : A JOURNAL OF ASIA PACIFIC MEDICINE & PUBLIC HEALTH 2018; 77:315-318. [PMID: 30533283 PMCID: PMC6277838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
The four serotypes of dengue virus (DENV) cause the most important and common arthropod-borne viral diseases in humans. There have been three major dengue outbreaks in Hawai'i since 1946. The most recent and largest outbreak occurred on Hawai'i Island in 2015-2016. This article reviews the public health response to dengue outbreaks over the period 2001-2016, as well as scientific literature on dengue outbreaks in Hawai'i. As summarized in the assessment by the Centers for Disease Control and Prevention in 2015, Hawaii's response to the dengue outbreak was timely, appropriate, and well-coordinated. All facets of a public health response to the outbreak were adequately addressed, but communications and medical entomologic capacities could be improved. The observations of Aedes aegypti on Hawai'i Island and of its co-localization with confirmed human cases highlight the importance of continuous vector surveillance and entomologic research. In-depth studies on the molecular epidemiology, entomology, and epidemiological investigation would provide new insights into the latest outbreak and into strategies to combat DENV and other arboviruses in the future.
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Affiliation(s)
- Rachel J Lew
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Manoa, Honolulu, HI (WYT, WKW)
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA (RJL)
| | - Wen-Yang Tsai
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Manoa, Honolulu, HI (WYT, WKW)
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA (RJL)
| | - Wei-Kung Wang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawai'i at Manoa, Honolulu, HI (WYT, WKW)
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA (RJL)
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4
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Cerón Gómez M, Yang HM. A simple mathematical model to describe antibody-dependent enhancement in heterologous secondary infection in dengue. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2018; 36:411-438. [DOI: 10.1093/imammb/dqy016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 11/14/2022]
Abstract
Abstract
We develop a mathematical model to describe the role of antibody-dependent enhancement (ADE) in heterologous secondary infections, assuming that antibodies specific to primary dengue virus (DENV) infection are being produced by immunological memory. The model has a virus-free equilibrium (VFE) and a unique virus-presence equilibrium (VPE). VFE is asymptotically stable when VPE is unstable; and unstable, otherwise. Additionally, there is an asymptotic attractor (not a fixed point) due to the fact that the model assumes unbounded increase in memory cells. In the analysis of the model, ADE must be accounted in the initial stage of infection (a window of time of few days), period of time elapsed from the heterologous infection until the immune system mounting an effective response against the secondary infection. We apply the results yielded by model to evaluate ADE phenomonon in heterologous DENV infection. We also associate the possible occurrence of severe dengue with huge viremia mediated by ADE phenomenon.
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Affiliation(s)
| | - Hyun Mo Yang
- Departamento de Matemática Aplicada, IMECC, UNICAMP, Praça Sérgio Buarque de Holanda, CEP, Campinas, SP, Brazil
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Wen S, Ma D, Lin Y, Li L, Hong S, Li X, Wang X, Xi J, Qiu L, Pan Y, Chen J, Shan X, Sun Q. Complete Genome Characterization of the 2017 Dengue Outbreak in Xishuangbanna, a Border City of China, Burma and Laos. Front Cell Infect Microbiol 2018; 8:148. [PMID: 29868504 PMCID: PMC5951998 DOI: 10.3389/fcimb.2018.00148] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/20/2018] [Indexed: 11/13/2022] Open
Abstract
A dengue outbreak abruptly occurred at the border of China, Myanmar, and Laos in June 2017. By November 3rd 2017, 1184 infected individuals were confirmed as NS1-positivein Xishuangbanna, a city located at the border. To verify the causative agent, complete genome information was obtained through PCR and sequencing based on the viral RNAs extracted from patient samples. Phylogenetic trees were constructed by the maximum likelihood method (MEGA 6.0). Nucleotide and amino acid substitutions were analyzed by BioEdit, followed by RNA secondary structure prediction of untranslated regions (UTRs) and protein secondary structure prediction in coding sequences (CDSs). Strains YN2, YN17741, and YN176272 were isolated from local residents. Stains MY21 and MY22 were isolated from Burmese travelers. The complete genome sequences of the five isolates were 10,735 nucleotides in length. Phylogenetic analysis classified all five isolates as genotype I of DENV-1, while isolates of local residents and Burmese travelers belonged to different branches. The three locally isolates were most similar to the Dongguan strain in 2011, and the other two isolates from Burmese travelers were most similar to the Laos strain in 2008. Twenty-four amino acid substitutions were important in eight evolutionary tree branches. Comparison with DENV-1SS revealed 658 base substitutions in the local isolates, except for two mutations exclusive to YN17741, resulting in 87 synonymous mutations. Compared with the local isolates, 52 amino acid mutations occurred in the CDS of two isolates from Burmese travelers. Comparing MY21 with MY22, 17 amino acid mutations were observed, all these mutations occurred in the CDS of non-structured proteins (two in NS1, 10 in NS2, two in NS3, three in NS5). Secondary structure prediction revealed 46 changes in the potential nucleotide and protein binding sites of the CDSs in local isolates. RNA secondary structure prediction also showed base changes in the 3′UTR of local isolates, leading to two significant changes in the RNA secondary structure. To our knowledge, this study is the first complete genome analysis of isolates from the 2017 dengue outbreak that occurred at the border areas of China, Burma, and Laos.
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Affiliation(s)
- Songjiao Wen
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
| | - Dehong Ma
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Xishuangbanna, China
| | - Yao Lin
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
| | - Lihua Li
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Xishuangbanna, China
| | - Shan Hong
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,School of Basic Medicine, Kunming Medical University, Kunming, China
| | - Xiaoman Li
- Institute of Pediatric Disease Research, The Affiliated Children's Hospital of Kunming Medical University, Kunming, China
| | - Xiaodan Wang
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
| | - Juemin Xi
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
| | - Lijuan Qiu
- Institute of Pediatric Disease Research, The Affiliated Children's Hospital of Kunming Medical University, Kunming, China
| | - Yue Pan
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
| | - Junying Chen
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
| | - Xiyun Shan
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Xishuangbanna, China
| | - Qiangming Sun
- Institute of Medical Biology, Peking Union Medical College, Chinese Academy of Medical Sciences, Kunming, China.,Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, China.,Yunnan Key Laboratory of Vector-borne Infectious Disease, Kunming, China
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Hyperendemic dengue transmission and identification of a locally evolved DENV-3 lineage, Papua New Guinea 2007-2010. PLoS Negl Trop Dis 2018; 12:e0006254. [PMID: 29494580 PMCID: PMC5849365 DOI: 10.1371/journal.pntd.0006254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/13/2018] [Accepted: 01/19/2018] [Indexed: 11/19/2022] Open
Abstract
Background Dengue is endemic in the Western Pacific and Oceania and the region reports more than 200,000 cases annually. Outbreaks of dengue and severe dengue occur regularly and movement of virus throughout the region has been reported. Disease surveillance systems, however, in many areas are not fully established and dengue incidence is underreported. Dengue epidemiology is likely least understood in Papua New Guinea (PNG), where the prototype DENV-2 strain New Guinea C was first isolated by Sabin in 1944 but where routine surveillance is not undertaken and little incidence and prevalence data is available. Methodology/Principal findings Serum samples from individuals with recent acute febrile illness or with non-febrile conditions collected between 2007–2010 were tested for anti-DENV neutralizing antibody. Responses were predominantly multitypic and seroprevalence increased with age, a pattern indicative of endemic dengue. DENV-1, DENV-2 and DENV-3 genomes were detected by RT-PCR within a nine-month period and in several instances, two serotypes were identified in individuals sampled within a period of 10 days. Phylogenetic analysis of whole genome sequences identified a DENV-3 Genotype 1 lineage which had evolved on the northern coast of PNG which was likely exported to the western Pacific five years later, in addition to a DENV-2 Cosmopolitan Genotype lineage which had previously circulated in the region. Conclusions/Significance We show that dengue is hyperendemic in PNG and identify an endemic, locally evolved lineage of DENV-3 that was associated with an outbreak of severe dengue in Pacific countries in subsequent years, although severe disease was not identified in PNG. Additional studies need to be undertaken to understand dengue epidemiology and burden of disease in PNG. Dengue virus (DENV) was first identified in Papua New Guinea (PNG) in 1944. Dengue is currently assumed to be an endemic disease in PNG although there is little incidence or prevalence data, and the evidence consensus for dengue presence is low. Routine surveillance is not undertaken and dengue is not a notifiable disease. Severe dengue is rarely identified by local clinicians and the reasons for this are unclear but may be related to poor recognition of dengue and a low index of suspicion, despite high incidence and prevalence rates in neighbouring countries. For example, Indonesia shares borders with PNG and regularly reports outbreaks of severe dengue and transmission of multiple DENV serotypes. DENV infection is identified in travellers from PNG however there are no data on locally circulating strains and how they may compare to viruses associated with severe dengue epidemics in other countries in the Asia Pacific region. We identified evidence for previous infection with all four DENV serotypes among people living on the northern coast of PNG, in Madang, and on Lihir Island in the Bismarck Archipelago off the northeastern coast. We also detected DENV-1, DENV-2, and DENV-3 virus in febrile patients, and we describe the first whole genome sequences of endemically circulating DENV since the prototype 1944 DENV-2New Guinea C strain was characterized. Of note, severe dengue was not diagnosed in any patient infected with these viruses in PNG although introduction of the PNG DENV-3 strain into the Solomon Islands five years later resulted in a large outbreak of severe dengue with hospitalizations and deaths in that country. Dengue epidemiology and burden of disease should be investigated in PNG.
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Wardhani P, Aryati A, Yohan B, Trimarsanto H, Setianingsih TY, Puspitasari D, Arfijanto MV, Bramantono B, Suharto S, Sasmono RT. Clinical and virological characteristics of dengue in Surabaya, Indonesia. PLoS One 2017; 12:e0178443. [PMID: 28575000 PMCID: PMC5456069 DOI: 10.1371/journal.pone.0178443] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 05/12/2017] [Indexed: 01/28/2023] Open
Abstract
Dengue disease is still a major health problem in Indonesia. Surabaya, the second largest city in the country, is endemic for dengue. We report here on dengue disease in Surabaya, investigating the clinical manifestations, the distribution of dengue virus (DENV) serotypes, and the relationships between clinical manifestations and the genetic characteristics of DENV. A total of 148 patients suspected of having dengue were recruited during February-August 2012. One hundred one (68%) of them were children, and 47 (32%) were adults. Dengue fever (DF) and Dengue hemorrhagic fever (DHF) were equally manifested in all of the patients. We performed DENV serotyping on all of the samples using real-time RT-PCR. Of 148, 79 (53%) samples were detected as DENV positive, with DENV-1 as the predominant serotype (73%), followed by DENV-2 (8%), DENV-4 (8%), and DENV-3 (6%), while 5% were mixed infections. Based on the Envelope gene sequences, we performed phylogenetic analyses of 24 isolates to genotype the DENV circulating in Surabaya in 2012, and the analysis revealed that DENV-1 consisted of Genotypes I and IV, DENV-2 was of the Cosmopolitan genotype, the DENV-3 viruses were of Genotype I, and DENV-4 was detected as Genotype II. We correlated the infecting DENV serotypes with clinical manifestations and laboratory parameters; however, no significant correlations were found. Amino acid analysis of Envelope protein did not find any unique mutations related to disease severity.
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Affiliation(s)
- Puspa Wardhani
- Department of Clinical Pathology, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Institute for Tropical Diseases, Universitas Airlangga, Surabaya, Indonesia
| | - Aryati Aryati
- Department of Clinical Pathology, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Institute for Tropical Diseases, Universitas Airlangga, Surabaya, Indonesia
| | | | | | | | - Dwiyanti Puspitasari
- Department of Pediatric, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Bramantono Bramantono
- Department of Internal Medicine, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Suharto Suharto
- Department of Internal Medicine, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - R. Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- * E-mail:
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8
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Ernst T, McCarthy S, Chidlow G, Luang-Suarkia D, Holmes EC, Smith DW, Imrie A. Emergence of a new lineage of dengue virus type 2 identified in travelers entering Western Australia from Indonesia, 2010-2012. PLoS Negl Trop Dis 2015; 9:e0003442. [PMID: 25635775 PMCID: PMC4311992 DOI: 10.1371/journal.pntd.0003442] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/24/2014] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) transmission is ubiquitous throughout the tropics. More than 70% of the current global dengue disease burden is borne by people who live in the Asia-Pacific region. We sequenced the E gene of DENV isolated from travellers entering Western Australia between 2010-2012, most of whom visited Indonesia, and identified a diverse array of DENV1-4, including multiple co-circulating viral lineages. Most viruses were closely related to lineages known to have circulated in Indonesia for some time, indicating that this geographic region serves as a major hub for dengue genetic diversity. Most notably, we identified a new lineage of DENV-2 (Cosmopolitan genotype) that emerged in Bali in 2011-2012. The spread of this lineage should clearly be monitored. Surveillance of symptomatic returned travellers provides important and timely information on circulating DENV serotypes and genotypes, and can reveal the herald wave of dengue and other emerging infectious diseases.
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Affiliation(s)
- Timo Ernst
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
| | - Suzi McCarthy
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Glenys Chidlow
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Dagwin Luang-Suarkia
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Edward C. Holmes
- Marie Bashir Institute for Emerging Diseases & Biosecurity, Charles Perkins Centre, School of Biological Sciences and Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - David W. Smith
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Allison Imrie
- School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- * E-mail:
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Ocwieja KE, Fernando AN, Sherrill-Mix S, Sundararaman SA, Tennekoon RN, Tippalagama R, Krishnananthasivam S, Premawansa G, Premawansa S, De Silva AD. Phylogeography and molecular epidemiology of an epidemic strain of dengue virus type 1 in Sri Lanka. Am J Trop Med Hyg 2014; 91:225-34. [PMID: 24799375 DOI: 10.4269/ajtmh.13-0523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In 2009, a severe epidemic of dengue disease occurred in Sri Lanka, with higher mortality and morbidity than any previously recorded epidemic in the country. It corresponded to a shift to dengue virus 1 as the major disease-causing serotype in Sri Lanka. Dengue disease reached epidemic levels in the next 3 years. We report phylogenetic evidence that the 2009 epidemic DENV-1 strain continued to circulate within the population and caused severe disease in the epidemic of 2012. Bayesian phylogeographic analyses suggest that the 2009 Sri Lankan epidemic DENV-1 strain may have traveled directly or indirectly from Thailand through China to Sri Lanka, and after spreading within the Sri Lankan population, it traveled to Pakistan and Singapore. Our findings delineate the dissemination route of a virulent DENV-1 strain in Asia. Understanding such routes will be of particular importance to global control efforts.
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Affiliation(s)
- Karen E Ocwieja
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Anira N Fernando
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Scott Sherrill-Mix
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Sesh A Sundararaman
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rashika N Tennekoon
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rashmi Tippalagama
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Shivankari Krishnananthasivam
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Gayani Premawansa
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Sunil Premawansa
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Aruna Dharshan De Silva
- University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania; Genetech Research Institute, Colombo, Sri Lanka; North Colombo Teaching Hospital, Ragama, Sri Lanka; Department of Zoology, University of Colombo, Colombo, Sri Lanka; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California
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10
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Yamashita A, Sasaki T, Kurosu T, Yasunaga T, Ikuta K. Origin and distribution of divergent dengue virus: novel database construction and phylogenetic analyses. Future Virol 2013. [DOI: 10.2217/fvl.13.99] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dengue virus (DENV), a mosquito-borne agent that exists as four serotypes (DENV-1–4), induces dengue illness. DENV has a positive-sense, ssRNA genome of approximately 11 kb that encodes a capsid protein, a premembrane protein and an envelope glycoprotein, in addition to seven nonstructural proteins. These individual genes show sequence variations that can be analyzed phylogenetically to yield several genotypes within each serotype. Here, the sequences of individual DENV genes were collected and used to construct a novel DENV database. This database was then used to characterize the evolution of individual genotypes in several countries. Interestingly, the database provided evidence for recombination between two or three different genotypes to yield new genotypes. This novel database will be available on the internet and is expected to be highly useful for dengue genetic studies, including phylogenetic analyses.
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Affiliation(s)
- Akifumi Yamashita
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
- National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Tadahiro Sasaki
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takeshi Kurosu
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Teruo Yasunaga
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuyoshi Ikuta
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
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Huang JH, Su CL, Yang CF, Liao TL, Hsu TC, Chang SF, Lin CC, Shu PY. Molecular characterization and phylogenetic analysis of dengue viruses imported into Taiwan during 2008-2010. Am J Trop Med Hyg 2012; 87:349-58. [PMID: 22855770 DOI: 10.4269/ajtmh.2012.11-0666] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We present our surveillance results on imported dengue cases in Taiwan during 2008-2010. A total of 734 imported dengue patients were identified. The travelers were arriving from 18 countries, including Southeast Asia, the Indian subcontinent, South Pacific islands, and Latin America. Gene sequences from 358 dengue virus (DENV) isolates were used to perform phylogenetic analyses, thus, providing an updated view of the geographic distribution and dynamic transmission of DENV strains circulating in these countries. Our results suggest that the DENV-1 genotype I and DENV-2 Cosmopolitan genotype comprise the predominant DENV strains circulating in Southeast Asian countries. The DENV-3 Genotype III strain was found to be newly emerging in several Southeast Asian countries, however, the Asian genotype 2 and the Asian/American genotype of DENV-2 strains appeared to be less prevalent in Southeast Asia. Furthermore, imported dengue viruses are representative of the overall patterns of serotype/genotype frequencies of dengue outbreaks that occurred in Taiwan.
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Affiliation(s)
- Jyh-Hsiung Huang
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, Republic of China
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12
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Steidel M, Fragnoud R, Guillotte M, Roesch C, Michel S, Meunier T, Paranhos-Baccalà G, Gervasi G, Bedin F. Nonstructural protein NS1 immunodominant epitope detected specifically in dengue virus infected material by a SELDI-TOF/MS based assay. J Med Virol 2012; 84:490-9. [PMID: 22246837 DOI: 10.1002/jmv.23204] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Dengue virus (DV) infection is the most common mosquito-born viral disease of public health significance. Though most patients only suffer from flu-like symptoms, a small group of patients experiences more severe forms of the disease. The viral nonstructural protein 1 (NS1), a secreted protein correlating with viremia, is a key element used for dengue diagnosis with potential implications in severe dengue prognosis. Capture-ELISAs for the early detection of the NS1 protein in the sera during the acute febrile stage are commonly used in routine by diagnostic laboratories. In this study, the detection of NS1 protein in DV-infected material was assessed by an alternative method combining a single NS1-directed monoclonal antibody and the SELDI-TOF/MS technology. According to the epitope mapping, the antibodies used are mainly directed against an immuno-dominant peptide located on the C-terminal part of the protein. The NS1 SELDI-TOF assay is specific, has a sensitivity level close to capture-ELISAs and is potentially useful for a coupled serotyping/detection assay or for the detection of subtle post-translational modifications on the protein.
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Affiliation(s)
- Marine Steidel
- Biomarker Department, BioMerieux SA, Chemin de l'Orme, Marcy l'Etoile, France
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13
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Use of serum and blood samples on filter paper to improve the surveillance of Dengue in Pacific Island Countries. J Clin Virol 2012; 55:23-9. [PMID: 22695001 DOI: 10.1016/j.jcv.2012.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/17/2012] [Indexed: 11/21/2022]
Abstract
BACKGROUND In Pacific Island Countries (PICs) the epidemiology of dengue is characterized by long-term transmission of a single dengue virus (DENV) serotype. The emergence of a new serotype in one island country often indicates major outbreaks with this serotype will follow in other PICs. OBJECTIVES Filter paper (FP) cards on which whole blood or serum from dengue suspected patients had been dried was evaluated as a method for transportation of this material by standard mail delivery throughout the Pacific. STUDY DESIGN Twenty-two FP-dried whole blood samples collected from patients in New Caledonia and Wallis & Futuna Islands, during DENV-1 and DENV-4 transmission, and 76 FP-dried sera collected from patients in Yap State, Majuro (Republic of Marshall Islands), Tonga and Fiji, before and during outbreaks of DENV-2 in Yap State and DENV-4 in Majuro, were tested for the presence of DENV RNA, by serotype specific RT-PCR, at the Institut Louis Malardé in French Polynesia. RESULTS The serotype of DENV could be determined, by a variety of RT-PCR procedures, in the FP-dried samples after more than three weeks of transport at ambient temperatures. In most cases, the sequencing of the envelope gene to genotype the viruses also was possible. CONCLUSIONS The serotype and genotype of DENV can be determined from FP-dried serum or whole blood samples transported over thousands of kilometers at ambient, tropical, temperatures. This simple and low-cost approach to virus identification should be evaluated in isolated and resource poor settings for surveillance for a range of significant viral diseases.
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Abstract
PURPOSE OF REVIEW Dengue is currently an expanding global health problem. Development of an effective tetravalent dengue vaccine is considered a high public health priority. The uniqueness of the dengue viruses (DENVs) and the spectrum of disease resulting from infection has made dengue vaccine development difficult. This review focuses on the current critical issues in dengue vaccine development. RECENT FINDINGS DENVs are arboviral flaviviruses transmitted by Aedes mosquitoes causing a spectrum of clinical disease. DENV infections are a significant global health problem; the WHO estimates that more than 120 countries have endemic DENV transmission resulting in 70-500 million infections, 2.1 million clinically severe cases, and 21 000 deaths annually. There are currently no licensed antivirals or vaccines to treat or prevent dengue. The DENV-host interaction of infection is unique with severe disease a consequence of sequential dengue infection, viral immune evasion, host antibody enhancement, host immune activation, and genetic predisposition. This unique pathogen-host interaction complicates dengue vaccine development and creates provocative questions in vaccine development such as identifying markers of protective immunogenicity, the potential role of antibody in vaccine failures, and the possible impact of large-scale vaccination on the evolution of wild-type DENV. SUMMARY Dengue is a unique and complex disease; developing a dengue vaccine has proven equally complex. In this review, the authors discuss issues that will prove to be critical to the success or failure of the dengue vaccine development effort.
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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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