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Kanampalliwar A, Singh DV. Virulence Pattern and Genomic Diversity of Vibrio cholerae O1 and O139 Strains Isolated From Clinical and Environmental Sources in India. Front Microbiol 2020; 11:1838. [PMID: 32982995 PMCID: PMC7479179 DOI: 10.3389/fmicb.2020.01838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/14/2020] [Indexed: 01/22/2023] Open
Abstract
Vibrio cholerae is an autochthonous inhabitant of the aquatic environment. Several molecular methods have been used for typing V. cholerae strains, but there is no proper database for such scheme, including multilocus sequence typing (MLST) for V. cholerae O1 and O139 strains. We used 54 V. cholerae O1 and three O139 strains isolated from clinical and environmental sources and regions of India during the time period of 1975-2015 to determine the presence of virulence genes and production of biofilm. We devised a MLST scheme and developed a database for typing V. cholerae strains. Also, we performed pulsed-field gel electrophoresis to see the genomic diversity among them and compared it with MLST. We used the MEGA 7.0 software for the alignment and comparison of different nucleotide sequences. The advanced cluster analysis was performed to define complexes. All strains of V. cholerae, except five strains, showed variation in phenotypic characteristics but carried virulence-associated genes indicating they belonged to the El Tor/hybrid/O139 variants. MLST analysis showed 455 sequences types among V. cholerae strains, irrespective of sources and places of isolation. With these findings, we set up an MLST database on PubMLST.org using the BIGSdb software for V. cholerae O1 and O139 strains, which is available at https://pubmlst.org/vcholerae/ under the O1/O139 scheme. The pulsed-field gel electrophoresis (PFGE) fingerprint showed six fingerprint patterns namely E, F, G, H, I, and J clusters among 33 strains including strain N16961 carrying El Tor ctxB of which cluster J representing O139 strain was entirely different from other El Tor strains. Twenty strains carrying Haitian ctxB showed a fingerprint pattern classified as cluster A. Of the five strains, four carrying classical ctxB comprising two each of El Tor and O139 strains and one El Tor strain carrying Haitian ctxB clustered together under cluster B along with V. cholerae 569B showing pattern D. This study thus indicates that V. cholerae strains are undergoing continuous genetic changes leading to the emergence of new strains. The MLST scheme was found more appropriate compared to PFGE that can be used to determine the genomic diversity and population structure of V. cholerae.
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Affiliation(s)
- Amol Kanampalliwar
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Durg Vijai Singh
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, India
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52
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Calvez E, Somlor S, Viengphouthong S, Balière C, Bounmany P, Keosenhom S, Caro V, Grandadam M. Rapid genotyping protocol to improve dengue virus serotype 2 survey in Lao PDR. PLoS One 2020; 15:e0237384. [PMID: 32764809 PMCID: PMC7413503 DOI: 10.1371/journal.pone.0237384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022] Open
Abstract
Dengue fever is one of the major public health problems in Lao PDR. Over the last decade, dengue virus (DENV) epidemics were characterized by a novel predominant serotype accompanied by at least two other serotypes. Since 2008, DENV-2 circulated at a low level in Lao PDR but its epidemiologic profile changed at the end of 2018. Indeed, the number of confirmed DENV-2 cases suddenly increased in October 2018 and DENV-2 became predominant at the country level in early 2019. We developed a Genotype Screening Protocol (GSP) to determine the origin(s) of the Lao DENV-2 and study their genetic polymorphism. With a good correlation with full envelope gene sequencing data, this molecular epidemiology tool evidence the co-circulation of two highly polymorphic DENV-2 genotypes, i.e. Asian I and Cosmopolitan genotypes, over the last five years, suggesting multiple introductions of DENV-2 in the country. GSP approach provides relevant first line information that may help countries with limited laboratory resources to reinforce their capabilities to DENV-2 and to follow the epidemics progresses and assess situations at the regional level.
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Affiliation(s)
- Elodie Calvez
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
- * E-mail:
| | - Somphavanh Somlor
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
| | | | | | | | - Sitsana Keosenhom
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
| | | | - Marc Grandadam
- Institut Pasteur du Laos, Vientiane, Lao People’s Democratic Republic
- Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
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Dengue virus co-infections with multiple serotypes do not result in a different clinical outcome compared to mono-infections. Epidemiol Infect 2020; 148:e119. [PMID: 32594967 PMCID: PMC7325333 DOI: 10.1017/s0950268820000229] [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] [Indexed: 01/31/2023] Open
Abstract
Circulation of multiple dengue virus (DENV) serotypes in a locale has resulted in individuals becoming infected with mixed serotypes. This research was undertaken to study the clinical presentation, presence of DENV serotypes and serological characteristics of DENV infected patients with co-infections from three Provinces of Sri Lanka where DENV-1 and -2 predominated during the study. A reverse transcription polymerase chain reaction was performed on 1249 patient samples and 301 were positive for DENV (24.1%). DENV-1 was the predominant serotype detected in 137 (45.51%) followed by DENV-2 in 65 (21.59%), DENV-3 in 59 (19.6%) and DENV-4 in 4 (1.32%) patients with mono-infections. Thirty-three patients (10.96%) had DENV co-infections with two or more serotypes. The highest number of co-infections was noted between DENV-1 and DENV-2 (57.57%) suggesting co-infection is driven by the frequency of the circulating serotypes. Platelet counts were significantly higher in DENV co-infected patients although clinical disease severity or white blood cell count, packed cell volume or viraemia were not significantly different in the co-infected compared to the mono-infected patients. Thus co-infection with multiple DENV serotypes does occur but with the exception of improved platelet counts in co-infected patients, there is no evidence that clinical or laboratory measures of disease are altered.
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54
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Syenina A, Vijaykrishna D, Gan ES, Tan HC, Choy MM, Siriphanitchakorn T, Cheng C, Vasudevan SG, Ooi EE. Positive epistasis between viral polymerase and the 3' untranslated region of its genome reveals the epidemiologic fitness of dengue virus. Proc Natl Acad Sci U S A 2020; 117:11038-11047. [PMID: 32366663 PMCID: PMC7245076 DOI: 10.1073/pnas.1919287117] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is a global health threat, causing repeated epidemics throughout the tropical world. While low herd immunity levels to any one of the four antigenic types of DENV predispose populations to outbreaks, viral genetic determinants that confer greater fitness for epidemic spread is an important but poorly understood contributor of dengue outbreaks. Here we report that positive epistasis between the coding and noncoding regions of the viral genome combined to elicit an epidemiologic fitness phenotype associated with the 1994 DENV2 outbreak in Puerto Rico. We found that five amino acid substitutions in the NS5 protein reduced viral genomic RNA (gRNA) replication rate to achieve a more favorable and relatively more abundant subgenomic flavivirus RNA (sfRNA), a byproduct of host 5'-3' exoribonuclease activity. The resulting increase in sfRNA relative to gRNA levels not only inhibited type I interferon (IFN) expression in infected cells through a previously described mechanism, but also enabled sfRNA to compete with gRNA for packaging into infectious particles. We suggest that delivery of sfRNA to new susceptible cells to inhibit type I IFN induction before gRNA replication and without the need for further de novo sfRNA synthesis could form a "preemptive strike" strategy against DENV.
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Affiliation(s)
- Ayesa Syenina
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, 117549 Singapore
| | - Dhanasekaran Vijaykrishna
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Esther Shuyi Gan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Milly M Choy
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Tanamas Siriphanitchakorn
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
- Department of Biological Sciences, National University of Singapore, 117558 Singapore
| | - Colin Cheng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857 Singapore;
- Saw Swee Hock School of Public Health, National University of Singapore, 117549 Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore
- SingHealth Duke-National University of Singapore Global Health Institute, 169857 Singapore
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Irenge LM, Ambroise J, Mitangala PN, Bearzatto B, Kabangwa RKS, Durant JF, Gala JL. Genomic analysis of pathogenic isolates of Vibrio cholerae from eastern Democratic Republic of the Congo (2014-2017). PLoS Negl Trop Dis 2020; 14:e0007642. [PMID: 32310947 PMCID: PMC7192507 DOI: 10.1371/journal.pntd.0007642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 04/30/2020] [Accepted: 03/12/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Over the past recent years, Vibrio cholerae has been associated with outbreaks in sub-Saharan Africa, notably in Democratic Republic of the Congo (DRC). This study aimed to determine the genetic relatedness of isolates responsible for cholera outbreaks in eastern DRC between 2014 and 2017, and their potential spread to bordering countries. METHODS/PRINCIPAL FINDINGS Phenotypic analysis and whole genome sequencing (WGS) were carried out on 78 clinical isolates of V. cholerae associated with cholera in eastern provinces of DRC between 2014 and 2017. SNP-based phylogenomic data show that most isolates (73/78) were V. cholerae O1 biotype El Tor with CTX-3 type prophage. They fell within the third transmission wave of the current seventh pandemic El Tor (7PET) lineage and were contained in the introduction event (T)10 in East Africa. These isolates clustered in two sub-clades corresponding to Multiple Locus Sequence Types (MLST) profiles ST69 and the newly assigned ST515, the latter displaying a higher genetic diversity. Both sub-clades showed a distinct geographic clustering, with ST69 isolates mostly restricted to Lake Tanganyika basin and phylogenetically related to V. cholerae isolates associated with cholera outbreaks in western Tanzania, whereas ST515 isolates were disseminated along the Albertine Rift and closely related to isolates in South Sudan, Uganda, Tanzania and Zambia. Other V. cholerae isolates (5/78) were non-O1/non-O139 without any CTX prophage and no phylogenetic relationship with already characterized non-O1/non-O139 isolates. CONCLUSIONS/SIGNIFICANCE Current data confirm the association of both DRC O1 7PET (T)10 sub-clades ST69 and ST515 with recurrent outbreaks in eastern DRC and at regional level over the past 10 years. Interestingly, while ST69 is predominantly a locally endemic sequence type, ST515 became adaptable enough to expand across DRC neighboring countries.
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Affiliation(s)
- Leonid M. Irenge
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
- Defence Laboratories Department, ACOS Ops&Trg, Belgian Armed Forces, Peutie, Belgium
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
| | | | - Jean-François Durant
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
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Barde PV, Shukla MK, Joshi P, Sahare L, Ukey MJ. Molecular studies on dengue viruses detected in patients from Central India. Indian J Med Microbiol 2019; 37:12-18. [PMID: 31424004 DOI: 10.4103/ijmm.ijmm_18_377] [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] [Indexed: 11/04/2022]
Abstract
Purpose Dengue viruses (DENVs), the causative agents of dengue (DEN), are classified into four serotypes and several genotypes. Identifying circulating serotypes and genotypes has clinical and epidemiological importance; however, limited information in this regard is available from Central India. This laboratory-based study was done to fill this lacuna. Materials and Methods The samples collected in the acute phase of illness were subjected to DEN NS1 ELISA, and NS1-positive samples (n = 80) were subjected to serotyping; representative samples from each serotype were sequenced to identify genotypes. Results Seventy-one (88.75%) samples could be serotyped. All the four DENV serotypes with dominance of DENV-3 (n = 33; 47%) were detected. DENV-4 was detected after a gap of 3 years. Cases with multiple DENV serotype infection were identified. Genotyping showed that DENV-1 belonging to genotype III, DENV-2 cosmopolitan (IV), DENV-3 genotype III lineage C and DENV-4 genotype I were in circulation in the year 2016. Conclusion Our study documents the molecular characteristics of DENV circulating in the area. Detection of heterologous DENV serotype with dominance of DENV-3 emphasises the need for regular molecular monitoring.
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Affiliation(s)
- Pradip V Barde
- Division of Virology and Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Mohan K Shukla
- Division of Virology and Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Piyush Joshi
- Division of Virology and Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Lalit Sahare
- Division of Virology and Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Mahendra J Ukey
- Division of Virology and Zoonoses, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
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Ghweil AA, Osman HA, Khodeary A, Okasha A, Hassan MH. Relative frequency of acute pancreatitis from dengue outbreaks as a late complication, in Egypt. Virusdisease 2019; 30:498-503. [PMID: 31890751 DOI: 10.1007/s13337-019-00556-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 11/15/2019] [Indexed: 01/19/2023] Open
Abstract
Patients with dengue virus infection have a different symptoms range from asymptomatic to sever form depending on primary and secondary immune status of host, infecting genotype and patient's age. The current study aimed to describe the clinical and laboratory profile of dengue fever outbreak and acute pancreatitis as a late complication, in Egypt, as two case reports only were available in literature regarding this issue. This prospective cohort study was carried out on 100 patients confirmed to have dengue disease out of 200 clinically suspected patients. Clinical, laboratory (serology for dengue specific IgM, real-time PCR for dengue virus, serum amylase and lipase) and abdominal multi-slice CT were done to all included patients. All patients presented with fever, headache and fatigue, which are the main clinical manifestations of dengue fever. The mean age of studied patients was 40.34 ± 15.74 years. Thirteen patients (13%), with their mean age 44.57 ± 11.53, presented after 3 months with typical clinical, laboratory and radiological manifestations of acute pancreatitis with positive serum dengue virus IgM, antibodies and negative serum dengue virus PCR. So, acute pancreatitis as a late complication of dengue fever disease should be keep in mind for its early diagnosis and management, thus minimize the morbidity and mortality from dengue fever.
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Affiliation(s)
- Ali A Ghweil
- 1Tropical Medicine and Gastroenterology Department, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Heba A Osman
- 1Tropical Medicine and Gastroenterology Department, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Ashraf Khodeary
- 2Clinical Pathology Department, Faculty of Medicine, Sohag University, Sohâg, Egypt
| | - Ahmed Okasha
- 3Radiology Department, Faculty of Medicine, South Valley University, Qena, Egypt
| | - Mohammed H Hassan
- 4Department of Medical Biochemistry, Faculty of Medicine, South Valley University, Qena, Egypt
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58
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Abe H, Ushijima Y, Loembe MM, Bikangui R, Nguema-Ondo G, Mpingabo PI, Zadeh VR, Pemba CM, Kurosaki Y, Igasaki Y, de Vries SG, Grobusch MP, Agnandji ST, Lell B, Yasuda J. Re-emergence of dengue virus serotype 3 infections in Gabon in 2016-2017, and evidence for the risk of repeated dengue virus infections. Int J Infect Dis 2019; 91:129-136. [PMID: 31821892 DOI: 10.1016/j.ijid.2019.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES Dengue outbreaks, mainly caused by dengue virus serotype 2 (DENV-2), occurred in 2007 and in 2010 in Gabon, Central Africa. However, information on DENV infections has been insufficient since 2010. The aim of this study was to investigate the current DENV infection scenario and the risk of repeated infections in Gabon. METHODS During 2015-2017, serum samples were collected from enrolled febrile participants and were tested for DENV infection using RT-qPCR. DENV-positive samples were analyzed for a history of previous DENV infection(s) using ELISA. The complete DENV genome was sequenced to analyze the phylogeny of Gabonese DENV strains. RESULTS DENV-3 was exclusively detected, with a high rate of anti-DENV IgG seropositivity among DENV-3-positive participants. DENV-3 showed higher infection rates in adults and the infection was seasonal with peaks in the rainy seasons. Phylogenetic analysis revealed that Gabonese DENV-3 originated from West African strains and has been circulating continuously in Gabon since at least 2010, when the first DENV-3 case was reported. CONCLUSIONS These findings indicate stable DENV-3 circulation and the risk of repeated DENV infections in Gabon, highlighting the need for continuous monitoring to control DENV infections.
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Affiliation(s)
- Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Yuri Ushijima
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Marguerite M Loembe
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Université des Sciences de la Santé de Libreville, Libreville, Gabon
| | - Rodrigue Bikangui
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Patrick I Mpingabo
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Vahid R Zadeh
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Christelle M Pemba
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Yohei Kurosaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Yui Igasaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Sophia G de Vries
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Martin P Grobusch
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Selidji T Agnandji
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan; National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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Islam MT, Mubarak MS. Diterpenes and their derivatives as promising agents against dengue virus and dengue vectors: A literature‐based review. Phytother Res 2019; 34:674-684. [DOI: 10.1002/ptr.6562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/13/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Muhammad Torequl Islam
- Department for Management of Science and Technology DevelopmentTon Duc Thang University Ho Chi Minh City Vietnam
- Faculty of PharmacyTon Duc Thang University Ho Chi Minh City Vietnam
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Castillo-Méndez M, Valverde-Garduño V. Aedes aegypti Immune Response and Its Potential Impact on Dengue Virus Transmission. Viral Immunol 2019; 33:38-47. [PMID: 31738698 DOI: 10.1089/vim.2019.0051] [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] [Indexed: 11/12/2022] Open
Abstract
Dengue virus (DENV) transmission to human populations requires infection of vector mosquitoes as an essential component of the transmission process. DENV transmission leads to infections that range from asymptomatic to life-threatening pathologies, such as dengue hemorrhagic fever and dengue shock syndrome. Aedes aegypti is the principal vector of DENV, and its vector competence consists of the intrinsic factors, genes, molecules, and pathways that allow infection, replication, and dissemination of this virus throughout the cells of mosquito tissues. In the search for mosquito molecular targets to block DENV transmission, the effect of DENV infection on mosquitoes has been an important focus of research. In this study, we review the findings of research on the effect of DENV infection on mosquito tissue cells and the immunity pathways and molecules that are involved in this infection. We emphasize the relevance of recent findings to understand the relationship between Ae. aegypti immune response, vector competence, and DENV transmission to human hosts.
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Affiliation(s)
- Manuel Castillo-Méndez
- Departamento de Infección e Inmunidad, Centro de Investigaciones Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México.,Escuela de Salud Pública de México, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Verónica Valverde-Garduño
- Departamento de Infección e Inmunidad, Centro de Investigaciones Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México.,Escuela de Salud Pública de México, Instituto Nacional de Salud Pública, Cuernavaca, México
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Abdul-Ghani R, Mahdy MAK, Al-Eryani SMA, Fouque F, Lenhart AE, Alkwri A, Al-Mikhlafi AM, Wilke ABB, Thabet AAQ, Beier JC. Impact of population displacement and forced movements on the transmission and outbreaks of Aedes-borne viral diseases: Dengue as a model. Acta Trop 2019; 197:105066. [PMID: 31226251 DOI: 10.1016/j.actatropica.2019.105066] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/31/2019] [Accepted: 06/17/2019] [Indexed: 01/06/2023]
Abstract
Population displacement and other forced movement patterns following natural disasters, armed conflicts or due to socioeconomic reasons contribute to the global emergence of Aedes-borne viral disease epidemics. In particular, dengue epidemiology is critically affected by situations of displacement and forced movement patterns, particularly within and across borders. In this respect, waves of human movements have been a major driver for the changing epidemiology and outbreaks of the disease on local, regional and global scales. Both emerging dengue autochthonous transmission and outbreaks in countries known to be non-endemic and co-circulation and hyperendemicity with multiple dengue virus serotypes have led to the emergence of severe disease forms such as dengue hemorrhagic fever and dengue shock syndrome. This paper reviews the emergence of dengue outbreaks driven by population displacement and forced movements following natural disasters and conflicts within the context of regional and sub-regional groupings.
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Affiliation(s)
- Rashad Abdul-Ghani
- Department of Parasitology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen; Tropical Disease Research Center, Faculty of Medicine and Health Sciences, University of Science and Technology, Sana'a, Yemen.
| | - Mohammed A K Mahdy
- Department of Parasitology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen; Tropical Disease Research Center, Faculty of Medicine and Health Sciences, University of Science and Technology, Sana'a, Yemen
| | - Samira M A Al-Eryani
- Department of Parasitology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen
| | - Florence Fouque
- UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Audrey E Lenhart
- Center for Global Health/Division of Parasitic Diseases and Malaria/Entomology Branch, U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Abdulsamad Alkwri
- Integrated Vector Management Unit, National Malaria Control Programme, Ministry of Public Health and Population, Sana'a, Yemen
| | - Abdulsalam M Al-Mikhlafi
- Department of Parasitology, Faculty of Medicine and Health Sciences, Sana'a University, Sana'a, Yemen
| | - André B B Wilke
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ahmed A Q Thabet
- Neglected Tropical Diseases and Pandemic Influenza Preparedness Department, WHO Office, Sana'a, Yemen
| | - John C Beier
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
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Molecular Epidemiology of Dengue in Panama: 25 Years of Circulation. Viruses 2019; 11:v11080764. [PMID: 31434193 PMCID: PMC6724401 DOI: 10.3390/v11080764] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
Dengue virus (DENV) is the most prevalent arbovirus in terms of human public health importance globally. In addition to DENV epidemiological surveillance, genomic surveillance may help investigators understand the epidemiological dynamics, geographic distribution, and temporal patterns of DENV circulation. Herein, we aimed to reconstruct the molecular epidemiology and phylogeny of DENV in Panama to connect the epidemiological history of DENV dispersal and circulation in Latin America. We retrospectively analyzed the epidemiological data obtained during 25 years of DENV surveillance in Panama. DENV was reintroduced in Panama in 1993 after a 35 year absence of autochthonous transmission. The increase in the number of total dengue cases has been accompanied by an increase in severe and fatal cases, with the highest case fatality rate recorded in 2011. All four serotypes were detected in Panama, which is characterized by serotype replacement and/or co-circulation of multiple serotypes. Phylogenetic analysis of datasets collected from envelope (E) gene sequences obtained from viruses isolated from human sera demonstrated that circulating viruses were highly diverse and clustered in distinct clades, with co-circulation of clades from the same genotype. Our analyses also suggest that Panamanian strains were related to viruses from different regions of the Americas, suggesting a continuous exchange of viruses within the Americas.
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Hamel R, Surasombatpattana P, Wichit S, Dauvé A, Donato C, Pompon J, Vijaykrishna D, Liegeois F, Vargas RM, Luplertlop N, Missé D. Phylogenetic analysis revealed the co-circulation of four dengue virus serotypes in Southern Thailand. PLoS One 2019; 14:e0221179. [PMID: 31415663 PMCID: PMC6695175 DOI: 10.1371/journal.pone.0221179] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/31/2019] [Indexed: 12/15/2022] Open
Abstract
Dengue fever is caused by dengue viruses (DENV) from the Flavivirus genus and is the most prevalent arboviral disease. DENV exists in four immunogenically distinct and genetically-related serotypes (DENV-1 to 4), each subdivided in genotypes. Despite the endemicity of all four DENV serotypes in Thailand, no prior study has characterized the circulation of DENV in the southern provinces of the country. To determine the genetic diversity of DENV circulating in Southern Thailand in 2015 and 2016, we investigated 46 viruses from 182 patients' sera confirmed positive for DENV by serological and Nested RT-PCR tests. Our dataset included 2 DENV-1, 20 DENV-2, 9 DENV-3 and 15 DENV-4. Phylogenetic analysis was performed on viral envelop sequences. This revealed that part of the identified genotypes from DENV-1 and DENV-4 had been predominant in Asia (genotype I for both serotypes), while genotype II for DENV-4 and the Cosmopolitan genotype DENV-2 were also circulating. Whereas DENV-3 genotype II had been predominantly detected in South East Asia during the previous decades, we found genotype III and genotype I in Southern Thailand. All DENV genotype identified in this study were closely related to contemporary strains circulating in Southeast Asian countries, emphasizing the regional circulation of DENV. These results provide new insights into the co-circulation of all four DENV serotypes in Southern Thailand, confirming the hyperendemicity of DENV in the region. These findings also suggest a new trend of dissemination for some DENV serotypes with a possible shift in genotype distribution; as recently observed in other Asian countries.
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Affiliation(s)
- Rodolphe Hamel
- MIVEGEC UMR 224, Université de Montpellier, IRD, CNRS, Montpellier, France.,Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | | | - Alexandra Dauvé
- Department of Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Celeste Donato
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Julien Pompon
- MIVEGEC UMR 224, Université de Montpellier, IRD, CNRS, Montpellier, France.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Dhanasekaran Vijaykrishna
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Florian Liegeois
- MIVEGEC UMR 224, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - Ronald Morales Vargas
- Department of Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natthanej Luplertlop
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Dorothée Missé
- MIVEGEC UMR 224, Université de Montpellier, IRD, CNRS, Montpellier, France
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64
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Lin F, Yang H, Zhang L, Fang SH, Zhan XF, Yang LY. The analysis of clinical and laboratory data: a large outbreak of dengue fever in Chaozhou, Guangdong province, China. Arch Virol 2019; 164:2131-2135. [PMID: 31102050 PMCID: PMC6591201 DOI: 10.1007/s00705-019-04266-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/13/2019] [Indexed: 10/26/2022]
Abstract
A large-scale dengue fever (DF) outbreak occurred in Chaozhou, Guangdong province, China 2015. In our study, 528 dengue-positive patient samples were collected for clinical and laboratory data analysis. 491 cases (93.0%) were primary dengue fever (PDF), 22 cases (4.2%) were dengue hemorrhagic fever (DHF) and 15 cases (2.8%) were diagnosed with severe dengue fever (SDF). All cases were infected by dengue virus serotype 2 (DENV-2), and the isolated strains belonged to cosmopolitan genotype, which were grouped closely with Malaysia strains from 2010 to 2014. Moreover, the study showed that laboratory indices have significantly difference in PDF, DHF and SDF patients. A comprehensive analysis of these data could assist and guide the clinical diagnosis for DF, which has an important significance for the control of dengue virus infection.
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Affiliation(s)
- Fen Lin
- Central Laboratory, Chaozhou Central Hospital Affiliated to Southern Medical University, Chaozhou, 521021, Guangdong, China
| | - Hui Yang
- Department of Laboratory Medicine, School of Medicine, Yangtze University, Jingzhou, Hubei, China
| | - Lin Zhang
- Central Laboratory, Chaozhou Central Hospital Affiliated to Southern Medical University, Chaozhou, 521021, Guangdong, China
| | - Sen-Hai Fang
- Central Laboratory, Chaozhou Central Hospital Affiliated to Southern Medical University, Chaozhou, 521021, Guangdong, China
| | - Xiao-Fen Zhan
- Central Laboratory, Chaozhou Central Hospital Affiliated to Southern Medical University, Chaozhou, 521021, Guangdong, China
| | - Li-Ye Yang
- Central Laboratory, Chaozhou Central Hospital Affiliated to Southern Medical University, Chaozhou, 521021, Guangdong, China.
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65
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Sang S, Liu-Helmersson J, Quam MBM, Zhou H, Guo X, Wu H, Liu Q. The evolutionary dynamics of DENV 4 genotype I over a 60-year period. PLoS Negl Trop Dis 2019; 13:e0007592. [PMID: 31356608 PMCID: PMC6663010 DOI: 10.1371/journal.pntd.0007592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/01/2019] [Indexed: 01/26/2023] Open
Abstract
Dengue virus serotype 4 (DENV 4) has had a relatively low prevalence worldwide for decades; however, likely due to data paucity, no study has investigated the epidemiology and evolutionary dynamics of DENV 4 genotype I (DENV 4-I). This study aims to understand the diversity, epidemiology and dynamics of DENV 4-I. We collected 404 full length DENV4-1 envelope (E) gene sequences from 14 countries using two sources: Yunnan Province in China (15 strains during 2013–2016) and GenBank (489 strains up to 2018-01-11). Conducting phylogenetic and phylogeographical analyses, we estimated the virus spread, population dynamics, and selection pressures using different statistical analysis methods (substitution saturation, likelihood mapping, Bayesian coalescent inference, and maximum likelihood estimation). Our results show that during the last 60 years (1956–2016), DENV 4-I was present in mainland and maritime Southeast Asia, the Indian subcontinent, the southern provinces of China, parts of Brazil and Australia. The recent spread of DENV 4-I likely originated in the Philippines and later spread to Thailand. From Thailand, it spread to adjacent countries and eventually the Indian subcontinent. Apparently diverging around years 1957, 1963, 1976 and 1990, the different Clades (Clade I-V) were defined. The mean overall evolution rate of DENV 4-I was 9.74 (95% HPD: 8.68–10.82) × 10−4 nucleotide substitutions/site/year. The most recent common ancestor for DENV 4-I traces back to 1956. While the demographic history of DENV 4-I fluctuated, peaks appeared around 1982 and 2006. While purifying selection dominated the majority of E-gene evolution of DENV 4-I, positive selection characterized Clade III (Vietnam). DENV 4-I evolved in situ in Southeast Asia and the Indian subcontinent. Thailand and Indian acted as the main and secondary virus distribution hubs globally and regionally. Our phylogenetic analysis highlights the need for strengthened regional cooperation on surveillance and sharing of sample sequences to improve global dengue control and cross-border transmission prevention efforts. Dengue virus (DENV) can be classified into four serotypes, DENV 1, 2, 3 and 4. Although DENV 4 is the first dengue serotype to diverge in phylogenetic analyses of the genus Flavivirus, this serotype occurs at a low prevalence worldwide and spreads the least rapidly. Similar to other serotypes, DENV 4 can also cause severe dengue (SD) disease manifestations, such as dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). To date, no study has investigated the epidemiology and dynamics of DENV 4 genotype I comprehensively. In this study, we seek to address this gap. Our study shows that the distribution of DENV 4-I is mainly restricted to Southeast Asia and the Indian subcontinent. The most recent spread of DENV 4-I likely originated from Southeast Asia–initially circulating in the Philippines, then Thailand and later on the Indian subcontinent. Viruses evolved in situ in Southeast Asia and the Indian subcontinent, respectively. Although DENV 4-I occasionally spread elsewhere, this genotype did not become widely established. The overall evolution rate of DENV 4-I was comparable with that of DENV 2–4. The nucleotide sequences indicates that the demographic history of DENV 4-I fluctuated with peaks apparent during parts of the 1980s and 2000s. Although a weak positive selection existed in Clade III -predominately in Vietnam, purifying selection dominated the E-gene evolution of DENV 4-I.
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Affiliation(s)
- Shaowei Sang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong, People's Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong, People's Republic of China
- * E-mail: (SS); (QL)
| | | | - Mikkel B. M. Quam
- Department of Epidemiology and Global Health, Umea University, Umea, Sweden
| | - Hongning Zhou
- Yunnan Provincial Center of Arborvirus Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan Institute of Parasitic Diseases, Pu'er, Yunnan, People's Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Center of Arborvirus Research, Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan Institute of Parasitic Diseases, Pu'er, Yunnan, People's Republic of China
| | - Haixia Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
| | - Qiyong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- * E-mail: (SS); (QL)
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Suzuki K, Phadungsombat J, Nakayama EE, Saito A, Egawa A, Sato T, Rahim R, Hasan A, Lin MYC, Takasaki T, Rahman M, Shioda T. Genotype replacement of dengue virus type 3 and clade replacement of dengue virus type 2 genotype Cosmopolitan in Dhaka, Bangladesh in 2017. INFECTION GENETICS AND EVOLUTION 2019; 75:103977. [PMID: 31351235 DOI: 10.1016/j.meegid.2019.103977] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/24/2019] [Accepted: 07/22/2019] [Indexed: 01/18/2023]
Abstract
Dengue is a mosquito-borne disease that has spread to >100 countries and is caused by the dengue virus (DENV), which belongs to the Flavivirus genus of the family Flaviviridae. DENV comprises 4 serotypes (DENV-1 to -4), and each serotype is further divided into distinct genotypes. In India, it is reported that all 4 serotypes of DENV co-circulate. Although Bangladesh is a neighboring country of India, very few reports have published DENV sequence data for the country, especially after 2012. To understand the current distribution of DENV genotypes in Bangladesh, we determined the nucleotide sequences of envelope regions obtained from 58 DENV-positive patients diagnosed at Apollo Hospitals Dhaka during the period between September 2017 and February 2018. We found 5 DENV-1, 47 DENV-2, and 6 DENV-3 serotypes. A phylogenetic analysis of the obtained viral sequences revealed that DENV-3 genotype I was present instead of DENV-3 genotype II, which was predominant in Bangladesh between 2000 and 2009. Furthermore, we found two distinct lineages of the Cosmopolitan genotype of DENV-2, one of which was closely related to strains from Southeast Asia and has never been reported previously in Bangladesh. These results indicated that DENVs in Bangladesh have increased in genotypic diversity and suggest that the DENV genotypic shift observed in other Asian countries also might have been taking place in Bangladesh.
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Affiliation(s)
- Keita Suzuki
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan; TANAKA Kikinzoku Kogyo K.K., 2-73, Shinmachi, Hiratsuka, Kanagawa 254-0076, Japan
| | - Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases, Mahidol University, 420/6 Ratchawithi road, Ratchathewi, Bangkok 10400, Thailand
| | - Emi E Nakayama
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Akatsuki Saito
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Akio Egawa
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tairyu Sato
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Rummana Rahim
- Apollo Hospitals Dhaka, Plot-81, Block-E, Bashundhara R/A, Dhaka 1229, Bangladesh
| | - Abu Hasan
- Apollo Hospitals Dhaka, Plot-81, Block-E, Bashundhara R/A, Dhaka 1229, Bangladesh
| | - Marco Yung-Cheng Lin
- Department of Medical Research, Mackay Memorial Hospital, No. 45, Minsheng Rd., Tamsui District, New Taipei City 25160, Taiwan
| | - Tomohiko Takasaki
- Kanagawa Prefectural Institute of Public Health, 1-3-1 Shimomachiya, Chigasaki, Kanagawa 253-0087, Japan
| | - Mizanur Rahman
- Apollo Hospitals Dhaka, Plot-81, Block-E, Bashundhara R/A, Dhaka 1229, Bangladesh
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, 3-1, Yamada-oka, Suita, Osaka 565-0871, Japan; Mahidol-Osaka Center for Infectious Diseases, Mahidol University, 420/6 Ratchawithi road, Ratchathewi, Bangkok 10400, Thailand
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67
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Ali A, Fatima Z, Wahid B, Rafique S, Idrees M. Cosmopolitan A1 lineage of dengue virus serotype 2 is circulating in Pakistan: A study from 2017 dengue viral outbreak. J Med Virol 2019; 91:1909-1917. [PMID: 31273791 DOI: 10.1002/jmv.25537] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 05/14/2019] [Indexed: 11/10/2022]
Abstract
Dengue viral infection has become a challenge in tropical and subtropical countries where dengue virus is endemic. Its epidemics are occurring at higher rates amid its circulation throughout the year. Since the first documented outbreak in Pakistan in 1994, this region has reported many sporadic cases and epidemics. There is availability of small scale demographic and epidemiological studies on dengue viral infection in Pakistan. The year 2017 witnessed a huge dengue outbreak in Peshawar city of Pakistan with 69 deaths and 24 807 laboratory-confirmed cases. We suspect that the circulation of a different lineage or genotype could be responsible for the enhanced number of infected patients in Pakistan's 2017 outbreak since previous studies have already described this phenomenon in other countries. For this, we collected 1447 suspected blood samples and their epidemiological data. After serotyping through polymerase chain reaction nine samples of Dengue virus2 (DENV2) were randomly selected and were subjected to Sanger's sequencing for genotyping analysis. The mean distance, genetic diversity, and phylogenetic analysis were carried out using K2 model. The phylogenetic analysis split Pakistani isolates into two lineages, the sequences from 2017 outbreak in Peshawar grouped within A1 lineage of cosmopolitan genotype (IV) of DENV2. The difference in distance, genetic diversity, and amino acids composition strongly back the results that the new lineage is circulating in the region. This is significant as Pakistan is struggling to control dengue epidemics which have caused much loss in both monetary and health sectors.
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Affiliation(s)
- Amjad Ali
- Department of Genetics, Hazara University, Mansehra, Khyber Pakhtunkhwa, Pakistan.,Molecular Virology Laboratory, Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Zareen Fatima
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Braira Wahid
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Shazia Rafique
- Divison of Virology, Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Divison of Virology, Center of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
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68
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Ayolabi CI, Olusola BA, Ibemgbo SA, Okonkwo GO. Detection of Dengue viruses among febrile patients in Lagos, Nigeria and phylogenetics of circulating Dengue serotypes in Africa. INFECTION GENETICS AND EVOLUTION 2019; 75:103947. [PMID: 31276800 DOI: 10.1016/j.meegid.2019.103947] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 11/16/2022]
Abstract
Dengue fever, a mosquito borne viral disease, is caused by Dengue virus. This virus and its vector is endemic in most tropical countries including Nigeria. Dengue presents with febrile symptoms and is a major cause of morbidity and mortality in affected countries. The infection presently has no licensed drugs and vaccine is only available for previously exposed individuals. Despite the endemicity of Dengue in Nigeria, very few studies have identified circulating Dengue genotypes in the country. There is also sparse information on the occurrence, distribution and temporal patterns of circulating dengue virus serotypes as well as genotypes in Africa. This situation creates barriers to effective control of the infection in the continent. This study identified Dengue serotypes and genotypes among febrile patients in two health centers in Lagos, Nigeria. Phylogenetic analysis of Dengue sequences previously collected from African countries and submitted to GenBank database from 1944 till date was also performed. One hundred and thirty febrile persons were recruited for the study between April and August 2018. Eleven (8.5%) persons were Dengue virus positive. Dengue virus serotypes 1 (genotype I) and 3 (genotype I) were identified as actively circulating in Lagos, Nigeria. DENV 1 genotype V, DENV 2 cosmopolitan genotype and DENV 3 genotype III has over the years been the predominant circulating Dengue strains in Africa. Relative genotypic stability of circulating Dengue serotypes in Africa occurred over the past five decades. This may be due to limited investigations on circulating Dengue serotypes among asymptomatic individuals in the region as most studies focused on disease outbreaks and imported cases. There is the need to describe circulating Dengue genotypes in northern Africa, southern Africa as well as among asymptomatic individuals in other parts of Africa as this will provide further information on the diversity of Dengue genotypes circulating in the region.
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Affiliation(s)
| | | | - Sylvester Agha Ibemgbo
- Department of Microbiology, University of Lagos, Lagos, Nigeria; Department of Biological Sciences, Mountain Top University, Ogun State, Nigeria.
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69
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Gutiérrez-Bugallo G, Piedra LA, Rodriguez M, Bisset JA, Lourenço-de-Oliveira R, Weaver SC, Vasilakis N, Vega-Rúa A. Vector-borne transmission and evolution of Zika virus. Nat Ecol Evol 2019; 3:561-569. [PMID: 30886369 PMCID: PMC8900209 DOI: 10.1038/s41559-019-0836-z] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022]
Abstract
Zika virus (ZIKV), discovered in the Zika Forest of Uganda in 1947, is a mosquito-borne flavivirus related to yellow fever, dengue and West Nile viruses. From its discovery until 2007, only sporadic ZIKV cases were reported, with mild clinical manifestations in patients. Therefore, little attention was given to this virus before epidemics in the South Pacific and the Americas that began in 2013. Despite a growing number of ZIKV studies in the past three years, many aspects of the virus remain poorly characterized, particularly the spectrum of species involved in its transmission cycles. Here, we review the mosquito and vertebrate host species potentially involved in ZIKV vector-borne transmission worldwide. We also provide an evidence-supported analysis regarding the possibility of ZIKV spillback from an urban cycle to a zoonotic cycle outside Africa, and we review hypotheses regarding recent emergence and evolution of ZIKV. Finally, we identify critical remaining gaps in the current knowledge of ZIKV vector-borne transmission.
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Affiliation(s)
- Gladys Gutiérrez-Bugallo
- Department of Vector Control, Center for Research, Diagnostic and Reference, Institute of Tropical Medicine Pedro Kourí, PAHO-WHO Collaborating Center for Dengue and its Control, Havana, Cuba
| | - Luis Augusto Piedra
- Department of Vector Control, Center for Research, Diagnostic and Reference, Institute of Tropical Medicine Pedro Kourí, PAHO-WHO Collaborating Center for Dengue and its Control, Havana, Cuba
| | - Magdalena Rodriguez
- Department of Vector Control, Center for Research, Diagnostic and Reference, Institute of Tropical Medicine Pedro Kourí, PAHO-WHO Collaborating Center for Dengue and its Control, Havana, Cuba
| | - Juan A Bisset
- Department of Vector Control, Center for Research, Diagnostic and Reference, Institute of Tropical Medicine Pedro Kourí, PAHO-WHO Collaborating Center for Dengue and its Control, Havana, Cuba
| | - Ricardo Lourenço-de-Oliveira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Mosquitos Transmissores de Hematozoários, Rio de Janeiro, Brazil
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Anubis Vega-Rúa
- Laboratory of Vector Control Research, Unit Transmission Reservoir and Pathogen Diversity, Institute Pasteur of Guadeloupe, Les Abymes, Guadeloupe, France.
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70
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Chetry S, Khan SA, Dutta P, Apum B, Medhi PS, Saikia DC, Temsu T, Mawii L, Marak BC. Dengue virus serotypes and genotypic characterization from northeast India. J Med Virol 2019; 91:918-927. [PMID: 30698841 DOI: 10.1002/jmv.25418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/11/2018] [Accepted: 11/24/2018] [Indexed: 12/31/2022]
Abstract
Dengue is a rapidly spreading acute arboviral infection transmitted through a human and Aedes mosquito cycle. Though northeast region of India has been experiencing dengue outbreaks regularly for over a decade, reports on genetic characterization of the virus from this region are limited. The present study was undertaken to detect the genotype and genetic composition of circulating dengue virus (DENV) in this region. Blood samples were collected from 918 suspected dengue patients of five northeast Indian states. Serological investigations, viz, nonstructural 1 (NS1) enzyme-linked immunosorbent assay (ELISA), immunoglobulin M (IgM) ELISA, and immunoglobulin G (IgG) ELISA were performed followed by molecular detection. Sequence analysis and phylogenetic tree construction based on capsid-premembrane (C-prM) gene junction was done by BioEdit and MEGA6 software, respectively. Serological detection showed 35.34% NS1 and 18.12% IgM positivity. Secondary infection was observed in 24.53%. All four serotypes were detected. Phylogenetic analysis demonstrated circulation of genotype III of DENV-1, genotype IV of DENV-2, and genotype III of DENV-3. Sequences from this region form distinct clades in the phylogenetic tree. Characterization of the C-prM gene junction reveals divergence among the DENV strains. As genetic variation within the DENV is known to be associated with diverse clinical outcomes, information regarding the genetic composition of circulating virus could be beneficial in designing an effective intervention strategy.
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Affiliation(s)
- Sumi Chetry
- ICMR- Regional Medical Research Centre, NE Region, Dibrugarh, Assam, India
| | - Siraj A Khan
- ICMR- Regional Medical Research Centre, NE Region, Dibrugarh, Assam, India
| | - Prafulla Dutta
- ICMR- Regional Medical Research Centre, NE Region, Dibrugarh, Assam, India
| | - Basumoti Apum
- Bakin Pertin General Hospital, Pasighat, Arunachal Pradesh, India
| | | | | | - Temjen Temsu
- Dimapur District Hospital, Dimapur, Nagaland, India
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71
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Genetic Determinants of the Re-Emergence of Arboviral Diseases. Viruses 2019; 11:v11020150. [PMID: 30759739 PMCID: PMC6410223 DOI: 10.3390/v11020150] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 01/06/2023] Open
Abstract
Mosquito-borne diseases constitute a large portion of infectious diseases, causing more than 700,000 deaths annually. Mosquito-transmitted viruses, such as yellow fever, dengue, West Nile, chikungunya, and Zika viruses, have re-emerged recently and remain a public health threat worldwide. Global climate change, rapid urbanization, burgeoning international travel, expansion of mosquito populations, vector competence, and host and viral genetics may all together contribute to the re-emergence of arboviruses. In this brief review, we summarize the host and viral genetic determinants that may enhance infectivity in the host, viral fitness in mosquitoes and viral transmission by mosquitoes.
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72
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Galarion MJ, Schwem B, Pangilinan C, Dela Tonga A, Petronio-Santos JA, Delos Reyes E, Destura R. Genotypic persistence of dengue virus in the Philippines. INFECTION GENETICS AND EVOLUTION 2019; 69:134-141. [PMID: 30682551 DOI: 10.1016/j.meegid.2019.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 11/16/2022]
Abstract
The Philippines is known to have one of the world's highest prevalences of dengue infection. The disease has been endemic in the country since 1956 and the severe form was first reported during an outbreak in Manila in 1954. Among all of the countries in the world, the Philippines had the highest case fatality rate from 2008 to 2012. With the increasing rate of international travel, the country is also considered one of the primary sources of imported dengue cases in non-endemic areas in Asia, Australia, and Europe. Despite this high prevalence, there is a dearth of literature describing the circulating strains in the Philippines at the genotype level. Using data from sequence databases, this study aimed to characterize all available Philippine sequences, at the molecular level. Capsid/pre-membrane (C/prM) junction gene and envelope (E) gene sequences of dengue serotypes 1, 2, 3 and 4 from 1956 to 2016 were used for phylogenetic analysis and genotypic identification. All four serotypes co-circulate in the country over the last 50 years with conspicuous genotypic characteristics. DENV-1 exhibited an apparent persistence of a single genotype since 1974. DENV-2 showed strong evidence of genotypic shift in 1999-2002 accompanied by a genotypic persistence thereafter. DENV-3 and DENV-4 displayed a temporal domination of a single genotype, with evidence of a minor co-circulating genotypic population. The persistence and pre-domination of specific DENV genotypes warrant continuous molecular surveillance for signs of genotypic shifts that can cause local outbreak events or an increased risk for severity.
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Affiliation(s)
- Ma Jowina Galarion
- National Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila, Philippines.
| | - Brian Schwem
- National Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila, Philippines
| | - Coleen Pangilinan
- National Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila, Philippines
| | - Angelo Dela Tonga
- National Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila, Philippines
| | - Joy Ann Petronio-Santos
- Biological Sciences Research and Services Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Diliman, Quezon City, Philippines
| | - Erlinda Delos Reyes
- The Medical City Hospital and Infectious Disease Practice and Innovations, Pasig City, Philippines
| | - Raul Destura
- National Institute of Molecular Biology and Biotechnology, National Institutes of Health, University of the Philippines Manila, Ermita, Manila, Philippines; The Medical City Hospital and Infectious Disease Practice and Innovations, Pasig City, Philippines; Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
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73
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Ahamed SF, Rosario V, Britto C, Dias M, Nayak K, Chandele A, Kaja MK, Shet A. Emergence of new genotypes and lineages of dengue viruses during the 2012-15 epidemics in southern India. Int J Infect Dis 2019; 84S:S34-S43. [PMID: 30639622 DOI: 10.1016/j.ijid.2019.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012-13/2014-15 outbreaks in southern India. METHODS Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n=612), a representative selection of DENV isolates (n=99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. RESULTS In 2012-13 (n=113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014-15 (n=499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012-13 and 2014-15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012-13, ceding to GI predominance (80.8%) in 2014-15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, 'GIVc'. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. CONCLUSIONS New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.
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Affiliation(s)
- Syed Fazil Ahamed
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore, 560064, Karnataka, India.
| | - Vivek Rosario
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Carl Britto
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK.
| | - Mary Dias
- Division of Infectious Diseases, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India; Department of Microbiology, St. John's Medical College Hospital, St. John's National Academy of Health Sciences, Bangalore, 560034, Karnataka, India.
| | - Kaustuv Nayak
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Murali-Krishna Kaja
- ICGEB-Emory Vaccine Centre, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Pediatrics, Emory University, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
| | - Anita Shet
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, 415 N Washington St, Baltimore 21231, USA.
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74
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Bonney JHK, Hayashi T, Dadzie S, Agbosu E, Pratt D, Nyarko S, Asiedu-Bekoe F, Ido E, Sarkodie B, Ohta N, Yamaoka S. Molecular detection of dengue virus in patients suspected of Ebola virus disease in Ghana. PLoS One 2018; 13:e0208907. [PMID: 30566466 PMCID: PMC6300295 DOI: 10.1371/journal.pone.0208907] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/26/2018] [Indexed: 12/28/2022] Open
Abstract
Dengue fever is known to be one of the most common arthropod-borne viral infectious diseases of public health importance. The disease is now endemic in more than 100 countries in Africa, the Americas, the Eastern Mediterranean, Southeast Asia and the Western Pacific with an estimated two fifths of the world's population being at risk. The notable endemic viral hemorrhagic fevers (VHFs) found in West Africa, including yellow fever, Lassa fever, Rift Valley fever, dengue fever and until recently Ebola have been responsible for most outbreaks with fatal consequences. These VHFs usually produce unclear acute febrile illness, especially in the acute phase of infection. In this study we detected the presence of 2 different serotypes (DENV-2 and DENV-3) of Dengue virus in 4 sera of 150 patients clinically suspected of Ebola virus disease during the Ebola Virus Disease (EVD) outbreak in West Africa with the use of serological and molecular test assays. Sequence data was successfully generated for DENV-3 and phylogenetic analysis of the envelope gene showed that the DENV-3 sequences had close homology with DENV-3 sequences from Senegal and India. This study documents molecular evidence of an indigenous Dengue fever viral infection in Ghana and therefore necessitates the need to have an efficient surveillance system to rapidly detect and control the dissemination of the different serotypes in the population which has the potential to cause outbreaks of dengue hemorrhagic fevers.
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Affiliation(s)
| | - Takaya Hayashi
- Virology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Legon, Ghana
- Tokyo Medical and Dental University, Tokyo, Japan
| | - Samuel Dadzie
- Virology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Legon, Ghana
| | - Esinam Agbosu
- Virology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Legon, Ghana
| | - Deborah Pratt
- Virology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Legon, Ghana
| | - Stephen Nyarko
- Virology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Legon, Ghana
| | | | - Eiji Ido
- Tokyo Medical and Dental University, Tokyo, Japan
| | - Badu Sarkodie
- Public Health Division, Ghana Health Service, Accra, Ghana
| | - Nobuo Ohta
- Tokyo Medical and Dental University, Tokyo, Japan
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75
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Phadungsombat J, Lin MYC, Srimark N, Yamanaka A, Nakayama EE, Moolasart V, Suttha P, Shioda T, Uttayamakul S. Emergence of genotype Cosmopolitan of dengue virus type 2 and genotype III of dengue virus type 3 in Thailand. PLoS One 2018; 13:e0207220. [PMID: 30419004 PMCID: PMC6231660 DOI: 10.1371/journal.pone.0207220] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/26/2018] [Indexed: 01/27/2023] Open
Abstract
Dengue is a mosquito-borne disease that has spread to over 100 countries. Dengue fever is caused by dengue virus (DENV), which belongs to the Flavivirus genus of the family Flaviviridae. DENV comprises 4 serotypes (DENV-1 to DENV-4), and each serotype is divided into distinct genotypes. Thailand is an endemic area where all 4 serotypes of DENV co-circulate. To understand the current genotype distribution of DENVs in Thailand, we enrolled 100 cases of fever with dengue-like symptoms at the Bamrasnaradura Infectious Diseases Institute during 2016–2017. Among them, 37 cases were shown to be dengue-positive by real-time PCR. We were able to isolate DENVs from 21 cases, including 1 DENV-1, 8 DENV-2, 4 DENV-3, and 8 DENV-4. To investigate the divergence of the viruses, RNA was extracted from isolated DENVs and viral near-whole genome sequences were determined. Phylogenetic analysis of the obtained viral sequences revealed that DENV-2 genotype Cosmopolitan was co-circulating with DENV-2 genotype Asian-I, the previously predominating genotype in Thailand. Furthermore, DENV-3 genotype III was found instead of DENV-3 genotype II. The DENV-2 Cosmopolitan and DENV-3 genotype III found in Thailand were closely related to the respective strains found in nearby countries. These results indicated that DENVs in Thailand have increased in genotypic diversity, and suggested that the DENV genotypic shift observed in other Asian countries also might be taking place in Thailand.
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Affiliation(s)
- Juthamas Phadungsombat
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Narinee Srimark
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Atsushi Yamanaka
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Emi E. Nakayama
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Visal Moolasart
- Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand
| | - Patama Suttha
- Bamrasnaradura Infectious Diseases Institute, Nonthaburi, Thailand
| | - Tatsuo Shioda
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- * E-mail:
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76
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Intrahost Selection Pressures Drive Rapid Dengue Virus Microevolution in Acute Human Infections. Cell Host Microbe 2018; 22:400-410.e5. [PMID: 28910637 PMCID: PMC5616187 DOI: 10.1016/j.chom.2017.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/06/2017] [Accepted: 08/07/2017] [Indexed: 11/24/2022]
Abstract
Dengue, caused by four dengue virus serotypes (DENV-1 to DENV-4), is a highly prevalent mosquito-borne viral disease in humans. Yet, selection pressures driving DENV microevolution within human hosts (intrahost) remain unknown. We employed a whole-genome segmented amplification approach coupled with deep sequencing to profile DENV-3 intrahost diversity in peripheral blood mononuclear cell (PBMC) and plasma samples from 77 dengue patients. DENV-3 intrahost diversity appears to be driven by immune pressures as well as replicative success in PBMCs and potentially other replication sites. Hotspots for intrahost variation were detected in 59%-78% of patients in the viral Envelope and pre-Membrane/Membrane proteins, which together form the virion surface. Dominant variants at the hotspots arose via convergent microevolution, appear to be immune-escape variants, and were evolutionarily constrained at the macro level due to viral replication defects. Dengue is thus an example of an acute infection in which selection pressures within infected individuals drive rapid intrahost virus microevolution.
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77
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Sun J, Zhang H, Tan Q, Zhou H, Guan D, Zhang X, Duan J, Cai S, Peng Z, He J, Ke C, Lin J, Liu T, Ma W, Wu D. The epidemiological characteristics and molecular phylogeny of the dengue virus in Guangdong, China, 2015. Sci Rep 2018; 8:9976. [PMID: 29967414 PMCID: PMC6028473 DOI: 10.1038/s41598-018-28349-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/21/2018] [Indexed: 11/29/2022] Open
Abstract
In 2015, an unexpected multiple outbreak of dengue occurred in Guangdong, China. In total, 1,699 cases were reported, of which 1,627 cases were verified to have DENV infections by nucleic acid or NS1 protein, including 44 DENV-1, 1126 DENV-2, 18 DENV-3 and 6 DENV-4, and the other cases were confirmed by NS1 ELISA. Phylogenetic analyses of DENV-1 isolates identified two genotypes (I and V). The predominant DENV-2 outbreak isolates were the Cosmopolitan genotypes, which likely originated from Malaysia. The DENV-3 isolates were assigned into genotype I and genotype III. All 6 DENV-4 isolates from imported cases were likely originally from Cambodia, Thailand and the Philippines. The entomological surveillance showed a moderate risk for the BI index in Chaozhou and Foshan and a low risk in Guangzhou. The imported cases were mostly detected in Guangzhou and Foshan. Surprisingly, the most serious outbreak occurred in Chaozhou, but not in Guangzhou or Foshan. A combined analyses demonstrated the multiple geographical origins of this outbreak, and highlight the detection of suspected cases after the alerting of imported cases, early implementation of control policies and reinforce the vector surveillance strategies were the key points in the chain of prevention and control of dengue epidemics.
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Affiliation(s)
- Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Huan Zhang
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Qiqi Tan
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Huiqiong Zhou
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Dawei Guan
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Xin Zhang
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Jinhua Duan
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Songwu Cai
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Zhiqiang Peng
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Jianfeng He
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Changwen Ke
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Jinyan Lin
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China.,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China
| | - Tao Liu
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - Wenjun Ma
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China
| | - De Wu
- Key Laboratory for Repository and Application of Pathogenic Microbiology, Research Center for Pathogens Detection Technology of Emerging Infectious Diseases, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, China. .,WHO Collaborating Centre for Surveillance, Research and Training of Emerging Infectious Diseases, Guangzhou, 511430, China.
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78
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Diversity of dengue virus-3 genotype III in Jeddah, Saudi Arabia. Acta Trop 2018; 183:114-118. [PMID: 29621534 DOI: 10.1016/j.actatropica.2018.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/25/2018] [Accepted: 04/01/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND Dengue is the most important arboviral disease in tropical and subtropical countries. Dispersal of the vector and an increase in migratory flow between countries have led to large epidemics and severe clinical outcomes. Over the past 20 years, dengue epidemics have become more wide-spread and frequent. Previous studies have shown that dengue is endemic in Jeddah, Makkah and Al-Madinah in western Saudi Arabia as well as in Jazan region in the southern part of the country. The four serotypes of dengue virus (DENV) have been reported from western Saudi Arabia. It has been suggested that pilgrims could play a significant and unique role in DENV-1 and DENV-2 introduction into Saudi Arabia, especially in the cities of Jeddah, Makkah and Al-Madinah during Hajj and Umrah seasons. However, only limited data on DENV-3 in Saudi Arabia are available. METHODS All available DENV-3 sequences published and unpublished from Saudi Arabia and other countries were retrieved from Genbank and gene sequence repository and phylogenetically analyzed to examine the diversity of DENV-3 into the city of Jeddah. RESULTS Based on the analysis of the envelope gene and non-structural 1 (E/NS1) junction sequences, we show that there were at least four independent introductions of DENV-3, all from genotype III into Jeddah. The first introduction was most probably before 1997 as Saudi virus isolates from 1997 formed a cluster without any close relationship to other globally circulating isolates, suggesting their local circulation from previous introduction events. Two introductions were most probably in 2004 with isolates closely-related to isolates from Africa and India (Asia), in addition to another introduction in 2014 with isolates clustering with those from Singapore (Asia). CONCLUSIONS Our data shows that only genotype III isolates of DENV-3 are circulating in Jeddah and highlights the potential role of pilgrims in DENV-3 importation into western Saudi Arabia and subsequent exportation to their home countries during Hajj and Umrah seasons. Therefore, it is highly recommended to establish DENV sentinel surveillance programs targeting clinical cases and the mosquito vector in the country to implement effective control measures and to minimize the burden of the disease in the kingdom.
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79
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Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context. Nat Commun 2018; 9:2355. [PMID: 29907741 PMCID: PMC6003961 DOI: 10.1038/s41467-018-04595-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
An extensive body of theory addresses the topic of pathogen virulence evolution, yet few studies have empirically demonstrated the presence of fitness trade-offs that would select for intermediate virulence. Here we show the presence of transmission-clearance trade-offs in dengue virus using viremia measurements. By fitting a within-host model to these data, we further find that the interaction between dengue and the host immune response can account for the observed trade-offs. Finally, we consider dengue virulence evolution when selection acts on the virus’s production rate. By combining within-host model simulations with empirical findings on how host viral load affects human-to-mosquito transmission success, we show that the virus’s transmission potential is maximized at production rates associated with intermediate virulence and that the optimal production rate critically depends on dengue’s epidemiological context. These results indicate that long-term changes in dengue’s global distribution impact the invasion and spread of virulent dengue virus genotypes. Theory predicts that pathogens will evolve towards intermediate virulence, yet the necessary trade-offs invoked by this theory have rarely been demonstrated empirically. Here, the authors show that dengue virus dynamics exhibit a trade-off between transmission and clearance rates.
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80
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Autochthonous spread of DENV-3 genotype III in Malaysia mitigated by pre-existing homotypic and heterotypic immunity. Epidemiol Infect 2018; 146:1635-1641. [PMID: 29860959 DOI: 10.1017/s0950268818001425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dengue virus type 3 genotype III (DENV-3/III) is widely distributed in most dengue-endemic regions. It emerged in Malaysia in 2008 and autochthonously spread in the midst of endemic DENV-3/I circulation. The spread, however, was limited and the virus did not cause any major outbreak. Spatiotemporal distribution study of DENV-3 over the period between 2005 and 2011 revealed that dengue cases involving DENV-3/III occurred mostly in areas without pre-existing circulating DENV-3. Neutralisation assays performed using sera of patients with the respective infection showed that the DENV-3/III viruses can be effectively neutralised by sera of patients with DENV-3 infection (50% foci reduction neutralisation titres (FRNT50) > 1300). Sera of patients with DENV-1 infection (FRNT50 ⩾ 190), but not sera of patients with DENV-2 infection (FRNT50 ⩽ 50), were also able to neutralise the virus. These findings highlight the possibility that the pre-existing homotypic DENV-3 and the cross-reacting heterotypic DENV-1 antibody responses could play a role in mitigating a major outbreak involving DENV-3/III in the Klang Valley, Malaysia.
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81
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Liao F, Mo Z, Chen M, Pang B, Fu X, Xu W, Jing H, Kan B, Gu W. Comparison and Evaluation of the Molecular Typing Methods for Toxigenic Vibrio cholerae in Southwest China. Front Microbiol 2018; 9:905. [PMID: 29867816 PMCID: PMC5951969 DOI: 10.3389/fmicb.2018.00905] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 11/15/2022] Open
Abstract
Vibrio cholerae O1 strains taken from the repository of Yunnan province, southwest China, were abundant and special. We selected 70 typical toxigenic V. cholerae (69 O1 and one O139 serogroup strains) isolated from Yunnan province, performed the pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and MLST of virulence gene (V-MLST) methods, and evaluated the resolution abilities for typing methods. The ctxB subunit sequence analysis for all strains have shown that cholera between 1986 and 1995 was associated with mixed infections with El Tor and El Tor variants, while infections after 1996 were all caused by El Tor variant strains. Seventy V. cholerae obtained 50 PFGE patterns, with a high resolution. The strains could be divided into three groups with predominance of strains isolated during 1980s, 1990s, and 2000s, respectively, showing a good consistency with the epidemiological investigation. We also evaluated two MLST method for V. cholerae, one was used seven housekeeping genes (adk, gyrB, metE, pntA, mdh, purM, and pyrC), and all the isolates belonged to ST69; another was used nine housekeeping genes (cat, chi, dnaE, gyrB, lap, pgm, recA, rstA, and gmd). A total of seven sequence types (STs) were found by using this method for all the strains; among them, rstA gene had five alleles, recA and gmd have two alleles, and others had only one allele. The virulence gene sequence typing method (ctxAB, tcpA, and toxR) showed that 70 strains were divided into nine STs; among them, tcpA gene had six alleles, toxR had five alleles, while ctxAB was identical for all the strains. The latter two sequences based typing methods also had consistency with epidemiology of the strains. PFGE had a higher resolution ability compared with the sequence based typing method, and MLST used seven housekeeping genes showed the lower resolution power than nine housekeeping genes and virulence genes methods. These two sequence typing methods could distinguish some epidemiological special strains in local area.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, First People's Hospital of Yunnan Province, Kunming, China
| | - Zhishuo Mo
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Meiling Chen
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Bo Pang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wen Xu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Huaiqi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Biao Kan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China.,Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical School, Kunming, China
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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83
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Tan KK, Zulkifle NI, Sulaiman S, Pang SP, NorAmdan N, MatRahim N, Abd-Jamil J, Shu MH, Mahadi NM, AbuBakar S. Emergence of the Asian lineage dengue virus type 3 genotype III in Malaysia. BMC Evol Biol 2018; 18:58. [PMID: 29699483 PMCID: PMC5921268 DOI: 10.1186/s12862-018-1175-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/11/2018] [Indexed: 01/16/2023] Open
Abstract
Background Dengue virus type 3 genotype III (DENV3/III) is associated with increased number of severe infections when it emerged in the Americas and Asia. We had previously demonstrated that the DENV3/III was introduced into Malaysia in the late 2000s. We investigated the genetic diversity of DENV3/III strains recovered from Malaysia and examined their phylogenetic relationships against other DENV3/III strains isolated globally. Results Phylogenetic analysis revealed at least four distinct DENV3/III lineages. Two of the lineages (DENV3/III-B and DENV3/III-C) are current actively circulating whereas the DENV3/III-A and DENV3/III-D were no longer recovered since the 1980s. Selection pressure analysis revealed strong evidence of positive selection on a number of amino acid sites in PrM, E, NS1, NS2a, NS2b, NS3, NS4a, and NS5. The Malaysian DENV3/III isolates recovered in the 1980s (MY.59538/1987) clustered into DENV3/III-B, which was the lineage with cosmopolitan distribution consisting of strains actively circulating in the Americas, Africa, and Asia. The Malaysian isolates recovered after the 2000s clustered within DENV3/III-C. This DENV3/III-C lineage displayed a more restricted geographical distribution and consisted of isolates recovered from Asia, denoted as the Asian lineage. Amino acid variation sites in NS5 (NS5–553I/M, NS5–629 T, and NS5–820E) differentiated the DENV3/III-C from other DENV3 viruses. The codon 629 of NS5 was identified as a positively selected site. While the NS5-698R was identified as unique to the genome of DENV3/III-C3. Phylogeographic results suggested that the recent Malaysian DENV3/III-C was likely to have been introduced from Singapore in 2008 and became endemic. From Malaysia, the virus subsequently spread into Taiwan and Thailand in the early part of the 2010s and later reintroduced into Singapore in 2013. Conclusions Distinct clustering of the Malaysian old and new DENV3/III isolates suggests that the currently circulating DENV3/III in Malaysia did not descend directly from the strains recovered during the 1980s. Phylogenetic analyses and common genetic traits in the genome of the strains and those from the neighboring countries suggest that the Malaysian DENV3/III is likely to have been introduced from the neighboring regions. Malaysia, however, serves as one of the sources of the recent regional spread of DENV3/III-C3 within the Asia region. Electronic supplementary material The online version of this article (10.1186/s12862-018-1175-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurul-Izzani Zulkifle
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Syuhaida Sulaiman
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sui-Ping Pang
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - NurAsyura NorAmdan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - NorAziyah MatRahim
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Juraina Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Meng-Hooi Shu
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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84
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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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85
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Shrivastava S, Tiraki D, Diwan A, Lalwani SK, Modak M, Mishra AC, Arankalle VA. Co-circulation of all the four dengue virus serotypes and detection of a novel clade of DENV-4 (genotype I) virus in Pune, India during 2016 season. PLoS One 2018; 13:e0192672. [PMID: 29470509 PMCID: PMC5823370 DOI: 10.1371/journal.pone.0192672] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/22/2018] [Indexed: 11/19/2022] Open
Abstract
Dengue is the most common mosquito-borne viral infection in tropical and sub-tropical countries. In recent years, India has reported increased incidences of concurrent infection with multiple serotypes of dengue viruses (DENV). In the present study, we have characterized DENV circulating during a single season of 2016 in Pune, India. A total of 64 serum samples from NS1 ELISA positive dengue patients were used for PCR amplification of CprM region of the viral genome and sequencing. Phylogenetic analysis documented circulation of all the four DENV serotypes with predominance of DENV-2 (40.6%). DENV genotyping classified DENV-1 to Genotype V, DENV-2 to Genotype IV, DENV-3 to Genotype III and DENV-4 to Genotype I. Further analysis revealed emergence of a novel clade (D) of genotype I of DENV-4. Subsequent isolation of three DENV-4 viruses in cell culture followed by complete genome sequence analysis confirmed this observation. Additionally, a new genotype within serotype-4 with >6.7% sequence variation from other genotypes was identified. This first report of significant co-circulation of all the four serotypes in a single outbreak in Pune reconfirms need for molecular monitoring of DENV.
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Affiliation(s)
- Shubham Shrivastava
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Divya Tiraki
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Arundhati Diwan
- Department of Medicine, Bharati Vidyapeeth Deemed University Medical College, Pune, Maharashtra, India
| | - Sanjay K. Lalwani
- Department of Pediatrics, Bharati Vidyapeeth Deemed University Medical College, Pune, Maharashtra, India
| | - Meera Modak
- Department of Microbiology, Bharati Vidyapeeth Deemed University Medical College, Pune, Maharashtra, India
| | - Akhilesh Chandra Mishra
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
| | - Vidya A. Arankalle
- Department of Communicable Diseases, Interactive Research School for Health Affairs, Bharati Vidyapeeth Deemed University, Pune, Maharashtra, India
- * E-mail:
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86
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Castro-Orozco R, Castro-García LR, Gómez-Camargo DE. [Phylogenetic analysis of South American sequences of the nonstructural protein-1 (ns1) of dengue serotype 2 associated with severe clinical bleeding]. Rev Salud Publica (Bogota) 2018; 18:459-469. [PMID: 28453108 DOI: 10.15446/rsap.v18n3.44078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 02/22/2016] [Indexed: 11/09/2022] Open
Abstract
Objective The objective of this in silico study was to compare nucleotide and amino acids DENV-2-NS1 sequences isolated from febrile patients, with and without disease severity, from different South American countries. Matherials and Methods A bayesian MCMC phylogenetic analysis was carried out using 28 complete sequences of the gene NS1 of the DENV-2 serotype (1 056 bp), using MrBayes v.3.2.0 software, with the model SYM+G (2.5 million generations). We also carried out a phylogenetic analysis with Neighbor-Joining method (Jukes-Cantor model). In addition, the amino acids sequences were aligned and compared with each other, using Clustal W included in MEGA v.5.2 software. Results In the amino acids sequences associated with bleeding, the most frequent substitution was isoleucine → threonine at posicion 93. These sequences showed a high percentage (94.6 %) of amino acid homology in comparison with the percentage of amino acids homology (74 %) of DENV-2 isolates not associated with bleeding. Five clades were identified that group the vast majority of the DENV-2-NS1 sequences analyzed (19/24; 79.2 %) with posterior probability values greater than or equal to 58 %. Seven sequences (87.5 %) associated with bleeding were phylogenetically related within clades 4 and 5, the posterior probability values were 58 % and 97 %, respectively. Conclusion Neither phylogenetic characteristics nor differences between amino acids of the DENV-2-NS1 sequences studied were found that could be associated directly with severity of the disease.
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87
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Abstract
Flaviviruses such as dengue (DENV), yellow fever (YFV), West Nile (WNV), and Zika (ZIKV) are human pathogens of global significance. In particular, DENV causes the most prevalent mosquito-borne viral diseases in humans, and ZIKV emerged from obscurity into the spotlight in 2016 as the etiologic agent of congenital Zika syndrome. Owing to the recent emergence of ZIKV as a global pandemic threat, the roles of the immune system during ZIKV infections are as yet unclear. In contrast, decades of DENV research implicate a dual role for the immune system in protection against and pathogenesis of DENV infection. As DENV and ZIKV are closely related, knowledge based on DENV studies has been used to prioritize investigation of ZIKV immunity and pathogenesis, and to accelerate ZIKV diagnostic, therapeutic, and vaccine design. This review discusses the following topics related to innate and adaptive immune responses to DENV and ZIKV: the interferon system as the key mechanism of host defense and viral target for immune evasion, antibody-mediated protection versus antibody-dependent enhancement, and T cell-mediated protection versus original T cell antigenic sin. Understanding the mechanisms that regulate the balance between immune-mediated protection and pathogenesis during DENV and ZIKV infections is critical toward development of safe and effective DENV and ZIKV therapeutics and vaccines.
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Affiliation(s)
- Annie Elong Ngono
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA;
| | - Sujan Shresta
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA;
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88
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Abstract
Dengue is a mosquito-borne acute viral infection that can develop into a potentially lethal complication known as severe dengue. It is endemic in more than 100 tropical and subtropical countries where the mosquito vectors, predominantly Aedes aegypti and Aedes albopictus, are found. Non-immune travellers are at risk of infection and with the rise in international travel and the availability of cheap holiday packages to endemic countries, many of which are popular tourist destinations, there has been a significant increase in spread of dengue viruses.
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89
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Abstract
Zika virus was discovered in East Africa in 1947 by the Rockefeller Foundation during investigations on the ecology of yellow fever. Although it was subsequently shown to have widespread distribution in Africa and Asia, it was not known to cause epidemics until 2007. This paper describes the history of the virus discovery, emergence and evolution as an epidemic virus, and the its evolving clinical spectrum.
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Affiliation(s)
- Duane J Gubler
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases/Center for Tropical Diseases Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Didier Musso
- Unit of Emerging Infectious Disease, Institut Louis Malardé Papeete, Tahiti, Polynésie
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90
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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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91
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Cecilia D, Patil J, Kakade M, Walimbe A, Alagarasu K, Anukumar B, Abraham A. Emergence of the Asian genotype of DENV-1 in South India. Virology 2017; 510:40-45. [DOI: 10.1016/j.virol.2017.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 10/19/2022]
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92
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Uehara A, Tissera HA, Bodinayake CK, Amarasinghe A, Nagahawatte A, Tillekeratne LG, Cui J, Reller ME, Palihawadana P, Gunasena S, Desilva AD, Wilder-Smith A, Gubler DJ, Woods CW, Sessions OM. Analysis of Dengue Serotype 4 in Sri Lanka during the 2012-2013 Dengue Epidemic. Am J Trop Med Hyg 2017; 97:130-136. [PMID: 28719296 DOI: 10.4269/ajtmh.16-0540] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The four serotypes of dengue virus (DENV-1, -2, -3, and -4) have had a rapidly expanding geographic range and are now endemic in over 100 tropical and subtropical countries. Sri Lanka has experienced periodic dengue outbreaks since the 1960s, but since 1989 epidemics have become progressively larger and associated with more severe disease. The dominant virus in the 2012 epidemic was DENV-1, but DENV-4 infections were also commonly observed. DENV-4 transmission was first documented in Sri Lanka when it was isolated from a traveler in 1978, but has been comparatively uncommon since dengue surveillance began in the early 1980s. To better understand the molecular epidemiology of DENV-4 infections in Sri Lanka, we conducted whole-genome sequencing on dengue patient samples from two different geographic locations. Phylogenetic analysis indicates that all sequenced DENV-4 strains belong to genotype 1 and are most closely related to DENV-4 viruses previously found in Sri Lanka and those recently found to be circulating in India and Pakistan.
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Affiliation(s)
| | | | | | | | | | | | - Jie Cui
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Megan E Reller
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | | | | | - Annelies Wilder-Smith
- Institute of Public Health, University of Heidelberg, Heidelberg, Germany.,Umea University, Umea, Sweden
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Tan KK, Zulkifle NI, Abd-Jamil J, Sulaiman S, Yaacob CN, Azizan NS, Che Mat Seri NAA, Samsudin NI, Mahfodz NH, AbuBakar S. Disruption of predicted dengue virus type 3 major outbreak cycle coincided with switching of the dominant circulating virus genotype. INFECTION GENETICS AND EVOLUTION 2017; 54:271-275. [PMID: 28698156 DOI: 10.1016/j.meegid.2017.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/19/2022]
Abstract
Dengue is hyperendemic in most of Southeast Asia. In this region, all four dengue virus serotypes are persistently present. Major dengue outbreak cycle occurs in a cyclical pattern involving the different dengue virus serotypes. In Malaysia, since the 1980s, the major outbreak cycles have involved dengue virus type 3 (DENV3), dengue virus type 1 (DENV1) and dengue virus type 2 (DENV2), occurring in that order (DENV3/DENV1/DENV2). Only limited information on the DENV3 cycles, however, have been described. In the current study, we examined the major outbreak cycle involving DENV3 using data from 1985 to 2016. We examined the genetic diversity of DENV3 isolates obtained during the period when DENV3 was the dominant serotype and during the inter-dominant transmission period. Results obtained suggest that the typical DENV3/DENV1/DENV2 cyclical outbreak cycle in Malaysia has recently been disrupted. The last recorded major outbreak cycle involving DENV3 occurred in 2002, and the expected major outbreak cycle involving DENV3 in 2006-2012 did not materialize. DENV genome analyses revealed that DENV3 genotype II (DENV3/II) was the predominant DENV3 genotype (67%-100%) recovered between 1987 and 2002. DENV3 genotype I (DENV3/I) emerged in 2002 followed by the introduction of DENV3 genotype III (DENV3/III) in 2008. These newly emerged DENV3 genotypes replaced DENV3/II, but there was no major upsurge of DENV3 cases that accompanied the emergence of these viruses. DENV3 remained in the background of DENV1 and DENV2 until now. Virus genome sequence analysis suggested that intrinsic differences within the different dengue virus genotypes could have influenced the transmission efficiency of DENV3. Further studies and continuous monitoring of the virus are needed for better understanding of the DENV transmission dynamics in hyperendemic regions.
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Affiliation(s)
- Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Nurul-Izzani Zulkifle
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Juraina Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Syuhaida Sulaiman
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Che Norainon Yaacob
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Noor Syahida Azizan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Nurul Asma Anati Che Mat Seri
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Nur Izyan Samsudin
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Nur Hidayana Mahfodz
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Choudhary MC, Gupta E, Sharma S, Hasnain N, Agarwala P. Genetic signatures coupled with lineage shift characterise endemic evolution of Dengue virus serotype 2 during 2015 outbreak in Delhi, India. Trop Med Int Health 2017; 22:871-880. [DOI: 10.1111/tmi.12898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Ekta Gupta
- Department of Virology; Institute of Liver and Biliary Sciences; New Delhi India
| | - Shvetank Sharma
- Molecular and Cellular Medicine Department; Institute of Liver and Biliary Sciences; New Delhi India
| | - Nadeem Hasnain
- Department of Virology; Institute of Liver and Biliary Sciences; New Delhi India
| | - Pragya Agarwala
- Department of Virology; Institute of Liver and Biliary Sciences; New Delhi India
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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: 4.1] [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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96
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Filomatori CV, Carballeda JM, Villordo SM, Aguirre S, Pallarés HM, Maestre AM, Sánchez-Vargas I, Blair CD, Fabri C, Morales MA, Fernandez-Sesma A, Gamarnik AV. Dengue virus genomic variation associated with mosquito adaptation defines the pattern of viral non-coding RNAs and fitness in human cells. PLoS Pathog 2017; 13:e1006265. [PMID: 28264033 PMCID: PMC5354447 DOI: 10.1371/journal.ppat.1006265] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/16/2017] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
The Flavivirus genus includes a large number of medically relevant pathogens that cycle between humans and arthropods. This host alternation imposes a selective pressure on the viral population. Here, we found that dengue virus, the most important viral human pathogen transmitted by insects, evolved a mechanism to differentially regulate the production of viral non-coding RNAs in mosquitos and humans, with a significant impact on viral fitness in each host. Flavivirus infections accumulate non-coding RNAs derived from the viral 3’UTRs (known as sfRNAs), relevant in viral pathogenesis and immune evasion. We found that dengue virus host adaptation leads to the accumulation of different species of sfRNAs in vertebrate and invertebrate cells. This process does not depend on differences in the host machinery; but it was found to be dependent on the selection of specific mutations in the viral 3’UTR. Dissecting the viral population and studying phenotypes of cloned variants, the molecular determinants for the switch in the sfRNA pattern during host change were mapped to a single RNA structure. Point mutations selected in mosquito cells were sufficient to change the pattern of sfRNAs, induce higher type I interferon responses and reduce viral fitness in human cells, explaining the rapid clearance of certain viral variants after host change. In addition, using epidemic and pre-epidemic Zika viruses, similar patterns of sfRNAs were observed in mosquito and human infected cells, but they were different from those observed during dengue virus infections, indicating that distinct selective pressures act on the 3’UTR of these closely related viruses. In summary, we present a novel mechanism by which dengue virus evolved an RNA structure that is under strong selective pressure in the two hosts, as regulator of non-coding RNA accumulation and viral fitness. This work provides new ideas about the impact of host adaptation on the variability and evolution of flavivirus 3’UTRs with possible implications in virulence and viral transmission. Flaviviruses constitute the most important and diverse group of arthropod-transmitted viruses, including relevant human pathogens such as dengue, Zika, yellow fever, and West Nile viruses. The natural alternation of these viruses between vertebrate and invertebrate hosts imposes a selective pressure on the viral population, with potential epidemiological implications. However, the selective forces and mechanisms that act on the viral RNA during host adaptation are largely unknown. Using dengue virus, we found that viral replication in mosquito or human cells leads to the accumulation of different patterns of viral non-coding RNAs that differently regulate viral fitness in each host. Carrying out this process requires changes of the structure of the viral 3’UTR that is under strong selective pressure in the two hosts. Our findings provide the first link between flavivirus host adaptation, fitness, and the production of viral non-coding RNAs, and support a model in which opposite selective pressures in the two hosts drive flavivirus 3’UTR evolution.
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Affiliation(s)
- Claudia V. Filomatori
- Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina
| | - Juan M. Carballeda
- Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina
| | - Sergio M. Villordo
- Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina
| | - Sebastian Aguirre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Horacio M. Pallarés
- Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina
| | - Ana M. Maestre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Irma Sánchez-Vargas
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Carol D. Blair
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Cintia Fabri
- Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", ANLIS, Pergamino, Argentina
| | - Maria A. Morales
- Departamento Investigación, Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", ANLIS, Pergamino, Argentina
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andrea V. Gamarnik
- Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires, Argentina
- * E-mail:
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97
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Yamanaka A, Moi ML, Takasaki T, Kurane I, Konishi E. Neutralizing and enhancing antibody responses to five genotypes of dengue virus type 1 (DENV-1) in DENV-1 patients. J Gen Virol 2017; 98:166-172. [PMID: 27911254 DOI: 10.1099/jgv.0.000669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) has four distinct serotypes, DENV-1-4, with four to six genotypes in each serotype. The World Health Organization recommends tetravalent formulations including one genotype of each serotype as safe and effective dengue vaccines. Here, we investigated the impact of genotype on the neutralizing antibody responses to DENV-1 in humans. Convalescent sera collected from patients with primary infection of DENV-1 were examined for neutralizing antibody against single-round infectious particles of the five DENV-1 genotypes (GI-GV). In both GI- and GIV-infected patients, their neutralizing antibody titres against the five genotypes were similar, differing ≤4-fold from the homogenotypic responses. The enhancing activities against the five genotypes were also similar in these sera. Thus, the genotype strains of DENV-1 showed no significant antigenic differences in these patients, suggesting that GI- or GIV-derived vaccine antigens should induce equivalent levels of neutralizing antibodies against all DENV-1 genotypes.
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Affiliation(s)
- Atsushi Yamanaka
- BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand.,BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Meng Ling Moi
- Present address: Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.,Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Present address: Kanagawa Prefectural Institute of Public Health, Kanagawa, Japan.,Department of Virology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ichiro Kurane
- National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Eiji Konishi
- BIKEN Endowed Department of Dengue Vaccine Development, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.,BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand
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98
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Pretzer C, Druzhinina IS, Amaro C, Benediktsdóttir E, Hedenström I, Hervio-Heath D, Huhulescu S, Schets FM, Farnleitner AH, Kirschner AKT. High genetic diversity of Vibrio cholerae in the European lake Neusiedler See is associated with intensive recombination in the reed habitat and the long-distance transfer of strains. Environ Microbiol 2017; 19:328-344. [PMID: 27871138 PMCID: PMC5718291 DOI: 10.1111/1462-2920.13612] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 10/27/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
Abstract
Coastal marine Vibrio cholerae populations usually exhibit high genetic diversity. To assess the genetic diversity of abundant V. cholerae non-O1/non-O139 populations in the Central European lake Neusiedler See, we performed a phylogenetic analysis based on recA, toxR, gyrB and pyrH loci sequenced for 472 strains. The strains were isolated from three ecologically different habitats in a lake that is a hot-spot of migrating birds and an important bathing water. We also analyzed 76 environmental and human V. cholerae non-O1/non-O139 isolates from Austria and other European countries and added sequences of seven genome-sequenced strains. Phylogenetic analysis showed that the lake supports a unique endemic diversity of V. cholerae that is particularly rich in the reed stand. Phylogenetic trees revealed that many V. cholerae isolates from European countries were genetically related to the strains present in the lake belonging to statistically supported monophyletic clades. We hypothesize that the observed phenomena can be explained by the high degree of genetic recombination that is particularly intensive in the reed stand, acting along with the long distance transfer of strains most probably via birds and/or humans. Thus, the Neusiedler See may serve as a bioreactor for the appearance of new strains with new (pathogenic) properties.
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Affiliation(s)
- Carina Pretzer
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Vienna, Austria.,Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria
| | - Irina S Druzhinina
- Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria
| | - Carmen Amaro
- ERI BioTecMed University of Valencia, Valencia, Spain
| | - Eva Benediktsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | | | - Franciska M Schets
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Andreas H Farnleitner
- Vienna University of Technology, Institute of Chemical Engineering, Vienna, Austria.,Interuniversity Cooperation Centre for Water & Health, (www.waterandhealth.at), Vienna, Austria
| | - Alexander K T Kirschner
- Medical University Vienna, Institute for Hygiene and Applied Immunology, Vienna, Austria.,Interuniversity Cooperation Centre for Water & Health, (www.waterandhealth.at), Vienna, Austria
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99
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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100
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Pham LD, Phung NHT, Le NTD, Vo TQ. Economic report on the cost of dengue fever in Vietnam: case of a provincial hospital. CLINICOECONOMICS AND OUTCOMES RESEARCH 2016; 9:1-8. [PMID: 28031723 PMCID: PMC5179203 DOI: 10.2147/ceor.s124023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Dengue is a mosquito-borne viral illness with the world's fastest rate of infection. In 2014, Vietnam had recorded 43,000 cases in 53 provinces, with 28 deaths. MATERIALS AND METHODS A 6-month cross-sectional study was conducted from September 2015 to March 2016 at Cu Chi General Hospital. Cost of illness in this study was estimated under the incidence-based approach from the societal perspective. RESULTS The average cost per case was US$139.3±$61.7. The average cost per child was higher than per adult, but not significant ($151.0±$63.5 and $132.7±$59.9, respectively; P=0.068). Meanwhile, 50.2% of the total cost was contributed by the cost of hospital bed. According to the sensitivity analysis, if both the costs of the hospital bed and ultrasound were reduced by 10%, the total treatment cost of dengue fever would fall by 5% and 1.6%, respectively. CONCLUSION This study is expected to be the basis for investment-plan formulation and fund allocation for the treatment and prevention of dengue. In an attempt to examine the entire socioeconomic encumbrance caused by the dengue virus, a larger scale study targeting both dengue and dengue hemorrhagic fever needs to be conducted in several hospitals.
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Affiliation(s)
- Luyen Dinh Pham
- Department of Pharmacy Administration, Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nhat Huy Tran Phung
- Department of Pharmacy Administration, Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nguyen Tu Dang Le
- Department of Pharmacy Administration, Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Trung Quang Vo
- Department of Pharmacy Administration, Faculty of Pharmacy, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
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