1
|
Phadungsombat J, Nakayama EE, Shioda T. Unraveling Dengue Virus Diversity in Asia: An Epidemiological Study through Genetic Sequences and Phylogenetic Analysis. Viruses 2024; 16:1046. [PMID: 39066210 PMCID: PMC11281397 DOI: 10.3390/v16071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Dengue virus (DENV) is the causative agent of dengue. Although most infected individuals are asymptomatic or present with only mild symptoms, severe manifestations could potentially devastate human populations in tropical and subtropical regions. In hyperendemic regions such as South Asia and Southeast Asia (SEA), all four DENV serotypes (DENV-1, DENV-2, DENV-3, and DENV-4) have been prevalent for several decades. Each DENV serotype is further divided into multiple genotypes, reflecting the extensive diversity of DENV. Historically, specific DENV genotypes were associated with particular geographical distributions within endemic regions. However, this epidemiological pattern has changed due to urbanization, globalization, and climate change. This review comprehensively traces the historical and recent genetic epidemiology of DENV in Asia from the first time DENV was identified in the 1950s to the present. We analyzed envelope sequences from a database covering 16 endemic countries across three distinct geographic regions in Asia. These countries included Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka from South Asia; Cambodia, Laos, Myanmar, Thailand, and Vietnam from Mainland SEA; and Indonesia, the Philippines, Malaysia, and Singapore from Maritime SEA. Additionally, we describe the phylogenetic relationships among DENV genotypes within each serotype, along with their geographic distribution, to enhance the understanding of DENV dynamics.
Collapse
Affiliation(s)
| | | | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (J.P.); (E.E.N.)
| |
Collapse
|
2
|
Dos Santos MAM, Pavon JAR, Dias LS, Viniski AE, Souza CLC, de Oliveira EC, de Azevedo VC, da Silva SP, Cruz ACR, Medeiros DBDA, Nunes MRT, Slhessarenko RD. Dengue virus serotype 2 genotype III evolution during the 2019 outbreak in Mato Grosso, Midwestern Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105487. [PMID: 37544570 DOI: 10.1016/j.meegid.2023.105487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/08/2023]
Abstract
DENV-2 was the main responsible for a 70% increase in dengue incidence in Brazil during 2019. That year, our metagenomic study by Illumina NextSeq on serum samples from acute febrile patients (n = 92) with suspected arbovirus infection, sampled in 22 cities of the state of Mato Grosso (MT), in the middle west of Brazil, revealed eight complete genomes and two near-complete sequences of DENV-2 genotype III, one Human parvovirus B19 genotype I (5,391 nt) and one Coxsackievirus A6 lineage D (4,514 nt). These DENV-2 sequences share the aminoacidic identities of BR4 lineage on E protein domains I, II and III, and were included in a clade with sequences of the same lineage circulating in the southeast of Brazil in the same year. Nevertheless, 11/34 non-synonymous mutations are unique to three strains inthis study, distributed in the E (n = 6), NS3 (n = 2) and NS5 (n = 3) proteins. Other 14 aa changes on C (n = 1), E (n = 3), NS1 (n = 2), NS2A (n = 1) and NS5 (n = 7) were first reported in a genotype III lineage, having been already reported only in other DENV-2 genotypes. All 10 sequences have mutations in the NS5 protein (14 different aa changes). Nine E protein aa changes found in two sequences, six of which are unique, are in the ectodomain; where the E:M272T change is on the hinge of the E protein at domain II, in a region critical for the anchoring to the host cell receptor. The NS5:G81R mutation, in the methyltransferase domain, was found in one strain of this study. Altogether, these data points to an important evolution of DENV-2 genotype III lineage BR4 during this outbreak in 2019 in MT. Genomic surveillance is essential to detect virus etiology and evolution, possibly related to immune evasion and viral fitness changes leading to future novel outbreaks.
Collapse
Affiliation(s)
- Marcelo Adriano Mendes Dos Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil; Faculdade de Medicina, Universidade do Estado de Mato Grosso, Cáceres, MT, Brazil
| | - Janeth Aracely Ramirez Pavon
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Lucas Silva Dias
- Curso de Graduação em Medicina, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Ana Elisa Viniski
- Laboratório Central de Saúde Pública do Estado de Mato Grosso, Secretaria de Estado da Saúde, Cuiabá, MT, Brazil
| | - Claudio Luis Campos Souza
- Laboratório Central de Saúde Pública do Estado de Mato Grosso, Secretaria de Estado da Saúde, Cuiabá, MT, Brazil
| | - Elaine Cristina de Oliveira
- Laboratório Central de Saúde Pública do Estado de Mato Grosso, Secretaria de Estado da Saúde, Cuiabá, MT, Brazil
| | - Vergínia Correa de Azevedo
- Laboratório Central de Saúde Pública do Estado de Mato Grosso, Secretaria de Estado da Saúde, Cuiabá, MT, Brazil
| | | | | | | | | | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
| |
Collapse
|
3
|
Wardhani P, Yohan B, Tanzilia M, Sunari EP, Wrahatnala BJ, Hakim FKN, Rohman A, Husada D, Hayati RF, Santoso MS, Sievers JTO, Aryati A, Sasmono RT. Genetic characterization of dengue virus 4 complete genomes from East Java, Indonesia. Virus Genes 2023; 59:36-44. [PMID: 36266496 PMCID: PMC9584228 DOI: 10.1007/s11262-022-01942-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/05/2022] [Indexed: 01/13/2023]
Abstract
Dengue is an endemic arboviral disease with continuous transmission in Indonesia for more than five decades. A recent outbreak in Jember, East Java province, demonstrated the predominance of DENV-4, a serotype known for its low global spread and limited transmission. While epidemiological factors such as new serotype introduction and lacking herd immunity may explain its predominance, viral factors may also contribute. Using next-generation sequencing, we generated 13 representative complete genomes of DENV-4 responsible for the outbreak. Phylogenetic and evolutionary analyses on complete genomes were performed to understand the spatial and temporal dynamics of the viruses. Further analyses were done to study amino acid variations in DENV genes, as well as the potential events of recombination and selection pressure within the genomes. We revealed the DENV-4 genetic factors that may lead to its predominance in the 2019 Jember dengue outbreak. A combination of selection pressure and mutational genetic changes may contribute to the DENV-4 predominance in East Java, Indonesia. The possible intra-serotype recombination events involving the non-structural protein 5 (NS5) gene were also observed. Altogether, these genetic factors may act as additional factors behind the complex dengue outbreak mechanism.
Collapse
Affiliation(s)
- Puspa Wardhani
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XInstitute for Tropical Diseases, Universitas Airlangga, Surabaya, 60115 Indonesia ,Dr. Soetomo General Academic Hospital, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XPost Graduate School, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Benediktus Yohan
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia ,grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Mayfanny Tanzilia
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Eka Putri Sunari
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Billy J. Wrahatnala
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Faradila K. N. Hakim
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Ali Rohman
- grid.440745.60000 0001 0152 762XDepartment of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, 60115 Indonesia
| | - Dominicus Husada
- Dr. Soetomo General Academic Hospital, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XDepartment of Pediatric, Faculty of Medicine Universitas Airlangga, Surabaya, 60286 Indonesia
| | - Rahma F. Hayati
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| | - Marsha S. Santoso
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| | - Justus T. O. Sievers
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| | - A. Aryati
- grid.440745.60000 0001 0152 762XDepartment of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Surabaya, 60286 Indonesia ,grid.440745.60000 0001 0152 762XInstitute for Tropical Diseases, Universitas Airlangga, Surabaya, 60115 Indonesia ,Dr. Soetomo General Academic Hospital, Surabaya, 60286 Indonesia
| | - R. Tedjo Sasmono
- Eijkman Research Center for Molecular Biology, National Agency for Research and Innovation, Jakarta, 10430 Indonesia
| |
Collapse
|
4
|
Full-genome sequencing and analysis of DENV-3 serotype isolated from Yemen. J Infect Public Health 2021; 14:803-810. [PMID: 34044250 DOI: 10.1016/j.jiph.2021.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/24/2021] [Accepted: 03/28/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Dengue virus causes the dengue fever as well as hemorrhagic fever in tropical and sub-tropical countries. It is now endemic in most parts of the South East Asia. Full-genome information of dengue virus 3 is not available from Yemen. METHODS In this study, the dengue virus 3 was detected by diagnostic tools like serology and RT-PCR in the samples isolated from a patient in Yemen. The full-genome was sequenced, and the identity, phylogenetic relationship and recombination analysis was performed by using BioEdit, MEGA X and RDP4 softwares. RESULTS The full-genome of the Yemen isolate was found to be 10,643 nt long with 3390 amino acids. The Yemen dengue virus 3 isolate showed the sequence similarity (98.5-92.4%) with dengue virus 3 isolates from China, Pakistan, India and Bangladesh respectively. The significant non-synonymous substitutions of amino acid in Yemen isolate were observed with selected isolates. The phylogenetic tree of Yemen isolate formed a unique clade within genotype III and sub-clade into lineage III. The Dengue virus isolate from Jeddah formed separated cluster with lineage IV. CONCLUSIONS This reveals the unique genetic variability among DENV-3 serotypes from Jeddah and earlier reported isolates from other regions.
Collapse
|
5
|
Vasey B, Shankar AH, Herrera BB, Becerra A, Xhaja K, Echenagucia M, Machado SR, Caicedo D, Miller J, Amedeo P, Naumova EN, Bosch I. Multivariate time-series analysis of biomarkers from a dengue cohort offers new approaches for diagnosis and prognosis. PLoS Negl Trop Dis 2020; 14:e0008199. [PMID: 32544159 PMCID: PMC7380649 DOI: 10.1371/journal.pntd.0008199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 07/24/2020] [Accepted: 03/05/2020] [Indexed: 11/18/2022] Open
Abstract
Dengue is a major public health problem worldwide with distinct clinical manifestations: an acute presentation (dengue fever, DF) similar to other febrile illnesses (OFI) and a more severe, life-threatening form (severe dengue, SD). Due to nonspecific clinical presentation during the early phase of dengue infection, differentiating DF from OFI has remained a challenge, and current methods to determine severity of dengue remain poor early predictors. We present a prospective clinical cohort study conducted in Caracas, Venezuela from 2001-2005, designed to determine whether clinical and hematological parameters could distinguish DF from OFI, and identify early prognostic biomarkers of SD. From 204 enrolled suspected dengue patients, there were 111 confirmed dengue cases. Piecewise mixed effects regression and nonparametric statistics were used to analyze longitudinal records. Decreased serum albumin and fibrinogen along with increased D-dimer, thrombin-antithrombin complex, activated partial thromboplastin time and thrombin time were prognostic of SD on the day of defervescence. In the febrile phase, the day-to-day rates of change in serum albumin and fibrinogen concentration, along with platelet counts, were significantly decreased in dengue patients compared to OFI, while the day-to-day rates of change of lymphocytes (%) and thrombin time were increased. In dengue patients, the absolute lymphocytes to neutrophils ratio showed specific temporal increase, enabling classification of dengue patients entering the critical phase with an area under the ROC curve of 0.79. Secondary dengue patients had elongation of Thrombin time compared to primary cases while the D-dimer formation (fibrinolysis marker) remained always lower for secondary compared to primary cases. Based on partial analysis of 31 viral complete genomes, a high frequency of C-to-T transitions located at the third codon position was observed, suggesting deamination events with five major hot spots of amino acid polymorphic sites outside in non-structural proteins. No association of severe outcome was statistically significant for any of the five major polymorphic sites found. This study offers an improved understanding of dengue hemostasis and a novel way of approaching dengue diagnosis and disease prognosis using piecewise mixed effect regression modeling. It also suggests that a better discrimination of the day of disease can improve the diagnostic and prognostic classification power of clinical variables using ROC curve analysis. The piecewise mixed effect regression model corroborated key early clinical determinants of disease, and offers a time-series approach for future vaccine and pathogenesis clinical studies.
Collapse
Affiliation(s)
- Baptiste Vasey
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Anuraj H. Shankar
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Bobby Brooke Herrera
- E25Bio Inc., Cambridge, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Aniuska Becerra
- Center for Infectious Diseases and Vaccine Research, University of Massachusetts, Worcester, Massachusetts, United States of America
| | - Kris Xhaja
- Center for Infectious Diseases and Vaccine Research, University of Massachusetts, Worcester, Massachusetts, United States of America
| | - Marion Echenagucia
- Centro Nacional de Hemofilia at Banco Municipal de Sangre, Universidad Central de Venezuela, Caracas, Venezuela
| | - Sara R. Machado
- Department of Health Policy, London School of Economics, London, United Kingdom
| | | | - John Miller
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Paolo Amedeo
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Elena N. Naumova
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, United States of America
| | - Irene Bosch
- E25Bio Inc., Cambridge, Massachusetts, United States of America
- Department of Medicine, Mount Sinai School of Medicine, New York, New York, United States of America
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Norma Blumenfeld deBosch
- Center for Infectious Diseases and Vaccine Research, University of Massachusetts, Worcester, Massachusetts, United States of America
| |
Collapse
|
6
|
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: 15] [Impact Index Per Article: 3.0] [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.
Collapse
|
7
|
Waman VP, Kale MM, Kulkarni-Kale U. Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study. INFECTION GENETICS AND EVOLUTION 2017; 49:234-240. [PMID: 28126562 DOI: 10.1016/j.meegid.2017.01.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/14/2017] [Accepted: 01/21/2017] [Indexed: 11/29/2022]
Abstract
Dengue virus serotype 3 (DENV-3), one of the four serotypes of Dengue viruses, is geographically diverse. There are five distinct genotypes (I-V) of DENV-3. Emerging strains and lineages of DENV-3 are increasingly being reported. Availability of genomic data for DENV-3 strains provides opportunity to study its population structure. Complete genome sequences are available for 860 strains of four genotypes (I, II, III and V) isolated worldwide and were analyzed using population genetics and evolutionary approaches to map landscape of genomic diversity. DENV-3 population is observed to be stratified into five major subpopulations. Genotype I and II formed independent subpopulations while genotype III is subdivided into three subpopulations (GIII-a, GIII-b and GIII-c) and is therefore heterogeneous. Genotypes I, II and GIII-a subpopulations comprise of Asian strains whereas GIII-c comprises of American strains. GIII-b subpopulation includes mainly of American strains along with a few strains from Sri Lanka. Genetic admixture is predominantly observed in Sri Lankan strains of genotype III and all strains of genotype V. Inter-genotype recombination was observed to occur in non-structural region of several Asian strains whereas extent of recombination was limited in American strains. Significant positive selection was found to be operational on all genes and observed to be the main driving force of genetic diversity. Positive selection was strongly operational on the branches leading to Asian genotypes and helped to delineate the genetic differences between Asian and American lineages. Thus, inter-genotype recombination, migration and adaptive evolution are the major determinants of evolution of DENV-3.
Collapse
Affiliation(s)
- Vaishali P Waman
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India
| | - Mohan M Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune 411007, Maharashtra, India.
| |
Collapse
|
8
|
Ramos-Castañeda J, Barreto dos Santos F, Martínez-Vega R, Galvão de Araujo JM, Joint G, Sarti E. Dengue in Latin America: Systematic Review of Molecular Epidemiological Trends. PLoS Negl Trop Dis 2017; 11:e0005224. [PMID: 28068335 PMCID: PMC5221820 DOI: 10.1371/journal.pntd.0005224] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 12/01/2016] [Indexed: 01/02/2023] Open
Abstract
Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed. A total of 396 relevant citations were identified, 57 of which fulfilled the inclusion criteria. All four dengue virus serotypes were present and co-circulated in many countries over the review period (with the predominance of individual serotypes varying by country and year). The number of countries in which more than one serotype circulated steadily increased during the period under review. Molecular epidemiology data were found for Argentina, Bolivia, Brazil, the Caribbean region, Colombia, Ecuador, Mexico and Central America, Paraguay, Peru and Venezuela. Distinct lineages with different dynamics were found in each country, with co-existence, extinction and replacement of lineages occurring over the review period. Despite some gaps in the literature limiting the possibility for comparison, our review has described the molecular epidemiological trends of dengue infection. However, several gaps in molecular epidemiological information across Latin America and the Caribbean were identified that provide avenues for future research; in particular, sequence determination of the dengue virus genome is important for more precise phylogenetic classification and correlation with clinical outcome and disease severity. The wide distribution of the mosquito vector and the co-circulation of multiple dengue virus serotypes has led to increases in the incidence of dengue in the Americas, where it is a major public health concern. Identifying molecular epidemiological trends may help to identify the reasons for the re-emergence of dengue across Latin America and the Caribbean, and, in turn, enable disease control and management. We conducted this review using well defined methods to search for and identify relevant research according to predetermined inclusion criteria. The objective was to obtain a clearer understanding of changes occurring within dengue serotypes that have resulted in substantial genetic diversity and the emergence of endemic and epidemic strains in different parts of the region. There remain fundamental gaps in our understanding of the epidemiological and evolutionary dynamics of dengue and its relation with disease, and it is not possible to correlate accurately spatial or temporal trends in disease epidemiology, disease severity, or the genetic diversity of DENV. It is important to maintain comprehensive epidemiological surveillance throughout the region (including sequencing of viral strains) to detect new DENV lineages and to understand the regional patterns of DENV dissemination.
Collapse
Affiliation(s)
- José Ramos-Castañeda
- Instituto Nacional de Salud Publica, Centro de Investigaciones sobre Enfermedades Infecciosas, Morelos, Mexico
| | - Flavia Barreto dos Santos
- Laboratório de Imunologia Viral, Instituto Oswaldo Cruz/ Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Josélio Maria Galvão de Araujo
- Laboratório de Biologia Molecular de Doenças Infecciosas e do Câncer, Departamento de Microbiologia e Parasitologia; Instituto de Medicina Tropical do Rio Grande do Norte; Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Graham Joint
- Synercom Ltd, Macclesfield, Cheshire, United Kingdom
| | | |
Collapse
|
9
|
Hapuarachchi HC, Koo C, Kek R, Xu H, Lai YL, Liu L, Kok SY, Shi Y, Chuen RLT, Lee KS, Maurer-Stroh S, Ng LC. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission. Sci Rep 2016; 6:22592. [PMID: 26940650 PMCID: PMC4778070 DOI: 10.1038/srep22592] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/17/2016] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013–2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.
Collapse
Affiliation(s)
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Relus Kek
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Helen Xu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Lilac Liu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Suet Yheng Kok
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yuan Shi
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Raphael Lee Tze Chuen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671
| | - Kim-Sung Lee
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Block 83, #04-00, 535 Clementi Road, Singapore 599489
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551.,National Public Health Laboratory (NPHL), Ministry of Health (MOH), 3 Biopolis Drive, #05-14 to 16, Synapse, Singapore 138623
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
| |
Collapse
|
10
|
Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes. Virology 2013; 447:45-51. [PMID: 24210098 DOI: 10.1016/j.virol.2013.08.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/18/2013] [Accepted: 08/19/2013] [Indexed: 12/25/2022]
Abstract
The Virus Pathogen Resource (ViPR; www.viprbrc.org) and Influenza Research Database (IRD; www.fludb.org) have developed a metadata-driven Comparative Analysis Tool for Sequences (meta-CATS), which performs statistical comparative analyses of nucleotide and amino acid sequence data to identify correlations between sequence variations and virus attributes (metadata). Meta-CATS guides users through: selecting a set of nucleotide or protein sequences; dividing them into multiple groups based on any associated metadata attribute (e.g. isolation location, host species); performing a statistical test at each aligned position; and identifying all residues that significantly differ between the groups. As proofs of concept, we have used meta-CATS to identify sequence biomarkers associated with dengue viruses isolated from different hemispheres, and to identify variations in the NS1 protein that are unique to each of the 4 dengue serotypes. Meta-CATS is made freely available to virology researchers to identify genotype-phenotype correlations for development of improved vaccines, diagnostics, and therapeutics.
Collapse
|
11
|
Bhattacharya MK, Maitra S, Ganguly A, Bhattacharya A, Sinha A. Dengue: a growing menace -- a snapshot of recent facts, figures & remedies. INTERNATIONAL JOURNAL OF BIOMEDICAL SCIENCE : IJBS 2013; 9:61-7. [PMID: 23847455 PMCID: PMC3708269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 04/01/2013] [Indexed: 11/21/2022]
Abstract
Dengue is specially owing to inadequate water supply and poor solid waste management , which are favorable for multiplication of the main vectors including the Aedes ageypti coupled with lack of proven anti viral therapy and no proven efficient vaccine .there are many cases of both dengue shock syndrome and dengue haemmorhagic fever making it a major public health burden sending ominous signal resulting both rising morbidity & mortality, deleterious effect on DALY [disability adjusted life year] & QALY [quality adjusted life year] & though it affect all section of society ,still it affect the poor & underprivileged section more, thereby growing menace in public health in general & in developing countries in particular.
Collapse
Affiliation(s)
| | - S. Maitra
- National Institute of Cholera & Enteric Disease, Kolkata
| | | | | | | |
Collapse
|
12
|
Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG. Unsupervised genome-wide recognition of local relationship patterns. BMC Genomics 2013; 14:347. [PMID: 23706020 PMCID: PMC3669000 DOI: 10.1186/1471-2164-14-347] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 05/08/2013] [Indexed: 12/05/2022] Open
Abstract
Background Phenomena such as incomplete lineage sorting, horizontal gene transfer, gene duplication and subsequent sub- and neo-functionalisation can result in distinct local phylogenetic relationships that are discordant with species phylogeny. In order to assess the possible biological roles for these subdivisions, they must first be identified and characterised, preferably on a large scale and in an automated fashion. Results We developed Saguaro, a combination of a Hidden Markov Model (HMM) and a Self Organising Map (SOM), to characterise local phylogenetic relationships among aligned sequences using cacti, matrices of pair-wise distance measures. While the HMM determines the genomic boundaries from aligned sequences, the SOM hypothesises new cacti in an unsupervised and iterative fashion based on the regions that were modelled least well by existing cacti. After testing the software on simulated data, we demonstrate the utility of Saguaro by testing two different data sets: (i) 181 Dengue virus strains, and (ii) 5 primate genomes. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to incomplete lineage sorting in the second dataset. Intriguingly for the primate data, Saguaro also classified an additional ~3% of the genome as most incompatible with the expected species phylogeny. A substantial fraction of these regions was found to overlap genes associated with both the innate and adaptive immune systems. Conclusions Saguaro detects distinct cacti describing local phylogenetic relationships without requiring any a priori hypotheses. We have successfully demonstrated Saguaro’s utility with two contrasting data sets, one containing many members with short sequences (Dengue viral strains: n = 181, genome size = 10,700 nt), and the other with few members but complex genomes (related primate species: n = 5, genome size = 3 Gb), suggesting that the software is applicable to a wide variety of experimental populations. Saguaro is written in C++, runs on the Linux operating system, and can be downloaded from http://saguarogw.sourceforge.net/.
Collapse
Affiliation(s)
- Neda Zamani
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Villabona-Arenas CJ, Mondini A, Bosch I, Schimitt D, Calzavara-Silva CE, de A Zanotto PM, Nogueira ML. Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006-2007. PLoS One 2013; 8:e63496. [PMID: 23667626 PMCID: PMC3646734 DOI: 10.1371/journal.pone.0063496] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022] Open
Abstract
Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.
Collapse
Affiliation(s)
- Christian Julian Villabona-Arenas
- Laboratório de Evolução Molecular e Bioinformática (LEMB), Departamento de Microbiologia, Instituto de Ciências Biomédicas. Universidade de São Paulo, São Paulo, Brazil
| | - Adriano Mondini
- Laboratório de Saúde Pública. Departamento de Ciências Biológicas. Faculdade de Ciências Farmacêuticas - Universidade Estadual Paulista “Júlio de Mesquita Filho” Araraquara/SP, Brazil
| | - Irene Bosch
- Division of Heath Science and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Diane Schimitt
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Carlos E. Calzavara-Silva
- Laboratório de Imunologia Celular e Molecular (LICM), Centro de Pesquisas Rene Rachou (CPqRR), Fundação Oswaldo Cruz (Fiocruz), Belo Horizonte, MG, Brazil
| | - Paolo M. de A Zanotto
- Laboratório de Evolução Molecular e Bioinformática (LEMB), Departamento de Microbiologia, Instituto de Ciências Biomédicas. Universidade de São Paulo, São Paulo, Brazil
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| |
Collapse
|
14
|
Drumond BP, Mondini A, Schmidt DJ, Bronzoni RVDM, Bosch I, Nogueira ML. Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization. PLoS One 2013; 8:e59422. [PMID: 23533624 PMCID: PMC3606110 DOI: 10.1371/journal.pone.0059422] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/14/2013] [Indexed: 01/05/2023] Open
Abstract
The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80′s. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998–2000) and BR3 (2003–05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.
Collapse
Affiliation(s)
- Betânia Paiva Drumond
- Laboratório de Virologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- * E-mail: (BPD); (MLN)
| | - Adriano Mondini
- Laboratório de Saúde Pública, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, Araraquara, São Paulo, Brazil
| | - Diane J. Schmidt
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | | | - Irene Bosch
- Genome Resources in Dengue Consortium, Massachusetts Institute of Technology. Cambridge, Massachusetts, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
- * E-mail: (BPD); (MLN)
| |
Collapse
|
15
|
Drumond BP, Mondini A, Schmidt DJ, Bosch I, Nogueira ML. Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement. Arch Virol 2012; 157:2061-73. [DOI: 10.1007/s00705-012-1393-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 05/18/2012] [Indexed: 11/25/2022]
|
16
|
Santiago GA, McElroy-Horne K, Lennon NJ, Santiago LM, Birren BW, Henn MR, Muñoz-Jordán JL. Reemergence and decline of dengue virus serotype 3 in Puerto Rico. J Infect Dis 2012; 206:893-901. [PMID: 22740715 DOI: 10.1093/infdis/jis426] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The dengue virus serotype 3 (DENV-3) Indian subcontinent strain emerged in Puerto Rico in 1998 after a 21-year absence. The rapid expansion of DENV-3 on the island correlated with the withdrawal of the other serotypes for 7 years. The DENV-3 prevalence declined in 2008 and remains undetected. METHODS We sequenced complete genomes of 92 DENV-3 clinical isolates to characterize the molecular evolution and phylogeography throughout 10 years of continued sampling (1998–2007). RESULTS We documented 8 distinct lineages that emerged simultaneously and evolved independently. Two of the 8 lineages were highly associated with transient introductions of foreign viruses, and 2 of the 3 endemic lineages covered the entire study period. We found evidence of temporal-geographical clustering only within the 3 endemic lineages. The phylogeography analysis combined with serotype-specific incidence data showed that transmission of a DENV serotype in a given location and time is usually correlated with the absence of the other serotype. CONCLUSIONS Our study shows the cotransmission of DENV-3 lineages through a complex dissemination pattern dissimilar to the evolutionary dynamics of the other serotypes in the island. High virus genetic diversity and a large naive population were underlying factors in the expansion and collapse of DENV-3 in Puerto Rico.
Collapse
Affiliation(s)
- Gilberto A Santiago
- Division of Vector-borne Infectious Diseases, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | | | | | | | | | | | | |
Collapse
|
17
|
Dugan VG, Saira K, Ghedin E. Large-scale sequencing and the natural history of model human RNA viruses. Future Virol 2012; 7:563-573. [PMID: 23682295 DOI: 10.2217/fvl.12.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA virus exploration within the field of medical virology has greatly benefited from technological developments in genomics, deepening our understanding of viral dynamics and emergence. Large-scale first-generation technology sequencing projects have expedited molecular epidemiology studies at an unprecedented scale for two pathogenic RNA viruses chosen as models: influenza A virus and dengue. Next-generation sequencing approaches are now leading to a more in-depth analysis of virus genetic diversity, which is greater for RNA than DNA viruses because of high replication rates and the absence of proofreading activity of the RNA-dependent RNA polymerase. In the field of virus discovery, technological advancements and metagenomic approaches are expanding the catalogs of novel viruses by facilitating our probing into the RNA virus world.
Collapse
Affiliation(s)
- Vivien G Dugan
- Viral Genomics, J Craig Venter Institute, Rockville, MD, USA
| | | | | |
Collapse
|
18
|
Rodriguez-Roche R, Villegas E, Cook S, Poh Kim PAW, Hinojosa Y, Rosario D, Villalobos I, Bendezu H, Hibberd ML, Guzman MG. Population structure of the dengue viruses, Aragua, Venezuela, 2006-2007. Insights into dengue evolution under hyperendemic transmission. INFECTION GENETICS AND EVOLUTION 2011; 12:332-44. [PMID: 22197765 PMCID: PMC3919160 DOI: 10.1016/j.meegid.2011.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/08/2011] [Accepted: 12/10/2011] [Indexed: 12/16/2022]
Abstract
During the past three decades there has been a notable increase in dengue disease severity in Venezuela. Nevertheless, the population structure of the viruses being transmitted in this country is not well understood. Here, we present a molecular epidemiological study on dengue viruses (DENV) circulating in Aragua State, Venezuela during 2006-2007. Twenty-one DENV full-length genomes representing all of the four serotypes were amplified and sequenced directly from the serum samples. Notably, only DENV-2 was associated with severe disease. Phylogenetic trees constructed using Bayesian methods indicated that only one genotype was circulating for each serotype. However, extensive viral genetic diversity was found in DENV isolated from the same area during the same period, indicating significant in situ evolution since the introduction of these genotypes. Collectively, the results suggest that the non-structural (NS) proteins may play an important role in DENV evolution, particularly NS1, NS2A and NS4B proteins. The phylogenetic data provide evidence to suggest that multiple introductions of DENV have occurred from the Latin American region into Venezuela and vice versa. The implications of the significant viral genetic diversity generated during hyperendemic transmission, particularly in NS protein are discussed and considered in the context of future development and use of human monoclonal antibodies as antivirals and tetravalent vaccines.
Collapse
|