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Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, de Oliveira T, Grubaugh ND. A new lineage nomenclature to aid genomic surveillance of dengue virus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.16.24307504. [PMID: 38798319 PMCID: PMC11118645 DOI: 10.1101/2024.05.16.24307504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador, Brazil
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Robert Gifford
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, UK
| | - Vi Thuy Tran
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tuyen Huynh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Sophie Yacoub
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Idrissa Dieng
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mignane Ndiaye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Diamilatou Balde
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Moussa M Diagne
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Faye
- Arboviruses and Haemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Richard Salvato
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference, Hamburg, Germany
- National Reference Center for Tropical Infectious Diseases. Bernhard, Hamburg, Germany
| | - Tatiana S Gregianini
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Fernanda M S Godinho
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (CDCT/CEVS/SES-RS), Rio Grande do Sul, Brazil
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mariana Leguia
- Genomics Laboratory, Pontificia Universidad Católica del Peru, Lima, Peru
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Gaspary Mwanyika
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Applied Sciences, Mbeya University of Science and Technology (MUST), Mbeya, Tanzania
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Italy
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Luiz C J Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Minas Gerais, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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2
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Zini N, Ávila MHT, Cezarotti NM, Parra MCP, Banho CA, Sacchetto L, Negri AF, Araújo E, Bittar C, Milhin BHGDA, Miranda Hernandes V, Dutra KR, Trigo LA, Cecílio da Rocha L, Alves da Silva R, Celestino Dutra da Silva G, Fernanda Pereira Dos Santos T, de Carvalho Marques B, Lopes Dos Santos A, Augusto MT, Mistrão NFB, Ribeiro MR, Pinheiro TM, Maria Izabel Lopes Dos Santos T, Avilla CMS, Bernardi V, Freitas C, Gandolfi FDA, Ferraz Júnior HC, Perim GC, Gomes MC, Garcia PHC, Rocha RS, Galvão TM, Fávaro EA, Scamardi SN, Rogovski KS, Peixoto RL, Benfatti L, Cruz LT, Chama PPDF, Oliveira MT, Watanabe ASA, Terzian ACB, de Freitas Versiani A, Dibo MR, Chiaravalotti-Neto F, Weaver SC, Estofolete CF, Vasilakis N, Nogueira ML. Cryptic circulation of chikungunya virus in São Jose do Rio Preto, Brazil, 2015-2019. PLoS Negl Trop Dis 2024; 18:e0012013. [PMID: 38484018 DOI: 10.1371/journal.pntd.0012013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/26/2024] [Accepted: 02/19/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Chikungunya virus (CHIKV) has spread across Brazil with varying incidence rates depending on the affected areas. Due to cocirculation of arboviruses and overlapping disease symptoms, CHIKV infection may be underdiagnosed. To understand the lack of CHIKV epidemics in São José do Rio Preto (SJdRP), São Paulo (SP), Brazil, we evaluated viral circulation by investigating anti-CHIKV IgG seroconversion in a prospective study of asymptomatic individuals and detecting anti-CHIKV IgM in individuals suspected of dengue infection, as well as CHIKV presence in Aedes mosquitoes. The opportunity to assess two different groups (symptomatic and asymptomatic) exposed at the same geographic region aimed to broaden the possibility of identifying the viral circulation, which had been previously considered absent. METHODOLOGY/PRINCIPAL FINDINGS Based on a prospective population study model and demographic characteristics (sex and age), we analyzed the anti-CHIKV IgG seroconversion rate in 341 subjects by ELISA over four years. The seroprevalence increased from 0.35% in the first year to 2.3% after 3 years of follow-up. Additionally, we investigated 497 samples from a blood panel collected from dengue-suspected individuals during the 2019 dengue outbreak in SJdRP. In total, 4.4% were positive for anti-CHIKV IgM, and 8.6% were positive for IgG. To exclude alphavirus cross-reactivity, we evaluated the presence of anti-Mayaro virus (MAYV) IgG by ELISA, and the positivity rate was 0.3% in the population study and 0.8% in the blood panel samples. In CHIKV and MAYV plaque reduction neutralization tests (PRNTs), the positivity rate for CHIKV-neutralizing antibodies in these ELISA-positive samples was 46.7%, while no MAYV-neutralizing antibodies were detected. Genomic sequencing and phylogenetic analysis revealed CHIKV genotype ECSA in São José do Rio Preto, SP. Finally, mosquitoes collected to complement human surveillance revealed CHIKV positivity of 2.76% of A. aegypti and 9.09% of A. albopictus (although it was far less abundant than A. aegypti) by RT-qPCR. CONCLUSIONS/SIGNIFICANCE Our data suggest cryptic CHIKV circulation in SJdRP detected by continual active surveillance. These low levels, but increasing, of viral circulation highlight the possibility of CHIKV outbreaks, as there is a large naïve population. Improved knowledge of the epidemiological situation might aid in outbreaks prevention.
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Affiliation(s)
- Nathalia Zini
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Matheus Henrique Tavares Ávila
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Natalia Morbi Cezarotti
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Maisa Carla Pereira Parra
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Cecília Artico Banho
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Livia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Andreia Francesli Negri
- Vigilância Epidemiológica, Secretaria de Saúde de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Emerson Araújo
- Department of Strategic Coordination of Health Surveillance, Secretary of Health Surveillance, Brazilian Ministry of Health, Rio de Janeiro, Brazil
| | - Cintia Bittar
- Laboratório de Estudos Genômicos, Instituto de Biociências, Letras & Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, São Paulo, Brazil
| | - Bruno Henrique Gonçalves de Aguiar Milhin
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Victor Miranda Hernandes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Karina Rocha Dutra
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Leonardo Agopian Trigo
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Leonardo Cecílio da Rocha
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Rafael Alves da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Gislaine Celestino Dutra da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Tamires Fernanda Pereira Dos Santos
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Beatriz de Carvalho Marques
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Andresa Lopes Dos Santos
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Marcos Tayar Augusto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Natalia Franco Bueno Mistrão
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Milene Rocha Ribeiro
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Tauyne Menegaldo Pinheiro
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Thayza Maria Izabel Lopes Dos Santos
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Clarita Maria Secco Avilla
- Laboratório de Estudos Genômicos, Instituto de Biociências, Letras & Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto, São Paulo, Brazil
| | - Victoria Bernardi
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Caroline Freitas
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Flora de Andrade Gandolfi
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Hélio Correa Ferraz Júnior
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Gabriela Camilotti Perim
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Mirella Cezare Gomes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Henrique Carrilho Garcia
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Rodrigo Sborghi Rocha
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Tayna Manfrin Galvão
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Eliane Aparecida Fávaro
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Samuel Noah Scamardi
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Karen Sanmartin Rogovski
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Renan Luiz Peixoto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | - Luiza Benfatti
- Laboratório de Investigação de Microrganismos, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
| | | | | | - Mânlio Tasso Oliveira
- Laboratório de Retrovirologia, Departamento de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Aripuanã Sakurada Aranha Watanabe
- Instituto de Ciências Biológicas, Departamento de Parasitologia e Microbiologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Ana Carolina Bernardes Terzian
- Laboratório de Imunologia Celular e Molecular, Instituto René Rachou, Fundação Osvaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Alice de Freitas Versiani
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Margareth Regina Dibo
- Laboratório de Entomologia, Superintendência de Controle de Endemias, São Paulo, Brazil
| | | | - Scott Cameron Weaver
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Cassia Fernanda Estofolete
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
- Hospital de Base, FUNFARME, São José Do Rio Preto, São Paulo, Brazil
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mauricio Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, São Paulo, Brazil
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Hospital de Base, FUNFARME, São José Do Rio Preto, São Paulo, Brazil
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3
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Amorim MT, Naveca FG, Hernández LHA, da Paz TYB, da Silva de Oliveira CC, da Conceição Miranda Santos A, Queiroz ALN, Wanzeller ALM, da Silva EVP, da Silva FS, da Silva SP, Nunes BTD, Cruz ACR. Detection of a Multiple Circulation Event of Dengue Virus 2 Strains in the Northern Region of Brazil. Trop Med Infect Dis 2024; 9:17. [PMID: 38251214 PMCID: PMC10818346 DOI: 10.3390/tropicalmed9010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/10/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Dengue virus serotype 2 (DENV-2) is responsible for dengue epidemics on a global scale and is associated with severe cases of the disease. This study conducted a phylogenetic investigation of DENV-2 isolates from 2017 to 2021 originating from the northern states of Brazil. A total of 32 samples from DENV-2 isolates were analyzed, including 12 from Acre, 19 from Roraima, and one from Tocantins. Only one lineage of the Asian-American genotype and one lineage of the cosmopolitan genotype were observed: Lineage 1, Asian-American genotype (connection to Puerto Rico); Lineage 5, cosmopolitan genotype (connection to Peru). Our results provide important data regarding the study of DENV genotypes and lineage distribution and open up possibilities for probable introduction and dissemination routes.
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Affiliation(s)
- Murilo Tavares Amorim
- Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil;
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Felipe Gomes Naveca
- Laboratory of Infectious Diseases Ecology in Amazon, Leonidas and Maria Deane Institute, Fiocruz, Manaus 69057-070, Brazil;
- Arbovirus and Hemorrhagic Virus Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Leonardo Henrique Almeida Hernández
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Thito Yan Bezerra da Paz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | | | - Alessandra da Conceição Miranda Santos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Alice Louize Nunes Queiroz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Ana Lucia Monteiro Wanzeller
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Eliana Vieira Pinto da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Fábio Silva da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Sandro Patroca da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Bruno Tardelli Diniz Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
| | - Ana Cecília Ribeiro Cruz
- Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil;
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ministry of Health, Ananindeua 67030-000, Brazil; (L.H.A.H.); (A.d.C.M.S.); (A.L.N.Q.); (A.L.M.W.); (E.V.P.d.S.); (S.P.d.S.); (B.T.D.N.)
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Prakash O, Verma AK, Paliwal A, Abbas F, Srivastava AK, Mishra VK, Radera S, Jain A. Circulating serotypes and genotypes of dengue virus in North India: An observational study. J Vector Borne Dis 2024; 61:117-122. [PMID: 38648413 DOI: 10.4103/0972-9062.392258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND OBJECTIVES This study reports observation on circulating serotypes and genotypes of Dengue Virus in North India. METHODS Serum samples were obtained from suspected cases of dengue referred to the virus diagnostic laboratory during 2014 to 2022. All samples were tested for anti-dengue virus IgM antibodies and NS1Ag by ELISA. NS1Ag positive samples were processed for serotyping and genotyping. RESULTS Total 41,476 dengue suspected cases were referred to the laboratory of which 12,292 (29.6%) tested positive. Anti-Dengue Virus IgM antibodies, NS1Ag, both IgM and NS1Ag, were positive in 7007 (57.4%); 3200 (26.0%) and 2085 (16.0%) cases respectively. Total 762 strains were serotyped during 9-year period. DENV-1, DENV-2, DENV-3 and DENV-4 serotypes were found in 79 (10.37%), 506 (66.40%), 151 (19.82%) and 26 (3.41%) cases respectively. DENV-1, DENV-2 and DENV-3 were in circulation throughout. Total 105 strains were genotyped. Genotype IV of DENV-1 serotype was circulating till 2014 which was later replaced by genotype V. A distinct seasonality with increase in number of cases in post-monsoon period was seen. INTERPRETATION CONCLUSION DENV-1, DENV-2 and DENV-3 were found to be in circulation in North India. Predominant serotype/genotype changed at times, but not at regular intervals.
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Affiliation(s)
- Om Prakash
- Department of Microbiology, King George's Medical University, Lucknow, India
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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.
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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.
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de Carvalho Marques B, Sacchetto L, Banho CA, Estofolete CF, Dourado FS, da Silva Cândido D, Dutra KR, da Silva Salles FC, de Jesus JG, Sabino EC, Faria NR, Nogueira ML. Genetic differences of dengue virus 2 in patients with distinct clinical outcome. Braz J Microbiol 2023; 54:1411-1419. [PMID: 37178262 PMCID: PMC10485208 DOI: 10.1007/s42770-023-01006-1] [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: 02/13/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
The genetic diversity of the dengue virus is characterized by four circulating serotypes, several genotypes, and an increasing number of existing lineages that may have differences in the potential to cause epidemics and disease severity. Accurate identification of the genetic variability of the virus is essential to identify lineages responsible for an epidemic and understanding the processes of virus spread and virulence. Here, we characterize, using portable nanopore genomic sequencing, different lineages of dengue virus 2 (DENV-2) detected in 22 serum samples from patients with and without dengue warning signs attended at Hospital de Base of São José do Rio Preto (SJRP) in 2019, during a DENV-2 outbreak. Demographic, epidemiological, and clinical data were also analyzed. The phylogenetic reconstruction and the clinical data showed that two lineages belonging to the American/Asian genotype of DENV-2-BR3 and BR4 (BR4L1 and BR4L2)-were co-circulating in SJRP. Although preliminary, these results indicate no specific association between clinical form and phylogenetic clustering at the virus consensus sequence level. Studies with larger sample sizes and which explore single nucleotide variants are needed. Therefore, we showed that portable nanopore genome sequencing could generate quick and reliable sequences for genomic surveillance to monitor viral diversity and its association with disease severity as an epidemic unfolds.
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Affiliation(s)
- Beatriz de Carvalho Marques
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cecília Artico Banho
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Cássia Fernanda Estofolete
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | - Fernanda Simões Dourado
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Karina Rocha Dutra
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil
| | | | - Jaqueline Góes de Jesus
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
| | - Nuno Rodrigues Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Instituto de Medicina Tropical da Faculdade de Medicina - Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
- The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas Em Virologia, Departamento de Doenças Dermatológicas, Infecciosas E Parasitárias, Faculdade de Medicina de São José Do Rio Preto, Avenida Brigadeiro Faria Lima, 5416 São José Do Rio Preto, São Paulo, 15090-000, Brazil.
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA.
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7
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Rivera JA, Rengifo AC, Rosales-Munar A, Díaz-Herrera TH, Ciro JU, Parra E, Alvarez-Díaz DA, Laiton-Donato K, Caldas ML. Genotyping of dengue virus from infected tissue samples embedded in paraffin. Virol J 2023; 20:100. [PMID: 37231481 DOI: 10.1186/s12985-023-02072-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/14/2023] [Indexed: 05/27/2023] Open
Abstract
Dengue has become one of the vector-borne diseases that affect humans worldwide. In Latin American countries, Colombia is historically one of the most affected by epidemics of this flavivirus. The underreporting of signs and symptoms of probable cases of dengue, the lack of characterization of the serotypes of the infection, and the few detailed studies of postmortem necropsies of patients are among other conditions that have delayed progress in the knowledge of the pathogenesis of the disease. This study presents the results of fragment sequencing assays on paraffin-embedded tissue samples from fatal DENV cases during the 2010 epidemic in Colombia. We found that the predominant serotype was DENV-2, with the Asian/American genotype of lineages 1 and 2. This work is one of the few reports of the circulating genotypes of dengue during the 2010 epidemic in Colombia, one of the most lethal dates in the country's history.
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Grants
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
- contract 757 project 2013 Instituto Nacional de Salud (INS), Dirección de Investigación en Salud Pública (DISP), and the Colombian Department of Science, Technology, and Innovation (Minciencias)
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Affiliation(s)
- Jorge Alonso Rivera
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| | - Aura Caterine Rengifo
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia.
| | - Alicia Rosales-Munar
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| | - Taylor H Díaz-Herrera
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
| | - José Usme Ciro
- CIST-Centro de Investigaciones en Salud Para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta, 47003, Colombia
| | - Edgar Parra
- Dirección de Redes en Salud Pública, Grupo de Patología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Diego A Alvarez-Díaz
- Dirección de investigación en Salud Pública, Grupo de Genómica de Microorganismos Emergentes, Instituto Nacional de Salud, Bogotá, Colombia
| | - Katherine Laiton-Donato
- Dirección de investigación en Salud Pública, Grupo de Genómica de Microorganismos Emergentes, Instituto Nacional de Salud, Bogotá, Colombia
| | - María Leonor Caldas
- Dirección de investigación en Salud Pública, Grupo de Morfología Celular, Instituto Nacional de Salud, Avenue 26 No. 51-20 - Zone 6 CAN, Bogotá, Colombia
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8
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Fritsch H, Moreno K, Lima IAB, Santos CS, Costa BGG, de Almeida BL, dos Santos RA, Francisco MVLDO, Sampaio MPS, de Lima MM, Pereira FM, Fonseca V, Tosta S, Xavier J, de Oliveira C, Adelino T, de Mello ALES, Gräf T, Alcantara LCJ, Giovanetti M, de Siqueira IC. Phylogenetic Reconstructions Reveal the Circulation of a Novel Dengue Virus-1V Clade and the Persistence of a Dengue Virus-2 III Genotype in Northeast Brazil. Viruses 2023; 15:1073. [PMID: 37243159 PMCID: PMC10224011 DOI: 10.3390/v15051073] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Dengue fever is among the most significant public health concerns in Brazil. To date, the highest number of Dengue notifications in the Americas has been reported in Brazil, with cases accounting for a total number of 3,418,796 reported cases as of mid-December 2022. Furthermore, the northeastern region of Brazil registered the second-highest incidence of Dengue fever in 2022. Due to the alarming epidemiological scenario, in this study, we used a combination of portable whole-genome sequencing, phylodynamic, and epidemiological analyses to reveal a novel DENV-1 genotype V clade and the persistence of DENV-2 genotype III in the region. We further report the presence of non-synonymous mutations associated with non-structural domains, especially the NS2A (non-structural protein 2A), as well as describe synonymous mutations in envelope and membrane proteins, distributed differently between clades. However, the absence of clinical data at the time of collection and notification, as well as the impossibility of monitoring patients in order to observe worsening or death, restricts our possibility of correlating mutational findings with possible clinical prognoses. Together, these results reinforce the crucial role of genomic surveillance to follow the evolution of circulating DENV strains and understand their spread across the region through inter-regional importation events, likely mediated by human mobility, and also the possible impacts on public health and outbreak management.
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Affiliation(s)
- Hegger Fritsch
- Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Keldenn Moreno
- Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Italo Andrade Barbosa Lima
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
| | - Cleiton Silva Santos
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
| | | | - Breno Lima de Almeida
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
| | - Ronald Alves dos Santos
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
| | | | - Maria Paula Souza Sampaio
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
| | - Maricelia Maia de Lima
- Secretaria Municipal de Saúde de Feira de Santana, Avenida João Durval Carneiro, s/n, Feira de Santana 44027-010, BA, Brazil
- Departamento de Saúde, Universidade Estadual de Feira de Santana, Avenida Transnordestina, s/n, Feira de Santana 44036-900, BA, Brazil
| | - Felicidade Mota Pereira
- Laboratório Central de Saúde Pública Prof Goncalo Moniz, Rua Waldemar Falcão, 123, Salvador 40295-010, BA, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana de Saúde/Organização Mundial de Saúde, Setor das Embaixadas, Lote 19, Avenida das Nações, Brasília 70-800400, SP, Brazil
| | - Stephane Tosta
- Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Joilson Xavier
- Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Carla de Oliveira
- Laboratório de Flavivírus, Lnstituto Oswaldo Cruz/Fundação Oswaldo Cruz, Avenida Brasil, 4365, Rio de Janeiro 21040-900, RJ, Brazil
| | - Talita Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Rua Conde Pereira Carneiro, 80, Belo Horizonte 30510-010, MG, Brazil
| | - Arabela Leal e Silva de Mello
- Departamento de Saúde, Universidade Estadual de Feira de Santana, Avenida Transnordestina, s/n, Feira de Santana 44036-900, BA, Brazil
| | - Tiago Gräf
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Avenida Professor Algacyr Munhoz Mader, 3775, Curitiba 81310-020, PA, Brazil
| | - Luiz Carlos Junior Alcantara
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Belo Horizonte 30190-002, MG, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Belo Horizonte 30190-002, MG, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, Via Álvaro del Portillo, 21, 00128 Rome, Italy
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9
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Milhim BHGA, da Rocha LC, Terzian ACB, Mazaro CCP, Augusto MT, Luchs A, Zini N, Sacchetto L, dos Santos BF, Garcia PHC, Rocha RS, Liso E, Brienze VMS, da Silva GCD, Vasilakis N, Estofolete CF, Nogueira ML. Arboviral Infections in Neurological Disorders in Hospitalized Patients in São José do Rio Preto, São Paulo, Brazil. Viruses 2022; 14:1488. [PMID: 35891468 PMCID: PMC9323204 DOI: 10.3390/v14071488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Arbovirus infections are increasingly important causes of disease, whose spectrum of neurological manifestations are not fully known. This study sought to retrospectively assess the incidence of arboviruses in cerebrospinal fluid samples of patients with neurological symptoms to inform diagnosis of central and peripheral nervous system disorders. A total of 255 cerebrospinal fluid (CSF) samples collected from January 2016 to December 2017 were tested for dengue virus (DENV 1-4), Zika virus (ZIKV), and Chikungunya virus (CHIKV) in addition to other neurotropic arboviruses of interest, using genetic and serologic assays. Of the 255 CSF samples analyzed, 3.53% (09/255) were positive for arboviruses presenting mainly as meningitis, encephalitis, and cerebrovascular events, of which ZIKV was detected in 2.74% (7/255), DENV in 0.78% (2/255), in addition to an identified ILHV infection that was described previously. All the cases were detected in adults aged 18 to 74 years old. Our findings highlight the scientific and clinical importance of neurological syndromes associated with arboviruses and demonstrate the relevance of specific laboratory methods to achieve accurate diagnoses as well as highlight the true dimension of these diseases to ultimately improve public health planning and medical case management.
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Affiliation(s)
- Bruno H. G. A. Milhim
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Leonardo C. da Rocha
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Ana C. B. Terzian
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
- Laboratório de Imunologia Celular e Molecular (LICM), Avenida Augusto de Lima, 1715, Centro, Belo Horizonte 30190-002, MG, Brazil
- Instituto René Rachou Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Centro, Belo Horizonte 30190-002, MG, Brazil
| | - Carolina C. P. Mazaro
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Marcos T. Augusto
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Adriana Luchs
- Enteric Disease Laboratory, Department of Virology, Adolfo Lutz Institute, Avenida Dr. Arnaldo, 355, São Paulo 01246-902, SP, Brazil;
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Livia Sacchetto
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Barbara F. dos Santos
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Pedro H. C. Garcia
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Rodrigo S. Rocha
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Elisabete Liso
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544-Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (E.L.); (V.M.S.B.)
| | - Vânia M. S. Brienze
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544-Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (E.L.); (V.M.S.B.)
| | - Gislaine C. D. da Silva
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
- Department of Preventive Medicine and Population Health, The University of Texas Medical Branch, Galveston, TX 77555-1150, USA
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Cássia F. Estofolete
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia [LPV], Faculdade de Medicina de São José do Rio Preto [FAMERP], Avenida Brigadeiro Faria Lima, 5544, Vila São Jose, São José do Rio Preto 15090-000, SP, Brazil; (B.H.G.A.M.); (L.C.d.R.); (A.C.B.T.); (C.C.P.M.); (M.T.A.); (N.Z.); (L.S.); (B.F.d.S.); (P.H.C.G.); (R.S.R.); (G.C.D.d.S.); (C.F.E.)
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
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10
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Sankaradoss A, Jagtap S, Nazir J, Moula SE, Modak A, Fialho J, Iyer M, Shastri JS, Dias M, Gadepalli R, Aggarwal A, Vedpathak M, Agrawal S, Pandit A, Nisheetha A, Kumar A, Bordoloi M, Shafi M, Shelar B, Balachandra SS, Damodar T, Masika MM, Mwaura P, Anzala O, Muthumani K, Sowdhamini R, Medigeshi GR, Roy R, Pattabiraman C, Krishna S, Sreekumar E. Immune profile and responses of a novel dengue DNA vaccine encoding an EDIII-NS1 consensus design based on Indo-African sequences. Mol Ther 2022; 30:2058-2077. [PMID: 34999210 PMCID: PMC8736276 DOI: 10.1016/j.ymthe.2022.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 12/30/2022] Open
Abstract
The ongoing COVID-19 pandemic highlights the need to tackle viral variants, expand the number of antigens, and assess diverse delivery systems for vaccines against emerging viruses. In the present study, a DNA vaccine candidate was generated by combining in tandem envelope protein domain III (EDIII) of dengue virus serotypes 1-4 and a dengue virus (DENV)-2 non-structural protein 1 (NS1) protein-coding region. Each domain was designed as a serotype-specific consensus coding sequence derived from different genotypes based on the whole genome sequencing of clinical isolates in India and complemented with data from Africa. This sequence was further optimized for protein expression. In silico structural analysis of the EDIII consensus sequence revealed that epitopes are structurally conserved and immunogenic. The vaccination of mice with this construct induced pan-serotype neutralizing antibodies and antigen-specific T cell responses. Assaying intracellular interferon (IFN)-γ staining, immunoglobulin IgG2(a/c)/IgG1 ratios, and immune gene profiling suggests a strong Th1-dominant immune response. Finally, the passive transfer of immune sera protected AG129 mice challenged with a virulent, non-mouse-adapted DENV-2 strain. Our findings collectively suggest an alternative strategy for dengue vaccine design by offering a novel vaccine candidate with a possible broad-spectrum protection and a successful clinical translation either as a stand alone or in a mix and match strategy.
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Affiliation(s)
- Arun Sankaradoss
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India,Corresponding author: National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.
| | - Suraj Jagtap
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Junaid Nazir
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shefta E. Moula
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Ayan Modak
- Molecular Virology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala 695014, India
| | - Joshuah Fialho
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Meenakshi Iyer
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayanthi S. Shastri
- Department of Microbiology, T.N.Medical College & B.y.L.Nair Hospital, Mumbai 400008, India
| | - Mary Dias
- Division of Infectious Disease, St. John's Medical College and Hospital, Bangalore 560034, India
| | - Ravisekhar Gadepalli
- Department of Microbiology, All India Institute of Medical Sciences, Jodhpur 342005, India
| | - Alisha Aggarwal
- Department of Microbiology, All India Institute of Medical Sciences, Jodhpur 342005, India
| | - Manoj Vedpathak
- Department of Microbiology, T.N.Medical College & B.y.L.Nair Hospital, Mumbai 400008, India
| | - Sachee Agrawal
- Department of Microbiology, T.N.Medical College & B.y.L.Nair Hospital, Mumbai 400008, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Amul Nisheetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Anuj Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Mahasweta Bordoloi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Mohamed Shafi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Bhagyashree Shelar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Swathi S. Balachandra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Tina Damodar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Moses Muia Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi 19676-00202, Kenya
| | - Patrick Mwaura
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi 19676-00202, Kenya
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi 19676-00202, Kenya
| | - Kar Muthumani
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | | | - Rahul Roy
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India,Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore 560029, India
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India,School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Ponda 404401, India
| | - Easwaran Sreekumar
- Molecular Virology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala 695014, India,Corresponding author: Molecular Virology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala 695014, India
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11
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Abbas I, Abbas A, Shalabi M, Mohamed H, Arjabey AMM, Babker AMA, Omer AFA. Molecular Characteristic of Dengue Virus against its Outbreak response of Red Sea State, Eastern Sudan - 2020. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.7983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Dengue fever is ranked by the World Health Organization as the most critical mosquito-borne viral disease, globally. More than 40% of the world’s population, in more than 100 countries are at risk of dengue infection.
AIM: The objective of this study was to determine the prevalence of dengue virus (DENV) genotypes and serotypes during disease outbreak 2020 in Port Sudan State, eastern Sudan.
METHODS: This study was a descriptive cross-sectional study conducted at Eastern Sudan (Port Sudan state). Three hundred and eighty serum samples were collected from febrile patients including any individual aged ≥5 years old and excluded all patients suffering from Tuberculosis, rheumatoid arthritis was excluded and those who have a history of travailing to an endemic area within the past 2 weeks. Reverse transcription polymerase chain reaction (RT-PCR) assays were used to amplify a fragment of the viral polyprotein gene. The PCR products of the amplified viral polyprotein gene were purified, and partial sequences were generated and used to confirm the specificity of DENV sequences and to identify the virus serotype. Data analysis was performed using Statistical Package for Social Sciences (SPSS, version 23.0).
RESULTS: Infection was confirmed in 27.9% in 106 samples out of 380 sampled sera, using DENVenzyme-linked immunoassay assay. The detection of DENV RNA was made possible using group-specific RT-PCR assay. The virus was DENV serotype 3 (DENV-3) serotype-specific RT-PCR assay.
CONCLUSION: The findings of this study indicate that DENV-3 of DENV is circulating and we did not detected DEN-1, 2 and DEN-4 in outbreak in eastern Sudan during the year 2020.
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12
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Genotype-Dependent Immunogenicity of Dengue Virus Type 2 Asian I and Asian/American Genotypes in Common Marmoset ( Callithrix jacchus): Discrepancy in Neutralizing and Infection-Enhancing Antibody Levels between Genotypes. Microorganisms 2021; 9:microorganisms9112196. [PMID: 34835327 PMCID: PMC8618970 DOI: 10.3390/microorganisms9112196] [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: 08/29/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
Owing to genotype-specific neutralizing antibodies, analyzing differences in the immunogenic variation among dengue virus (DENV) genotypes is central to effective vaccine development. Herein, we characterized the viral kinetics and antibody response induced by DENV type 2 Asian I (AI) and Asian/American (AA) genotypes using marmosets (Callithrix jacchus) as models. Two groups of marmosets were inoculated with AI and AA genotypes, and serial plasma samples were collected. Viremia levels were determined using quantitative reverse transcription-PCR, plaque assays, and antigen enzyme-linked immunosorbent assay (ELISA). Anti-DENV immunoglobulin M and G antibodies, neutralizing antibody titer, and antibody-dependent enhancement (ADE) activity were determined using ELISA, plaque reduction neutralization test, and ADE assay, respectively. The AI genotype induced viremia for a longer duration, but the AA genotype induced higher levels of viremia. After four months, the neutralizing antibody titer induced by the AA genotype remained high, but that induced by the AI genotype waned. ADE activity toward Cosmopolitan genotypes was detected in marmosets inoculated with the AI genotype. These findings indicate discrepancies between heterologous genotypes that influence neutralizing antibodies and viremia in marmosets, a critical issue in vaccine development.
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13
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Alagarasu K, Patil JA, Kakade MB, More AM, Yogesh B, Newase P, Jadhav SM, Parashar D, Kaur H, Gupta N, Vijay N, Narayan J, Shah PS. Serotype and genotype diversity of dengue viruses circulating in India: a multi-centre retrospective study involving the Virus Research Diagnostic Laboratory Network in 2018. Int J Infect Dis 2021; 111:242-252. [PMID: 34428547 DOI: 10.1016/j.ijid.2021.08.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES A retrospective study was undertaken to investigate the circulating dengue virus (DENV) serotypes and genotypes in India in 2018. METHODS In total, 4963 samples referred to virus research diagnostic laboratories (n=21), the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) and ICMR-NIV field units (n=2) for diagnosis of dengue in 2018 were tested using a real-time reverse transcription polymerase chain reaction assay for the presence of DENV serotypes. Representative samples were sequenced for the envelope (E) gene. RESULTS Regional diversity was observed with regard to the dominant circulating serotypes. DENV-2 was found to be the most common serotype in many states. Thrombocytopenia, petechiae and malaise were associated with DENV-2 infection. Phylogenetic analyses of DENV E gene sequences revealed the circulation of genotypes I and V of DENV-1, two lineages of DENV-2 genotype IV, DENV-3 genotype III and DENV-4 genotype I. CONCLUSIONS This study found regional differences in the prevalence of circulating DENV serotypes in India, and provides baseline data for continuous molecular surveillance. Molecular surveillance may have implications for predicting large-scale outbreaks of dengue if regional shifts in the predominantly circulating serotypes and genotypes are detected during the early phase of the dengue season.
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Affiliation(s)
- K Alagarasu
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India.
| | - J A Patil
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - M B Kakade
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - A M More
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - B Yogesh
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - P Newase
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - S M Jadhav
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - D Parashar
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - H Kaur
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - N Gupta
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - N Vijay
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - J Narayan
- Virology Unit, Indian Council of Medical Research, New Delhi, India
| | - P S Shah
- Dengue and Chikungunya Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
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Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil. Nat Commun 2021; 12:2619. [PMID: 33976183 PMCID: PMC8113494 DOI: 10.1038/s41467-021-22921-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/07/2021] [Indexed: 12/19/2022] Open
Abstract
After the Zika virus (ZIKV) epidemic in the Americas in 2016, both Zika and dengue incidence declined to record lows in many countries in 2017–2018, but in 2019 dengue resurged in Brazil, causing ~2.1 million cases. In this study we use epidemiological, climatological and genomic data to investigate dengue dynamics in recent years in Brazil. First, we estimate dengue virus force of infection (FOI) and model mosquito-borne transmission suitability since the early 2000s. Our estimates reveal that DENV transmission was low in 2017–2018, despite conditions being suitable for viral spread. Our study also shows a marked decline in dengue susceptibility between 2002 and 2019, which could explain the synchronous decline of dengue in the country, partially as a result of protective immunity from prior ZIKV and/or DENV infections. Furthermore, we performed phylogeographic analyses using 69 newly sequenced genomes of dengue virus serotype 1 and 2 from Brazil, and found that the outbreaks in 2018–2019 were caused by local DENV lineages that persisted for 5–10 years, circulating cryptically before and after the Zika epidemic. We hypothesize that DENV lineages may circulate at low transmission levels for many years, until local conditions are suitable for higher transmission, when they cause major outbreaks. Zika and dengue incidence in the Americas declined in 2017–2018, but dengue resurged in 2019 in Brazil. This study uses epidemiological, climatological and genomic data to show that the decline of dengue may be explained by protective immunity from pre-exposure to ZIKV and/or DENV in prior years.
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15
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Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, de Filippis AMB, de Abreu AL, de Jesus R, de Albuquerque CFC, Rico JM, do Carmo Said RF, Silva JA, de Moura NFO, Leite P, Frutuoso LCV, Haddad SK, Martínez A, Barreto FK, Vazquez CC, da Cunha RV, Araújo ELL, de Oliveira Tosta SF, de Araújo Fabri A, Chalhoub FLL, da Silva Lemos P, de Bruycker-Nogueira F, de Castro Lichs GG, Zardin MCSU, Segovia FMC, Gonçalves CCM, Grillo ZDCF, Slavov SN, Pereira LA, Mendonça AF, Pereira FM, de Magalhães JJF, Dos Santos Júnior ADCM, de Lima MM, Nogueira RMR, Góes-Neto A, de Carvalho Azevedo VA, Ramalho DB, Oliveira WK, Macario EM, de Medeiros AC, Pimentel V, Holmes EC, de Oliveira T, Lourenço J, Alcantara LCJ. Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil. Nat Commun 2021; 12:2296. [PMID: 33863880 PMCID: PMC8052316 DOI: 10.1038/s41467-021-22607-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.
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Affiliation(s)
- Talita Émile Ribeiro Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Vagner Fonseca
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joilson Xavier
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Álvaro Salgado de Abreu
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Valdinete Alves do Nascimento
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil
| | | | | | | | | | | | - Roselene Hans Santos
- Laboratório Central de Saúde Pública Dr. Milton Bezerra Sobral, Recife, Pernambuco, Brazil
| | | | | | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Maria Bispo de Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Luiz de Abreu
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Ronaldo de Jesus
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | - Jairo Mendez Rico
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | | | - Joscélio Aguiar Silva
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Noely Fabiana Oliveira de Moura
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Priscila Leite
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Lívia Carla Vinhal Frutuoso
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | | | | | | | | | - Emerson Luiz Lima Araújo
- Coordenação Geral dos Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | - Allison de Araújo Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávia Löwen Levy Chalhoub
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | - Luiz Augusto Pereira
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Ana Flávia Mendonça
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | | | | | | | | | - Rita Maria Ribeiro Nogueira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Dario Brock Ramalho
- Secretaria de Saúde do Estado de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Victor Pimentel
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK.
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
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Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka. Viruses 2021; 13:v13030421. [PMID: 33807922 PMCID: PMC8001906 DOI: 10.3390/v13030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Genetic variations in dengue virus (DENV) play a distinct role in epidemic emergence. The DENV 3′ UTR has become a recent interest in research. The objective of the study was to examine the genetic variation in the domain II, 3′ UTR region of human and mosquito-derived DENV. DENV-infected human sera were orally infected to laboratory reared Aedes aegypti mosquitoes. The domain II, 3′ UTR of each human- and mosquito-derived sample was amplified. The nucleotide sequence variation, phylogenetic and secondary structure analysis was carried out incorporating respective regions of so far recorded Sri Lankan and the reference genotype strains of the DENV3 and DENV1 serotypes. The human- and mosquito-derived domain II, 3′ UTR were identical in nucleotide sequences within the serotypes isolated, indicating the conserved nature of the region during host switch. The sequence analysis revealed distinct variations in study isolates compared to so far recorded Sri Lankan isolates. However, despite single nucleotide variations, the maintenance of structural integrity was evident in related strains within the serotypes in the secondary structure analysis. The phylogenetic analysis revealed distinct clade segregation of the study sequences from so far reported Sri Lankan isolates and illustrated the phylogenetic relations of the study sequences to the available global isolates of respective serotypes.
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17
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Torres MC, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Fonseca V, Ribeiro MS, Brandão AP, Venâncio da Cunha R, Dias AI, Santos Vilas Boas L, Felix AC, Alves Pereira M, de Oliveira Pinto LM, Sakuntabhai A, Bispo de Filippis AM. Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes. Viruses 2021; 13:v13020349. [PMID: 33672226 PMCID: PMC7926750 DOI: 10.3390/v13020349] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/07/2021] [Accepted: 02/13/2021] [Indexed: 02/07/2023] Open
Abstract
Intrahost genetic diversity is thought to facilitate arbovirus adaptation to changing environments and hosts, and it might also be linked to viral pathogenesis. Dengue virus serotype 2 (DENV-2) has circulated in Brazil since 1990 and is associated with severe disease and explosive outbreaks. Intending to shed light on the viral determinants for severe dengue pathogenesis, we sought to analyze the DENV-2 intrahost genetic diversity in 68 patient cases clinically classified as dengue fever (n = 31), dengue with warning signs (n = 19), and severe dengue (n = 18). Unlike previous DENV intrahost diversity studies whose approaches employed PCR, here we performed viral whole-genome deep sequencing from clinical samples with an amplicon-free approach, representing the real intrahost diversity scenario. Striking differences were detected in the viral population structure between the three clinical categories, which appear to be driven mainly by different infection times and selection pressures, rather than being linked with the clinical outcome itself. Diversity in the NS2B gene, however, showed to be constrained, irrespective of clinical outcome and infection time. Finally, 385 non-synonymous intrahost single-nucleotide variants located along the viral polyprotein, plus variants located in the untranslated regions, were consistently identified among the samples. Of them, 124 were exclusively or highly detected among cases with warning signs and among severe cases. However, there was no variant that by itself appeared to characterize the cases of greater severity, either due to its low intrahost frequency or the conservative effect on amino acid substitution. Although further studies are necessary to determine their real effect on viral proteins, this heightens the possibility of epistatic interactions. The present analysis represents an initial effort to correlate DENV-2 genetic diversity to its pathogenic potential and thus contribute to understanding the virus’s dynamics within its human host.
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Affiliation(s)
- Maria Celeste Torres
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, 21040-360 Rio de Janeiro, Brazil; (M.C.L.d.M.); (C.D.d.S.R.); (A.M.B.d.F.)
- Correspondence:
| | - Marcos Cesar Lima de Mendonça
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, 21040-360 Rio de Janeiro, Brazil; (M.C.L.d.M.); (C.D.d.S.R.); (A.M.B.d.F.)
| | | | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 4041 Durban, South Africa;
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, 70719-040 Distrito Federal, Brazil
| | - Mario Sergio Ribeiro
- Superintendência Secretaria de Vigilância em Saúde do Estado do Rio de Janeiro, 20031-142 Rio de Janeiro, Brazil;
| | - Ana Paula Brandão
- Laboratório Central Noel Nutels/LACEN, 20231-092 Rio de Janeiro, Brazil;
| | - Rivaldo Venâncio da Cunha
- Coordenação de Vigilância em Saúde e Laboratórios de Referência da Fundação Oswaldo Cruz, FIOCRUZ, 21040-360 Rio de Janeiro, Brazil;
| | - Ana Isabel Dias
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, 05403-000 São Paulo, Brazil; (A.I.D.); (L.S.V.B.); (A.C.F.)
| | - Lucy Santos Vilas Boas
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, 05403-000 São Paulo, Brazil; (A.I.D.); (L.S.V.B.); (A.C.F.)
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, 05403-000 São Paulo, Brazil; (A.I.D.); (L.S.V.B.); (A.C.F.)
| | | | | | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases, Department of Global Health, Institut Pasteur, 75015 Paris, France;
| | - Ana Maria Bispo de Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, 21040-360 Rio de Janeiro, Brazil; (M.C.L.d.M.); (C.D.d.S.R.); (A.M.B.d.F.)
| | - on behalf of ZikAction Consortium
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, 21040-360 Rio de Janeiro, Brazil; (M.C.L.d.M.); (C.D.d.S.R.); (A.M.B.d.F.)
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18
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Allicock OM, Sahadeo N, Lemey P, Auguste AJ, Suchard MA, Rambaut A, Carrington CVF. Determinants of dengue virus dispersal in the Americas. Virus Evol 2021; 6:veaa074. [PMID: 33408877 PMCID: PMC7772473 DOI: 10.1093/ve/veaa074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dengue viruses (DENVs) are classified into four serotypes, each of which contains multiple genotypes. DENV genotypes introduced into the Americas over the past five decades have exhibited different rates and patterns of spatial dispersal. In order to understand factors underlying these patterns, we utilized a statistical framework that allows for the integration of ecological, socioeconomic, and air transport mobility data as predictors of viral diffusion while inferring the phylogeographic history. Predictors describing spatial diffusion based on several covariates were compared using a generalized linear model approach, where the support for each scenario and its contribution is estimated simultaneously from the data set. Although different predictors were identified for different serotypes, our analysis suggests that overall diffusion of DENV-1, -2, and -3 in the Americas was associated with airline traffic. The other significant predictors included human population size, the geographical distance between countries and between urban centers and the density of people living in urban environments.
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Affiliation(s)
- Orchid M Allicock
- Department of Preclinical Sciences, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nikita Sahadeo
- Department of Preclinical Sciences, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Philippe Lemey
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Leuven, Belgium
| | - Albert J Auguste
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, The Kings Buildings, Edinburgh, EH9 3FL, UK
| | - Christine V F Carrington
- Department of Preclinical Sciences, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
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19
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Milhim BHGA, Estofolete CF, da Rocha LC, Liso E, Brienze VMS, Vasilakis N, Terzian ACB, Nogueira ML. Fatal Outcome of Ilheus Virus in the Cerebrospinal Fluid of a Patient Diagnosed with Encephalitis. Viruses 2020; 12:v12090957. [PMID: 32872425 PMCID: PMC7552055 DOI: 10.3390/v12090957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 01/06/2023] Open
Abstract
Ilheus virus is an arbovirus with the potential for central nervous system involvement. Accurate diagnosis is a challenge due to similar clinical symptoms and serologic cross-reactivity with other flaviviruses. Here, we describe the first documented case of a fatal outcome following the identification of Ilheus virus in the cerebrospinal fluid (CSF) of a patient with cerebral encephalitis in Brazil.
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Affiliation(s)
- Bruno H. G. A. Milhim
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Cássia F. Estofolete
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Leonardo C. da Rocha
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Elisabete Liso
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, SP 15090-000 São José do Rio Preto, Brazil; (E.L.); (V.M.S.B.)
| | - Vânia M. S. Brienze
- Hospital de Base, Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, SP 15090-000 São José do Rio Preto, Brazil; (E.L.); (V.M.S.B.)
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA;
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Ana C. B. Terzian
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Faculdade de Medicina de São José do Rio Preto (FAMERP), Avenida Brigadeiro Faria Lima, 5544 - Vila Sao Jose, 15090-000 São José do Rio Preto, Brazil; (B.H.G.A.M.); (C.F.E.); (L.C.d.R.); (A.C.B.T.)
- Correspondence: ; Tel.: +55-1798811-0550
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20
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Estofolete CF, Milhim BHGA, Zini N, Scamardi SN, Selvante JD, Vasilakis N, Nogueira ML. Flavivirus Infection Associated with Cerebrovascular Events. Viruses 2020; 12:v12060671. [PMID: 32580374 PMCID: PMC7354470 DOI: 10.3390/v12060671] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
Arthropod-borne viruses (arboviruses) of the genus Flavivirus are distributed globally and cause significant human disease and mortality annually. Flavivirus infections present a spectrum of clinical manifestations, ranging from asymptomatic to severe manifestations, including hemorrhage, encephalitis and death. Herein, we describe 3 case reports of cerebrovascular involvement in patients infected by dengue and Zika viruses in Sao Jose do Rio Preto, São Paulo State, Brazil, a hyperendemic area for arbovirus circulation, including dengue, yellow fever, chikungunya and Saint Louis encephalitis viruses. Our findings highlight the potential threat that unusual clinical manifestations may pose to arbovirus disease management and recovery.
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Affiliation(s)
- Cássia F Estofolete
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Bruno H G A Milhim
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Nathalia Zini
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Samuel N Scamardi
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Joana D'Arc Selvante
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0610, USA
| | - Maurício L Nogueira
- Department of Infectious, Dermatological and Parasitic Infections, Sao Jose do Rio Preto Medical School, Sao Jose do Rio Preto 15090-000, Brazil
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21
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de Jesus JG, Dutra KR, Sales FCDS, Claro IM, Terzian AC, Candido DDS, Hill SC, Thézé J, Torres C, D'Agostini TL, Felix AC, Reis AFN, Alcantara LCJ, de Abreu AL, Croda JH, de Oliveira WK, de Filipis AMB, Camis MDCRDS, Romano CM. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019. Mem Inst Oswaldo Cruz 2020; 115:e190423. [PMID: 32428189 PMCID: PMC7227788 DOI: 10.1590/0074-02760190423] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 04/06/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Despite efforts to mitigate the impact of dengue virus (DENV) epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo State in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES To understand the origin and dynamics of the 2019 DENV outbreak. METHODS Here using portable nanopore sequencing we generated20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of São Paulo State, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.
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Affiliation(s)
| | - Karina Rocha Dutra
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | | | - Ingra Morales Claro
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana Carolina Terzian
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto, SP, Brazil
| | | | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Celeste Torres
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Tatiana Lang D'Agostini
- Coordenadoria de Controle de Doenças, Centro de Vigilância Epidemiológica Professor Alexandre Vranjac, Secretaria de Estado da Saúde, São Paulo, SP, Brasil
| | - Alvina Clara Felix
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - André L de Abreu
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Júlio Hr Croda
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Wanderson K de Oliveira
- Coordenação Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Ana Maria Bispo de Filipis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Camila Malta Romano
- Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo, SP, Brazil
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22
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Torres MC, de Bruycker Nogueira F, Fernandes CA, Louzada Silva Meira G, Ferreira de Aguiar S, Chieppe AO, Bispo de Filippis AM. Re-introduction of dengue virus serotype 2 in the state of Rio de Janeiro after almost a decade of epidemiological silence. PLoS One 2019; 14:e0225879. [PMID: 31825989 PMCID: PMC6905541 DOI: 10.1371/journal.pone.0225879] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/14/2019] [Indexed: 01/16/2023] Open
Abstract
The Asian/American genotype of dengue virus serotype 2 (DENV-2) has been introduced in Brazil through the state of Rio de Janeiro around 1990, and since then it has been spreading and evolving, leading to several waves of dengue epidemics throughout the country that cause a major public health problem. Of particular interest has been the epidemic of 2008, whose highest impact was evidenced in the state of Rio de Janeiro, with a higher number of severe cases and mortality rate, compared to previous outbreaks. Interestingly, no circulation of DENV-2 was witnessed in this region during the preceding 9-year period. By early 2010, phylogenetic analysis of the 2008 epidemic strain revealed that the outbreak was caused by a new viral lineage of the Asian/American genotype, which was pointed as responsible for the outbreak severity as well. The same scenario is repeating in 2019 in this state; however, only a few cases have been detected yet. To provide information that helps to the understanding of DENV-2 dynamics in the state of Rio de Janeiro, and thereafter contribute to public health control and prevention actions, we employed phylogenetic studies combined with temporal and dynamics geographical features to determine the origin of the current viral strain. To this effect, we analyzed a region of 1626 nucleotides entailing the Envelope/NS1 viral genes. Our study reveals that the current strain belongs to the same lineage that caused the 2008 outbreak, however, it is phylogenetically distant from any Brazilian strain identified so far. Indeed, it seemed to be originated in Puerto Rico around 2002 and has been introduced into the state in late 2018. Taking into account that no DENV-2 case was reported over the last decade in the state (representing a whole susceptible children generation), and the fact that a new viral strain may be causing current dengue infections, these results will be influential in strengthening dengue surveillance and disease control, mitigating the potential epidemiological consequences of virus spread.
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Affiliation(s)
- María Celeste Torres
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
- * E-mail:
| | | | | | | | | | - Alexandre Otávio Chieppe
- Secretaria Estadual de Saúde, Superintendência de Vigilância Sanitária do Estado do Rio de Janeiro, Brazil
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23
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Aragão CF, Pinheiro VCS, Nunes Neto JP, da Silva EVP, Pereira GJG, do Nascimento BLS, Castro KDS, Maia AM, Catete CP, Martins LC, Tadei WP, da Silva SP, Cruz ACR. Natural Infection of Aedes aegypti by Chikungunya and Dengue type 2 Virus in a Transition Area of North-Northeast Brazil. Viruses 2019; 11:E1126. [PMID: 31817553 PMCID: PMC6949906 DOI: 10.3390/v11121126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 01/16/2023] Open
Abstract
Dengue fever, chikungunya, and Zika are diseases caused by viruses transmitted by Aedes aegypti and Aedes albopictus. In Brazil, the number of human infections is high, but few studies are performed in mosquito vectors. This study aimed to investigate the presence of Zika, Dengue and Chikungunya viruses in Ae. aegypti and Ae. albopictus from the municipalities of Alto Alegre, Caxias, Codó, and São Mateus do Maranhão, located in the state of Maranhão, Northeast Brazil. The mosquitoes were collected with a mechanical aspirator, identified, triturated, and then submitted to RNA extraction and RT-qPCR. The positive samples were confirmed by virus isolation and genome sequencing. Three hundred and forty-eight Ae. aegypti (176 males and 172 females) and 12 Ae. albopictus (eight males and four females) were collected and tested. Ae. aegypti was the only vector positive in two municipalities-Codó, with detection of Chikungunya virus (CHIKV) belonging to the East-Central-South African genotype, and in Caxias, with detection of Dengue virus (DENV)-2 belonging to the Asian/American genotype. The detection of CHIKV and DENV-2 is evidence that those viruses are maintained in arthropod vectors, and shows the epidemiological risk in the area for chikungunya cases and a possible increase of severe dengue cases, associated with the occurrence of dengue hemorrhagic fever.
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Affiliation(s)
- Carine Fortes Aragão
- Programa de Pós-Graduação em Biologia dos Agentes Infecciosos e Parasitários, Universidade Federal do Pará, Belém, PA 66075-110, Brazil;
| | - Valéria Cristina Soares Pinheiro
- Laboratório de Entomologia Médica, Centro de Estudos Superiores de Caxias, Universidade Estadual do Maranhão, Caxias, MA 65604-380, Brazil;
| | - Joaquim Pinto Nunes Neto
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
| | - Eliana Vieira Pinto da Silva
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
| | - Glennda Juscely Galvão Pereira
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
| | - Bruna Laís Sena do Nascimento
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
| | - Karoline da Silva Castro
- Programa de Pós-Graduação em Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém, PA 66087-670, Brazil; (K.d.S.C.); (A.M.M.)
| | - Ariadne Mendonça Maia
- Programa de Pós-Graduação em Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém, PA 66087-670, Brazil; (K.d.S.C.); (A.M.M.)
| | - Clistenes Pamplona Catete
- Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil;
| | - Lívia Carício Martins
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
| | - Wanderli Pedro Tadei
- Laboratório de Malária e Dengue, Instituto Nacional de Pesquisas da Amazônia, Manaus, CEP 69060-001, Manaus - AM, Brazil;
| | - Sandro Patroca da Silva
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
| | - Ana Cecília Ribeiro Cruz
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Secretaria de Vigilância e Saúde, Ministério da Saúde, Ananindeua, PA 67030-000, Brazil; (J.P.N.N.); (E.V.P.d.S.); (G.J.G.P.); (B.L.S.d.N.); (L.C.M.); (S.P.d.S.)
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Colombo TE, Versiani AF, Dutra KR, Rubiato JGD, Galvão TM, Negri Reis AF, Nogueira ML. Performance of CDC Trioplex qPCR during a dengue outbreak in Brazil. J Clin Virol 2019; 121:104208. [PMID: 31707203 DOI: 10.1016/j.jcv.2019.104208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND In recent years real‑time reverse transcription polymerase chain reaction (real-time RT-PCR) has become a leading technique for nucleic acid detection and quantification of flaviviruses, including Dengue virus (DENV). Trioplex real-time RT-PCR has the advantages of providing the concurrent detection of Zika virus (ZIKV), DENV, and Chikungunya virus (CHIKV) RNA in human serum. OBJECTIVE This study sought to compare the sensitivity and specificity of the Trioplex real-time RT-PCR assay to those provided by CDC DENV TaqMan® RT-qPCR assay and conventional PCR when used for DENV detection in the context of a dengue epidemic. STUDY DESIGN We analyzed 1656 serum samples from symptomatic patients with acute febrile disease for 5 days less between December 2018 and May 2019. The samples were tested using the various PCR-based assays. RESULTS Of the 1656 serum samples analyzed, 713 (43%) were laboratory-confirmed as arboviruses: 99.86% (712/713) were confirmed as DENV and 0.14% (1/713) were confirmed as ZIKV. Next, 590 samples were selected, and of these, 331 samples (56.1%) were determined to be positive (Ct < 38) and 259 samples (43.9%) were determined to be negative (Ct > 38) using the Trioplex real-time RT-PCR assay. The multiplex method found that the test exhibits 95% sensitivity and 100% specificity. CONCLUSION This evaluation demonstrates the capacity of the Trioplex real-time RT-PCR assay to detect DENV at a high sensitivity and specificity in a geographic area with a current dengue outbreak and a lower co-circulation of other arboviruses - such as ZIKV and CHIKV, and the results prove it´s applicability as clinical screening test that can serve as a confirmatory test.
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Affiliation(s)
- Tatiana Elias Colombo
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil; Universidade Paulista (UNIP), São José do Rio Preto, SP, Brazil
| | - Alice Freitas Versiani
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
| | - Karina Rocha Dutra
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
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Laiton-Donato K, Alvarez DA, Peláez-Carvajal D, Mercado M, Ajami NJ, Bosch I, Usme-Ciro JA. Molecular characterization of dengue virus reveals regional diversification of serotype 2 in Colombia. Virol J 2019; 16:62. [PMID: 31068191 PMCID: PMC6505283 DOI: 10.1186/s12985-019-1170-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/25/2019] [Indexed: 11/24/2022] Open
Abstract
Dengue is hyperendemic in Colombia, where a cyclic behavior of serotype replacement leading to periodic epidemics has been observed for decades. This level of endemicity favors accumulation of dengue virus genetic diversity and could be linked to disease outcome. To assess the genetic diversity of dengue virus type 2 in Colombia, we sequenced the envelope gene of 24 virus isolates from acute cases of dengue or severe dengue fever during the period 2013–2016. The phylogenetic analysis revealed the circulation of the Asian-American genotype of dengue virus type 2 in Colombia during that period, the intra-genotype variability leading to divergence in two recently circulating lineages with differential geographic distribution, as well as the presence of nonsynonymous substitutions accompanying their emergence and diversification.
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Affiliation(s)
- Katherine Laiton-Donato
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Avenida Calle 26 N° 51-20 CAN, Bogotá DC, Colombia
| | - Diego A Alvarez
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Avenida Calle 26 N° 51-20 CAN, Bogotá DC, Colombia
| | - Dioselina Peláez-Carvajal
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Avenida Calle 26 N° 51-20 CAN, Bogotá DC, Colombia
| | - Marcela Mercado
- Dirección de Vigilancia y Análisis del Riesgo en Salud Pública, Instituto Nacional de Salud, Bogotá DC, 111321, Colombia
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Irene Bosch
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02142-1601, USA
| | - José A Usme-Ciro
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Avenida Calle 26 N° 51-20 CAN, Bogotá DC, Colombia. .,Current Address: Centro de Investigación en Salud para el Trópico - CIST, Facultad de Medicina, Universidad Cooperativa de Colombia, Troncal del Caribe Sector Mamatoco, Santa Marta, Colombia.
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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: 5.8] [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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Jiménez-Silva CL, Carreño MF, Ortiz-Baez AS, Rey LA, Villabona-Arenas CJ, Ocazionez RE. Evolutionary history and spatio-temporal dynamics of dengue virus serotypes in an endemic region of Colombia. PLoS One 2018; 13:e0203090. [PMID: 30157270 PMCID: PMC6114916 DOI: 10.1371/journal.pone.0203090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 08/14/2018] [Indexed: 12/27/2022] Open
Abstract
Dengue is a prevalent disease in Colombia and all dengue virus serotypes (DENV-1 to -4) co-circulate in the country since 2001. However, the relative impact of gene flow and local diversification on epidemic dynamics is unknown due to heterogeneous sampling and lack of sufficient genetic data. The region of Santander is one of the areas with the highest incidence of dengue in Colombia. To provide a better understanding of the epidemiology of dengue, we inferred DENV population dynamics using samples collected between 1998 and 2015. We used Bayesian phylogenetic analysis and included 143 new envelope gene sequences from Colombia, mainly from the region of Santander, and 235 published sequences from representative countries in the Americas. We documented one single genotype for each serotype but multiple introductions. Whereas the majority of DENV-1, DENV-2, and DENV-4 strains fell into one single lineage, DENV-3 strains fell into two distinct lineages that co-circulated. The inferred times to the most recent common ancestors for the most recent clades of DENV-1, DENV-2, and DENV-4 fell between 1977 and 1987, and for DENV-3 was around 1995. Demographic reconstructions suggested a gradual increase in viral diversity over time. A phylogeographical analysis underscored that Colombia mainly receives viral lineages and a significant diffusion route between Colombia and Venezuela. Our findings contribute to a better understanding of the viral diversity and dengue epidemiology in Colombia.
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Affiliation(s)
- Cinthy L. Jiménez-Silva
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Universidad Industrial de Santander, Bucaramanga, Colombia
| | - María Fernanda Carreño
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Ayda Susana Ortiz-Baez
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Luz Aida Rey
- Unidad de Epidemiología Clínica, Escuela de Medicina, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Christian Julián Villabona-Arenas
- Laboratoire TransVIHMI, Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Institut de Biologie Computationnelle (IBC), Université de Montpellier, Montpellier, France
| | - Raquel E. Ocazionez
- Laboratorio de Arbovirus, Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Universidad Industrial de Santander, Bucaramanga, Colombia
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Low socioeconomic condition and the risk of dengue fever: A direct relationship. Acta Trop 2018; 180:47-57. [PMID: 29352990 DOI: 10.1016/j.actatropica.2018.01.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 02/05/2023]
Abstract
This study aimed to characterize the first dengue fever epidemic in Várzea Paulista, São Paulo, Brazil, and its spatial and spatio-temporal distribution in order to assess the association of socioeconomic factors with dengue occurrence. We used autochthonous dengue cases confirmed in a 2007 epidemic, the first reported in the city, available in the Information System on Diseases of Compulsory Declaration database. These cases where geocoded by address. We identified spatial and spatio-temporal clusters of high- and low-risk dengue areas using scan statistics. To access the risk of dengue occurrence and to evaluate its relationship with socioeconomic level we used a population-based case-control design. Firstly, we fitted a generalized additive model (GAM) to dengue cases and controls without considering the non-spatial covariates to estimate the odds ratios of the occurrence of the disease. The controls were drawn considering the spatial distribution of the household of the study area and represented the source population of the dengue cases. After that, we assessed the relationship between socioeconomic variables and dengue using the GAM and obtained the effect of these covariates in the occurrence of dengue adjusted by the spatial localization of the cases and controls. Cluster analysis and GAM indicated that northeastern area of Várzea Paulista was the most affected area during the epidemic. The study showed a positive relationship between low socioeconomic condition and increased risk of dengue. We studied the first dengue epidemic in a highly susceptible population at the beginning of the outbreak and therefore it may have allowed to identify an association between low socioeconomic conditions and increased risk of dengue. These results may be useful to predict the occurrence and to identify priority areas to develop control measures for dengue, and also for Zika and Chikungunya; diseases that recently reached Latin America, especially Brazil.
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Sedda L, Vilela APP, Aguiar ERGR, Gaspar CHP, Gonçalves ANA, Olmo RP, Silva ATS, de Cássia da Silveira L, Eiras ÁE, Drumond BP, Kroon EG, Marques JT. The spatial and temporal scales of local dengue virus transmission in natural settings: a retrospective analysis. Parasit Vectors 2018; 11:79. [PMID: 29394906 PMCID: PMC5797342 DOI: 10.1186/s13071-018-2662-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/19/2018] [Indexed: 11/10/2022] Open
Abstract
Background Dengue is a vector-borne disease caused by the dengue virus (DENV). Despite the crucial role of Aedes mosquitoes in DENV transmission, pure vector indices poorly correlate with human infections. Therefore there is great need for a better understanding of the spatial and temporal scales of DENV transmission between mosquitoes and humans. Here, we have systematically monitored the circulation of DENV in individual Aedes spp. mosquitoes and human patients from Caratinga, a dengue endemic city in the state of Minas Gerais, in Southeast Brazil. From these data, we have developed a novel stochastic point process pattern algorithm to identify the spatial and temporal association between DENV infected mosquitoes and human patients. Methods The algorithm comprises of: (i) parameterization of the variogram for the incidence of each DENV serotype in mosquitoes; (ii) identification of the spatial and temporal ranges and variances of DENV incidence in mosquitoes in the proximity of humans infected with dengue; and (iii) analysis of the association between a set of environmental variables and DENV incidence in mosquitoes in the proximity of humans infected with dengue using a spatio-temporal additive, geostatistical linear model. Results DENV serotypes 1 and 3 were the most common virus serotypes detected in both mosquitoes and humans. Using the data on each virus serotype separately, our spatio-temporal analyses indicated that infected humans were located in areas with the highest DENV incidence in mosquitoes, when incidence is calculated within 2.5–3 km and 50 days (credible interval 30–70 days) before onset of symptoms in humans. These measurements are in agreement with expected distances covered by mosquitoes and humans and the time for virus incubation. Finally, DENV incidence in mosquitoes found in the vicinity of infected humans correlated well with the low wind speed, higher air temperature and northerly winds that were more likely to favor vector survival and dispersal in Caratinga. Conclusions We have proposed a new way of modeling bivariate point pattern on the transmission of arthropod-borne pathogens between vector and host when the location of infection in the latter is known. This strategy avoids some of the strong and unrealistic assumptions made by other point-process models. Regarding virus transmission in Caratinga, our model showed a strong and significant association between high DENV incidence in mosquitoes and the onset of symptoms in humans at specific spatial and temporal windows. Together, our results indicate that vector surveillance must be a priority for dengue control. Nevertheless, localized vector control at distances lower than 2.5 km around premises with infected vectors in densely populated areas are not likely to be effective. Electronic supplementary material The online version of this article (10.1186/s13071-018-2662-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luigi Sedda
- Centre for Health Information Computation and Statistics (CHICAS), Furness Building, Lancaster University, Lancaster, LA1 4YG, UK
| | - Ana Paula Pessoa Vilela
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil.,Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil.,Present Address: Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahia, 40110-100, Brazil
| | - Caio Henrique Pessoa Gaspar
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - André Nicolau Aquime Gonçalves
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Ana Teresa Saraiva Silva
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Lízia de Cássia da Silveira
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Álvaro Eduardo Eiras
- Department of Parasitology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Betânia Paiva Drumond
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - Erna Geessien Kroon
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil
| | - João Trindade Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30270-901, Brazil.
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Carrillo-Hernández MY, Ruiz-Saenz J, Villamizar LJ, Gómez-Rangel SY, Martínez-Gutierrez M. Co-circulation and simultaneous co-infection of dengue, chikungunya, and zika viruses in patients with febrile syndrome at the Colombian-Venezuelan border. BMC Infect Dis 2018; 18:61. [PMID: 29382300 PMCID: PMC5791178 DOI: 10.1186/s12879-018-2976-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/23/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In Colombia, the dengue virus (DENV) has been endemic for decades, and with the recent entry of the chikungunya virus (CHIKV) (2014) and the Zika virus (ZIKV) (2015), health systems are overloaded because the diagnosis of these three diseases is based on clinical symptoms, and the three diseases share a symptomatology of febrile syndrome. Thus, the objective of this study was to use molecular methods to identify their co-circulation as well as the prevalence of co-infections, in a cohort of patients at the Colombian-Venezuelan border. METHODS A total of 157 serum samples from patients with febrile syndrome consistent with DENV were collected after informed consent and processed for the identification of DENV (conventional PCR and real-time PCR), CHIKV (conventional PCR), and ZIKV (real-time PCR). DENV-positive samples were serotyped, and some of those positive for DENV and CHIKV were sequenced. RESULTS Eighty-two patients were positive for one or more viruses: 33 (21.02%) for DENV, 47 (29.94%) for CHIKV, and 29 (18.47%) for ZIKV. The mean age range of the infected population was statistically higher in the patients infected with ZIKV (29.72 years) than in those infected with DENV or CHIKV (21.09 years). Both co-circulation and co-infection of these three viruses was found. The prevalence of DENV/CHIKV, DENV/ZIKV, and CHIKV/ZIKV co-infection was 7.64%, 6.37%, and 5.10%, with attack rates of 14.90, 12.42, and 9.93 cases per 100,000 inhabitants, respectively. Furthermore, three patients were found to be co-infected with all three viruses (prevalence of 1.91%), with an attack rate of 4.96 cases per 100,000 inhabitants. CONCLUSION Our results demonstrate the simultaneous co-circulation of DENV, CHIKV, ZIKV and their co-infections at the Colombian-Venezuelan border. Moreover, it is necessary to improve the differential diagnosis in patients with acute febrile syndrome and to study the possible consequences of this epidemiological overview of the clinical outcomes of these diseases in endemic regions.
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Affiliation(s)
- Marlen Yelitza Carrillo-Hernández
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Calle 30A #, 33-51, Bucaramanga, Colombia.,Universidad de Santander UDES, Facultad de Ciencias de la Salud, Programa de Bacteriología y Laboratorio clínico, Grupo de investigación en manejo clínico - CLINIUDES, Bucaramanga, Colombia.,Maestría en Investigación en Enfermedades Infecciosas, Universidad de Santander, Bucaramanga, Colombia.,Doctorado en Ciencias Básicas Biomedicas, Universidad de Antioquia, Medellin, Colombia
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Calle 30A #, 33-51, Bucaramanga, Colombia
| | - Lucy Jaimes Villamizar
- Laboratorio Clínico, E.S.E. Jorge Cristo Sahium Hospital, Norte de Santander, Cúcuta, Colombia
| | - Sergio Yebrail Gómez-Rangel
- Universidad de Santander UDES, Facultad de Ciencias de la Salud, Programa de Bacteriología y Laboratorio clínico, Grupo de investigación en manejo clínico - CLINIUDES, Bucaramanga, Colombia
| | - Marlen Martínez-Gutierrez
- Grupo de Investigación en Ciencias Animales-GRICA, Universidad Cooperativa de Colombia, Calle 30A #, 33-51, Bucaramanga, Colombia.
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Complete Coding Sequences of Two Dengue Virus Type 2 Strains Isolated from an Outbreak in Burkina Faso in 2016. GENOME ANNOUNCEMENTS 2017; 5:5/17/e00209-17. [PMID: 28450505 PMCID: PMC5408103 DOI: 10.1128/genomea.00209-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report here the complete coding sequences of two strains of dengue virus type 2, isolated in France from patients returning from Burkina Faso in November 2016. Both strains (cosmopolitan genotype) are almost identical (99.91% nucleotide identity) and closely related to a strain circulating in Burkina Faso in 1983.
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32
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Wei K, Li Y. Global evolutionary history and spatio-temporal dynamics of dengue virus type 2. Sci Rep 2017; 7:45505. [PMID: 28378782 PMCID: PMC5381229 DOI: 10.1038/srep45505] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/27/2017] [Indexed: 11/08/2022] Open
Abstract
DENV-2 spread throughout the tropical and subtropical regions globally, which is implicated in deadly outbreaks of DHF and DSS. Since dengue cases have grown dramatically in recent years, about half of the world's population is now at risk. Our timescale analysis indicated that the most recent common ancestor existed about 100 years ago. The rate of nucleotide substitution was estimated to be 8.94 × 10-4 subs/site/year. Selection pressure analysis showed that two sites 160 and 403 were under positive selection, while E gene is mainly shaped by stronger purifying selection. BSP analysis showed that estimating effective population size from samples of sequences has undergone three obvious increases, additionally, Caribbean and Puerto Rico maintained higher levels of genetic diversity relative to other 6 representative geographical populations using GMRF method. The phylogeographic analysis indicated that two major transmission routes are from South America to Caribbean and East&SouthAsia to Puerto Rico. The trunk reconstruction confirmed that the viral evolution spanned 50 years occurred primarily in Southeast Asia and East&South Asia. In addition, phylogeographic association-trait analysis indicated that the viral phenotypes are highly correlated with phylogeny in Nicaragua and Puerto Rico (P < 0.05).
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
| | - Yuhan Li
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
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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: 79] [Impact Index Per Article: 11.3] [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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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.
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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
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What caused the 2012 dengue outbreak in Pucallpa, Peru? A socio-ecological autopsy. Soc Sci Med 2016; 174:122-132. [PMID: 28024241 DOI: 10.1016/j.socscimed.2016.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/21/2016] [Accepted: 12/07/2016] [Indexed: 01/12/2023]
Abstract
Dengue is highly endemic in Peru, with increases in transmission particularly since vector re-infestation of the country in the 1980s. Pucallpa, the second largest city in the Peruvian Amazon, experienced a large outbreak in 2012 that caused more than 10,000 cases and 13 deaths. To date, there has been limited research on dengue in the Peruvian Amazon outside of Iquitos, and no published review or critical analysis of the 2012 Pucallpa dengue outbreak. This study describes the incidence, surveillance, and control of dengue in Ucayali to understand the factors that contributed to the 2012 Pucallpa outbreak. We employed a socio-ecological autopsy approach to consider distal and proximal contributing factors, drawing on existing literature and interviews with key personnel involved in dengue control, surveillance and treatment in Ucayali. Spatio-temporal analysis showed that relative risk of dengue was higher in the northern districts of Calleria (RR = 2.18), Manantay (RR = 1.49) and Yarinacocha (RR = 1.25) compared to all other districts between 2004 and 2014. The seasonal occurrence of the 2012 outbreak is consistent with typical seasonal patterns for dengue incidence in the region. Our assessment suggests that the outbreak was proximally triggered by the introduction of a new virus serotype (DENV-2 Asian/America) to the region. Increased travel, rapid urbanization, and inadequate water management facilitated the potential for virus spread and transmission, both within Pucallpa and regionally. These triggers occurred within the context of failures in surveillance and control programming, including underfunded and ad hoc vector control. These findings have implications for future prevention and control of dengue in Ucayali as new diseases such as chikungunya and Zika threaten the region.
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Dutra KR, Drumond BP, de Rezende IM, Nogueira ML, de Oliveira Lopes D, Calzavara Silva CE, Siqueira Ferreira JM, Dos Santos LL. Molecular surveillance of dengue in Minas Gerais provides insights on dengue virus 1 and 4 circulation in Brazil. J Med Virol 2016; 89:966-973. [PMID: 27926790 DOI: 10.1002/jmv.24729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 11/11/2022]
Abstract
Dengue, caused by any of the four types of Dengue virus (DENV) is the most important arbovirus in the world. In this study we performed a molecular surveillance of dengue during the greatest dengue outbreak that took place in Divinópolis, Minas Gerais state, Southeast Brazil, in 2013. Samples from 100 patients with clinical symptoms of dengue were studied and 26 were positive. The capsid/premembrane (CprM) and envelope gene sequences of some samples were amplified and sequenced. Molecular analyses demonstrated that two DENV-1 lineages, belonging to genotype V were introduced and co-circulated in Divinópolis. When compared to each other, those lineages presented high genetic diversity and showed unique amino acids substitutions in the envelope protein, including in domains I, II, and III. DENV-4 strains from Divinópolis clustered within genotype IIb and the most recent common ancestor was probably introduced into the city three years before the 2013 epidemic. Here we demonstrated for the first time the circulation of DENV-4 and the co-circulation of two DENV-1 lineages in Midwest region of Minas Gerais, Brazil. Moreover our analysis indicated the introduction of five DENV-1 lineages, genotype V into Brazil, in different times. J. Med. Virol. 89:966-973, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Karina Rocha Dutra
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del Rei (UFSJ), Divinópolis, Minas Gerais, Brazil
| | - Betânia Paiva Drumond
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.,Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Izabela Maurício de Rezende
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.,Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | | | - Débora de Oliveira Lopes
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del Rei (UFSJ), Divinópolis, Minas Gerais, Brazil
| | | | | | - Luciana Lara Dos Santos
- Campus Centro-Oeste Dona Lindu, Universidade Federal de São João Del Rei (UFSJ), Divinópolis, Minas Gerais, Brazil
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37
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Colombo TE, Vedovello D, Pacca-Mazaro CC, Mondini A, Araújo JP, Cabrera E, Lopes JC, Penha dos Santos IN, Negri Reis AF, Costa FR, Antônio Cruz LEA, Ferreira J, de Oliveira Rocha ES, Kroon EG, de Morais Bronzoni RV, Vasilakis N, Nogueira ML. Dengue virus surveillance: Detection of DENV-4 in the city of São José do Rio Preto, SP, Brazil. Acta Trop 2016; 164:84-89. [PMID: 27609639 DOI: 10.1016/j.actatropica.2016.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/14/2022]
Abstract
Dengue viruses are the most common arbovirus infection worldwide and are caused by four distinct serotypes of the dengue virus (DENV). In the present study, we assessed DENV transmission in São José do Rio Preto (SJRP) from 2010 to 2014. We analyzed blood samples from febrile patients who were attended at health care centers in SJRP. DENV detection was performed using multiplex RT-PCR, using flavivirus generic primers, based on the genes of the non-structural protein (NS5), followed by nested-PCR assay with species-specific primers. We analyzed 1549 samples, of which 1389 were positive for NS1 by rapid test. One thousand and eight-seven samples (78%) were confirmed as positive by multiplex RT-PCR: DENV-4, 48.5% (528/1087); DENV-1, 41.5% (449/1087); DENV-2, 9.5% (104/1087); and co-infection (5 DENV-1/DENV-4, 1 DENV-1/DENV-2), 0.5% (6/1087). Phylogenetic analysis of the DENV-4 grouped the isolates identified in this study with the American genotype and the showed a relationship between isolates from SJRP and isolates from the northern region of South America. Taken together, our data shows the detection and emergence of new dengue genotype in a new region and reiterate the importance of surveillance programs to detect and trace the evolution of DENV.
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Furlan NB, Tukasan C, Estofolete CF, Nogueira ML, da Silva NS. Low sensitivity of the tourniquet test for differential diagnosis of dengue: an analysis of 28,000 trials in patients. BMC Infect Dis 2016; 16:627. [PMID: 27809813 PMCID: PMC5095934 DOI: 10.1186/s12879-016-1947-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/20/2016] [Indexed: 01/15/2023] Open
Abstract
Background The aim of this study was to evaluate the utility of the tourniquet test (TT) for dengue diagnosing. To our knowledge, no previous study with such a large sample, of this duration, with as many laboratory methods referenced, or relating the results of the TT to the 2009 WHO classification of severity has been conducted thus far. Methods In this study, we analyzed the records of 119,589 suspected dengue cases in a Brazilian city, with 30,670 confirmed cases. The Cohen’s Kappa test was applied to evaluate the degree of agreement between the tests, and the sensitivity and specificity was calculated for the TT. Results Twenty-eight thousand six hundred thirty-five TT were performed. No association between the outcome of the TT and greater severity of infection, according to the 2009 guideline, was observed (P = 0.28); furthermore, relevant agreement with the final diagnosis (κ = 0.01; 95 % CI = 0.00 to 0.02) or individually with the IgM enzyme-linked immunoassay was not observed (κ = 0.05; 95 % CI = 0.04 to 0.06), and was even lower with PCR (κ = 0.27; 95 % CI = 0.06 to 0.49). Most importance of the TT was shown in relation to specificity (88.9 %; 95 % CI = 0.88 to 0.89) and negative predictive value (70.3 %; CI 95 % = 0.70 to 0.71). Conclusions TT was more effective in detecting cases that were truly negative than positive. These results suggest that the TT should not be used as diagnosis of dengue.
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Affiliation(s)
- Nathália Barbosa Furlan
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil
| | - Caroline Tukasan
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil
| | - Cássia Fernanda Estofolete
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil.,Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil
| | - Natal Santos da Silva
- Faculdade de Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil. .,Laboratório de Pesquisas em Virologia, Faculdade de Medicina de São José do Rio Preto, São Paulo, Brazil. .,Laboratório de Modelagens Matemática e Estatística em Medicina, União das Faculdades dos Grandes Lagos, São José do Rio Preto, São Paulo, Brazil. .,Laboratório de Modelagens Matemática e Estatística em Medicina, Faculdade de Medicina, União das Faculdades dos Grandes Lagos, Rua Dr. Eduardo Nielsem, 960 Jardim Novo Aeroporto, São Jose do Rio Preto, São Paulo, CEP 15030-070, Brazil.
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Zhao Y, Li L, Ma D, Luo J, Ma Z, Wang X, Pan Y, Chen J, Xi J, Yang J, Qiu L, Bai C, Jiang L, Shan X, Sun Q. Molecular Characterization and Viral Origin of the 2015 Dengue Outbreak in Xishuangbanna, Yunnan, China. Sci Rep 2016; 6:34444. [PMID: 27681163 PMCID: PMC5041078 DOI: 10.1038/srep34444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/13/2016] [Indexed: 11/17/2022] Open
Abstract
A total of 1067 serum samples were collected from febrile patients in Xishuangbanna, Yunnan, 2015. Of these, 852 cases were confirmed to be dengue NS1-positive. 76 structural protein genes were sequenced through RT-PCR based on the viral RNAs extracted from serum samples. Phylogenetic analysis revealed that all strains were classified as cosmopolitan genotype of DENV-2. After comparing with the DENV-2SS, 173 base substitutions were found in 76 sequences, resulting in 43 nonsynonymous mutations, of which 22 mutations existed among all samples. According to secondary structure prediction, 8 new possible nucelotide/protein binding sites were found and another 4 sites were lost among the 775 amino acids of DENV structural proteins as compared with DENV-2SS. Meanwhile, 6 distinct amino acid changes were found in the helix and strand regions, and the distribution of the exposed and buried regions was slightly altered. The results indicated that the epidemic dengue strains of Xishuangbanna in 2015 are most similar to the Indian strain in 2001 and the Sri Lankan strain in 2004. Moreover, it also show a very strong similarity to the epidemic strains of Fujian province in 1999 and 2010, which show that there is an internal recycling epidemic trend of DENV in China.
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Affiliation(s)
- Yujiao Zhao
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Lihua Li
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Dehong Ma
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Jia Luo
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
- Kunming Medical University, Kunming 650500, PR China
| | - Zhiqiang Ma
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Xiaodan Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Junying Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Juemin Xi
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Jiajia Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Lijuan Qiu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Chunhai Bai
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Liming Jiang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Xiyun Shan
- Xishuangbanna Dai Autonomous Prefecture People's Hospital, Jinghong 666100, PR China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China
- Yunnan Key Laboratory of Vaccine Research &Development on Severe Infectious Diseases, Kunming 650118, PR China
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Heinen LBDS, Zuchi N, Cardoso BF, Santos MAMD, Nogueira ML, Dezengrini-Slhessarenko R. DENGUE OUTBREAK IN MATO GROSSO STATE, MIDWESTERN BRAZIL. Rev Inst Med Trop Sao Paulo 2016; 57:489-96. [PMID: 27049702 PMCID: PMC4727134 DOI: 10.1590/s0036-46652015000600005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/05/2015] [Indexed: 12/29/2022] Open
Abstract
Dengue virus (DENV) is the most frequent arbovirus worldwide. In this study, we report a large outbreak in Mato Grosso State (MT). Serum samples from 604 patients with acute febrile illness for less than five days were inoculated in C6/36 cells, then infected cells were subjected to an indirect immunofluorescence test for DENV serotypes and yellow fever virus. Serum samples were submitted to a multiplex-semi-nested-RT-PCR for 11 flaviviruses. DENV-4 was isolated in 150/604 (24.8%) and DENV-1 in 19/604 (3.1%) specimens. By RT-PCR, 331 (54.8%) samples tested positive for DENV; 321 had single infections (DENV-4 n = 305; DENV-1 n = 15; DENV-3 n = 1), nine had co-infections of DENV-1/DENV-4, and one of DENV-2/DENV-4. DENV-4 was detected in 315/331 (95.2%) positive patients from 17 municipalities, and DENV-1 in 24/331 (7.2%) patients from five cities in north-central MT and the city of Cuiaba. The incidence of infection was higher in patients aged 20-39 (142/331; 42.9%). The NS5 partial nucleotide sequence of DENV-1 was most similar to that of genotype V, DENV-2 to Southeast Asian/American, DENV-3 to genotype III, and DENV-4 to genotype II strains, considered the most frequent strains in Brazil. This outbreak coincided with the introduction of DENV-4 in the state. Cuiaba was hyperendemic for the four DENV serotypes, highlighting the necessity for arbovirus surveillance in MT.
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Affiliation(s)
| | - Nayara Zuchi
- Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brasil
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Waman VP, Kolekar P, Ramtirthkar MR, Kale MM, Kulkarni-Kale U. Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes. PeerJ 2016; 4:e2326. [PMID: 27635316 PMCID: PMC5012332 DOI: 10.7717/peerj.2326] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Dengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages. METHODS Complete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches. RESULTS DENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach. DISCUSSION Complete genome-based analysis revealed that the worldwide population of DENV-2 strains is subdivided into fifteen lineages. The population structure of DENV-2 is spatiotemporal and is shaped by episodic positive selection and recombination. Intra-genotype diversity was observed in four genotypes (Asian/American, Asian I, cosmopolitan and sylvatic). Episodic positive selection on envelope and non-structural genes translates into antigenic diversity and appears to be responsible for emergence of strains/lineages in DENV-2 genotypes. Understanding of the genotype diversity and emerging lineages will be useful to design strategies for epidemiological surveillance and vaccine design.
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Affiliation(s)
- Vaishali P. Waman
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
| | - Pandurang Kolekar
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
| | - Mukund R. Ramtirthkar
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
| | - Mohan M. Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, Maharashtra, India
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Soo KM, Khalid B, Ching SM, Chee HY. Meta-Analysis of Dengue Severity during Infection by Different Dengue Virus Serotypes in Primary and Secondary Infections. PLoS One 2016; 11:e0154760. [PMID: 27213782 PMCID: PMC4877104 DOI: 10.1371/journal.pone.0154760] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/19/2016] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Dengue virus (DENV) infection is currently a major cause of morbidity and mortality in the world; it has become more common and virulent over the past half-century and has gained much attention. Thus, this review compared the percentage of severe cases of both primary and secondary infections with different serotypes of dengue virus. METHODS Data related to the number of cases involving dengue fever (DF), dengue hemorrhagic fever (DHF), dengue shock syndrome (DSS) or severe dengue infections caused by different serotypes of dengue virus were obtained by using the SCOPUS, the PUBMED and the OVID search engines with the keywords "(dengue* OR dengue virus*) AND (severe dengue* OR severity of illness index* OR severity* OR DF* OR DHF* OR DSS*) AND (serotypes* OR serogroup*)", according to the MESH terms suggested by PUBMED and OVID. RESULTS Approximately 31 studies encompassing 15,741 cases reporting on the dengue serotypes together with their severity were obtained, and meta-analysis was carried out to analyze the data. This study found that DENV-3 from the Southeast Asia (SEA) region displayed the greatest percentage of severe cases in primary infection (95% confidence interval (CI), 31.22-53.67, 9 studies, n = 598, I2 = 71.53%), whereas DENV-2, DENV-3, and DENV-4 from the SEA region, as well as DENV-2 and DENV-3 from non-SEA regions, exhibited the greatest percentage of severe cases in secondary infection (95% CI, 11.64-80.89, 4-14 studies, n = 668-3,149, I2 = 14.77-96.20%). Moreover, DENV-2 and DENV-4 from the SEA region had been found to be more highly associated with dengue shock syndrome (DSS) (95% CI, 10.47-40.24, 5-8 studies, n = 642-2,530, I2 = 76.93-97.70%), while DENV-3 and DENV-4 from the SEA region were found to be more highly associated with dengue hemorrhagic fever (DHF) (95% CI, 31.86-54.58, 9 studies, n = 674-2,278, I2 = 55.74-88.47%), according to the 1997 WHO dengue classification. Finally, DENV-2 and DENV-4 from the SEA region were discovered to be more highly associated with secondary infection compared to other serotypes (95% CI, 72.01-96.32, 9-12 studies, n = 671-2,863, I2 = 25.01-96.75%). CONCLUSION This study provides evidence that the presence of certain serotypes, including primary infection with DENV-3 from the SEA region and secondary infection with DENV-2, DENV-3, and DENV-4 also from the SEA region, as well as DENV-2 and DENV-3 from non SEA regions, increased the risk of severe dengue infections. Thus, these serotypes are worthy of special consideration when making clinical predictions upon the severity of the infection. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42015026093 (http://www.crd.york.ac.uk/PROSPERO).
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Affiliation(s)
- Kuan-Meng Soo
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Bahariah Khalid
- Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siew-Mooi Ching
- Department of Family Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Malaysian Research Institute on Ageing, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hui-Yee Chee
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Cunha MDP, Guimarães VN, Souza M, de Paula Cardoso DDD, de Almeida TNV, de Oliveira TS, Fiaccadori FS. Phylodynamics of DENV-1 reveals the spatiotemporal co-circulation of two distinct lineages in 2013 and multiple introductions of dengue virus in Goiás, Brazil. INFECTION GENETICS AND EVOLUTION 2016; 43:130-4. [PMID: 27223633 DOI: 10.1016/j.meegid.2016.05.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/02/2023]
Abstract
Dengue virus type 1 (DENV-1) was the first serotype introduced in Brazil, during in the 1980s. Since then, this virus has spread in the Brazilian territory, causing several outbreaks. In 2013 the highest number of dengue cases was notified, when compared to the previous years in Brazil, and the state of Goiás reported over 160 thousand cases. In this study, we aimed to present the Phylodynamics of DENV-1 isolates from the state of Goiás, Brazil, during 2013 outbreak, based on the envelope gene (E) sequences. Phylogenetic analysis revealed that Brazilian DENV-1 isolates are grouped together with viruses from genotype V in two distinct lineages (lineage I and lineage II) reflecting co-circulation. Phylogeographic analyses showed that these lineages were introduced in different moments in Goiás, Brazil, using distinct routes, likely originated from the Caribbean. Lineage I was first introduced coming from Rio de Janeiro (2007-2012), followed by the introduction from Argentina (2010-2013). Lineage II was introduced in a single moment from Rio de Janeiro and this clade has existed since 2007-2010. The different viral introduction events demonstrate the viral dispersion process with neighboring regions, which is essential for the maintenance of outbreaks and introduction of new emerging viruses. In conclusion, obtained data reveals the importance of continuous molecular surveillance of this virus in different regions, providing a better understanding of DENV-1 circulation, considering the evolutionary and virus spread patterns.
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Affiliation(s)
| | | | - Menira Souza
- Federal University of Goiás, Goiânia, Goiás, Brazil
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Poloni TR, Dornas FP, Dos Santos NN, Soares AM, Amarilla AA, Alfonso HL, Trigueiro S, Lavrador MAS, Yamamoto AY, Aquino VH. High prevalence of clinically unsuspected dengue disease among children in Ribeirao Preto city, Brazil. J Med Virol 2016; 88:1711-9. [PMID: 27004990 DOI: 10.1002/jmv.24533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2016] [Indexed: 11/12/2022]
Abstract
The aim of this study was to analyze the characteristics of Dengue virus (DENV)-infected children and the accuracy of dengue diagnosis based on clinical presentations. The inclusion criteria were children ≥1-year-old presenting febrile illness with 1-7 days of onset. Children (n = 110) aged 2-15 years were included in this study. DENV infection was confirmed with virological tests using serum, salvia, and/or urine samples. The attending pediatricians classified 56/110 (50.91%) of the children as suspected dengue cases. The DENV infection was confirmed by specific laboratory tests in 52/56 (92.9%) of the suspected dengue cases but also in 44/54 (81.5%) of the unsuspected dengue cases; total of 96/110 (87.27%) confirmed dengue cases. The clinical diagnosis gave an overall sensitivity of 54.2% (52/96) and a specificity of 71.4% (10/14). The positive predictive value of the clinical diagnosis was 92.8% and negative predictive value was 18.5%. After the third day of onset of symptoms, the DENV genome detection rate was similar in serum and saliva samples, suggesting that saliva samples represent an alternative to blood samples for early dengue diagnosis. Vaccination against Yellow fever virus did not influence the antibody response against DENV-1, DENV-2, and DENV-3, which circulated during the study period. Although the signs and symptoms were compatible with dengue, the attending pediatricians did not suspect the disease in several children. Therefore, the inclusion of virological tests for early diagnosis in the protocols for dengue surveillance would help in the implementation of prompt treatment of patients and epidemic containment strategies. J. Med. Virol. 88:1711-1719, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Telma Regina Poloni
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Fabio Pio Dornas
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Nilton Nascimento Dos Santos
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Adriana Moreira Soares
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Alberto Anastacio Amarilla
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Helda Liz Alfonso
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Sabrina Trigueiro
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marco Aurélio Sicchiroli Lavrador
- Laboratory of Bioinformatics and Biostatistics, Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Aparecida Yulie Yamamoto
- Department of Pediatrics, School of Medicine of Ribeirao Preto, University of São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Victor Hugo Aquino
- Laboratory of Virology, Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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Pang EL, Loh HS. Current perspectives on dengue episode in Malaysia. ASIAN PAC J TROP MED 2016; 9:395-401. [PMID: 27086160 DOI: 10.1016/j.apjtm.2016.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/20/2016] [Indexed: 11/29/2022] Open
Abstract
Prevalence of dengue transmission has been alarmed by an estimate of 390 million infections per annum. Urban encroachment, ecological disruption and poor sanitation are all contributory factors of increased epidemiology. Complication however arises from the fact that dengue virus inherently exists as four different serotypes. Secondary infection is often manifested in the more severe form, such that antibody-dependent enhancement (ADE) could aggravate ailment by allowing pre-existing antibodies to form complexes with infecting viruses as means of intrusion. Consequently, increased viraemic titter and suppression of antiviral response are observed. Deep concerns are thus expressed in regards to escalating trend of hospitalisation and mortality rates. In Malaysia, situation is exacerbated by improper clinical management and pending vector control operations. As a preparedness strategy against the potential deadly dengue pandemic, the call for development of a durable and cost-effective dengue vaccine against all infecting serotypes is intensified. Even though several vaccine candidates are currently being evaluated in clinical trials, uncertainties in regards to serotypes interference, incomplete protection and dose adequacy have been raised. Instead of sole reliance on outsourcing, production of local vaccine should be considered in coherent to government's efforts to combat against dengue.
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Affiliation(s)
- Ee Leen Pang
- School of Biosciences, Faculty of Science, The University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Hwei-San Loh
- School of Biosciences, Faculty of Science, The University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia; Biotechnology Research Centre, The University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
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Nunes PCG, Sampaio SAF, da Costa NR, de Mendonça MCL, Lima MDRQ, Araujo SEM, dos Santos FB, Simões JBS, Gonçalves BDS, Nogueira RMR, de Filippis AMB. Dengue severity associated with age and a new lineage of dengue virus-type 2 during an outbreak in Rio De Janeiro, Brazil. J Med Virol 2016; 88:1130-6. [PMID: 27061403 DOI: 10.1002/jmv.24464] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2015] [Indexed: 02/03/2023]
Abstract
Dengue virus-type 2 (DENV-2) caused three outbreaks, in the years 1990, 1998, and 2008, in Rio de Janeiro, Brazil. The 2008 outbreak was the most severe in reported cases, hospitalizations, and deaths. To investigate virological and epidemiological factors that may have contributed to the pathogenic profile of 2008 epidemic, 102 patients sera obtained during the epidemic and inter-epidemic periods of three outbreaks were analysed by qRT-PCR to estimate viremia levels and their correlation with the clinical, immunological, and demographic patient characteristics. DENV-2 isolates from the outbreaks were sequenced. Two DENV-2 lineages (I and II) of the American/Asian genotype were confirmed, each exclusive for 1990-2002 and 2007-2011, respectively. The mean viremia level in the 2008 samples was two orders of magnitude higher than that of the 1990-2002 samples. Severe dengue cases increased from 31% in 1990-2002 to 69% in 2007-2011; in patients aged ≤15 years, from 3% in 1990-2002 to 37% in 2007-2011. The DENV-2 lineage II and younger age significantly contributed to the pathogenic profile of 2008 epidemic in Rio de Janeiro.
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Affiliation(s)
| | | | | | | | | | - Saraiva Eliane M Araujo
- Flavivirus Laboratory, Oswaldo Cruz Foundation/Oswaldo Cruz Institute, Rio de Janeiro, Brazil
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Tahir U, Khan UH, Zubair MS, Bahar-E-Mustafa. Wolbachia pipientis: A potential candidate for combating and eradicating dengue epidemics in Pakistan. ASIAN PAC J TROP MED 2015; 8:989-998. [PMID: 26706669 DOI: 10.1016/j.apjtm.2015.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/20/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022] Open
Abstract
Dengue virus syndrome is an emerging global health challenge which is endemic in tropical countries like Pakistan. In recent years dengue incidences have increased considerably in different areas of Pakistan with more sever impacts on urban and peri-urban populations. This review is an effort to highlight the changing epidemiology of dengue fever, role of Government of Pakistan in disease management and control using preventive and community based approaches in the region. Moreover, there is an emphasis on application of Wolbachia as novel, inexpensive and environmentally benign candidate for control and eradication of dengue transmitting vectors.
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Affiliation(s)
- Uruj Tahir
- Department of Environmental Sciences, Fatima Jinnah Women University, Rawalpindi, Pakistan.
| | - Umair Hassan Khan
- Department of Microbiology, University of Agriculture Faisalabad, Sub-Campus Toba Tek Singh, Pakistan
| | | | - Bahar-E-Mustafa
- Department of Microbiology, University of Agriculture Faisalabad, Sub-Campus Toba Tek Singh, Pakistan
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Singh S, Gupta BP, Manakkadan A, Manandhar KD, Sreekumar E. Phylogenetic study reveals co-circulation of Asian II and Cosmopolitan genotypes of Dengue virus serotype 2 in Nepal during 2013. INFECTION GENETICS AND EVOLUTION 2015; 34:402-9. [DOI: 10.1016/j.meegid.2015.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/03/2015] [Accepted: 07/05/2015] [Indexed: 10/23/2022]
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Chiaravalloti-Neto F, Pereira M, Fávaro EA, Dibo MR, Mondini A, Rodrigues-Junior AL, Chierotti AP, Nogueira ML. Assessment of the relationship between entomologic indicators of Aedes aegypti and the epidemic occurrence of dengue virus 3 in a susceptible population, São José do Rio Preto, São Paulo, Brazil. Acta Trop 2015; 142:167-77. [PMID: 25484110 DOI: 10.1016/j.actatropica.2014.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/26/2022]
Abstract
The aims of this study were to describe the occurrence of dengue in space and time and to assess the relationships between dengue incidence and entomologic indicators. We selected the dengue autochthonous cases that occurred between September 2005 and August 2007 in São José do Rio Preto to calculate incidence rates by month, year and census tracts. The monthly incidence rates of the city were compared to the monthly Breteau indices (BI) of the São José do Rio Region. Between December 2006 and February 2007, an entomological survey was conducted to collect immature forms of Aedes aegypti in Jaguaré, a São José do Rio Preto neighborhood, and to obtain entomological indices. These indices were represented using statistical interpolation. To represent the occurrence of dengue in the Jaguaré neighborhood in 2006 and 2007, we used the Kernel ratio and to evaluate the relationship between dengue and the entomological indices, we used a generalized additive model in a spatial case-control design. Between September 2005 and August 2007, the occurrence of dengue in São José do Rio Preto was almost entirely caused by DENV3, and the monthly incidence rates presented high correlation coefficients with the monthly BI. In Jaguaré neighborhood, the entomological indices calculated by hectare were better predictors of the spatial distribution of dengue than the indices calculated by properties, but the pupae quantification did not show better prediction qualities than the indices based on the container positivity, in relation to the risk of dengue occurrence. The fact that the municipality's population had a high susceptibility to the serotype DENV3 before the development of this research, along with the almost total predominance of the occurrence of this serotype between 2005 and 2007, facilitated the analysis of the epidemiological situation of the disease and allowed us to connect it to the entomological indicators.
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Sardar T, Rana S, Bhattacharya S, Al-Khaled K, Chattopadhyay J. A generic model for a single strain mosquito-transmitted disease with memory on the host and the vector. Math Biosci 2015; 263:18-36. [PMID: 25645185 DOI: 10.1016/j.mbs.2015.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
Abstract
In the present investigation, three mathematical models on a common single strain mosquito-transmitted diseases are considered. The first one is based on ordinary differential equations, and other two models are based on fractional order differential equations. The proposed models are validated using published monthly dengue incidence data from two provinces of Venezuela during the period 1999-2002. We estimate several parameters of these models like the order of the fractional derivatives (in case of two fractional order systems), the biting rate of mosquito, two probabilities of infection, mosquito recruitment and mortality rates, etc., from the data. The basic reproduction number, R0, for the ODE system is estimated using the data. For two fractional order systems, an upper bound for, R0, is derived and its value is obtained using the published data. The force of infection, and the effective reproduction number, R(t), for the three models are estimated using the data. Sensitivity analysis of the mosquito memory parameter with some important responses is worked out. We use Akaike Information Criterion (AIC) to identify the best model among the three proposed models. It is observed that the model with memory in both the host, and the vector population provides a better agreement with epidemic data. Finally, we provide a control strategy for the vector-borne disease, dengue, using the memory of the host, and the vector.
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Affiliation(s)
- Tridip Sardar
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, West Bengal, India.
| | - Sourav Rana
- Department of Statistics, Visva-Bharati University, Santiniketan, West Bengal, India
| | - Sabyasachi Bhattacharya
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, West Bengal, India
| | - Kamel Al-Khaled
- Department of Mathematics and Statistics, Jordan University of Science and Technology, P.O. Box: 3030, Irbid, 22110, Jordan; Department of Mathematics and Statistics, Sultan Qaboos University, P.O. Box: 36, PC 123, Al-Khod, Muscat, Oman
| | - Joydev Chattopadhyay
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, West Bengal, India.
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