1
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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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Adelino T, Lima M, Guimarães NR, Xavier J, Fonseca V, Tomé LMR, Pereira MA, Machado VF, Alcantara LCJ, Iani FCDM, Giovanetti M. Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report. Pathogens 2024; 13:202. [PMID: 38535545 PMCID: PMC10974589 DOI: 10.3390/pathogens13030202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 04/01/2024] Open
Abstract
This report provides a detailed overview of the resurgence of DENV-3 in the state of Minas Gerais, Brazil, which is a concerning scenario in the context of dengue, a mosquito-borne viral disease. Historically, Brazil has grappled with dengue epidemics caused primarily by the DENV-1 and DENV-2 serotypes. However, in 2023, a significant shift in this pattern was observed as DENV-3 made a notable resurgence. This resurgence was characterized by the increase in DENV-3 cases within the country and the region of the Americas. Given the absence of sustained DENV-3 circulation in Brazil in previous years, this situation poses a significant risk, making the population highly susceptible to a potential novel epidemic. In November 2023, a 31-year-old male patient in Belo Horizonte exhibited symptoms of acute febrile syndrome. Multiplex RT-qPCR using the Kit Molecular ZC D-Tipagem confirmed DENV-3 infection, suggesting a likely autochthonous case, as the patient reported no travel history. To promptly assess this resurgence, we applied the nanopore sequencing technology. This allowed for the rapid characterization of the initial DENV-3 case isolated in Minas Gerais in 2023, representing a 13-year interval since the serotype's previous documented circulation in that state. This case report underscores the critical importance of proactive monitoring and the swift implementation of targeted control strategies to address the evolving dynamics of dengue, with a specific emphasis on the resurgence of DENV-3 in the state.
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Affiliation(s)
- Talita Adelino
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (T.A.); (M.L.); (N.R.G.); (L.M.R.T.); (M.A.P.)
| | - Maurício Lima
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (T.A.); (M.L.); (N.R.G.); (L.M.R.T.); (M.A.P.)
| | - Natália R. Guimarães
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (T.A.); (M.L.); (N.R.G.); (L.M.R.T.); (M.A.P.)
| | - Joilson Xavier
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil (L.C.J.A.)
| | - Vagner Fonseca
- Department of Exact and Earth Science, University of the State of Bahia, Salvador 41192-010, Brazil;
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
| | - Luiz Marcelo R. Tomé
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (T.A.); (M.L.); (N.R.G.); (L.M.R.T.); (M.A.P.)
| | - Maira Alves Pereira
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (T.A.); (M.L.); (N.R.G.); (L.M.R.T.); (M.A.P.)
| | | | - Luiz Carlos Junior Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil (L.C.J.A.)
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
| | - Felipe C. de Melo Iani
- Fundação Ezequiel Dias, Belo Horizonte 30510-010, Brazil; (T.A.); (M.L.); (N.R.G.); (L.M.R.T.); (M.A.P.)
| | - Marta Giovanetti
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Brazil (L.C.J.A.)
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Roma, Italy
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3
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Naveca FG, Santiago GA, Maito RM, Ribeiro Meneses CA, do Nascimento VA, de Souza VC, do Nascimento FO, Silva D, Mejía M, Gonçalves L, de Figueiredo RMP, Ribeiro Cruz AC, Diniz Nunes BT, Presibella MM, Quallio Marques NF, Riediger IN, de Mendonça MCL, de Bruycker-Nogueira F, Sequeira PC, de Filippis AMB, Resende P, Campos T, Wallau GL, Gräf T, Delatorre E, Kopp E, Morrison A, Muñoz-Jordán JL, Bello G. Reemergence of Dengue Virus Serotype 3, Brazil, 2023. Emerg Infect Dis 2023; 29:1482-1484. [PMID: 37347884 PMCID: PMC10310385 DOI: 10.3201/eid2907.230595] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
We characterized 3 autochthonous dengue virus serotype 3 cases and 1 imported case from 2 states in the North and South Regions of Brazil, 15 years after Brazil's last outbreak involving this serotype. We also identified a new Asian lineage recently introduced into the Americas, raising concerns about future outbreaks.
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4
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Yu X, Cheng G. Contribution of phylogenetics to understanding the evolution and epidemiology of dengue virus. Animal Model Exp Med 2022; 5:410-417. [PMID: 36245335 PMCID: PMC9610151 DOI: 10.1002/ame2.12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) is one of the most important arboviral pathogens in the tropics and subtropics, and nearly one‐third of the world's population is at risk of infection. The transmission of DENV involves a sylvatic cycle between nonhuman primates (NHP) and Aedes genus mosquitoes, and an endemic cycle between human hosts and predominantly Aedes aegypti. DENV belongs to the genus Flavivirus of the family Flaviviridae and consists of four antigenically distinct serotypes (DENV‐1‐4). Phylogenetic analyses of DENV have revealed its origin, epidemiology, and the drivers that determine its molecular evolution in nature. This review discusses how phylogenetic research has improved our understanding of DENV evolution and how it affects viral ecology and improved our ability to analyze and predict future DENV emergence.
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Affiliation(s)
- Xi Yu
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Gong Cheng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China.,Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China.,Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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5
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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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6
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Utomo DIS, Pambudi S, Sjatha F, Kato T, Park EY. Production of dengue virus-like particles serotype-3 in silkworm larvae and their ability to elicit a humoral immune response in mice. AMB Express 2020; 10:147. [PMID: 32804287 PMCID: PMC7431508 DOI: 10.1186/s13568-020-01087-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/11/2020] [Indexed: 02/08/2023] Open
Abstract
To develop monovalent dengue virus-like particle for serotype 3 (DENV-LP/3), we prepared and expressed two structural polyprotein constructs using silkworm and Bm5 cells: DENV-3 Capsid-premembrane-envelope (DENV-3CprME) and premembrane-envelope (DENV-3prME). The expressed PA-tagged 3CprME and 3prME polypeptides were partially purified by PA-tag affinity chromatography and had molecular weights of 85 and 75 kDa, respectively. Expressed proteins were separately verified using the following primary antibodies: the anti-PA tag antibody, DENV premembrane polyclonal antibody, and DENV envelope polyclonal antibody. Transmission electron microscopy revealed that these DENV-3CprME and 3prME formed rough, spherical DENV-LPs (DENV-LP/3CprME and DENV-LP/3prME), respectively, with a diameter of 30–55 nm. The heparin-binding assay demonstrated that these DENV-LPs contained the envelope protein domain III on their surfaces. Both DENV-LPs showed an affinity to sera from human dengue patients and immunized mice. Immunization of mice with DENV-LP/3prME significantly induced the level of antibodies compared with DENV-LP/3CprME. These results indicate that DENV-LP/3prME is suitable as a vaccine candidate compared with DENV-LP/3CprME.
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7
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Revisiting Key Entry Routes of Human Epidemic Arboviruses into the Mainland Americas through Large-Scale Phylogenomics. Int J Genomics 2018; 2018:6941735. [PMID: 30402454 PMCID: PMC6196792 DOI: 10.1155/2018/6941735] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 11/18/2022] Open
Abstract
The rapid worldwide spread of chikungunya (CHIKV), dengue (DENV), and Zika (ZIKV) viruses have raised great international concern. Knowledge about the entry routes and geographic expansion of these arboviruses to the mainland Americas remain incomplete and controversial. Epidemics caused by arboviruses continue to cause socioeconomic burden globally, particularly in countries where vector control is difficult due to climatic or infrastructure factors. Understanding how the virus circulates and moves from one country to another is of paramount importance to assist government and health officials in anticipating future epidemics, as well as to take steps to help control or mitigate the spread of the virus. Through the analyses of the sequences of arbovirus genomes collected at different locations over time, we identified patterns of accumulated mutations, being able to trace routes of dispersion of these viruses. Here, we applied robust phylogenomic methods to trace the evolutionary dynamics of these arboviruses with special focus on Brazil, the epicenter of these triple epidemics. Our results show that CHIKV, DENV-1–4, and ZIKV followed a similar path prior to their first introductions into the mainland Americas, underscoring the need for systematic arboviral surveillance at major entry points of human population movement between countries such as airports and seaports.
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8
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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9
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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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10
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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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Mota MTDO, Terzian AC, Silva MLCR, Estofolete C, Nogueira ML. Mosquito-transmitted viruses - the great Brazilian challenge. Braz J Microbiol 2016; 47 Suppl 1:38-50. [PMID: 27818091 PMCID: PMC5156505 DOI: 10.1016/j.bjm.2016.10.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
Arboviruses pose a serious threat to public health worldwide, overloading the healthcare system and causing economic losses. These viruses form a very diverse group, and in Brazil, arboviruses belonging to the families Flaviviridae and Togaviridae are predominant. Unfortunately, the number of arboviruses increases in proportion with factors such as deforestation, poor sanitation, climate changes, and introduction of new viruses like Chikungunya virus and Zika virus. In Brazil, dengue is endemic, along with the presence of other arboviruses. The situation is complicated by the scarcity of diagnostic infrastructure and the absence of approved vaccines for these diseases. Disease control, thus, relies solely on vector control. Therefore, enhanced clinical knowledge and improved general awareness about these arboviruses are indispensable to tackle diagnostic inadequacies.
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Affiliation(s)
| | - Ana Carolina Terzian
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
| | | | - Cássia Estofolete
- Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
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12
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Epidemiological Scenario of Dengue in Brazil. BIOMED RESEARCH INTERNATIONAL 2015; 2015:321873. [PMID: 26413514 PMCID: PMC4568054 DOI: 10.1155/2015/321873] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/09/2015] [Indexed: 01/12/2023]
Abstract
Dengue is the most important reemerging mosquito-borne viral disease worldwide. It is caused by any of four Dengue virus types or serotypes (DENV-1 to DENV-4) and is transmitted by mosquitoes from the genus Aedes. Ecological changes have favored the geographic expansion of the vector and, since the dengue pandemic in the Asian and Pacific regions, the infection became widely distributed worldwide, reaching Brazil in 1845. The incidence of dengue in Brazil has been frequently high, and the number of cases in the country has at some point in time represented up to 60% of the dengue reported cases worldwide. This review addresses vector distribution, dengue outbreaks, circulating serotypes and genotypes, and prevention approaches being utilized in Brazil.
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Tittarelli E, Mistchenko AS, Barrero PR. Dengue virus 1 in Buenos Aires from 1999 to 2010: towards local spread. PLoS One 2014; 9:e111017. [PMID: 25343372 PMCID: PMC4208802 DOI: 10.1371/journal.pone.0111017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 09/19/2014] [Indexed: 01/07/2023] Open
Abstract
Dengue virus (DENV) is a public health problem representing the most important arthropod-borne viral disease in humans. In Argentina, Northern provinces have reported autochthonous cases since 1997, though these outbreaks have originated in bordering countries, where co-circulation of more than one serotype has been reported. In the last decade, imported dengue cases have been reported in Buenos Aires, the urban area of Argentina with the highest population density. In 2009, a dengue outbreak affected Buenos Aires and, for the first time, local transmission was detected. All cases of this outbreak were caused by DENV-1. In this report, we present the full-length sequences of 27 DENV-1 isolates, corresponding to imported cases of 1999–2000, as well as local and imported cases of the 2009 and 2010 outbreaks. We analyzed their phylogenetic and phylodynamic relationships and their global and local spread. Additionally, we characterized their genomic and phenotypic features. All cases belonged to DENV-1 genotype V. The most recent ancestor for this genotype was dated ∼1934, whereas that for the 2009 outbreak was dated ∼2007. The mean rates of nucleotide substitution were 4.98E-4 and 8.53E-4 subs./site/yr, respectively. We inferred an introduction from Paraguay in 1999–2000 and mainly from Venezuela during 2009–2010. Overall, the number of synonymous substitutions per synonymous site significantly exceeded the number of non-synonymous substitutions per site and 12 positively selected sites were detected. These analyses could contribute to a better understanding regarding spread and evolution of this pathogen in the Southern Cone of South America.
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Affiliation(s)
- Estefanía Tittarelli
- Laboratorio de Virología, Hospital de Niños “Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
| | - Alicia S. Mistchenko
- Laboratorio de Virología, Hospital de Niños “Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC), Buenos Aires, Argentina
| | - Paola R. Barrero
- Laboratorio de Virología, Hospital de Niños “Ricardo Gutiérrez”, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Mir D, Romero H, Fagundes de Carvalho LM, Bello G. Spatiotemporal dynamics of DENV-2 Asian-American genotype lineages in the Americas. PLoS One 2014; 9:e98519. [PMID: 24897118 PMCID: PMC4045713 DOI: 10.1371/journal.pone.0098519] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/03/2014] [Indexed: 12/30/2022] Open
Abstract
The Asian/American (AS/AM) genotype of dengue virus type 2 (DENV-2) has been evolving in the Americas over the last 30 years, leading to several waves of dengue epidemics and to the emergence of different viral lineages in the region. In this study, we investigate the spatiotemporal dissemination pattern of the DENV-2 lineages at a regional level. We applied phylogenetic and phylogeographic analytical methods to a comprehensive data set of 582 DENV-2 E gene sequences of the AS/AM genotype isolated from 29 different American countries over a period of 30 years (1983 to 2012). Our study reveals that genetic diversity of DENV-2 AS/AM genotype circulating in the Americas mainly resulted from one single founder event and can be organized in at least four major lineages (I to IV), which emerged in the Caribbean region at the early 1980s and then spread and die out with different dynamics. Lineages I and II dominate the epidemics in the Caribbean region during the 1980s and early 1990s, lineage III becomes the prevalent DENV-2 one in the Caribbean and South America during the 1990s, whereas lineage IV dominates the epidemics in South and Central America during the 2000s. Suriname and Guyana seem to represent important entry points for DENV-2 from the Lesser Antilles to South America, whereas Venezuela, Brazil and Nicaragua were pointed as the main secondary hubs of dissemination to other mainland countries. Our study also indicates that DENV-2 AS/AM genotype was disseminated within South America following two main routes. The first route hits Venezuela and the western side of the Andes, while the second route mainly hits Brazil and the eastern side of the Andes. The phenomenon of DENV-2 lineage replacement across successive epidemic outbreaks was a common characteristic in all American countries, although the timing of lineage replacements greatly vary across locations.
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Affiliation(s)
- Daiana Mir
- Laboratorio de Organización y Evolución del Genoma, Dpto. Ecología y Evolución, Facultad de Ciencias CURE, Universidad de la República, Montevideo, Uruguay
- * E-mail:
| | - Hector Romero
- Laboratorio de Organización y Evolución del Genoma, Dpto. Ecología y Evolución, Facultad de Ciencias CURE, Universidad de la República, Montevideo, Uruguay
| | | | - Gonzalo Bello
- Laboratorio de AIDS & Imunologia Molecular. Instituto Oswaldo Cruz - FIOCRUZ. Rio de Janeiro, Brazil
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Nunes MRT, Palacios G, Faria NR, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DBA, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PFC, Lipkin WI. Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLoS Negl Trop Dis 2014; 8:e2769. [PMID: 24743730 PMCID: PMC3990485 DOI: 10.1371/journal.pntd.0002769] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/18/2014] [Indexed: 01/01/2023] Open
Abstract
Dengue virus and its four serotypes (DENV-1 to DENV-4) infect 390 million people and are implicated in at least 25,000 deaths annually, with the largest disease burden in tropical and subtropical regions. We investigated the spatial dynamics of DENV-1, DENV-2 and DENV-3 in Brazil by applying a statistical framework to complete genome sequences. For all three serotypes, we estimated that the introduction of new lineages occurred within 7 to 10-year intervals. New lineages were most likely to be imported from the Caribbean region to the North and Northeast regions of Brazil, and then to disperse at a rate of approximately 0.5 km/day. Joint statistical analysis of evolutionary, epidemiological and ecological data indicates that aerial transportation of humans and/or vector mosquitoes, rather than Aedes aegypti infestation rates or geographical distances, determine dengue virus spread in Brazil.
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Affiliation(s)
- Marcio R. T. Nunes
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Gustavo Palacios
- Center for Genomic Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, Maryland, United States of America
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | | | - Jamilla A. Pantoja
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Sueli G. Rodrigues
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Valéria L. Carvalho
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Daniele B. A. Medeiros
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Guy Baele
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California - Los Angeles, Los Angeles, California, United States of America
| | - Philippe Lemey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Pedro F. C. Vasconcelos
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
- Universidade do Estado do Pará, Belém, Pará, Brazil
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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Drumond BP, Mondini A, Schmidt DJ, Bronzoni RVDM, Bosch I, Nogueira ML. Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization. PLoS One 2013; 8:e59422. [PMID: 23533624 PMCID: PMC3606110 DOI: 10.1371/journal.pone.0059422] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/14/2013] [Indexed: 01/05/2023] Open
Abstract
The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80′s. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998–2000) and BR3 (2003–05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.
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Affiliation(s)
- Betânia Paiva Drumond
- Laboratório de Virologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- * E-mail: (BPD); (MLN)
| | - Adriano Mondini
- Laboratório de Saúde Pública, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista, Araraquara, São Paulo, Brazil
| | - Diane J. Schmidt
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | | | - Irene Bosch
- Genome Resources in Dengue Consortium, Massachusetts Institute of Technology. Cambridge, Massachusetts, United States of America
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisa em Virologia, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
- * E-mail: (BPD); (MLN)
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