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Rojas A, Shen J, Cardozo F, Bernal C, Caballero O, Ping S, Key A, Haider A, de Guillén Y, Langjahr P, Acosta ME, Aria L, Mendoza L, Páez M, Von-Horoch M, Luraschi P, Cabral S, Sánchez MC, Torres A, Pinsky BA, Piantadosi A, Waggoner JJ. Characterization of Dengue Virus 4 Cases in Paraguay, 2019-2020. Viruses 2024; 16:181. [PMID: 38399957 PMCID: PMC10892180 DOI: 10.3390/v16020181] [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: 10/26/2023] [Revised: 01/16/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
In 2019-2020, dengue virus (DENV) type 4 emerged to cause the largest DENV outbreak in Paraguay's history. This study sought to characterize dengue relative to other acute illness cases and use phylogenetic analysis to understand the outbreak's origin. Individuals with an acute illness (≤7 days) were enrolled and tested for DENV nonstructural protein 1 (NS1) and viral RNA by real-time RT-PCR. Near-complete genome sequences were obtained from 62 DENV-4 positive samples. From January 2019 to March 2020, 799 participants were enrolled: 253 dengue (14 severe dengue, 5.5%) and 546 other acute illness cases. DENV-4 was detected in 238 dengue cases (94.1%). NS1 detection by rapid test was 52.5% sensitive (53/101) and 96.5% specific (387/401) for dengue compared to rRT-PCR. DENV-4 sequences were grouped into two clades within genotype II. No clustering was observed based on dengue severity, location, or date. Sequences obtained here were most closely related to 2018 DENV-4 sequences from Paraguay, followed by a 2013 sequence from southern Brazil. DENV-4 can result in large outbreaks, including severe cases, and is poorly detected with available rapid diagnostics. Outbreak strains seem to have been circulating in Paraguay and Brazil prior to 2018, highlighting the importance of sustained DENV genomic surveillance.
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Affiliation(s)
- Alejandra Rojas
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - John Shen
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - Fátima Cardozo
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
- Departamento de Laboratorio de Análisis Clínicos, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.C.S.); (A.T.)
| | - Cynthia Bernal
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Oliver Caballero
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Sara Ping
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
| | - Autum Key
- Department of Pathology, Emory University, Atlanta, GA 30322, USA;
| | - Ali Haider
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
| | - Yvalena de Guillén
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Patricia Langjahr
- Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo 111421, Paraguay;
| | - Maria Eugenia Acosta
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Laura Aria
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Laura Mendoza
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Malvina Páez
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo 111241, Paraguay; (F.C.); (C.B.); (O.C.); (Y.d.G.); (M.E.A.); (L.A.); (L.M.); (M.P.)
| | - Marta Von-Horoch
- Departamento de Epidemiología, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.V.-H.); (P.L.); (S.C.)
| | - Patricia Luraschi
- Departamento de Epidemiología, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.V.-H.); (P.L.); (S.C.)
| | - Sandra Cabral
- Departamento de Epidemiología, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.V.-H.); (P.L.); (S.C.)
| | - María Cecilia Sánchez
- Departamento de Laboratorio de Análisis Clínicos, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.C.S.); (A.T.)
| | - Aurelia Torres
- Departamento de Laboratorio de Análisis Clínicos, Hospital Central—Instituto de Previsión Social, Asunción 001531, Paraguay; (M.C.S.); (A.T.)
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anne Piantadosi
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
- Department of Pathology, Emory University, Atlanta, GA 30322, USA;
| | - Jesse J. Waggoner
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
- Department of Medicine, Division of Infectious Diseases, Emory University, 1760 Haygood Drive NE, Room E-169, Bay E-1, Atlanta, GA 30322, USA; (S.P.); (A.H.); (A.P.)
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Islam A, Deeba F, Tarai B, Gupta E, Naqvi IH, Abdullah M, Dohare R, Ahmed A, Almajhdi FN, Hussain T, Parveen S. Global and local evolutionary dynamics of Dengue virus serotypes 1, 3, and 4. Epidemiol Infect 2023; 151:e127. [PMID: 37293986 PMCID: PMC10540175 DOI: 10.1017/s0950268823000924] [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: 10/12/2022] [Revised: 04/01/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Evolutionary studies on Dengue virus (DENV) in endemic regions are necessary since naturally occurring mutations may lead to genotypic variations or shifts in serotypes, which may lead to future outbreaks. Our study comprehends the evolutionary dynamics of DENV, using phylogenetic, molecular clock, skyline plots, network, selection pressure, and entropy analyses based on partial CprM gene sequences. We have collected 250 samples, 161 in 2017 and 89 in 2018. Details for the 2017 samples were published in our previous article and that of 2018 are presented in this study. Further evolutionary analysis was carried out using 800 sequences, which incorporate the study and global sequences from GenBank: DENV-1 (n = 240), DENV-3 (n = 374), and DENV-4 (n = 186), identified during 1944-2020, 1956-2020, and 1956-2021, respectively. Genotypes V, III, and I were identified as the predominant genotypes of the DENV-1, DENV-3, and DENV-4 serotypes, respectively. The rate of nucleotide substitution was found highest in DENV-3 (7.90 × 10-4 s/s/y), followed by DENV-4 (6.23 × 10-4 s/s/y) and DENV-1 (5.99 × 10-4 s/s/y). The Bayesian skyline plots of the Indian strains revealed dissimilar patterns amongst the population size of the three serotypes. Network analyses showed the presence of different clusters within the prevalent genotypes. The data presented in this study will assist in supplementing the measures for vaccine development against DENV.
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Affiliation(s)
- Arshi Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Bansidhar Tarai
- Department of Microbiology and Infection Control, Max Superspeciality Hospital, New Delhi, India
| | - Ekta Gupta
- Department of Clinical Virology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Irshad H. Naqvi
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Mohd. Abdullah
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fahad N. Almajhdi
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Tajamul Hussain
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Vernal S, Nahas AK, Chiaravalloti Neto F, Prete Junior CA, Cortez AL, Sabino EC, Luna EJDA. Geoclimatic, demographic and socioeconomic characteristics related to dengue outbreaks in Southeastern Brazil: an annual spatial and spatiotemporal risk model over a 12-year period. Rev Inst Med Trop Sao Paulo 2021; 63:e70. [PMID: 34586304 PMCID: PMC8494490 DOI: 10.1590/s1678-9946202163070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022] Open
Abstract
Dengue fever is re-emerging worldwide, however the reasons of this new emergence
are not fully understood. Our goal was to report the incidence of dengue in one
of the most populous States of Brazil, and to assess the high-risk areas using a
spatial and spatio-temporal annual models including geoclimatic, demographic and
socioeconomic characteristics. An ecological study with both, a spatial and a
temporal component was carried out in Sao Paulo State, Southeastern Brazil,
between January 1st, 2007 and December 31st, 2019. Crude
and Bayesian empirical rates of dengue cases following by Standardized Incidence
Ratios (SIR) were calculated considering the municipalities as the analytical
units and using the Integrated Nested Laplace Approximation in a Bayesian
context. A total of 2,027,142 cases of dengue were reported during the studied
period. The spatial model allocated the municipalities in four groups according
to the SIR values: (I) SIR<0.8; (II) SIR 0.8<1.2; (III) SIR 1.2<2.0 and
SIR>2.0 identified the municipalities with higher risk for dengue outbreaks.
“Hot spots” are shown in the thematic maps. Significant correlations between SIR
and two climate variables, two demographic variables and one socioeconomical
variable were found. No significant correlations were found in the
spatio-temporal model. The incidence of dengue exhibited an inconstant and
unpredictable variation every year. The highest rates of dengue are concentrated
in geographical clusters with lower surface pressure, rainfall and altitude, but
also in municipalities with higher degree of urbanization and better
socioeconomic conditions. Nevertheless, annual consolidated variations in
climatic features do not influence in the epidemic yearly pattern of dengue in
southeastern Brazil.
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Affiliation(s)
- Sebastian Vernal
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Andressa K Nahas
- Universidade de São Paulo, Faculdade de Saúde Pública, Departamento de Epidemiologia, São Paulo, São Paulo, Brazil
| | - Francisco Chiaravalloti Neto
- Universidade de São Paulo, Faculdade de Saúde Pública, Departamento de Epidemiologia, São Paulo, São Paulo, Brazil
| | - Carlos A Prete Junior
- Universidade de São Paulo, Escola Politécnica, Departamento de Engenharia de Sistemas Eletrônicos, São Paulo, São Paulo, Brazil
| | - André L Cortez
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas e Parasitárias, São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
| | - Expedito José de Albuquerque Luna
- Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento de Medicina Preventiva, São Paulo, São Paulo, Brazil
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Different Profiles of Cytokines, Chemokines and Coagulation Mediators Associated with Severity in Brazilian Patients Infected with Dengue Virus. Viruses 2021; 13:v13091789. [PMID: 34578370 PMCID: PMC8473164 DOI: 10.3390/v13091789] [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] [Received: 06/30/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 12/27/2022] Open
Abstract
The incidence of dengue in Latin America has increased dramatically during the last decade. Understanding the pathogenic mechanisms in dengue is crucial for the identification of biomarkers for the triage of patients. We aimed to characterize the profile of cytokines (IFN-γ, TNF-α, IL-1β, IL-6, IL-18 and IL-10), chemokines (CXCL8/IL-8, CCL2/MCP-1 and CXCL10/IP-10) and coagulation mediators (Fibrinogen, D-dimer, Tissue factor-TF, Tissue factor pathway inhibitor-TFPI and Thrombomodulin) during the dengue-4 epidemic in Brazil. Laboratory-confirmed dengue cases had higher levels of TNF-α (p < 0.001), IL-6 (p = 0.005), IL-10 (p < 0.001), IL-18 (p = 0.001), CXCL8/IL-8 (p < 0.001), CCL2/MCP-1 (p < 0.001), CXCL10/IP-10 (p = 0.001), fibrinogen (p = 0.037), D-dimer (p = 0.01) and TFPI (p = 0.042) and lower levels of TF (p = 0.042) compared to healthy controls. A principal component analysis (PCA) distinguished between two profiles of mediators of inflammation and coagulation: protective (TNF-α, IL-1β and CXCL8/IL-8) and pathological (IL-6, TF and TFPI). Lastly, multivariate logistic regression analysis identified high aspartate aminotransferase-to-platelet ratio index (APRI) as independent risk factors associated with severity (adjusted OR: 1.33; 95% CI 1.03–1.71; p = 0.027), the area under the receiver operating characteristics curve (AUC) was 0.775 (95% CI 0.681–0.869) and an optimal cutoff value was 1.4 (sensitivity: 76%; specificity: 79%), so it could be a useful marker for the triage of patients attending primary care centers.
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Cunha MDP, Duarte-Neto AN, Pour SZ, Hajjar LA, Frassetto FP, Dolhnikoff M, Saldiva PHDN, Zanotto PMDA. Systemic dengue infection associated with a new dengue virus type 2 introduction in Brazil - a case report. BMC Infect Dis 2021; 21:311. [PMID: 33794785 PMCID: PMC8015031 DOI: 10.1186/s12879-021-05959-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 03/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dengue infection is caused by an arbovirus with a wide range of presentations, varying from asymptomatic disease to unspecific febrile illness and haemorrhagic syndrome with shock, which can evolve to death. In Brazil, the virus circulates since the 1980s with many introductions of new serotypes, genotypes, and lineages since then. Here we report a fatal case of dengue associated with a Dengue virus (DENV) lineage not detected in the country until now. CASE PRESENTATION The patient, a 58-year-old man arrived at the hospital complaining of fever and severe abdominal pain due to intense gallbladder edema, mimicking acute abdomen. After 48 h of hospital admission, he evolved to refractory shock and death. DENV RNA was detected in all tissues collected (heart, lung, brain, kidney, spleen, pancreas, liver, and testis). Viral sequencing has shown that the virus belongs to serotype 2, American/Asian genotype, in a new clade, which has never been identified in Brazil before. The virus was phylogenetically related to isolates from central America [Puerto Rico (2005-2007), Martinique (2005), and Guadeloupe (2006)], most likely arriving in Brazil from Puerto Rico. CONCLUSION In summary, this was the first fatal documented case with systemic dengue infection associated with the new introduction of Dengue type 2 virus in Brazil during the 2019 outbreak.
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Affiliation(s)
- Marielton Dos Passos Cunha
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
| | | | - Shahab Zaki Pour
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Ludhmila Abrahão Hajjar
- Intensive Care Unit, Heart Institute (InCor), Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Marisa Dolhnikoff
- Pathology Department, Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.
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Origin and Spread of the Dengue Virus Type 1, Genotype V in Senegal, 2015-2019. Viruses 2021; 13:v13010057. [PMID: 33406660 PMCID: PMC7824722 DOI: 10.3390/v13010057] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/20/2023] Open
Abstract
Dengue virus (DENV) is the most widespread arthropod-borne virus, with the number and severity of outbreaks increasing worldwide in recent decades. Dengue is caused by genetically distinct serotypes, DENV-1–4. Here, we present data on DENV-1, isolated from patients with dengue fever during an outbreak in Senegal and Mali (Western Africa) in 2015–2019, that were analyzed by sequencing the envelope (E) gene. The emergence and the dynamics of DENV-1 in Western Africa were inferred by using maximum likelihood and Bayesian methods. The DENV-1 grouped into a monophyletic cluster that was closely related to those from Southeast Asia. The virus appears to have been introduced directly into Medina Gounass (Suburb of Dakar), Senegal (location probability = 0.301, posterior = 0.76). The introduction of the virus in Senegal occurred around 2014 (95% HPD = 2012.88–2014.84), and subsequently, the virus moved to regions within Senegal (e.g., Louga and Fatick), causing intense outbreaks in the subsequent years. The virus appears to have been introduced in Mali (a neighboring country) after its introduction in Senegal. In conclusion, we present evidence that the outbreak caused by DENV-1 in urban environments in Senegal and Mali after 2015 was caused by a single viral introduction from Asia.
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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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8
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Pollett S, Fauver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND. Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks. J Infect Dis 2020; 221:S308-S318. [PMID: 31711190 PMCID: PMC11095994 DOI: 10.1093/infdis/jiz302] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.
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Affiliation(s)
- S. Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University, Bethesda, Maryland
- Marie Bashir Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - J. R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | | | - L. D. Gillis
- Bureau of Public Health Laboratories–Miami, Florida Department of Health
| | - M. A. Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - R. G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - N. D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
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Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases. Sci Rep 2019; 9:20418. [PMID: 31892699 PMCID: PMC6938505 DOI: 10.1038/s41598-019-56650-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/11/2019] [Indexed: 01/03/2023] Open
Abstract
The largest outbreak of yellow fever of the 21st century in the Americas began in 2016, with intense circulation in the southeastern states of Brazil, particularly in sylvatic environments near densely populated areas including the metropolitan region of São Paulo city (MRSP) during 2017–2018. Herein, we describe the origin and molecular epidemiology of yellow fever virus (YFV) during this outbreak inferred from 36 full genome sequences taken from individuals who died following infection with zoonotic YFV. Our analysis revealed that these deaths were due to three genetic variants of sylvatic YFV that belong the South American I genotype and that were related to viruses previously isolated in 2017 from other locations in Brazil (Minas Gerais, Espírito Santo, Bahia and Rio de Janeiro states). Each variant represented an independent virus introduction into the MRSP. Phylogeographic and geopositioning analyses suggested that the virus moved around the peri-urban area without detectable human-to-human transmission, and towards the Atlantic rain forest causing human spill-over in nearby cities, yet in the absence of sustained viral transmission in the urban environment.
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Poveda-Cuevas SA, Etchebest C, Barroso da Silva FL. Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method. J Chem Inf Model 2019; 60:944-963. [DOI: 10.1021/acs.jcim.9b00895] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sergio A. Poveda-Cuevas
- Universidade de São Paulo, Programa Interunidades em Bioinformática, Rua do Matão, 1010, BR, 05508-090 São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. Café, s/no−Campus da USP, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
- University of São Paulo-Université Sorbonne Paris Cité International Laboratory in Structural Bioinformatics, Av. do Café, s/no−FCFRP, Bloco B, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Catherine Etchebest
- Université de Paris, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, F-75015 Paris, France
- Equipe 2, Dynamique des Structures et des Interactions Moléculaires, Université Paris Diderot−Paris 7, INTS, 6 Rue Alexandre Cabanel, 75015 Paris, France
- Laboratoire d’Excellence GR-Ex, Paris, France
- University of São Paulo-Université Sorbonne Paris Cité International Laboratory in Structural Bioinformatics, Av. do Café, s/no−FCFRP, Bloco B, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Fernando L. Barroso da Silva
- Universidade de São Paulo, Programa Interunidades em Bioinformática, Rua do Matão, 1010, BR, 05508-090 São Paulo, São Paulo, Brazil
- Universidade de São Paulo, Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. Café, s/no−Campus da USP, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
- University of São Paulo-Université Sorbonne Paris Cité International Laboratory in Structural Bioinformatics, Av. do Café, s/no−FCFRP, Bloco B, BR, 14040-903 Ribeirão Preto, São Paulo, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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Ayolabi CI, Olusola BA, Ibemgbo SA, Okonkwo GO. Detection of Dengue viruses among febrile patients in Lagos, Nigeria and phylogenetics of circulating Dengue serotypes in Africa. INFECTION GENETICS AND EVOLUTION 2019; 75:103947. [PMID: 31276800 DOI: 10.1016/j.meegid.2019.103947] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 11/16/2022]
Abstract
Dengue fever, a mosquito borne viral disease, is caused by Dengue virus. This virus and its vector is endemic in most tropical countries including Nigeria. Dengue presents with febrile symptoms and is a major cause of morbidity and mortality in affected countries. The infection presently has no licensed drugs and vaccine is only available for previously exposed individuals. Despite the endemicity of Dengue in Nigeria, very few studies have identified circulating Dengue genotypes in the country. There is also sparse information on the occurrence, distribution and temporal patterns of circulating dengue virus serotypes as well as genotypes in Africa. This situation creates barriers to effective control of the infection in the continent. This study identified Dengue serotypes and genotypes among febrile patients in two health centers in Lagos, Nigeria. Phylogenetic analysis of Dengue sequences previously collected from African countries and submitted to GenBank database from 1944 till date was also performed. One hundred and thirty febrile persons were recruited for the study between April and August 2018. Eleven (8.5%) persons were Dengue virus positive. Dengue virus serotypes 1 (genotype I) and 3 (genotype I) were identified as actively circulating in Lagos, Nigeria. DENV 1 genotype V, DENV 2 cosmopolitan genotype and DENV 3 genotype III has over the years been the predominant circulating Dengue strains in Africa. Relative genotypic stability of circulating Dengue serotypes in Africa occurred over the past five decades. This may be due to limited investigations on circulating Dengue serotypes among asymptomatic individuals in the region as most studies focused on disease outbreaks and imported cases. There is the need to describe circulating Dengue genotypes in northern Africa, southern Africa as well as among asymptomatic individuals in other parts of Africa as this will provide further information on the diversity of Dengue genotypes circulating in the region.
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Affiliation(s)
| | | | - Sylvester Agha Ibemgbo
- Department of Microbiology, University of Lagos, Lagos, Nigeria; Department of Biological Sciences, Mountain Top University, Ogun State, Nigeria.
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