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Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil

The dengue virus has a single-stranded positive-sense RNA genome of ∼10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DEN...

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Autores principales: Mondini, Adriano, Bronzoni, Roberta Vieira de Moraes, Nunes, Silvia Helena Pereira, Chiaravalloti Neto, Francisco, Massad, Eduardo, Alonso, Wladimir J., Lázzaro, Eduardo S. M., Ferraz, Amena Alcântara, de Andrade Zanotto, Paolo Marinho, Nogueira, Maurício Lacerda
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682200/
https://www.ncbi.nlm.nih.gov/pubmed/19478848
http://dx.doi.org/10.1371/journal.pntd.0000448
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author Mondini, Adriano
Bronzoni, Roberta Vieira de Moraes
Nunes, Silvia Helena Pereira
Chiaravalloti Neto, Francisco
Massad, Eduardo
Alonso, Wladimir J.
Lázzaro, Eduardo S. M.
Ferraz, Amena Alcântara
de Andrade Zanotto, Paolo Marinho
Nogueira, Maurício Lacerda
author_facet Mondini, Adriano
Bronzoni, Roberta Vieira de Moraes
Nunes, Silvia Helena Pereira
Chiaravalloti Neto, Francisco
Massad, Eduardo
Alonso, Wladimir J.
Lázzaro, Eduardo S. M.
Ferraz, Amena Alcântara
de Andrade Zanotto, Paolo Marinho
Nogueira, Maurício Lacerda
author_sort Mondini, Adriano
collection PubMed
description The dengue virus has a single-stranded positive-sense RNA genome of ∼10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1–4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000–2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.
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spelling pubmed-26822002009-05-27 Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil Mondini, Adriano Bronzoni, Roberta Vieira de Moraes Nunes, Silvia Helena Pereira Chiaravalloti Neto, Francisco Massad, Eduardo Alonso, Wladimir J. Lázzaro, Eduardo S. M. Ferraz, Amena Alcântara de Andrade Zanotto, Paolo Marinho Nogueira, Maurício Lacerda PLoS Negl Trop Dis Research Article The dengue virus has a single-stranded positive-sense RNA genome of ∼10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1–4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000–2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area. Public Library of Science 2009-05-26 /pmc/articles/PMC2682200/ /pubmed/19478848 http://dx.doi.org/10.1371/journal.pntd.0000448 Text en Mondini et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Mondini, Adriano
Bronzoni, Roberta Vieira de Moraes
Nunes, Silvia Helena Pereira
Chiaravalloti Neto, Francisco
Massad, Eduardo
Alonso, Wladimir J.
Lázzaro, Eduardo S. M.
Ferraz, Amena Alcântara
de Andrade Zanotto, Paolo Marinho
Nogueira, Maurício Lacerda
Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
title Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
title_full Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
title_fullStr Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
title_full_unstemmed Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
title_short Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
title_sort spatio-temporal tracking and phylodynamics of an urban dengue 3 outbreak in são paulo, brazil
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682200/
https://www.ncbi.nlm.nih.gov/pubmed/19478848
http://dx.doi.org/10.1371/journal.pntd.0000448
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