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Dengue virus 1 in Buenos Aires from 1999 to 2010: towards local spread.

Tittarelli E, Mistchenko AS, Barrero PR - PLoS ONE (2014)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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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Most clade credibility tree obtained by a discrete phylogeographic analysis of DENV-1 genotype V.The probable country location and age of the ancestors are shown on the nodes (5E+8 generations sampling every 5E+4). Sequences included in the analysis are noted as GenBank accession number/collection date/source country for sequences downloaded from GenBank, and as HNRGnumber/collection date/source country for sequences obtained in our laboratory. Abbreviations of the countries are as follows: AR: Argentina, BI: British Virgin Islands, BRcen: Center of Brazil, BRnor: North of Brazil, CO: Colombia, FG: French Guiana, IN: India, MX: Mexico, NI: Nicaragua, PE: Peru, PR: Puerto Rico (USA), PY: Paraguay, TH: Thailand, VE: Venezuela.
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pone-0111017-g003: Most clade credibility tree obtained by a discrete phylogeographic analysis of DENV-1 genotype V.The probable country location and age of the ancestors are shown on the nodes (5E+8 generations sampling every 5E+4). Sequences included in the analysis are noted as GenBank accession number/collection date/source country for sequences downloaded from GenBank, and as HNRGnumber/collection date/source country for sequences obtained in our laboratory. Abbreviations of the countries are as follows: AR: Argentina, BI: British Virgin Islands, BRcen: Center of Brazil, BRnor: North of Brazil, CO: Colombia, FG: French Guiana, IN: India, MX: Mexico, NI: Nicaragua, PE: Peru, PR: Puerto Rico (USA), PY: Paraguay, TH: Thailand, VE: Venezuela.

Mentions: Viral phylodynamics and phylogeographic reconstructions were evaluated for genotype V under the TIM2+I+G evolution model. The best demographic and clock models were Coalescent Bayesian Skyline and Lognormal relaxed clock (uncorrelated), respectively. Coalescent analyses showed that the most recent ancestor of DENV-1 genotype V was dated approximately 76 years ago (∼1934) (95% HPD 58.40–94.95). Since then, the population has had a steady size until a first decay inferred around 1998. A deeper second decay was inferred around 2007 (Figure 2). The mean rate of nucleotide substitution was 4.9821E-4 subs./site/yr (95% HPD 3.98E-4-5.97E-4). We found an initial spread from Thailand to India in two waves: the first around 1956, with extensive geographical spread (95% HPD 1944–1965), and a second one without further spread. We inferred an introduction of the virus into the Americas, specifically to Puerto Rico and British Virgin Islands around 1966 (95% HPD 1958–1974) and 1983 (95% HPD 1981–1984), respectively. From these two Caribbean countries, the virus spread to different Latin American countries, such as Colombia, Northern and Center of Brazil, and Paraguay, with the highest state probabilities (SP) (0.28, 0.68, 0.27 and 0.89 respectively). After reaching Colombia, the virus spread to Peru, Nicaragua and diversified into different clades into Venezuela (with SP = 0.56 for the clade related to Argentina). Viruses from Nicaragua spread to Mexico and viruses from the Center of Brazil spread to Paraguay (SP = 0.62). Also, viruses from two different sources of Paraguay and Venezuela reached Argentina around 1999 (95% HPD 1999–2000) and 2006 (95% HPD 2005–2007), with SP = 0.73, 0.90 and 0.99, respectively. The discrete phylogeographic analyses are depicted by the MCCT in Figure 3, and the diffusion process is summarized in Figure 4 and Video S1.


Dengue virus 1 in Buenos Aires from 1999 to 2010: towards local spread.

Tittarelli E, Mistchenko AS, Barrero PR - PLoS ONE (2014)

Most clade credibility tree obtained by a discrete phylogeographic analysis of DENV-1 genotype V.The probable country location and age of the ancestors are shown on the nodes (5E+8 generations sampling every 5E+4). Sequences included in the analysis are noted as GenBank accession number/collection date/source country for sequences downloaded from GenBank, and as HNRGnumber/collection date/source country for sequences obtained in our laboratory. Abbreviations of the countries are as follows: AR: Argentina, BI: British Virgin Islands, BRcen: Center of Brazil, BRnor: North of Brazil, CO: Colombia, FG: French Guiana, IN: India, MX: Mexico, NI: Nicaragua, PE: Peru, PR: Puerto Rico (USA), PY: Paraguay, TH: Thailand, VE: Venezuela.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4208802&req=5

pone-0111017-g003: Most clade credibility tree obtained by a discrete phylogeographic analysis of DENV-1 genotype V.The probable country location and age of the ancestors are shown on the nodes (5E+8 generations sampling every 5E+4). Sequences included in the analysis are noted as GenBank accession number/collection date/source country for sequences downloaded from GenBank, and as HNRGnumber/collection date/source country for sequences obtained in our laboratory. Abbreviations of the countries are as follows: AR: Argentina, BI: British Virgin Islands, BRcen: Center of Brazil, BRnor: North of Brazil, CO: Colombia, FG: French Guiana, IN: India, MX: Mexico, NI: Nicaragua, PE: Peru, PR: Puerto Rico (USA), PY: Paraguay, TH: Thailand, VE: Venezuela.
Mentions: Viral phylodynamics and phylogeographic reconstructions were evaluated for genotype V under the TIM2+I+G evolution model. The best demographic and clock models were Coalescent Bayesian Skyline and Lognormal relaxed clock (uncorrelated), respectively. Coalescent analyses showed that the most recent ancestor of DENV-1 genotype V was dated approximately 76 years ago (∼1934) (95% HPD 58.40–94.95). Since then, the population has had a steady size until a first decay inferred around 1998. A deeper second decay was inferred around 2007 (Figure 2). The mean rate of nucleotide substitution was 4.9821E-4 subs./site/yr (95% HPD 3.98E-4-5.97E-4). We found an initial spread from Thailand to India in two waves: the first around 1956, with extensive geographical spread (95% HPD 1944–1965), and a second one without further spread. We inferred an introduction of the virus into the Americas, specifically to Puerto Rico and British Virgin Islands around 1966 (95% HPD 1958–1974) and 1983 (95% HPD 1981–1984), respectively. From these two Caribbean countries, the virus spread to different Latin American countries, such as Colombia, Northern and Center of Brazil, and Paraguay, with the highest state probabilities (SP) (0.28, 0.68, 0.27 and 0.89 respectively). After reaching Colombia, the virus spread to Peru, Nicaragua and diversified into different clades into Venezuela (with SP = 0.56 for the clade related to Argentina). Viruses from Nicaragua spread to Mexico and viruses from the Center of Brazil spread to Paraguay (SP = 0.62). Also, viruses from two different sources of Paraguay and Venezuela reached Argentina around 1999 (95% HPD 1999–2000) and 2006 (95% HPD 2005–2007), with SP = 0.73, 0.90 and 0.99, respectively. The discrete phylogeographic analyses are depicted by the MCCT in Figure 3, and the diffusion process is summarized in Figure 4 and Video S1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

Show MeSH
Related in: MedlinePlus