Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics

Abstract

BackgroundDengue is the most important mosquito-borne viral disease worldwide. Dengue virus comprises four antigenically related viruses named dengue virus type 1 to 4 (DENV1-4). DENV-3 was re-introduced into the Americas in 1994 causing outbreaks in Nicaragua and Panama. DENV-3 was introduced in Brazil in 2000 and then spread to most of the Brazilian States, reaching the neighboring country, Paraguay in 2002. In this study, we have analyzed the phylogenetic relationship of DENV-3 isolated in Brazil and Paraguay with viruses isolated worldwide. We have also analyzed the evolutionary divergence dynamics of DENV-3 viruses.ResultsThe entire open reading frame (ORF) of thirteen DENV-3 isolated in Brazil (n = 9) and Paraguay (n = 4) were sequenced for phylogenetic analysis. DENV-3 grouped into three main genotypes (I, II and III). Several internal clades were found within each genotype that we called lineage and sub-lineage. Viruses included in this study belong to genotype III and grouped together with viruses isolated in the Americas within the lineage III. The Brazilian viruses were further segregated into two different sub-lineage, A and B, and the Paraguayan into the sub-lineage B. All three genotypes showed internal grouping. The nucleotide divergence was in average 6.7% for genotypes, 2.7% for lineages and 1.5% for sub-lineages. Phylogenetic trees constructed with any of the protein gene sequences showed the same segregation of the DENV-3 in three genotypes.ConclusionOur results showed that two groups of DENV-3 genotypes III circulated in Brazil during 2002–2009, suggesting different events of introduction of the virus through different regions of the country. In Paraguay, only one group DENV-3 genotype III is circulating that is very closely related to the Brazilian viruses of sub-lineage B. Different degree of grouping can be observed for DENV-3 and each group showed a characteristic evolutionary divergence. Finally, we have observed that any protein gene sequence can be used to identify the virus genotype.

Clinical and Virological Descriptive Study in the 2011 Outbreak of Dengue in the Amazonas, Brazil

“…DENV-3 belonged to genotype III introduced from the Caribbean Islands and present in Brazil since the last 15 years [32], [33]. All DENV-4 analyzed in this study belonged to genotype II.…”

Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India

“…Genotypes are defined based on the nucleotide divergence of 6%-8% within each serotype (Holmes and Twiddy, 2003;Sim and Hibberd, 2016). Within a genotype, the group of DENV strains which form phylogenetically distinct monophyletic clusters with bootstrap support of at least 75% (Foster et al, 2004) and a nucleotide divergence of 2.4%-4.9% (mean 2.7%) (Alfonso et al, 2012), are classified as 'lineages', (dos Santos et al, 2011;Foster et al, 2004;Sharma et al, 2011) and the term 'clade' is used to characterize strains clustered under lineages (Uehara et al, 2017).…”

High prevalence of clinically unsuspected dengue disease among children in Ribeirao Preto city, Brazil

“…After the introduction of DENV‐4 in Boa Vista, Roraima State, in 2010, all four serotypes are now circulating in the Brazil [Nogueira et al, ; Amarilla et al, ; Aquino et al, ; Temporao et al, ; Alfonso et al, ; Carneiro et al, ; Drumond et al, , ]. Dengue occurs mainly in young adults [Siqueira et al, ; Teixeira et al, ; San Martín et al, ].…”