Abstract
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 R0 = 1.53 and values for lineage 2 of R0 = 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.
Highlights
The genus Flavivirus includes 53 arthropod borne viruses that can cause severe encephalitis, hemorrhagic fever and febrile illness in humans [1]
Our study describes the patterns of spread of different lineages of dengue 3 virus circulating in a medium-sized city from Brazil, and we analyzed the dynamics and microevolution of the disease during the 2006 outbreak
The pattern of dengue virus circulation might be similar to many other settings all over the world, and the information provided by our study can help a better understanding of dengue outbreaks, providing important information for public-health systems
Summary
The genus Flavivirus includes 53 arthropod borne viruses that can cause severe encephalitis, hemorrhagic fever and febrile illness in humans [1]. Dengue viruses (DENV), Saint Louis Encephalitis virus (SLEV), and Yellow Fever virus (YFV) belong to this genus and are important public health issues in most tropical and subtropical countries [2]. Dengue virus has a single-stranded positive-sense RNA genome of ,10,700 nucleotides that is surrounded by a nucleocapsid and covered by a lipid envelope with viral glycoproteins. The RNA genome contains a single open reading frame (ORF) flanked by two untranslated regions (UTRs 39 and 59). The disease is caused by four antigenically distinct virus serotypes (DENV 1–4) and each serotype harbors phylogenetically defined genotypes [5] that have been experiencing massive bursts of genetic diversity as a consequence of the exponentially increasing human population during the last 200 years [5,6,7]
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