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 (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

Concurrent dengue and malaria in the Amazon region

Introduction: The Amazon region has extensive forested areas and natural ecosystems, providing favorable conditions for the existence of innumerous arboviruses. Over 200 arboviruses have been isolated in Brazil and about 40 are associated with human disease. Four out of 40 are considered to be of public health importance in Brazil: Dengue viruses (1-4), Oropouche, Mayaro and Yellow Fever. Along with these viruses, about 98% of the malaria cases are restricted to the Legal Amazon region. Methods: This study aimed to investigate the presence of arboviruses in 111 clinical serum samples from patients living in Novo Repartimento (Para), Placido de Castro (Acre), Porto Velho (Rondonia) and Oiapoque (Amapa). The viral RNA was extracted and RT-PCR was performed followed by a Multiplex-Nested-PCR, using Flavivirus, Alphavirus and Orthobunyavirus generic and species-specific primers. Results: Dengue virus serotype 2 was detected in two patients living in Novo Repartimento (Para) that also presented active Plasmodium vivax infection. Conclusions: Despite scant data, this situation is likely to occur more frequently than detected in the Amazon region. Finally, it is important to remember that both diseases have similar clinical findings, thus the diagnosis could be made concomitantly for dengue and malaria in patients living or returning from areas where both diseases are endemic or during dengue outbreaks.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Hantavirus antibodies among phyllostomid bats from the arc of deforestation in Southern Amazonia, Brazil

In order to determine whether southern Amazonian bats could harbour hantaviruses we, serologically and molecularly, screened blood, saliva, excreta and organ tissues of 47 bats captured from September to December 2015. We found that only phyllostomid bats presented antibodies against hantavirus. The seropositive bats belonged to two species of Phyllostomid bats: the greater spear-nosed bat Phyllostomus hastatus (omnivorous) and the gnome fruit-eating bat Dermanura gnoma. The overall seroprevalence was of 4.2%. Therefore, we show here that hantaviruses are circulating among phyllostomid bats in the Amazonian arc of deforestation

Urban census tracts.

<p>Urban census tracts (<i>i.e.</i>, continuous and homogeneous areas comprising 300 buildings on average, IBGE 2002) according to socioeconomic levels (quartile) and dengue cases with molecular analysis according to strains from January 2006 to June 2006 (A); urban census tracts according to incidence coefficients of dengue cases (quartile) reported to the Surveillance System from September 2005 to August 2006 (B).</p

Bayesian skyline (BSL) plot and number of dengue reported cases.

<p>A) Bayesian skyline (BSL) plot of the virus genealogy-based estimate of the number of new infections (presented as <i>Ne.g</i>) indicated as the median for 82 DENV-3 isolates showing the increase from 180 to 120 days before the last sampling (from present day 0 or day of the last sample taken to the past), which matches with uncanny precision the rise in number of reported cases per 100,000 inhabitants from December of 2005. Apparent differences in overall population sizes are due to both the fact that the BSL shows accumulated number of new infections and to scaling problems or misreport. B) Number of Dengue reported cases in SJRP during the seasons of 2001–2002 (01_02), 2003 (02_03), 2004 (03_04), 2005 (04_05) and 2006 (05_06). It is noticeable that the maximum number of reported cases in 2006 happened in April, when the zenith of the epidemics, determined by the Bayesian skyline plot, was around February.</p