Dataset Information

Spatial-Temporal Assessment of Environmental Factors Related to Dengue Outbreaks in Sao Paulo, Brazil.

ABSTRACT: Dengue fever, a disease caused by a vector-borne flavivirus, is endemic to tropical countries, but its occurrence has been reported worldwide. This study aimed to understand important factors contributing to the spatial and temporal patterns of dengue occurrence in São Paulo, the largest municipality of Brazil. The temporal assessment of dengue occurrence covered the 2011-2016 time period and was based on climatological data, such as the El Niño indices and time series statistical tools such as the continuous wavelet transformation. The spatial assessment used Landsat 8 data for years 2014-2016 to estimate land surface temperature and normalized indices for vegetation, urban areas, and leaf water. Results from a cross correlation for the temporal analysis found a relationship between the sea surface temperature anomalies index and the number of reported dengue cases in São Paulo (r = 0.5) with a lag of +29 (weeks) between the climatic event and the response on the dengue incidence. This relationship, initially nonlinear, became linear after correcting for the lag period. For the spatial assessment, the linear stepwise regression model detected a low relationship between dengue incidence and minimum surface temperature (r = 0.357) and no relationship with other environmental parameters. The poor relationship might be due to confounding effects of socioeconomic factors as these seem to influence the spatial dynamics of dengue incidence. More testing is needed to validate these methods in other locations. Nevertheless, we presented possible tools to be used for the improvement of dengue control programs.

SUBMITTER: Ogashawara I

PROVIDER: S-EPMC7007072 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Spatial-Temporal Assessment of Environmental Factors Related to Dengue Outbreaks in São Paulo, Brazil.

Ogashawara I I Li L L Moreno-Madriñán M J MJ

GeoHealth 20190821 8

Dengue fever, a disease caused by a vector-borne flavivirus, is endemic to tropical countries, but its occurrence has been reported worldwide. This study aimed to understand important factors contributing to the spatial and temporal patterns of dengue occurrence in São Paulo, the largest municipality of Brazil. The temporal assessment of dengue occurrence covered the 2011-2016 time period and was based on climatological data, such as the El Niño indices and time series statistical tools such as ...[more]

PMID: 32159042

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Project description:The dengue virus has a single-stranded positive-sense RNA genome of approximately 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.

Project description:Species of the genus Flavivirus are widespread in Brazil and are a major public health concern. The country's largest city, São Paulo, is in a highly urbanized area with a few forest fragments which are commonly used for recreation. These can be considered to present a potential risk of flavivirus transmission to humans as they are home simultaneously to vertebrate hosts and mosquitoes that are potential flavivirus vectors. The aim of this study was to conduct flavivirus surveillance in field-collected mosquitoes in the Capivari-Monos Environmental Protection Area (EPA) and identify the flavivirus species by sequence analysis in flavivirus IFA-positive pools. Monthly mosquito collections were carried out from March 2016 to April 2017 with CO2-baited CDC light traps. Specimens were identified morphologically and grouped in pools of up to 10 individuals according to their taxonomic category. A total of 260 pools of non-engorged females were inoculated into C6/36 cell culture, and the cell suspensions were analyzed by indirect immunofluorescence assay (IFA) after the incubation period. IFA-positive pools were tested by qRT-PCR with genus-specific primers targeting the flavivirus NS5 gene to confirm IFA-positive results and sequenced to identify the species. Anopheles cruzii (19.5%) and Wyeomyia confusa (15.3%) were the most frequent vector species collected. IFA was positive for flaviviruses in 2.3% (6/260) of the sample pools. This was confirmed by qRT-PCR in five pools (83.3%). All five flavivirus-positive pools were successfully sequenced and the species identified. DENV serotype 2 (DENV-2) was detected in Culex spp. and Culex vaxus pools, while ZIKV was identified in An. cruzii, Limatus durhamii and Wy. confusa pools. To the best of our knowledge, detection of flavivirus species of medical importance has never previously been reported in these species of wild-caught mosquitoes. The finding of DENV-2 and ZIKV circulating in wild mosquitoes suggests the existence of an enzootic cycle in the area. In-depth studies of DENV-2 and ZIKV, including investigation of mosquito infection, vector competence and infection in sylvatic hosts, are needed to shed light on the transmission dynamics of these important viruses and the potential risk of future outbreaks of DENV-2 and ZIKV infections in the region.

Dataset Information

Spatial-Temporal Assessment of Environmental Factors Related to Dengue Outbreaks in Sao Paulo, Brazil.

Publications

Spatial-Temporal Assessment of Environmental Factors Related to Dengue Outbreaks in São Paulo, Brazil.

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