A tale of 141 municipalities: the spatial distribution of dengue in Mato Grosso, Brazil.

BACKGROUND: In recent years, the state of Mato Grosso has presented one of the highest dengue incidence rates in Brazil. The meeting of the Amazon, Cerrado and Pantanal biomes results in a large variation of rainfall and temperature across different regions of the state. In addition, Mato Grosso has been undergoing intense urban growth since the 1970s, mainly due to the colonization of the Mid-North and North regions. We analyzed factors involved in dengue incidence in Mato Grosso from 2008 to 2019. METHODS: The Moran Global Index was used to assess spatial autocorrelation of dengue incidence using explanatory variables such as temperature, precipitation, deforestation, population density and municipal development index. Areas at risk of dengue were grouped by the Local Moran Indicator. RESULTS: We noticed that areas at risk of dengue expanded from the Mid-North region to the North; the same pattern occurred from the Southeast to the Northeast; the South region remained at low-risk levels. The increase in incidence was influenced by precipitation, deforestation and the municipal development index. CONCLUSIONS: The identification of risk areas for dengue in space and time enables public health authorities to focus their control and prevention efforts, reducing infestation and the potential impact of dengue in the human population.

COVID-19 Patterns in Araraquara, Brazil: A Multimodal Analysis.

The epidemiology of COVID-19 presented major shifts during the pandemic period. Factors such as the most common symptoms and severity of infection, the circulation of different variants, the preparedness of health services, and control efforts based on pharmaceutical and non-pharmaceutical interventions played important roles in the disease incidence. The constant evolution and changes require the continuous mapping and assessing of epidemiological features based on time-series forecasting. Nonetheless, it is necessary to identify the events, patterns, and actions that were potential factors that affected daily COVID-19 cases. In this work, we analyzed several databases, including information on social mobility, epidemiological reports, and mass population testing, to identify patterns of reported cases and events that may indicate changes in COVID-19 behavior in the city of Araraquara, Brazil. In our analysis, we used a mathematical approach with the fast Fourier transform (FFT) to map possible events and machine learning model approaches such as Seasonal Auto-regressive Integrated Moving Average (ARIMA) and neural networks (NNs) for data interpretation and temporal prospecting. Our results showed a root-mean-square error (RMSE) of about 5 (more precisely, a 4.55 error over 71 cases for 20 March 2021 and a 5.57 error over 106 cases for 3 June 2021). These results demonstrated that FFT is a useful tool for supporting the development of the best prevention and control measures for COVID-19.

Detection of Saint Louis encephalitis virus in two Brazilian states.

We describe the circulation of Saint Louis encephalitis virus (SLEV) in two Brazilian States during outbreaks of Dengue and Zika viruses. We detected the virus in a patient from Araraquara, State of São Paulo, and in patients and in a mosquito pool of Culex quinquefasciatus from Sinop, State of Mato Grosso. Phylogenetic analysis grouped samples from this study within genotype V, which are closely related to other strains that previously circulated in other parts of the country. Genotype V seems to have established circulation in Brazil.

National Holidays and Social Mobility Behaviors: Alternatives for Forecasting COVID-19 Deaths in Brazil.

In this paper, we investigate the influence of holidays and community mobility on the transmission rate and death count of COVID-19 in Brazil. We identify national holidays and hallmark holidays to assess their effect on disease reports of confirmed cases and deaths. First, we use a one-variate model with the number of infected people as input data to forecast the number of deaths. This simple model is compared with a more robust deep learning multi-variate model that uses mobility and transmission rates (R0, Re) from a SEIRD model as input data. A principal components model of community mobility, generated by the principal component analysis (PCA) method, is added to improve the input features for the multi-variate model. The deep learning model architecture is an LSTM stacked layer combined with a dense layer to regress daily deaths caused by COVID-19. The multi-variate model incremented with engineered input features can enhance the forecast performance by up to 18.99% compared to the standard one-variate data-driven model.

Detection of the Asian II genotype of dengue virus serotype 2 in humans and mosquitoes in Brazil.

INTRODUCTION: DENV-2 is the cause of most dengue epidemics worldwide and is associated with severe cases. METHODS: We investigated arboviruses in 164 serum samples collected from patients presenting with clinical symptoms of dengue fever and 152 mosquito pools. RESULTS: We detected the Asian II genotype of DENV-2 in humans and mosquitoes. Our results confirmed the circulation of the Asian II genotype in Brazil, in addition to the prevalent Asian/American genotype. CONCLUSIONS: The detection of Asian II genotype of DENV-2 in mosquito pools collected in a forest park may be related to a spillback event of human dengue virus.

Serological point-of-care and label-free capacitive diagnosis of dengue virus infection.

Dengue non-structural protein 1 (NS1 DENV) is considered a biomarker for dengue fever in an early stage. A sensitive and rapid assay for distinguishing positive from negative dengue infection samples is imperative for epidemic control and public health in tropical regions because it enables the development of instantaneous updatable databases and effective surveillance systems. Presently, we successfully report, for the first time, the use of the electrochemical capacitive method for the detection of NS1 DENV biomarker in human serum samples. By using a ferrocene-tagged peptide modified surface containing anti-NS1 as the receptor, it was possible to differentiate positive from negative samples with a p < 0.01 in a reagentless and label-free capacitive format. This capacitive assay had a cut-off of 1.36% (confidence interval of 99.99%); it therefore opens new avenues for developing miniature label-free electrochemical devices for infectious diseases.

Ecological aspects of potential arbovirus vectors (Diptera: Culicidae) in an urban landscape of Southern Amazon, Brazil.

Amazon has been under intense human pressure, especially in the so-called "Arc of Deforestation" in the Eastern and Southern regions. Changes in biodiversity due to landscape disturbance in municipalities at the Arc of Deforestation are likely to impact mosquito species leading to the potential for emergence of arboviruses. Our aim was to describe the composition and structure of culicids in Sinop, a municipality located in the Southern Amazon at the State of Mato Grosso, as well as their presence in urban habitats, analyzing climate variables and potential risk of arbovirus transmission. Mosquitoes were collected in four habitats located in urban environments for 12 months. We recovered 5,210 adult mosquitoes from mosquito traps. Among the 33 species identified, 19 are associated with arbovirus transmission. Higher abundance, richness, diversity, and equitability of mosquito species were observed in urban forest parks and in new neighborhoods located in the outskirts of the city, nearby forest fragments and agricultural areas. As the environment consolidates as urban, both abundance and richness decrease. Highly urbanized neighborhoods had higher dominance of Culex quinquefasciatus, a mosquito associated with different arboviruses, including West Nile and Saint Louis encephalitis virus. The medically important species Cx. declarator, Cx. (Melanoconion) ssp., Aedeomyia squamipennis and Aedes scapularis were found in the four habitats. It is possible that these mosquitoes are adapting to different habitats and as a consequence, they are reaching urbanized areas. Mosquito abundance was higher in the days of high temperature and low precipitation in urban forest parks and in highly urbanized neighborhoods. These results suggest that Sinop region is a key area for surveillance of arbovirus vectors.

Detection of the Asian II genotype of dengue virus serotype 2 in humans and mosquitoes in Brazil

Abstract INTRODUCTION: DENV-2 is the cause of most dengue epidemics worldwide and is associated with severe cases. METHODS: We investigated arboviruses in 164 serum samples collected from patients presenting with clinical symptoms of dengue fever and 152 mosquito pools. RESULTS: We detected the Asian II genotype of DENV-2 in humans and mosquitoes. Our results confirmed the circulation of the Asian II genotype in Brazil, in addition to the prevalent Asian/American genotype. CONCLUSIONS: The detection of Asian II genotype of DENV-2 in mosquito pools collected in a forest park may be related to a spillback event of human dengue virus.

Field-deployable viral diagnostics using CRISPR-Cas13.

Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field deployable. In this study, we demonstrate that the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015-2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

Dengue in Araraquara, state of São Paulo: epidemiology, climate and Aedes aegypti infestation.

OBJECTIVE To describe the epidemiology of dengue in a medium-sized city in the state of São Paulo. METHODS Data, such as circulating serotypes, severe cases and deaths, age group, sex, among others, were obtained on reported and confirmed dengue cases in Araraquara, state of São Paulo, between 1991 and 2015. Climatic and infestation data were also analyzed. These variables were evaluated descriptively, using statistical measures such as frequencies, averages, minimum and maximum. Dengue incidence rates were calculated according to month, year, age and sex, and time series of dengue cases, infestation, and climatic variables. RESULTS Approximately 16,500 cases of dengue fever were reported between 1991 and 2015. The highest number of reports was recorded in 2015 (7,811 cases). In general, the age group with the highest number of reports is between 20 and 59 years old. The highest incidences, generally between March and May, occurred after the increase in rainfall and infestation in January. CONCLUSIONS Increased levels of infestation due to rainfall are reflected in incidence rates of the disease. It is fundamental to know the epidemiology of dengue in medium-sized cities. Such information can be extended to diseases such as Zika and Chikungunya, which are transmitted by the same vector and were reported in the city. The intensification of surveillance efforts in periods before epidemics could be a strategy to be considered to control the viral spread.

Using adult Aedes aegypti females to predict areas at risk for dengue transmission: A spatial case-control study.

INTRODUCTION: Traditional indices for measuring dengue fever risk in a given area are based on the immature forms of the vector (larvae and pupae surveys). However, this is inefficient because only adult female mosquitoes actually transmit the virus. Based on these assumptions, our objective was to evaluate the association between an entomological index obtained from adult mosquito traps and the occurrence of dengue in a hyperendemic area. Additionally, we compared its cost to that of the Breteau Index (BI). MATERIAL AND METHODS: We performed this study in São José do Rio Preto, SP, Brazil, between the epidemiological weeks of 36/2012 and 19/2013. BG-Sentinel and BG-Mosquitito traps were installed to capture adult mosquitoes. Positive and negative cases of dengue fever were computed and geocoded. We generated biweekly thematic maps of the entomological index, generated by calculating the number of adult Aedes aegypti females (NAF) per 100 households during a week by kriging, and based on the number of mosquitoes captured. The relation between the occurrence of dengue fever and the NAF was tested using a spatial case-control design and a generalized additive model and was controlled by the coordinates of the positive and negative cases of dengue fever. RESULTS: Our analyses showed that increases in dengue fever cases occurred in parallel with increases in the number of Ae. aegypti females. The entomological index produced in our study correlates positively with the incidence of dengue, particularly during intervals when vector control measures were applied less intensively. The operational costs of our index were lower than those of the BI: NAF used 71.5% less human resources necessary to measure the BI. CONCLUSIONS: Spatial analysis techniques and the number of adult Ae. aegypti females were used to produce an indicator of dengue risk. The index can be applied at various levels of spatial aggregation for an entire study area, as well as for sub-areas, such as city blocks. Even though the index is adequate to predict dengue risk, it should be tested and validated in various scenarios before routine use.

Dengue in Araraquara, state of São Paulo: epidemiology, climate and Aedes aegypti infestation / Dengue em Araraquara, SP: epidemiologia, clima e infestação por Aedes aegypti

ABSTRACT OBJECTIVE To describe the epidemiology of dengue in a medium-sized city in the state of São Paulo. METHODS Data, such as circulating serotypes, severe cases and deaths, age group, sex, among others, were obtained on reported and confirmed dengue cases in Araraquara, state of São Paulo, between 1991 and 2015. Climatic and infestation data were also analyzed. These variables were evaluated descriptively, using statistical measures such as frequencies, averages, minimum and maximum. Dengue incidence rates were calculated according to month, year, age and sex, and time series of dengue cases, infestation, and climatic variables. RESULTS Approximately 16,500 cases of dengue fever were reported between 1991 and 2015. The highest number of reports was recorded in 2015 (7,811 cases). In general, the age group with the highest number of reports is between 20 and 59 years old. The highest incidences, generally between March and May, occurred after the increase in rainfall and infestation in January. CONCLUSIONS Increased levels of infestation due to rainfall are reflected in incidence rates of the disease. It is fundamental to know the epidemiology of dengue in medium-sized cities. Such information can be extended to diseases such as Zika and Chikungunya, which are transmitted by the same vector and were reported in the city. The intensification of surveillance efforts in periods before epidemics could be a strategy to be considered to control the viral spread.

RESUMO OBJETIVO Descrever a epidemiologia da dengue em cidade de médio porte do estado de São Paulo. MÉTODOS Foram obtidas informações sobre os casos notificados e confirmados de dengue em Araraquara, SP, entre 1991 e 2015, como sorotipos circulantes, casos graves e óbitos, faixa etária, sexo, entre outras. Também foram levantadas as informações climáticas e de infestação pelo vetor. Essas variáveis foram trabalhadas descritivamente, utilizando-se medidas estatísticas como frequências, médias, mínimo e máximo. Calcularam-se taxas de incidência de dengue segundo mês, ano, idade e sexo, e série histórica de casos de dengue, infestação e variáveis climáticas. RESULTADOS Foram confirmados 16.431 casos de dengue entre 1991 e 2015. O maior número de notificações foi registrado em 2015 (7.811 casos). De forma geral, a faixa etária com o maior número de notificações encontra-se entre 20 e 59 anos. As maiores incidências, geralmente entre março e maio, ocorreram após o aumento da pluviosidade e infestação, em janeiro. CONCLUSÕES Os altos níveis de infestação que aumentam com as chuvas refletem-se nas taxas de incidência da doença. É fundamental conhecer a epidemiologia da dengue em cidades de médio porte. Seus resultados podem ser estendidos para doenças como Zika e Chikungunya (transmitidas pelo mesmo vetor e notificadas na cidade). A intensificação dos esforços de vigilâncias em períodos que precedem as epidemias poderia ser uma estratégia a ser considerada para o controle da dispersão viral.

Dengue virus surveillance: Detection of DENV-4 in the city of São José do Rio Preto, SP, Brazil.

Dengue viruses are the most common arbovirus infection worldwide and are caused by four distinct serotypes of the dengue virus (DENV). In the present study, we assessed DENV transmission in São José do Rio Preto (SJRP) from 2010 to 2014. We analyzed blood samples from febrile patients who were attended at health care centers in SJRP. DENV detection was performed using multiplex RT-PCR, using flavivirus generic primers, based on the genes of the non-structural protein (NS5), followed by nested-PCR assay with species-specific primers. We analyzed 1549 samples, of which 1389 were positive for NS1 by rapid test. One thousand and eight-seven samples (78%) were confirmed as positive by multiplex RT-PCR: DENV-4, 48.5% (528/1087); DENV-1, 41.5% (449/1087); DENV-2, 9.5% (104/1087); and co-infection (5 DENV-1/DENV-4, 1 DENV-1/DENV-2), 0.5% (6/1087). Phylogenetic analysis of the DENV-4 grouped the isolates identified in this study with the American genotype and the showed a relationship between isolates from SJRP and isolates from the northern region of South America. Taken together, our data shows the detection and emergence of new dengue genotype in a new region and reiterate the importance of surveillance programs to detect and trace the evolution of DENV.

Detection of Mayaro virus infections during a dengue outbreak in Mato Grosso, Brazil.

Arboviruses are common agents of human febrile illness worldwide. In dengue-endemic areas illness due to other arboviruses have been misdiagnosed as dengue based only on clinical-epidemiological data. In this study we investigated the presence of Brazilian arboviruses in sera of 200 patients presenting acute febrile illness, during a dengue outbreak in Sinop, MT, Brazil. The results showed that 38 samples were positive to Dengue virus (DENV) type 1, two samples to DENV type 4, and six to Mayaro virus. These results indicate that arboviruses others than DENV are circulating in Sinop and the surrounding region, which are going undiagnosed. In addition, molecular and evolutionary analyses indicate that two MAYV genotypes are co-circulating in Mato Grosso, Brazil. Thus, a strong surveillance program must be implemented to evaluate and monitor the distribution and the true importance of non-dengue arboviruses in the etiology of acute febrile illnesses.

Assessment of the relationship between entomologic indicators of Aedes aegypti and the epidemic occurrence of dengue virus 3 in a susceptible population, São José do Rio Preto, São Paulo, Brazil.

The aims of this study were to describe the occurrence of dengue in space and time and to assess the relationships between dengue incidence and entomologic indicators. We selected the dengue autochthonous cases that occurred between September 2005 and August 2007 in São José do Rio Preto to calculate incidence rates by month, year and census tracts. The monthly incidence rates of the city were compared to the monthly Breteau indices (BI) of the São José do Rio Region. Between December 2006 and February 2007, an entomological survey was conducted to collect immature forms of Aedes aegypti in Jaguaré, a São José do Rio Preto neighborhood, and to obtain entomological indices. These indices were represented using statistical interpolation. To represent the occurrence of dengue in the Jaguaré neighborhood in 2006 and 2007, we used the Kernel ratio and to evaluate the relationship between dengue and the entomological indices, we used a generalized additive model in a spatial case-control design. Between September 2005 and August 2007, the occurrence of dengue in São José do Rio Preto was almost entirely caused by DENV3, and the monthly incidence rates presented high correlation coefficients with the monthly BI. In Jaguaré neighborhood, the entomological indices calculated by hectare were better predictors of the spatial distribution of dengue than the indices calculated by properties, but the pupae quantification did not show better prediction qualities than the indices based on the container positivity, in relation to the risk of dengue occurrence. The fact that the municipality's population had a high susceptibility to the serotype DENV3 before the development of this research, along with the almost total predominance of the occurrence of this serotype between 2005 and 2007, facilitated the analysis of the epidemiological situation of the disease and allowed us to connect it to the entomological indicators.

Co-infection ofddengue virus by serotypes 1 and4 in patient from medium sized city from Brazil / Co-infeccao por virus dengue, sorotipos 1 e 4, em paciente de cidade de porte medio no Brasil

SUMMARY The natural co-infection with dengue virus can occur in highly endemic areas where different serotypes have been observed for many years. We report one case of DENV-1/DENV-4 co-infection in human serum detected by molecular tests. Phylogenetic analysis of the sequences obtained indicated the presence of genotype V and II for DENV-1 and DENV-4, respectively. .

RESUMO A co-infecção por dengue vírus pode ocorrer em áreas com circulação endêmica, nas quais diferentes sorotipos vêm circulando durante muitos anos. Neste trabalho relatamos um caso de co-infecção por DENV-1/DENV-4 em soro humano, detectado por testes moleculares. Análises filogenéticas das sequências obtidas indicaram a presença do genótipo V e II de DENV-1 e DENV-4, respectivamente. .

Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006-2007.

Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.

Circulation of different lineages of Dengue virus 2, genotype American/Asian in Brazil: dynamics and molecular and phylogenetic characterization.

The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80's. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998-2000) and BR3 (2003-05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.

Serological detection of West Nile virus in horses and chicken from Pantanal, Brazil

In an effort to detect West Nile virus (WNV) in Brazil, we sampled serum from horses and chickens from the Pantanal region of the state of Mato Grosso and tested for flavivirus-reactive antibodies by blocking ELISA. The positive samples were further confirmed for serological evidence of WNV infection in three (8%) of the 38 horses and one (3.2%) of the 31 chickens using an 80% plaque-reduction neutralisation test (PRNT80). These results provide evidence of the circulation of WNV in chickens and horses in Pantanal.

First identification of Culex flavivirus (Flaviviridae) in Brazil.

INTRODUCTION: Culex flavivirus (CxFV) was first isolated in 2007 from Culex pipiens in Japan and then identified in several other countries. Characterization of the CxFV showed that all strains are related to the cell fusing agent virus. In this manuscript we report the first identification of CxFV in South America. MATERIAL AND METHODS: We have collected Culex sp. mosquitoes using BG-Sentinel traps and manual aspirators. They were pooled according to genus, species, sex and location. Viral RNA was extracted and multiplex nested PCR was performed to test the presence of Flavivirus. The positive samples were isolated in C6/36 cells and sequenced for phylogenetic analyses. RESULTS: 265 female Culex mosquitoes pooled in 83 pools were tested with specific CxFV, Saint Louis encephalitis virus (SLEV) and West Nile virus (WNV) primers. Our sequence data indicated maximum sequence similarity of 97% with CxFV. DISCUSSION: In this study we report the circulation of CxFV in an urban setting where SLEV had previously caused an outbreak. In terms of public health, this is an important finding due to the assumption that the previous exposition of mosquitoes to CxFV might lessen the susceptibility of these mosquitoes to other flaviviruses.