Zika Virus Changes Methylation of Genes Involved in Immune Response and Neural Development in Brazilian Babies Born With Congenital Microcephaly.

The recent increase in babies born with brain and eye malformations in Brazil is associated with Zika virus (ZIKV) infection in utero. ZIKV alters host DNA methylation in vitro. Using genome-wide DNA methylation profiling we compared 18 babies born with congenital ZIKV microcephaly with 20 controls. We found ZIKV-associated alteration of host methylation patterns, notably at RABGAP1L which is important in brain development, at viral host immunity genes MX1 and ISG15, and in an epigenetic module containing the causal microcephaly gene MCPH1. Our data support the hypothesis that clinical signs of congenital ZIKV are associated with changes in DNA methylation.

Spectroscopy with computational analysis in virological studies: A decade (2006-2016).

This review presents a retrospective of the studies carried out in the last 10 years (2006-2016) using spectroscopic methods as a research tool in the field of virology. Spectroscopic analyses are sensitive to variations in the biochemical composition of the sample, are non-destructive, fast and require the least sample preparation, making spectroscopic techniques tools of great interest in biological studies. Herein important chemometric algorithms that have been used in virological studies are also evidenced as a good alternative for analyzing the spectra, discrimination and classification of samples. Techniques that have not yet been used in the field of virology are also suggested. This methodology emerges as a new and promising field of research, and may be used in the near future as diagnosis tools for detecting diseases caused by viruses.

Dengue in the State of Rio Grande do Norte, Brazil, 2010-2012.

OBJECTIVE: To present results of virological surveillance and epidemiological aspects of dengue in the State of Rio Grande do Norte, Brazil. METHODS: A total of 1581 cases, reported from 2010 to 2012 at various health centres in the state, were analysed by viral isolation and/or RT-PCR for viral detection and typing. To identify whether different genotypes were circulating in the state during this period, sequencing of the complete E gene for DENV (1485 bp in length) was performed directly from patient serum samples. RESULTS: All four serotypes of dengue virus circulated in Rio Grande do Norte, with the introduction of DENV-4 in the state in 2011. In 2012, DENV-4 represented 100% of positive confirmed cases. 53.97% of cases occurred in Natal. Case numbers peaked in April (21%) and May (23%). Genetic characterisation of circulating strains confirmed the circulation of genotypes V, south-east Asian/American and II, respectively, for DENV-1, DENV-2 and DENV-4. CONCLUSIONS: This work furthers a better understanding of dengue viruses in the State of Rio Grande do Norte. Strengthening control efforts in the region is important considering the impact of dengue.

Infrared spectroscopy (NIRS and ATR-FTIR) together with multivariate classification for non-destructive differentiation between female mosquitoes of Aedes aegypti recently infected with dengue vs. uninfected females.

One of the most important steps in preventing arboviruses is entomological surveillance. The main entomological surveillance action is to detect vector foci in the shortest possible stages. In this work, near and medium infrared spectra collected from female Aedes aegypti mosquitoes recently infected and not infected with dengue were used in order to build chemometric models capable of differentiating the spectra of each class. For this, computational algorithms such as Successive Projection Algorithm (SPA) and Genetic Algorithm (GA) were used together with Linear Discriminant Analysis (LDA). The constructed models were evaluated with sensitivity and specificity calculations. It was observed that models based on near infrared (NIR) spectra have better classification results when compared to mid infrared (MIR) spectra, as well as models based on GA present better results when compared to those based on SPA. Thus, NIR-GA-LDA obtained the best results, reaching 100.00 % for sensitivity and specificity. NIR spectroscopy is 18 times faster and 116 times cheaper than RT-qPCR. The findings reported in this study may have important applications in the field of entomological surveillance, prevention and control of dengue vectors. In the future, mosquito traps equipped with portable NIR instruments capable of detecting infected mosquitoes may be used, in order to enable an action plan to prevent future outbreaks of the disease.

Identification of promiscuous T cell epitopes on Mayaro virus structural proteins using immunoinformatics, molecular modeling, and QM:MM approaches.

The Mayaro virus (MAYV) belongs to genus Alphavirus (family Togaviridae) and has been reported in several countries, especially in tropical regions of America. Due to its outbreaks and potential lack of medication, an effective vaccine formulation is strongly required. This study aimed to predict promiscuous T cell epitopes from structural polyproteins of MAYV using an immunoinformatics approach. For this purpose, consensus sequences were used to identify short protein sequences capable of binding to MHC class I and class II alleles. Our analysis pointed out 4 MHC-I/TCD8+ and 21 MHC-II/TCD4+ epitopes on capside (1;3), E1 (2;5), E2 (1;10), E3 (0;2), and 6 K (0;1) proteins. These predicted epitopes were characterized by high antigenicity, immunogenicity, conservancy, non-allergenic, non-toxic, and good population coverage rate values for North and South American geographical areas. Afterwards, we used the crystal structure of human toll-like receptor 3 (TLR3) ectodomain as a template to predict, through docking essays, the placement of a vaccine prototype at the TLR3 receptor binding site. Finally, classical and quantum mechanics/molecular mechanics (QM:MM) computations were employed to improve the quality of docking calculations, with the QM part of the simulations being accomplished by using the density functional theory (DFT) formalism. These results provide important insights into the advancement of diagnostic platforms, the development of vaccines, and immunotherapeutic interventions.

Molecular fluorescence spectroscopy with multi-way analysis techniques detects spectral variations distinguishing uninfected serum versus dengue or chikungunya viral infected samples.

Significant attempts are being made worldwide in an attempt to develop a tool that, with a simple analysis, is capable of distinguishing between different arboviruses. Herein, we employ molecular fluorescence spectroscopy as a sensitive and specific rapid tool, with simple methodology response, capable of identifying spectral variations between serum samples with or without the dengue or chikungunya viruses. Towards this, excitation emission matrices (EEM) of clinical samples from patients with dengue or chikungunya, in addition to uninfected controls, were separated into a training or test set and analysed using multi-way classification models such as n-PLSDA, PARAFAC-LDA and PARAFAC-QDA. Results were evaluated based on calculations of accuracy, sensitivity, specificity and F score; the most efficient model was identified to be PARAFAC-QDA, whereby 100% was obtained for all figures of merit. QDA was able to predict all samples in the test set based on the scores present in the factors selected by PARAFAC. The loadings obtained by PARAFAC can be used in future studies to prove the direct or indirect relationship of spectral changes caused by the presence of these viruses. This study demonstrates that molecular fluorescence spectroscopy has a greater capacity to detect spectral variations related to the presence of such viruses when compared to more conventional techniques.

Epidemiologic and clinical investigations during a chikungunya outbreak in Rio Grande do Norte State, Brazil.

The first autochthonous case of chikungunya virus (CHIKV) infection in Brazil was in September 2014 in the State of Amapá, and from there it rapidly spread across the country. The present study was conducted in 2016 in the state of Rio Grande do Norte, and the aims were to describe the epidemiological and the clinical aspects of the CHIKV outbreak. Biological samples from 284 chikungunya suspected cases were screened for CHIKV and Flavivirus (FV) RNA using qRT-PCR. Negative PCR samples were also screened for anti-CHIKV and anti-FVIgM by ELISA. CHIKV RNA were detected in 125 samples mostly occurring from January through March (46%), mainly affecting adults and older adults. We found a gradual decrease in viral RNA over the disease time. Anti-CHIKV IgM was found in 47.5% after negative CHIKV qRT-PCR. Interestingly, 45.0% simultaneously had positive results for CHIKV and FV IgM, suggesting the occurrence of virus co-circulation. The most frequent symptom was fever (91%). Women presented more chance to develop nausea and abdominal pain compared to men. Our data described and allows us to better understand the clinical and epidemiological aspects of the 2016 chikungunya outbreak in Rio Grande do Norte and can help in the early clinical diagnosis of the virus.

Accuracy of the SD BIOLINE Dengue Duo for rapid point-of-care diagnosis of dengue.

BACKGROUND: Rapid diagnosis tests (RDTs) are easy to carry out, provide fast results, and could potentially guide medical treatment decisions. We investigated the performance of a commercially available RDT, which simultaneously detects the non-structural 1 (NS1) dengue virus (DENV) antigen, and IgM and IgG DENV antibodies, using representative serum samples from individuals in a dengue endemic area in Salvador, Brazil. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the accuracy of the SD BIOLINE Dengue Duo RDT (Abbott, Santa Clara, USA; former Alere Inc, Waltham, USA) in a random collection of sera. Samples included acute-phase sera from 246 laboratory-confirmed dengue cases and 108 non-dengue febrile patients enrolled in a surveillance study for dengue detection, 73 healthy controls living in the same surveillance community, and 73 blood donors. RDT accuracy was blindly assessed based on the combined results for the NS1 and the IgM test components. The RDT sensitivity was 46.8% (38.6% for the NS1 component and 13.8% for the IgM component). Sensitivity was greater for samples obtained from patients with secondary DENV infections (49.8%) compared to primary infections (31.1%) (P: 0.02) and was also influenced by the result in the confirmatory dengue diagnostic test, ranging from 39.7% for samples of cases confirmed by IgM-ELISA seroconversion between paired samples to 90.4% for samples of cases confirmed by a positive NS1-ELISA. The RDT specificity was 94.4% for non-dengue febrile patients, 87.7% for the community healthy controls, and 95.9% for the blood donors. CONCLUSIONS/SIGNIFICANCE: The SD BIOLINE Dengue Duo RDT showed good specificities, but low sensitivity, suggesting that it may be more useful to rule in than to rule out a dengue diagnosis in dengue endemic regions.

A seminested PCR assay for detection and typing of human papillomavirus based on E1 gene sequences.

HPV infection is considered one of the leading causes of cervical cancer in the world. To date, more than 180 types of HPV have been described and viral typing is critical for defining the prognosis of cancer. In this work, a seminested PCR which allow fast and inexpensively detection and typing of HPV is presented. The system is based on the amplification of a variable length region within the viral gene E1, using three primers that potentially anneal in all HPV genomes. The amplicons produced in the first step can be identified by high resolution electrophoresis or direct sequencing. The seminested step includes nine specific primers which can be used in multiplex or individual reactions to discriminate the main types of HPV by amplicon size differentiation using agarose electrophoresis, reducing the time spent and cost per analysis.

Dengue virus in Aedes aegypti and Aedes albopictus in urban areas in the state of Rio Grande do Norte, Brazil: Importance of virological and entomological surveillance.

BACKGROUND: Vector control remains the sole effective method to prevent dengue virus (DENV) transmission, although a vaccine for dengue has recently become available and testing of its efficacy and coverage is being performed in multiple places. Entomological surveillance is a key factor in alerting authorities to possible outbreaks, but until now natural DENV infection of mosquito populations has been scarcely used as an early warning system to monitor fluctuating prevalence of infected mosquitoes. The purpose of this study was to determine the burden of adult and larval/pupae of Aedes aegypti and Aedes albopictus with DENV in urban areas in the state of Rio Grande do Norte, Brazil. METHODOLOGY/PRINCIPAL FINDINGS: Immature insect forms (larvae and pupae) were collected from April 2011 to March 2012, whereas the collection of adults was conducted along 3 years: May 2011 to April 2014. Total RNAs of the samples were extracted and the nested reverse transcriptase PCR assay for detecting and typing DENV was performed. Of the 1333 immature insects collected during the study period, 1186 (89%) were A. aegypti and 147 (11%) A. albopictus. DENV-4 was identified in pools of A. aegypti larvae. The rate of DENV infection in immature A. aegypti was expressed as MIR = 3.37. DENV wasnot detected in immature A. albopictus. A total of 1360 adult female mosquitoes of the Aedes genus were captured from May 2011 to April 2014. Of this total, 1293 were A. aegypti (95%) and 67 were A. albopictus (5%). From the 130 pools studied, 27 (20.7%) were positive for DENV. DENV-1 was identified in 2/27 (7.4%) pools; 1of A. albopictus and 1 of A. aegypti. DENV-2 was identified in only 1/27 (3.7%) A. aegypti pools. DENV-4 was the most prevalent, identified in 24/27 (88.8%) of the positive pools, with 19 being of A. aegypti and 5 of A. albopictus pools. The minimum infection rate for adults of the Aedes genus was 19.8, considering both A. aegypti and A. albopictus. CONCLUSIONS/SIGNIFICANCE: This work represents the most complete study to date on the interaction between dengue viruses and Aedes mosquitoes in the State of Rio Grande do Norte, and raises important questions about a possible role of A. albopictus in the transmission of dengue virus in Brazil.

Spatial Distribution of Dengue in a Brazilian Urban Slum Setting: Role of Socioeconomic Gradient in Disease Risk.

BACKGROUND: Few studies of dengue have shown group-level associations between demographic, socioeconomic, or geographic characteristics and the spatial distribution of dengue within small urban areas. This study aimed to examine whether specific characteristics of an urban slum community were associated with the risk of dengue disease. METHODOLOGY/PRINCIPAL FINDINGS: From 01/2009 to 12/2010, we conducted enhanced, community-based surveillance in the only public emergency unit in a slum in Salvador, Brazil to identify acute febrile illness (AFI) patients with laboratory evidence of dengue infection. Patient households were geocoded within census tracts (CTs). Demographic, socioeconomic, and geographical data were obtained from the 2010 national census. Associations between CTs characteristics and the spatial risk of both dengue and non-dengue AFI were assessed by Poisson log-normal and conditional auto-regressive models (CAR). We identified 651 (22.0%) dengue cases among 2,962 AFI patients. Estimated risk of symptomatic dengue was 21.3 and 70.2 cases per 10,000 inhabitants in 2009 and 2010, respectively. All the four dengue serotypes were identified, but DENV2 predominated (DENV1: 8.1%; DENV2: 90.7%; DENV3: 0.4%; DENV4: 0.8%). Multivariable CAR regression analysis showed increased dengue risk in CTs with poorer inhabitants (RR: 1.02 for each percent increase in the frequency of families earning ≤1 times the minimum wage; 95% CI: 1.01-1.04), and decreased risk in CTs located farther from the health unit (RR: 0.87 for each 100 meter increase; 95% CI: 0.80-0.94). The same CTs characteristics were also associated with non-dengue AFI risk. CONCLUSIONS/SIGNIFICANCE: This study highlights the large burden of symptomatic dengue on individuals living in urban slums in Brazil. Lower neighborhood socioeconomic status was independently associated with increased risk of dengue, indicating that within slum communities with high levels of absolute poverty, factors associated with the social gradient influence dengue transmission. In addition, poor geographic access to health services may be a barrier to identifying both dengue and non-dengue AFI cases. Therefore, further spatial studies should account for this potential source of bias.

Preliminary evaluation on the efficiency of the kit Platelia Dengue NS1 Ag-ELISA to detect dengue virus in dried Aedes aegypti: a potential tool to improve dengue surveillance.

BACKGROUND: Surveillance is a critical component of any dengue prevention and control programme. Herein, we investigate the efficiency of the commercial kit Platelia Dengue NS1 Ag-ELISA to detect dengue virus (DENV) antigens in Aedes aegypti mosquitoes infected under laboratory conditions. METHODS: Under insectary conditions, four to five day-old mosquitoes were orally challenged with DENV-2 titer of 3.6 x 105 PFU equivalent/ml, incubated for 14 days and then killed. At ten time-points following mosquito death (0, 6, 12, 24, 72, 96, 120, 144 and 168 h), i.e., during a one-week period, dried mosquitoes were comparatively tested for the detection of the NS1 antigen with other methods of detection, such as qRT-PCR and virus isolation in C6/36 cells. RESULTS: We first observed that the NS1 antigen was more effective in detecting DENV-2 in Ae. aegypti between 12 and 72 h after mosquito death when compared with qRT-PCR. A second round involved comparing the sensitivity of detection of the NS1 antigen and virus isolation in C6/36 cells. The NS1 antigen was also more effective than virus isolation, detecting DENV-2 at all time-points, i.e., up to 168 h after mosquito death. Meanwhile, virus isolation was successful up to 96 h after Ae. aegypti death, but the number of positive samples per time period presented a tendency to decline progressively over time. From the 43 samples positive by the virus isolation technique, 38 (88.4%) were also positive by the NS1 test. CONCLUSION: Taken together, these results are the first to indicate that the NS1 antigen might be an interesting complementary tool to improve dengue surveillance through DENV detection in dried Ae. aegypti females.

Herpes simplex virus type 1 is the main cause of genital herpes in women of Natal, Brazil.

OBJECTIVES: The purpose of this study was to assess the prevalence of HSV-1 and HSV-2 in sexually active women who participated in the cervical cancer screening program in Natal, Brazil. STUDY DESIGN: The study included 261 sexually active women resident in the metropolitan area of Natal, Brazil and attending a public clinic for cervical screening. From each participant, a sample of exfoliated uterine cervical cells was collected, using a cytobrush which was conditioned in a tube containing a preserving solution (PBS+vancomycin+nystatin) and sent to a laboratory where it was processed for DNA extraction. The samples were analyzed for the presence of HSV-1 and HSV-2 DNA in separate reactions by PCRs using specific primers. RESULTS: HSV-1 in genital infection is four times more prevalent than HSV-2 in the population analyzed. The highest prevalence rates for both viruses were found in women aged 31-39years. We did not observe any association between the presence of both virus serotypes and socio-demographic characteristics in the population studied, nor with some classical risk factors for sexually transmitted diseases. CONCLUSIONS: HSV-1 was the major cause of genital infection by Herpes simplex virus in the women included in this study. No association was found between HSV infection and the socio-demographic characteristics or some classical risk factors for sexually transmitted diseases.

Phylogeography and evolutionary history of dengue virus type 3.

In this study, we revisited the phylogeography of the three of major DENV-3 genotypes and estimated its rate of evolution, based on the analysis of the envelope (E) gene of 200 strains isolated from 31 different countries around the world over a time period of 50 years (1956-2006). Our phylogenetic analysis revealed a geographical subdivision of DENV-3 population in several country-specific clades. Migration patterns of the main DENV-3 genotypes showed that genotype I was mainly circumspect to the maritime portion of Southeast-Asia and South Pacific, genotype II stayed within continental areas in South-East Asia, while genotype III spread across Asia, East Africa and into the Americas. No evidence for rampant co-circulation of distinct genotypes in a single locality was found, suggesting that some factors, other than geographic proximity, may limit the continual dispersion and reintroduction of new DENV-3 variants. Estimates of the evolutionary rate revealed no significant differences among major DENV-3 genotypes. The mean evolutionary rate of DENV-3 in areas with long-term endemic transmissions (i.e., Indonesia and Thailand) was similar to that observed in the Americas, which have been experiencing a more recent dengue spread. We estimated the origin of DENV-3 virus around 1890, and the emergence of current diversity of main DENV-3 genotypes between the middle 1960s and the middle 1970s, coinciding with human population growth, urbanization, and massive human movement, and with the description of the first cases of DENV-3 hemorrhagic fever in Asia.

Quantification of dengue virus type 3 RNA in fatal and non-fatal cases in Brazil, 2002.

We examined levels of dengue virus type 3 (DENV-3) RNA in association with the type of infection (primary or secondary) in 42 patients with fatal and non-fatal outcomes in Rio de Janeiro, Brazil, 2002. Subjects with fatal outcomes had mean virus titers significantly higher than those who survived (12.5 vs. 7.9 log(10) RNA copies/ml). Because primary infections were confirmed among the fatal cases (52.1%), antibody-dependent enhancement alone did not explain all the cases of severe disease in this study population. These findings suggest that high levels of DENV-3 may have contributed to the severe form of dengue in Rio de Janeiro, 2002.