Dataset Information

Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.

ABSTRACT: The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016-2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolates from two main cities located in the metropolitan mesoregion, obtained directly from clinical samples. Our phylogenetic reconstructions suggest the 2019-CHIKV-ECSA epidemic in RJ state was characterized by the co-circulation of multiple clade (clade A and B), highlighting that two independent introduction events of CHIKV-ECSA into RJ state have occurred between 2016-2019, both mediated from the northeastern region. Interestingly, we identified that the two-clade displaying eighteen characteristic amino acids changes among structural and non-structural proteins. Our findings reinforce that genomic data can provide information about virus genetic diversity and transmission dynamics, which might assist in the arbovirus epidemics establishing of an effective surveillance framework.

SUBMITTER: Fabri AA

PROVIDER: S-EPMC7759993 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.

Fabri Allison Araújo AA Rodrigues Cintia Damasceno Dos Santos CDDS Santos Carolina Cardoso Dos CCD Chalhoub Flávia Löwen Levy FLL Sampaio Simone Alves SA Faria Nieli Rodrigues da Costa NRDC Torres Maria Celeste MC Fonseca Vagner V Brasil Patricia P Calvet Guilherme G Alcantara Luiz Carlos Junior LCJ Filippis Ana Maria Bispo de AMB Giovanetti Marta M de Bruycker-Nogueira Fernanda F

Pathogens (Basel, Switzerland) 20201126 12

The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016-2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolat ...[more]

PMID: 33255865

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Project description:Phenylketonuria (PKU) is an autosomal recessive disease resulting from mutations in the PAH gene. Most of the patients are compound heterozygotes, and genotype is a major factor in determining the phenotypic variability of PKU. More than 1,000 variants have been described in the PAH gene. Rio de Janeiro's population has a predominance of Iberian, followed by African and Amerindian ancestries. It is expected that most PKU variants in this Brazilian state have originated in the Iberian Peninsula. However, rare European, African or pathogenic variants that are characteristic of the admixed population of the state might also be found. A total of 102 patients were included in this study. Genomic DNA was isolated from dried blood spots. Sanger sequencing was used for PAH gene variant identification. Deletions and duplications were also screened using MLPA analysis. Haplotypes were also determined. Nine (8.8%) homozygous and 93 (91.2%) compound heterozygous patients were found. The spectrum included 37 causative mutations. Missense, nonsense, and splicing pathogenic variants corresponded to 63.7%, 2.9%, and 22.6% of the mutant alleles, respectively. Large (1.5%), and small deletions, inframe (5.4%) and with frameshift (3.9%), comprised the remainder. The most frequent pathogenic variants were: p.V388M (12.7%), p.R261Q (11.8%), IVS10-11G>A (10.3%), IVS2+5G>C (6.4%), p.S349P (6.4%), p.R252W (5.4%), p.I65T (4.4%), p.T323del (4.4%), and p.P281L (3.4%). One novel variant was detected: c.934G>T (p.G312C) [rs763115697]. The three most frequent pathogenic variants in our study (34.8% of the alleles) were also the most common in other Brazilian states, Portugal, and Spain (p.V388M, p.R261Q, IVS10-11G>A), corroborating that the Iberian Peninsula is the major source of PAH mutations in Rio de Janeiro. Pathogenic variants that have other geographical origins, such IVS2+5G>C, p.G352Vfs*48, and IVS12+1G>A were also detected. Genetic drift and founder effect may have also played a role in the mutation spectrum we observed.

Project description:BACKGROUND:Genetic heterogeneity and compound heterozygosis give rise to a continuous spectrum of phenylalanine hydroxylase deficiency and metabolic phenotypes in phenylketonuria (PKU). The most used parameters for evaluating phenotype in PKU are pretreatment phenylalanine (Phe) levels, tolerance for dietary Phe, and Phe overloading test. Phenotype can vary from a "classic" (severe) form to mild hyperphenylalaninemia, which does not require dietary treatment. A subset of patients is responsive to treatment by the cofactor tetrahydrobiopterin (BH4 ). Genotypes of PKU patients from Rio de Janeiro, Brazil, were compared to predicted and observed phenotypes. Genotype-based estimations of responsiveness to BH4 were also conducted. METHODS:Phenotype was defined by pretreatment Phe levels. A standard prediction system based on arbitrary assigned values was employed to measure genotype-phenotype concordance. Patients were also estimated as BH4 -responders according to the responsiveness previously reported for their mutations and genotypes. RESULTS:A 48.3% concordance rate between genotype-predicted and observed phenotypes was found. When the predicted phenotypes included those reported at the BIOPKU database, the concordance rate reached 77%. A total of 18 genotypes from 30 patients (29.4%) were estimated as of potential or probable BH4 responsiveness. Inconsistencies were observed in genotypic combinations including the common "moderate" mutations p.R261Q, p.V388M, and p.I65T and the mild mutations p.L48S, p.R68S, and p.L249F. CONCLUSION:The high discordance rate between genotype-predicted and observed metabolic phenotypes in this study seems to be due partially to the high frequency of the so-called "moderate" common mutations, p.R261Q, p.V388M, and p.I65T, which are reported to be associated to erratic or more severe than expected metabolic phenotypes. Although our results of BH4 estimated responsiveness must be regarded as tentative, it should be emphasized that genotyping and genotype-phenotype association studies are important in selecting patients to be offered a BH4 overload test, especially in low-resource settings like Brazil.

Project description:Trichophyton, Microsporum, Nannizzia and Epidermophyton genera cause dermatophytosis, the most common and highly contagious infectious skin disease. Rio de Janeiro is one of the most visited cities in the Southern Hemisphere, located in the most visited state of Brazil. This retrospective study investigated epidemiological and laboratorial aspects of dermatophytosis in Rio de Janeiro state, Brazil, by using spatiotemporal analysis. More than half of all individuals were infected by one or more dermatophytes. A variation between 18 and 106 years-old of the studied population was verified, and women more frequently affected. Patients were more frequently infected by Trichophyton spp., most of them T. rubrum, followed by T. mentagrophytes. M. canis and N. gypsea were more frequently isolated in the age group between 40 and 60 years old, while T. rubrum predominates among younger patients. All species presented homogeneous distribution while T. tonsurans appears to be restricted to the Rio de Janeiro capital and E. floccosum to the municipality of Macaé (190 Km apart from RJ). Rio de Janeiro state presented spatial clusters of dermatophytosis with high density in Guanabara Bay (E. floccosum, M. canis, N. gypsea, T. tonsurans) and Niterói (T. rubrum, T. mentagrophytes) but low density in Macaé (E. floccosum). Significant spatiotemporal clusters on dermatophytosis cases were detected in distinct municipalities (p-value ≤ 0.05). The Vulnerability Index (r = 0.293) and Demographic Density (r = 0.652) distributed according to neighborhoods in Niterói were direct related with dermatophytosis cases whereas Income (r = -0.306) was inversely correlated (p-value ≤ 0.05). The dermatophytosis spatiotemporal distinct distribution after two major international events in Rio de Janeiro, Brazil, highlight the pressing need for specific measures of its prevention and controlling. This is particularly relevant in touristic tropical localities which must consider both socio-economical and traveler's medicine variables.

Project description:BackgroundViolence and other traumatic events, as well as psychiatric disorders are frequent in developing countries, but there are few population studies to show the actual impact of traumatic events in the psychiatric morbidity in low and middle-income countries (LMIC).AimsTo study the relationship between traumatic events and prevalence of mental disorders in São Paulo and Rio de Janeiro, Brazil.MethodsCross-sectional survey carried out in 2007-2008 with a probabilistic representative sample of 15- to 75-year-old residents in Sao Paulo and Rio de Janeiro, Brazil, using the Composite International Diagnostic Interview.ResultsThe sample comprised 3744 interviews. Nearly 90% of participants faced lifetime traumatic events. Lifetime prevalence of any disorders was 44% in Sao Paulo and 42.1% in Rio de Janeiro. One-year estimates were 32.5% and 31.2%. One-year prevalence of traumatic events was higher in Rio de Janeiro than Sao Paulo (35.1 vs. 21.7; p<0.001). Participants from Rio de Janeiro were less likely to have alcohol dependence (OR?=?0.55; p?=?0.027), depression (OR?=?0.6; p?=?0.006) generalized anxiety (OR?=?0.59; p?=?0.021) and post-traumatic stress disorder (OR?=?0.62; p?=?0.027). Traumatic events correlated with all diagnoses--e.g. assaultive violence with alcohol dependence (OR?=?5.7; p<0.001) and with depression (OR?=?1.7; p?=?0.001).ConclusionOur findings show that psychiatric disorders and traumatic events, especially violence, are extremely common in Sao Paulo and Rio de Janeiro, supporting the idea that neuropsychiatric disorders and external causes have become a major public health priority, as they are amongst the leading causes of burden of disease in low and middle-income countries. The comparison between the two cities regarding patterns of violence and psychiatric morbidity suggests that environmental factors may buffer the negative impacts of traumatic events. Identifying such factors might guide the implementation of interventions to improve mental health and quality of life in LMIC urban centers.

Dataset Information

Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.

Publications

Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.

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