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1.
Obes Sci Pract ; 10(3): e756, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38708040

RESUMO

Background: Anti-obesity medications (AOMs) have historically had limited weight-loss efficacy. However, newer glucagon-like peptide-1 receptor agonist (GLP-1 RA)-based therapies seem to be more effective, including dual agonists of GLP-1R and the glucagon receptor (GCGR) or glucose-dependent insulinotropic polypeptide receptor. Objective: To explore healthcare professionals' (HCPs) experience in obesity treatment and their understanding of agonists of GCGR, glucose-dependent insulinotropic polypeptide (GIP) RA, and GLP-1 RA. Methods: This cross-sectional online survey of HCPs prescribing AOMs was conducted in the United States in 2023 with a questionnaire designed to evaluate prescribing behavior and understanding of GCGR, GIP RA, and GLP-1 RA. Results: The 785 respondents (251 primary-care physicians [PCPs], 263 endocrinologists, and 271 advanced practice providers [APPs]) reported 55% of their patients had obesity (body mass index ≥30 kg/m2 or ≥27 with weight-related complications) and recommended AOMs to 49% overall, significantly more endocrinologists (57% of patients, p < 0.0005) than PCPs (43%) or APPs (46%). The greatest barriers to treatment were medication cost/lack of insurance (mean 4.2 on 1-5 scale [no barrier-extreme barrier]), low patient engagement/adherence (3.3), and inadequate time/staff (3.1). Metformin was the type 2 diabetes (T2D) medication most commonly prescribed to treat obesity in T2D patients (92.5% of respondents). Most HCPs (65%) were very/extremely familiar with GLP-1 RA, but only 30% with GIP RA and 16% with GCGR. Most HCPs expected dual GCGR/GLP-1 RA to benefit many obesity-related conditions; however, only a minority of HCPs perceived that they would benefit non-cardiometabolic complications of obesity. Conclusions: Among HCPs prescribing AOMs, gaps exist in the management of people living with obesity as <50% are prescribed AOMs. Barriers to treatment indicate a need to improve access to AOMs. HCPs were less familiar with GCGR or GIP RA than GLP-1 RA but expect dual GCGR/GLP-1 RA may offer additional benefits, potentially addressing treatment barriers and access. Thus, there is a need for greater education among HCPs regarding the mechanism of action and therapeutic effects of GCGR agonists, and dual GCGR/GLP-1 RA, so that the full range of obesity-related complications can be effectively treated.

2.
Curr Diab Rep ; 22(12): 549-569, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36422793

RESUMO

PURPOSE OF REVIEW: There is a notable lack of consistency in the measurement of psychosocial factors affecting youth with type 1 diabetes, resulting in a need for increased measurement standardization and establishment of measures tailored to capture unique experiences faced by youth. This review sought to assess 10 years of extant literature (2011 to 2020) to identify which established measurement tools are commonly used and to evaluate new measurement tools that were introduced during this period. RECENT FINDINGS: There are a variety of psychosocial factors affecting youth, and assessment of these measures has shown substantial variability. Our review found that most frequently cited scales were those pertaining to self-efficacy, diabetes distress, family conflict, autonomy, and fear of hypoglycemia. During our review period, experts developed and validated 21 new scales, the majority of which sought to evaluate areas pertaining to diabetes distress. Of the common scales and newly developed scales identified in this review, psychometric properties showcase high reliability and validity, and items are becoming increasingly specific to youth but still lack assessment of how youth perceive technology's impact on diabetes management. The field would benefit from measures employing more nuanced age specificity and addressing technology usage.


Assuntos
Diabetes Mellitus Tipo 1 , Hipoglicemia , Adolescente , Humanos , Reprodutibilidade dos Testes , Medo , Tecnologia
3.
J Health Commun ; 26(9): 626-635, 2021 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-34649469

RESUMO

Adolescents with type 1 diabetes (T1D) face a variety of challenges in disease management, and many struggle to achieve optimal glycemic control. Health communication through didactic messaging about the importance of self-management is a commonly used strategy for this population, but narratives have been underutilized. The purpose of this study was to determine if narratives would provide a better tool to improve disease management for adolescents overcoming T1D-specific issues. Adolescent ages 12-17 (N = 191) were enrolled in an online experiment and viewed sets of narratives or standard of care messages. Outcomes were broken into three categories: message evaluation, specifically perceived message effectiveness (PME), and positive emotional reactions; beliefs such as self-efficacy, outcome expectations, and stress and burnout perceptions, and behaviors including disease management and interpersonal communication. Narratives did not significantly outperform standard of care messages, but both message types scored high on PME and other outcomes. We conclude that both narrative and didactic formats may offer utility for healthcare providers working with adolescents, in that narratives provide stories that may inspire positive emotions while standard of care messages provide the necessary clinical information needed to set goals for self-management.


Assuntos
Diabetes Mellitus Tipo 1 , Comunicação em Saúde , Autogestão , Adolescente , Criança , Diabetes Mellitus Tipo 1/terapia , Humanos , Narração , Padrão de Cuidado
4.
Artigo em Inglês | MEDLINE | ID: mdl-34574783

RESUMO

In the small city of St. John's, NL (2020 population ~114,000), 100% of the soils of the pre-1926 properties exceeded the Canadian soil Pb standard, 140 mg/kg. The Pb was traced to high-Pb coal ash used for heating and disposed on the soils outside. Analytical instruments became available in the late 1960s and 1970s and were first used for blood Pb and clinical studies and repurposed for measuring environmental Pb. The environmental research part of this study compared four common soil Pb analysis methods on the same set (N = 96) of St. John's soil samples. The methods: The US EPA method 3050B, portable X-ray fluorescence spectrometry (pXRF), The Chaney-Mielke leachate extraction (1 M nitric acid), and the relative bioaccessibility leaching procedure (US EPA method 1340). Correlation is not the same as agreement ℜ. There is strong agreement (Berry-Mielke's Universal ℜ) among the four soil Pb analytical methods. Accordingly, precaution is normally advisable to protect children from the high-Pb garden soils and play areas. A public health reality check by Health Canada surveillance of St. John's children (N = 257) noted remarkably low blood Pb. The low blood Pb of St. John's' children is contrary to the soil Pb results. Known urban processes causing the rise of environmental Pb and children's Pb exposure includes particle size, aerosol emission by traffic congestion, and quantities of leaded petrol during the 20th century. Smaller cities had minor traffic congestion and limited combustion particles from leaded petrol. From the perspective of the 20th century era of urban Pb pollution, St. John's, NL, children have blood Pb characteristics of a small city.


Assuntos
Poluentes do Solo , Solo , Canadá , Criança , Cidades , Humanos , Chumbo , Terra Nova e Labrador , Poluentes do Solo/análise
5.
Viruses ; 12(7)2020 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-32640609

RESUMO

Hepatitis B virus (HBV) is the primary cause of liver-related malignancies worldwide, and there is no effective cure for chronic HBV infection (CHB) currently. Strong immunological responses induced by T cells are associated with HBV clearance during acute infection; however, the repertoire of epitopes (epi) presented by major histocompatibility complexes (MHCs) to elicit these responses in various African populations is not well understood. In silico approaches were used to map and investigate 15-mers HBV peptides restricted to 9 HLA class II alleles with high population coverage in Botswana. Sequences from 44 HBV genotype A and 48 genotype D surface genes (PreS/S) from Botswana were used. Of the 1819 epi bindings predicted, 20.2% were strong binders (SB), and none of the putative epi bind to all the 9 alleles suggesting that multi-epitope, genotype-based, population-based vaccines will be more effective against HBV infections as opposed to previously proposed broad potency epitope-vaccines which were assumed to work for all alleles. In total, there were 297 unique epi predicted from the 3 proteins and amongst, S regions had the highest number of epi (n = 186). Epitope-densities (Depi) between genotypes A and D were similar. A number of mutations that hindered HLA-peptide binding were observed. We also identified antigenic and genotype-specific peptides with characteristics that are well suited for the development of sensitive diagnostic kits. This study identified candidate peptides that can be used for developing multi-epitope vaccines and highly sensitive diagnostic kits against HBV infection in an African population. Our results suggest that viral variability may hinder HBV peptide-MHC binding, required to initiate a cascade of immunological responses against infection.


Assuntos
Antígenos HLA/imunologia , Vírus da Hepatite B/imunologia , Leucócitos/imunologia , Alelos , Botsuana/epidemiologia , Simulação por Computador , Epitopos de Linfócito T/imunologia , Genes MHC da Classe II/imunologia , Hepatite B/imunologia , Antígenos de Superfície da Hepatite B/imunologia , Humanos , Linfócitos T/imunologia
6.
Health Commun ; 35(2): 148-157, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-30482058

RESUMO

Target audience ratings of the likely impact of persuasive messages, known as perceived message effectiveness (PME), are commonly used in health communication campaigns. However, applications of PME rely on a critical assumption-that is, that PME is a valid indicator of the likely effectiveness of messages. To examine the evidence supporting this assumption, we conducted a systematic review and meta-analysis of longitudinal studies in the tobacco education campaigns literature. Six longitudinal studies examining the predictive validity of PME met inclusion criteria. Results indicated that PME ratings were significantly associated with the majority of outcomes studied. In fact, each of the six studies found PME to be associated with at least one outcome, and across the six studies, PME was associated with message recall, conversations about ads, beliefs about smoking and quitting smoking, quit intentions, and cessation behavior. Meta-analyses demonstrated that PME predicted quit intentions (r = .256, p < .001) and cessation behavior (r = .201, p < .001), revealing effects that were small to medium in magnitude. Our results suggest that PME provides some predictive value as to the likely effectiveness of messages, although additional work using different validation designs, with other health behaviors, and among other populations is needed.


Assuntos
Educação em Saúde , Promoção da Saúde , Intenção , Comunicação Persuasiva , Abandono do Hábito de Fumar , Uso de Tabaco/efeitos adversos , Humanos , Estudos Longitudinais
7.
Health Commun ; 34(9): 949-957, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-29521518

RESUMO

Parents of children with type 1 diabetes (T1D) face uncertainty about the illness. This uncertainty can have negative health consequences for parents and their children. However, little is known about the types of uncertainty associated with T1D diagnosis and subsequent treatment and how this uncertainty is managed. Using uncertainty management theory (UMT) as a framework and 29 in-depth interviews with parents of children with T1D, this study found that parents experienced medical, social, and financial forms of uncertainty. Most parents viewed uncertainty negatively and sought to reduce it by seeking information, joining support groups, and turning to technology. However, some parents preferred uncertainty to the certainty of knowing their child had T1D and, at least initially, chose to maintain uncertainty about the disease by avoiding information. This study also provides practical outcomes that health-care providers can use to help parents of children with T1D reduce and manage uncertainty.


Assuntos
Diabetes Mellitus Tipo 1/psicologia , Pais/psicologia , Incerteza , Adolescente , Adulto , Criança , Pré-Escolar , Diabetes Mellitus Tipo 1/diagnóstico , Diabetes Mellitus Tipo 1/terapia , Feminino , Humanos , Entrevistas como Assunto , Masculino , Pessoa de Meia-Idade , Pais/educação , Teoria Psicológica
8.
J Med Virol ; 91(5): 758-764, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30515847

RESUMO

Both hepatitis B virus (HBV) and human immunodeficiency virus (HIV) infection are highly endemic in sub-Saharan Africa. This study examined serological and clinical follow-up data from 39 HBV DNA-positive, HIV-positive black South African adults, who returned for follow-up at 3, 6, 12, and 18 months post-initiation of antiretroviral therapy (ART). Of the 39 participants, 10 experienced full suppression of HBV and 29 experienced no suppression, with 10 of these showing a virological breakthrough. All 10 patients who fully suppressed were HBsAg-negative, with 16 of the 29 who did not suppress being HBsAg-positive and 13 HBsAg-negative (P < 0.05). Participants fully suppressing the virus had significantly lower aminotransferase levels and were all HBsAg-negative compared to those who did not suppress (P < 0.05). HBV viral loads between HBsAg-positive and HBsAg-negative samples were similar at baseline and at the final time-point. In these South African patients with HBV/HIV coinfection, HBsAg-negative status at baseline was a predictor of the outcome of HBV suppression in response to ART containing lamivudine.


Assuntos
Antirretrovirais/uso terapêutico , Coinfecção/tratamento farmacológico , Infecções por HIV/complicações , Infecções por HIV/tratamento farmacológico , Vírus da Hepatite B/isolamento & purificação , Hepatite B/complicações , Lamivudina/uso terapêutico , Adolescente , Adulto , Criança , Estudos de Coortes , Feminino , Antígenos de Superfície da Hepatite B/sangue , Humanos , Masculino , Pessoa de Meia-Idade , África do Sul , Resultado do Tratamento , Carga Viral , Adulto Jovem
9.
Genes (Basel) ; 9(9)2018 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-30205537

RESUMO

The World Health Organization plans to eliminate hepatitis B and C Infections by 2030. Therefore, there is a need to study and understand hepatitis B virus (HBV) epidemiology and viral evolution further, including evaluating occult (HBsAg-negative) HBV infection (OBI), given that such infections are frequently undiagnosed and rarely treated. We aimed to molecularly characterize HBV genomes from 108 individuals co-infected with human immunodeficiency virus (HIV) and chronic hepatitis B (CHB) or OBI identified from previous HIV studies conducted in Botswana from 2009 to 2012. Full-length (3.2 kb) and nearly full-length (~3 kb) genomes were amplified by nested polymerase chain reaction (PCR). Sequences from OBI participants were compared to sequences from CHB participants and GenBank references to identify OBI-unique mutations. HBV genomes from 50 (25 CHB and 25 OBI) individuals were successfully genotyped. Among OBI participants, subgenotype A1 was identified in 12 (48%), D3 in 12 (48%), and E in 1 (4%). A similar genotype distribution was observed in CHB participants. Whole HBV genome sequences from Botswana, representing OBI and CHB, were compared for the first time. There were 43 OBI-unique mutations, of which 26 were novel. Future studies using larger sample sizes and functional analysis of OBI-unique mutations are warranted.

10.
Genes (Basel) ; 9(9)2018 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-30134551

RESUMO

Occult hepatitis B infections (OBI) represent a reservoir of undiagnosed and untreated hepatitis B virus (HBV), hence the need to identify mutations that lead to this phenotype. Functionally characterizing these mutations by in vitro studies is time-consuming and expensive. To bridge this gap, in silico approaches, which predict the effect of amino acid (aa) variants on HBV protein function, are necessary. We developed an algorithm for determining the relevance of OBI-associated mutations using in silico approaches. A 3 kb fragment of subgenotypes A1 and D3 from 24 chronic HBV-infected (CHB) and 24 OBI participants was analyzed. To develop and validate the algorithm, the effects of 68 previously characterized occult-associated mutations were determined using three computational tools: PolyPhen2, SNAP2, and PROVEAN. The percentage of deleterious mutations (with impact on protein function) predicted were 52 (76.5%) by PolyPhen2, 55 (80.9%) by SNAP2, and 65 (95.6%) by PROVEAN. At least two tools correctly predicted 59 (86.8%) mutations as deleterious. To identify OBI-associated mutations exclusive to Botswana, study sequences were compared to CHB sequences from GenBank. Of the 43 OBI-associated mutations identified, 26 (60.5%) were predicted by at least two tools to have an impact on protein function. To our knowledge, this is the first study to use in silico approaches to determine the impact of OBI-associated mutations, thereby identifying potential candidates for functional analysis to facilitate mechanistic studies of the OBI phenotype.

11.
PLoS One ; 13(2): e0193647, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29489899

RESUMO

Benthic habitat maps, including maps of seabed sediments, have become critical spatial-decision support tools for marine ecological management and conservation. Despite the increasing recognition that environmental variables should be considered at multiple spatial scales, variables used in habitat mapping are often implemented at a single scale. The objective of this study was to evaluate the potential for using environmental variables at multiple scales for modelling and mapping seabed sediments. Sixteen environmental variables were derived from multibeam echosounder data collected near Qikiqtarjuaq, Nunavut, Canada at eight spatial scales ranging from 5 to 275 m, and were tested as predictor variables for modelling seabed sediment distributions. Using grain size data obtained from grab samples, we tested which scales of each predictor variable contributed most to sediment models. Results showed that the default scale was often not the best. Out of 129 potential scale-dependent variables, 11 were selected to model the additive log-ratio of mud and sand at five different scales, and 15 were selected to model the additive log-ratio of gravel and sand, also at five different scales. Boosted Regression Tree models that explained between 46.4 and 56.3% of statistical deviance produced multiscale predictions of mud, sand, and gravel that were correlated with cross-validated test data (Spearman's ρmud = 0.77, ρsand = 0.71, ρgravel = 0.58). Predictions of individual size fractions were classified to produce a map of seabed sediments that is useful for marine spatial planning. Based on the scale-dependence of variables in this study, we concluded that spatial scale consideration is at least as important as variable selection in seabed mapping.


Assuntos
Ecossistema , Sedimentos Geológicos , Oceanos e Mares , Modelos Estatísticos , Análise Espacial
12.
Commun Methods Meas ; 12(4): 295-313, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-31428217

RESUMO

Target audience ratings of the likely impact of persuasive messages, known as perceived message effectiveness (PME), are commonly used during message development and selection. PME is also used to examine receptivity of messages after they are fully developed or deployed. Despite this, we know little about the conceptual and methodological characteristics of extant PME measures used in the literature. We conducted a systematic review of tobacco education video, print, and audio campaign studies to examine conceptual and methodological characteristics of PME measures. One hundred twenty-six PME measures from 75 studies conducted in 21 countries with more than 61,000 participants were reviewed. Results indicated considerable variability in measures' focus on general perceptions of a message (i.e., message perceptions) versus perceptions of expected message effects (i.e., effects perceptions). Considerable variability was also found on underlying persuasive constructs, use of referents, and referencing of behavior in PME items and measures. We conclude with several recommendations for future research on PME measurement and validation.

13.
Springerplus ; 5(1): 1896, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27843753

RESUMO

BACKGROUND: Hepatitis B virus (HBV) DNA sequence data from thousands of samples are present in the public sequence databases. No publicly available, up-to-date, multiple sequence alignments, containing full-length and subgenomic fragments per genotype, are available. Such alignments are useful in many analysis applications, including data-mining and phylogenetic analyses. RESULTS: By issuing a query, all HBV sequence data from the GenBank public database was downloaded (67,893 sequences). Full-length and subgenomic sequences, which were genotyped by the submitters (30,852 sequences), were placed into a multiple sequence alignment, for each genotype (genotype A: 5868 sequences, B: 4630, C: 7820, D: 8300, E: 2043, F: 985, G: 189, H: 108, I: 23), according to the results of offline BLAST searches against a custom reference library of full-length sequences. Further curation was performed to improve the alignment. CONCLUSIONS: The algorithm described in this paper generates, for each of the nine HBV genotypes, multiple sequence alignments, which contain full-length and subgenomic fragments. The alignments can be updated as new sequences become available in the online public sequence databases. The alignments are available at http://hvdr.bioinf.wits.ac.za/alignments.

14.
Viruses ; 7(2): 781-97, 2015 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-25690798

RESUMO

DNA sequence analysis is undertaken in many biological research laboratories. The workflow consists of several steps involving the bioinformatic processing of biological data. We have developed a suite of web-based online bioinformatic tools to assist with processing, analysis and curation of DNA sequence data. Most of these tools are genome-agnostic, with two tools specifically designed for hepatitis B virus sequence data. Tools in the suite are able to process sequence data from Sanger sequencing, ultra-deep amplicon resequencing (pyrosequencing) and chromatograph (trace files), as appropriate. The tools are available online at no cost and are aimed at researchers without specialist technical computer knowledge. The tools can be accessed at http://hvdr.bioinf.wits.ac.za/SmallGenomeTools, and the source code is available online at https://github.com/DrTrevorBell/SmallGenomeTools.


Assuntos
Biologia Computacional/métodos , Genoma Viral , Genômica/métodos , Vírus da Hepatite B/genética , Algoritmos , Vírus da Hepatite B/classificação , Humanos , Internet
15.
PLoS One ; 9(4): e95377, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24740330

RESUMO

AIMS: The aims of this study were to develop bioinformatics tools to explore ultra-deep pyrosequencing (UDPS) data, to test these tools, and to use them to determine the optimum error threshold, and to compare results from UDPS and cloning based sequencing (CBS). METHODS: Four serum samples, infected with either genotype D or E, from HBeAg-positive and HBeAg-negative patients were randomly selected. UDPS and CBS were used to sequence the basic core promoter/precore region of HBV. Two online bioinformatics tools, the "Deep Threshold Tool" and the "Rosetta Tool" (http://hvdr.bioinf.wits.ac.za/tools/), were built to test and analyze the generated data. RESULTS: A total of 10952 reads were generated by UDPS on the 454 GS Junior platform. In the four samples, substitutions, detected at 0.5% threshold or above, were identified at 39 unique positions, 25 of which were non-synonymous mutations. Sample #2 (HBeAg-negative, genotype D) had substitutions in 26 positions, followed by sample #1 (HBeAg-negative, genotype E) in 12 positions, sample #3 (HBeAg-positive, genotype D) in 7 positions and sample #4 (HBeAg-positive, genotype E) in only four positions. The ratio of nucleotide substitutions between isolates from HBeAg-negative and HBeAg-positive patients was 3.5 ∶ 1. Compared to genotype E isolates, genotype D isolates showed greater variation in the X, basic core promoter/precore and core regions. Only 18 of the 39 positions identified by UDPS were detected by CBS, which detected 14 of the 25 non-synonymous mutations detected by UDPS. CONCLUSION: UDPS data should be approached with caution. Appropriate curation of read data is required prior to analysis, in order to clean the data and eliminate artefacts. CBS detected fewer than 50% of the substitutions detected by UDPS. Furthermore it is important that the appropriate consensus (reference) sequence is used in order to identify variants correctly.


Assuntos
Biologia Computacional/métodos , DNA Viral/genética , Vírus da Hepatite B/genética , Filogenia , Análise de Sequência de DNA/estatística & dados numéricos , Proteínas do Core Viral/genética , Adulto , Clonagem Molecular , Biologia Computacional/instrumentação , DNA Viral/química , Genótipo , Antígenos E da Hepatite B/sangue , Vírus da Hepatite B/classificação , Vírus da Hepatite B/isolamento & purificação , Hepatite B Crônica/sangue , Hepatite B Crônica/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Dados de Sequência Molecular , Mutação , Proteínas do Core Viral/química
16.
Viruses ; 5(3): 824-33, 2013 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-23482300

RESUMO

While PCR amplicons extend to a few thousand bases, the length of sequences from direct Sanger sequencing is limited to 500-800 nucleotides. Therefore, several fragments may be required to cover an amplicon, a gene or an entire genome. These fragments are typically sequenced in an overlapping fashion and assembled by manually sliding and aligning the sequences visually. This is time-consuming, repetitive and error-prone, and further complicated by circular genomes. An online tool merging two to twelve long overlapping sequence fragments was developed. Either chromatograms or FASTA files are submitted to the tool, which trims poor quality ends of chromatograms according to user-specified parameters. Fragments are assembled into a single sequence by repeatedly calling the EMBOSS merger tool in a consecutive manner. Output includes the number of trimmed nucleotides, details of each merge, and an optional alignment to a reference sequence. The final merge sequence is displayed and can be downloaded in FASTA format. All output files can be downloaded as a ZIP archive. This tool allows for easy and automated assembly of overlapping sequences and is aimed at researchers without specialist computer skills. The tool is genome- and organism-agnostic and has been developed using hepatitis B virus sequence data.


Assuntos
Vírus da Hepatite B/genética , Sistemas On-Line/instrumentação , Alinhamento de Sequência/instrumentação , Alinhamento de Sequência/métodos , Análise de Sequência de DNA/métodos , Bases de Dados de Ácidos Nucleicos , Vírus da Hepatite B/química , Internet , Análise de Sequência de DNA/instrumentação , Software
17.
Virol J ; 10: 62, 2013 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-23433201

RESUMO

BACKGROUND: An online tool, which extracts and summarises nucleotide or amino acid sequence data at specified loci of interest, was developed and tested using the basic core promoter/precore (BCP/PC) region of the hepatitis B virus (HBV). The tool is aimed at researchers without specialist computer skills. METHODS: The tool consists of a web-based front-end, with a CGI script, which runs Python code to generate an output web-page. The Python code searches the input sequence data for a specified anchor motif, after which it generates summary tables and graphs of residue and motif distributions. RESULTS: After the user provides an input file in FASTA format containing aligned sequence data (nucleotides or amino acids) and specifies an anchor motif at a known coordinate, the tool summarizes the nucleotides or amino acids at the specified loci, their frequency and analyzes motif patterns of the loci.The tool can output a graph that displays the frequency of mutations relative to a reference sequence. The tool was used to analyze the BCP/PC region of HBV belonging to subgenotypes A1, A2 and subgenotype D and to serotype HBV. The "Discovery Mode" ignores conserved loci and assists in identifying potential loci of interest. CONCLUSIONS: Although HBV was used to demonstrate the utility of the Mutation Reporter Tool, the tool has wide application as it is genome-agnostic: nucleotide or amino acid sequence data from any organism can be processed. Rapid characterisation of many sequences can be achieved easily when the loci of interest are known. The tool is available online, without charge, at http://hvdr.bioinf.wits.ac.za/tools.


Assuntos
Biologia Computacional/métodos , Mutação , Vírus da Hepatite B/genética , Humanos , Internet , Virologia/métodos
18.
PLoS One ; 7(9): e46345, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23029487

RESUMO

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) are hyperendemic in sub-Saharan Africa. The HBV genotypes prevailing in HIV-infected Africans are unknown. Our aim was to determine the HBV genotypes in HIV-infected participants and to identify clinically significant HBV mutations. From 71 HBV DNA(+ve) HIV-infected participants, 49 basic core promoter/precore (BCP/PC) and 29 complete S regions were successfully sequenced. Following phylogenetic analysis of 29 specimens in the complete S region, 28 belonged to subgenotype A1 and one to D3. Mutations affecting HBeAg expression at the transcriptional (1762T1764A), translational (Kozak 1809-1812, initiation 1814-1816, G1896A with C1858T), or post translational levels (G1862T), were responsible for the high HBeAg-negativity observed. The G1862T mutation occurred only in subgenotype A1 isolates, which were found in one third (7/21) of HBsAg(-ve) participants, but in none of the 18 HBsAg(+ve) participants (p<0.05). Pre-S deletion mutants were detected in four HBsAg(+ve) and one HBsAg(-ve) participant/s. The following mutations occurred significantly more frequently in HBV isolated in this study than in strains of the same cluster of the phylogenetic tree: ps1F25L, ps1V88L/A; ps2Q10R, ps2 R48K/T, ps2A53V and sQ129R/H, sQ164A/V/G/D, sV168A and sS174N (p<0.05). ps1I48V/T occurred more frequently in females than males (p<0.05). Isolates with sV168A occurred more frequently in participants with viral loads >200 IU per ml (p<0.05) and only sS174N occurred more frequently in HBsAg(-ve) than in HBsAg(+ve) individuals (p<0.05). Prior to initiation of ART, ten percent, 3 of 29 isolates sequenced, had drug resistance mutations rtV173L, rtL180M+rtM204V and rtV214A, respectively. This study has provided important information on the molecular characteristics of HBV in HIV-infected southern Africans prior to ART initiation, which has important clinical relevance in the management of HBV/HIV co-infection in our unique setting.


Assuntos
Infecções por HIV/virologia , HIV-1/fisiologia , Antígenos de Superfície da Hepatite B/genética , Antígenos E da Hepatite B/genética , Vírus da Hepatite B/genética , Hepatite B Crônica/virologia , Adolescente , Adulto , Fármacos Anti-HIV/administração & dosagem , Criança , Pré-Escolar , Coinfecção , Feminino , Expressão Gênica , Técnicas de Genotipagem , Infecções por HIV/tratamento farmacológico , Vírus da Hepatite B/classificação , Vírus da Hepatite B/isolamento & purificação , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Filogenia , Análise de Sequência de DNA , Fatores Sexuais , África do Sul , Fatores de Tempo , Carga Viral
19.
PLoS One ; 7(10): e45750, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23049685

RESUMO

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) share transmission routes and are endemic in sub-Saharan Africa. The objective of the present study was to use the Taormina definition of occult HBV infection, together with stringent amplification conditions, to determine the prevalence and characteristics of HBV infection in antiretroviral treatment (ART)-naïve HIV(+ve) adults in a rural cohort in South Africa. The presence of HBV serological markers was determined by enzyme linked immunoassay (ELISA) tests. HBV DNA-positivity was determined by polymerase chain reaction (PCR) of at least two of three different regions of the HBV genome. HBV viral loads were determined by real-time PCR. Liver fibrosis was determined using the aspartate aminotransferase-to-platelet ratio index. Of the 298 participants, 231 (77.5%) showed at least one HBV marker, with 53.7% HBV DNA(-ve) (resolved) and 23.8% HBV DNA(+ve) (current) [8.7% HBsAg(+ve): 15.1% HBsAg(-ve)]. Only the total number of sexual partners distinguished HBV DNA(+ve) and HBV DNA(-ve) participants, implicating sexual transmission of HBV and/or HIV. It is plausible that sexual transmission of HBV and/or HIV may result in a new HBV infection, superinfection and re-activation as a consequence of immunesuppression. Three HBsAg(-ve) HBV DNA(+ve) participants had HBV viral loads <200 IU/ml and were therefore true occult HBV infections. The majority of HBsAg(-ve) HBV DNA(+ve) participants did not differ from HBsAg(+ve) HBV DNA(+ve) (overt) participants in terms of HBV viral loads, ALT levels or frequency of liver fibrosis. Close to a quarter of HIV(+ve) participants were HBV DNA(+ve), of which the majority were HBsAg(-ve) and were only detected using nucleic acid testing. Detection of HBsAg(-ve) HBV DNA(+ve) subjects is advisable considering they were clinically indistinguishable from HBsAg(+ve) HBV DNA(+ve) individuals and should not be overlooked, especially if lamivudine is included in the ART.


Assuntos
Infecções por HIV/complicações , Infecções por HIV/epidemiologia , Hepatite B/complicações , Hepatite B/epidemiologia , Adulto , Aspartato Aminotransferases/sangue , Biomarcadores/metabolismo , Primers do DNA/genética , Ensaio de Imunoadsorção Enzimática , Feminino , Infecções por HIV/transmissão , Hepatite B/transmissão , Vírus da Hepatite B/genética , Humanos , Cirrose Hepática/etiologia , Cirrose Hepática/patologia , Masculino , Prevalência , Reação em Cadeia da Polimerase em Tempo Real , População Rural , Testes Sorológicos , África do Sul/epidemiologia , Estatísticas não Paramétricas
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