Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Métodos diagnósticos para detecção da Leucemia viral felina

The feline leukemia virus (FeLV) was described in 1964 by William Jarrett and collaborators wen find viral particles attached to the membrane of lymphoblasts in cat with lymphoma. The virus belongs to the family Retroviridae, subfamily oncornavirus. With worldwide distribution, the occurrence of FeLV has 1.6% in healthy cats and 10.8% in sick cats in Brazil. The mortality of persistently viremic animals in catteries is about 50% in two years and 80% in three years. In catteries that have endemic feline Coronavirus (FCoV), FeLV and / or Feline Immunodeficiency Virus (FIV), the FeLV infection has greater contribution to mortality. The test for infection and FeLV positive cats segregation is the main way to prevent the spread of infection. The diagnostic methods are based on clinical signs and changes compatible with FeLV infection observed by physical examination, complete blood count, X-ray, bone marrow aspirate and biochemical. The viral p27 protein is produced in infected cells in high amounts and is found in abundance in the cytoplasm and in body fluids enabling diagnosed methods such as enzyme-linked immunosorbent assay - ELISA and direct immunofluorescence, detection of viral genome (Chain Reaction Polymerase - PCR) and detection of the virus by virus isolation. Although diagnostic tests are highly sensitive, it should be made more than a confirmatory test, especially serological due to variable characteristic of the progress of infection

Carga viral e genotipagem do vírus de Epstein-Barr (EBV) e análise da frequência das variantes do gene viral BNLF-1 em indivíduos portadores do vírus da imunodeficiência humana (HIV)

Indivíduos imunocomprometidos possuem maior risco de desenvolver linfomas associados ao EBV. A detecção desse vírus em sangue periférico e a determinação de sua carga viral podem ter importância na evolução clínica de indivíduos portadores do HIV. Foram avaliadas 156 amostras de pacientes HIVpositivos pela reação em cadeia da polimerase em tempo real (qPCR) para detecção e quantificação da carga viral do EBV. 123/156 (78,8%) casos apresentaram carga viral detectável para o EBV, sendo que a carga viral média foi de 6,9x10-3 cópias de EBV/célula. Foi detectada elevada carga viral do EBV em indivíduos com falha terapêutica ou sem HAART (p =0,0076), em coinfectados pelos EBVs 1 e 2 (p=0,0205), em pacientes com altas cargas de HIV (rho=0,27614, p=0,0005) e longos períodos de infecção pelo HIV (rho= 0,24164, p =0,0026) e os que apresentavam altos níveis de linfócitos T CD8 + (rho=0,19286, p =0,0159). A amplificação do gene EBNA-2 para realização da tipagem viral foi possível em 95/123 (77,2%) amostras, das quais 72 (75,8%) revelaram infecção pelo EBV-1, 9 (9,5%) pelo EBV-2 e 14 (14,7%) apresentavam coinfecção entre os EBVs 1 e 2. Esses dados estão de acordo com a literatura visto que o tipo 1 é predominante em países ocidentais e 70,0% da coorte era composta por indivíduos caucasianos e heterossexuais. A maioria dos pacientes que apresentaram coinfecção pelos EBVs 1 e 2 tiveram contagem de linfócitos T CD4 + entre 200 e 499 células/μL de sangue segundo classificação CDC (p =0,0272). Quanto a analise do gene BNLF-1, a amplificação foi possível em 99/123 (80,5%). Desses 50/99 (50,5%) apresentavam a deleção de 30pb no gene, enquanto 49/99 (49,5%) não a possuíam. Em conjunto, os resultados obtidos evidenciam deterioração do sistema imunitário, caracterizada...(Resumo completo, clicar acesso eletrônico abaixo)

Pirossequenciamento de alta cobertura da região hipervariável 1 do Vírus da Hepatite C

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Pesquisa de genomas virais em primatas não humanos do novo mundo por metagenômica

Pós-graduação em Medicina Veterinária - FMVZ

Natural compounds isolated from Brazilian plants are potent inhibitors of hepatitis C virus replication in vitro

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Prevalência de anticorpos contra o vírus da diarreia viral bovina em suínos

Pós-graduação em Medicina Veterinária - FCAV

Use of uniform designs in combination with neural networks for viral infection process development

This work aimed to compare the predictive capacity of empirical models, based on the uniform design utilization combined to artificial neural networks with respect to classical factorial designs in bioprocess, using as example the rabies virus replication in BHK-21 cells. The viral infection process parameters under study were temperature (34°C, 37°C), multiplicity of infection (0.04, 0.07, 0.1), times of infection, and harvest (24, 48, 72 hours) and the monitored output parameter was viral production. A multilevel factorial experimental design was performed for the study of this system. Fractions of this experimental approach (18, 24, 30, 36 and 42 runs), defined according uniform designs, were used as alternative for modelling through artificial neural network and thereafter an output variable optimization was carried out by means of genetic algorithm methodology. Model prediction capacities for all uniform design approaches under study were better than that found for classical factorial design approach. It was demonstrated that uniform design in combination with artificial neural network could be an efficient experimental approach for modelling complex bioprocess like viral production. For the present study case, 67% of experimental resources were saved when compared to a classical factorial design approach. In the near future, this strategy could replace the established factorial designs used in the bioprocess development activities performed within biopharmaceutical organizations because of the improvements gained in the economics of experimentation that do not sacrifice the quality of decisions.

Prevalence of the hepatitis C virus among university employees in São Paulo, southeastern Brazil: predictive factors and geoprocessing spatial analysis

Background There are limited studies on the prevalence and risk factors associated with hepatitis C virus (HCV) infection. Objective Identify the prevalence and risk factors for HCV infection in university employees of the state of São Paulo, Brazil. Methods Digital serological tests for anti-HCV have been performed in 3153 volunteers. For the application of digital testing was necessary to withdraw a drop of blood through a needlestick. The positive cases were performed for genotyping and RNA. Chi-square and Fisher’s exact test were used, with P-value <0.05 indicating statistical significance. Univariate and multivariate logistic regression were also used. Results Prevalence of anti-HCV was 0.7%. The risk factors associated with HCV infection were: age >40 years, blood transfusion, injectable drugs, inhalable drugs (InDU), injectable Gluconergam®, glass syringes, tattoos, hemodialysis and sexual promiscuity. Age (P=0.01, OR 5.6, CI 1.4 to 22.8), InDU (P<0.0001, OR=96.8, CI 24.1 to 388.2), Gluconergam® (P=0.0009, OR=44.4, CI 4.7 to 412.7) and hemodialysis (P=0.0004, OR=90.1, CI 7.5 – 407.1) were independent predictors. Spatial analysis of the prevalence with socioeconomic indices, Gross Domestic Product and Human Development Index by the geoprocessing technique showed no positive correlation. Conclusions The prevalence of HCV infection was 0.7%. The independent risk factors for HCV infection were age, InDU, Gluconergan® and hemodialysis. There was no spatial correlation of HCV prevalence with local economic factors.

Determinação da carga viral em transplantados renais como parâmetro preditivo para o desenvolvimento da doença infecciosa por Citomegalovírus

Pós-graduação em Microbiologia - IBILCE

Epidemiological profile of hepatitis C virus infection in patients from west region of Minas Gerais State, Brazil

Hepatitis C virus (HCV) is a serious public health problem and is the leading cause of liver transplantation due to cirrhosis and hepatocellular carcinoma. In Brazil, it is estimated that there are approximately 2 to 3 million HCV chronic carriers. Few data regarding HCV infection are available in West region of Minas Gerais State. Due to the absence of an effective vaccine against this important human pathogen and the high costs of antiviral treatment, it is important to conduct epidemiological studies with the purpose of carry out the planning and implementation of measures to prevent hepatitis C in different populations. Therefore, the aim of this study is to describe the epidemiological aspects of HCV patients from West region of Minas Gerais State, Brazil. Sociodemographic data and risk factors for HCV infection were determined from 74 HCV patients from Uberlandia city (Minas Gerais State). Reactive anti-HCV sera samples were submitted to HCV RNA and genotype detection. Most of individuals were male (63.5%) with mean age of 51 years and presenting low socioeconomic status. HCV genotype was determined among 40 samples and the frequencies were: genotype 2 (45%), 1 (37.5%) and 3 (17.5%). Hepatitis C virus (HCV) infection was common among male and low socioeconomic status individuals.

Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of canonical siRNA and dicer substrate RNA for inhibition of hepatitis C virus genome replication: a comparative study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hepatitis C virus and dental health workers: an update

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Clinical and laboratory description of a series of cases of acute viral myositis

Describe the clinical and laboratory profile, follow-up, and outcome of a series of cases of acute viral myositis. A retrospective analysis of suspected cases under observation in the emergency department was performed, including outpatient follow-up with the recording of respiratory infection and musculoskeletal symptoms, measurement of muscle enzymes, creatine phosphokinase (CPK), lactate dehydrogenase (LDH), transaminases (AST and ALT), blood count, C-reactive protein, and erythrocyte sedimentation rate in the acute phase and during follow-up until normalization. Between 2000 and 2009, 42 suspected cases were identified and 35 (27 boys) were included. The median age was 7 years and the diagnosis was reported in 89% in the first emergency visit. The observed respiratory symptoms were cough (31%), rhinorrhea (23%), and fever (63%), with a mean duration of 4.3 days. Musculoskeletal symptoms were localized pain in the calves (80%), limited ambulation (57%), gait abnormality (40%), and muscle weakness in the lower limbs (71%), with a mean duration of 3.6 days. There was significant increase in CPK enzymes (5507±9180U/L), LDH (827±598U/L), and AST (199±245U/L), with a tendency to leukopenia (4590±1420) leukocytes/mm(3). The complete recovery of laboratory parameters was observed in 30 days (median), and laboratory and clinical recurrence was documented in one case after 10 months. Typical symptoms with increased muscle enzymes after diagnosis of influenza and self-limited course of the disease were the clues to the diagnosis. The increase in muscle enzymes indicate transient myotropic activity related to seasonal influenza, which should be considered, regardless of the viral identification, possibly associated with influenza virus or other respiratory viruses.