Use of synthetic oligonucleotides for determination of HTLV-1 proviral load by real-time PCR: a helpful alternative approach in the clinical management.

AIMS: To evaluate the potential use of synthetic oligonucleotides as a standard curve for proviral load (PVL) of human T-cell leukaemia virus type 1 (HTLV-1) quantification in peripheral blood mononuclear cells (PBMC) of HTLV-1-infected individuals by quantitative real-time polymerase chain reaction (qPCR) analysis. METHODS AND RESULTS: Synthetic oligonucleotides based on HTLV-1 genome were customized to use as a standard curve. Twelve anti-HTLV-1-positive samples with known HTLV-1 PVL, previously quantified by qPCR assay using TARL-2 cells as a conventional standard curve, were submitted to the new protocol. The proviral quantification levels had a high concordance with qPCR results using a conventional standard curve. The results demonstrate that the conventional standard curve can be replaced by a synthetic standard curve due to its ability to quantification based on the linearity and qPCR efficiency and similar results with a validated qPCR assay using a conventional standard curve. CONCLUSIONS: Synthetic oligonucleotides standard curves could be a very useful tool on HTLV-1 diagnosis and absolute HTLV-1 PVL quantification. SIGNIFICANCE AND IMPACT OF THE STUDY: HTLV-1 PVL determination using synthetic oligonucleotides standard curve by qPCR could be a helpful alternative for the laboratories that monitor infected patients as an important prognostic factor in HTLV-1-associated diseases progression. Also, it can decrease costs and overcome the biological limitations of the plasmid curve.

Detection and quantification of hepatitis E virus in the absence of IgG and IgM anti-HEV in HIV-positive patients.

AIMS: To improve RT-qPCR with an internal control and a synthetic standard curve to detect HEV in HIV co-infected patients. METHODS AND RESULTS: A single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA) synthetic curve were designed, compared to the international reference panel for HEV genotypes, and tested to quantify and detect a reference panel for HEV genotypes. The detection limit of the RNA synthetic curve (50 copies per ml) was better than the DNA synthetic curve (100 copies per ml) and the WHO standard curve (250 copies per ml). Then, 280 serum samples from HIV-positive patients were tested for HEV RNA, which was detected in 3·6% of serum samples. The viral load ranged from 2 × 102 copies per ml to 4·78 × 108 copies per ml. HEV IgM/IgG antibodies were not detected in the RNA-positive patients. Sequencing analysis of HEV showed that the virus belongs to genotype 3 (HEV GT3). CONCLUSIONS: Real-time PCR was a useful tool to estimate co-infection with HEV/HIV, even in patients with low viral loads and undetectable anti-HEV IgG and IgM antibodies. SIGNIFICANCE AND IMPACT OF THE STUDY: Hepatitis E virus genotype 3 (HEV GT3) has been associated with silent chronic hepatitis and cirrhosis in HIV-positive subjects worldwide, but there is a lack of data on this co-infection in Brazil.

Recombinant expression of Ixolaris, a Kunitz-type inhibitor from the tick salivary gland, for NMR studies.

Ixolaris is an anticoagulant protein identified in the tick saliva of Ixodes scapularis. Ixolaris contains 2 Kunitz like domains and binds to Factor Xa or Factor X as a scaffold for inhibition of the Tissue Factor (TF)/Factor VIIa (FVIIa). In contrast to tissue factor pathway inhibitor (TFPI), however, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite. Due to its potent and long-lasting antithrombotic activity, Ixolaris is a promising agent for anticoagulant therapy. Although numerous functional studies of Ixolaris exist, three-dimensional structure of Ixolaris has not been obtained at atomic resolution. Using the pET32 vector, we successfully expressed a TRX-His6-Ixolaris fusion protein. By combining Ni-NTA chromatography, enterokinase protease cleavage, and reverse phase HPLC (RP-HPLC), we purified isotopically labeled Ixolaris for NMR studies. 1D 1H and 2D 15N-1H NMR analysis yielded high quality 2D 15N-1H HSQC spectra revealing that the recombinant protein is folded. These studies represent the first steps in obtaining high-resolution structural information by NMR for Ixolaris enabling the investigation of the molecular basis for Ixolaris-coagulation factors interactions.

Bet v 1--a Trojan horse for small ligands boosting allergic sensitization?

BACKGROUND: Birch pollen allergy represents the main cause of winter and spring pollinosis in the temperate climate zone of the northern hemisphere and sensitization towards Bet v 1, the major birch pollen allergen, affects over 100 million allergic patients. The major birch pollen allergen Bet v 1 has been described as promiscuous acceptor for a wide variety of hydrophobic ligands. OBJECTIVE: In search of intrinsic properties of Bet v 1, which account responsible for the high allergenic potential of the protein, we thought to investigate the effects of ligand-binding on immunogenic as well as allergenic properties. METHODS: As surrogate ligand of Bet v 1 sodium deoxycholate (DOC) was selected. Recombinant and natural Bet v 1 were characterised physico-chemically as well as immunologically in the presence or absence of DOC, and an animal model of allergic sensitization was established. Moreover, human IgE binding to Bet v 1 was analysed by nuclear magnetic resonance (NMR) spectroscopy. RESULTS: Ligand-binding had an overall stabilizing effect on Bet v 1. This translated in a Th2 skewing of the immune response in a mouse model. Analyses of human IgE binding on Bet v 1 in mediator release assays revealed that ligand-bound allergen-induced degranulation at lower concentrations; however, in basophil activation tests with human basophils ligand-binding did not show this effect. For the first time, human IgE epitopes on Bet v 1 were determined using antibodies isolated from patients' sera. The IgE epitope mapping of Bet v 1 demonstrated the presence of multiple binding regions. CONCLUSIONS AND CLINICAL RELEVANCE: Deoxycholate binding stabilizes conformational IgE epitopes on Bet v 1; however, the epitopes themselves remain unaltered. Therefore, we speculate that humans are exposed to both ligand-bound and free Bet v 1 during sensitization, disclosing the ligand-binding cavity of the allergen as key structural element.

Kinetics of hepatitis A virus replication in vivo and in vitro using negative-strand quantitative PCR.

The replication of hepatitis A virus (HAV) is via a complementary negative-strand RNA. Each negative strand may serve as a template for the synthesis of many positive strands. The aim of this study was to detect the intermediate replicative (negative strand) of HAV in order to monitor its replication in vitro and in vivo. Real-time polymerase chain reaction (PCR) was standardized to detect the intermediate replicative of HAV in cell culture and liver from non-human primates infected experimentally. HAV primers from the 5' non-translated region and VP3 were used in the cDNA synthesis of negative-strand RNA. The negative strand was detected in the infected cell lines and liver by highly strand-specific rTth recombinant Thermus thermophilus DNA polymerase reverse transcription followed by quantitative PCR. The results indicate that the negative-strand HAV RNA can be detected in vivo and in vitro. This model is an approach for assessing the dynamic patterns of replication and should represent a valuable tool for the monitoring of HAV replications in cell cultures and for the evaluation of experimental infections in animal models.

Changes in hepatitis A virus seroepidemiology in HIV-infected Brazilian patients.

Shifting of hepatitis A virus (HAV) epidemiology from a high towards an intermediate endemicity pattern and use of antiretroviral therapy increased the risk of HIV/HAV coinfection in developing countries. The aim of this study was to investigate the presence of HAV markers in a cohort of HIV-infected patients from 1988 to 2004. The presence of serum anti-HAV antibodies and HAV-RNA by real-time polymerase chain reaction was investigated in 581 patients. Total anti-HAV antibodies was found in 464/581 (79.8%) patients, however, a changing epidemiologic pattern of hepatitis A among HIV-infected patients from 1988 to 2004 was observed. Among patients susceptible to HAV (n = 117), 5 (4.2%) were coinfected with HAV, all of them had IgM anti-HAV antibodies and were serum HAV-RNA-positive. The high prevalence of anti-HAV antibodies in HIV-infected patients suggests that screening tests for anti-HAV antibodies should be performed before implementation of hepatitis A vaccination, especially in those patients from endemic countries.

Hepatitis A virus in environmental water samples from the Amazon Basin.

Hepatitis A virus (HAV) is a significant waterborne human pathogen. Of the global supply of potable water, Brazil retains 13%, of which 75% resides in the Amazon Basin. Although hepatitis A morbidity has declined progressively in Brazil as a whole, it remains high in the Amazon region. We used nested and real-time reverse-transcription polymerase chain reaction (RT-PCR) to detect and quantify the viral load in water samples from the Amazon Basin. Most samples tested positive (92%), with viral loads varying from 60 to 5500 copies /L, depending on sanitary conditions and the degree of flooding. Nested RT-PCR of the VP1-2A region detected HAV RNA in 23% of the samples. In low viral load samples, HAV was detected only with real-time RT-PCR, suggesting that this technique is useful for monitoring HAV contamination. The presence of HAV in water samples constitutes a serious public health problem.

Prevalence of Neospora caninum and Toxoplasma gondii in sheep and dogs from Guarapuava farms, Paraná State, Brazil.

Sheep and dog blood samples were collected from nine farms in the county of Guarapuava, Paraná, Brazil. The indirect fluorescent antibody test (IFAT) was used to detect Neospora caninum and Toxoplasma gondii antibodies. Herein, serum samples from 305 sheep were evaluated, being 29 (9.5%) and 157 (51.5%) seropositives to N. caninum and T. gondii, respectively. Seven (29.1%) and five (20.8%) out of 24 dogs were seropositives to N. caninum and T. gondii, respectively. There were no differences among the sheep serology for N. caninum and reproductive problems, management and animal feeding variables, neurological problems and presence of other animals species on the farm (P>or=0.05). The simultaneous frequency of antibodies between N. caninum and T. gondii was 5.2% in the herds. Age, breed, farm size, semi-intensive activity, mineral salt supplementation, water origin, stage of the pregnancy when reproduction problems occurred, neurological problems in lambs, presence of rodents in the food room and pasture cat access were identified as associated factors for the occurrence of toxoplasmosis in sheep (P<0.05). There were no differences among the seropositivity in dogs for N. caninum and T. gondii and breed, age and sex (P>or=0.05). The present work is the first report on serum prevalence of N. caninum in sheep from the state of Paraná, Brazil.

1H, 15N and 13C resonance assignments of Ixolaris, a tissue factor pathway inhibitor from the tick salivary gland.

Ixolaris is a two-Kunitz tick salivary gland protein identified in Ixodes scapularis that presents sequence homology to TFPI (tissue factor pathway inhibitor). It binds to the coagulation enzyme factor Xa (FXa) or to its zymogen form, FX, and further inhibits tissue factor/FVIIa complex (extrinsic Xnase compex). Differently from TFPI, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite, which may also results in decreased FXa activity into the prothrombinase complex. The Ixolaris-FXa/FX complex formation has been characterized by using a combination of biophysical and biochemical technics although no structural data is currently available. In this study, we reported the NMR chemical shift assignment of Ixolaris, as a first step to further establishing the structure, dynamics and function relationship for this protein.

Detection of hepatitis A virus RNA in serum during the window period of infection.

BACKGROUND: Hepatitis A virus (HAV) infection is the leading cause of clinically apparent viral hepatitis in many parts of the world, including developed and developing countries. Only limited information is available regarding the seronegative viremic window that follows HAV infection, and no systematic search has been reported for HAV RNA positive, IgM anti-HAV negative serum samples during hepatitis A outbreaks. OBJECTIVES: To determine the proportion of HAV infected individuals among (i) children who were tested negative for anti-HAV antibodies during hepatitis A outbreaks which occurred in a public school (n = 157) and a child care center (n = 38); (ii) subjects (n = 46) initially classified as acute non-A-C hepatitis patients after clinical examination and serological tests (sporadic cases). STUDY DESIGN: Reverse transcription (RT)-PCR was performed to detect the presence of HAV genome in serum samples collected from anti-HAV negative, susceptible subjects. RESULTS: HAV RNA was detected in 19/157 (12%) and 5/38 (13%) anti-HAV negative children from the public school and child care center, respectively. Twelve (26%) out of the 46 acute hepatitis patients (sporadic cases) were also HAV RNA positive. From nine of these 12 patients, a second blood sample was obtained 18-34 days after the first one: all nine had seroconverted to IgM anti-HAV, and their serum transaminases had reached elevated levels (mean ALT, 418; mean AST, 241). CONCLUSIONS: Detection of HAV RNA before IgM anti-HAV seroconversion may be used as an early diagnosis method during hepatitis A outbreaks. HAV RNA testing should also help to elucidate acute hepatitis cases of unknown etiology.

Hepatitis A virus infection in hepatitis C Brazilian patients.

OBJECTIVE: HAV infection in patients with pre-existing chronic liver disease has been associated with increased rate of fulminant hepatitis and mortality. The aim of this study was to investigate the presence of serological and molecular HAV markers in a population of HCV infected patients. PATIENTS AND METHODS: The presence of total and IgM anti-HAV antibodies was investigated in 197 patients (mean age 44.8+/-12.5 years) referred to the Brazilian Reference Center for Viral Hepatitis and who tested positive for anti-HCV antibodies and HCV RNA. HAV RNA was investigated by reverse transcription-nested PCR in these patients.Results. One hundred seventy patients (86%) had total, but not IgM anti-HAV antibodies, being therefore, immune to hepatitis A, while 27 (14%) were not. A high proportion (6/27, 22%) of the susceptible patients presented markers of recent HAV infection: One patient was IgM anti-HAV positive, three were HAV RNA positive, and two presented both markers. By nucleotide sequencing, it was demonstrated that the HAV isolates infecting these patients belonged to subgenotypes 1A and 1B. CONCLUSIONS: Superinfection with HAV was a common event in the group of HCV infected patients under study. Implementation of hepatitis A vaccination should be considered for this population.

Prevalence of anti-Toxoplasma gondii and anti-Neospora caninum antibodies in ovine from São Paulo State, Brazil.

Serum samples from 597 sheep from São Paulo State, in the southeastern region of Brazil, were tested to determine the prevalence of antibodies directed against Toxoplasma gondii (> or = 1:64) and Neospora caninum (> or = 1:50) using the indirect fluorescent antibody test (IFAT). The animals were divided into three groups based on their age: < or = 1 year, 1-4 years, and > or = 4 years. Antibodies to T. gondii were observed in 34.7% of the samples with titers ranging from 64 to 16,384 and IgG antibodies directed against N. caninum were observed in 9.2%, with titers ranging from 50 to 3200. Only 3.5% of the sheep were positive for both agents. All farms had at least one positive animal for T. gondii, and 26 of the 30 farms had at least one positive animal for N. caninum. An association between seroprevalence and age was observed for T. gondii (P = 0.001), but not to N. caninum (P = 0.343). It was not possible to associate seroprevalence to T. gondii and the presence of domestic or feral cats, since in all farms there was at least one positive sheep. There was no association between seropositivity to N. caninum and the presence of domestic (P = 1.000) and feral dogs (P = 0.550).

Structural basis for the interaction of human ß-defensin 6 and its putative chemokine receptor CCR2 and breast cancer microvesicles.

Human ß-defensins (hBDs) are believed to function as alarm molecules that stimulate the adaptive immune system when a threat is present. In addition to its antimicrobial activity, defensins present other activities such as chemoattraction of a range of different cell types to the sites of inflammation. We have solved the structure of the hBD6 by NMR spectroscopy that contains a conserved ß-defensin domain followed by an extended C-terminus. We use NMR to monitor the interaction of hBD6 with microvesicles shed by breast cancer cell lines and with peptides derived from the extracellular domain of CC chemokine receptor 2 (Nt-CCR2) possessing or not possessing sulfation on Tyr26 and Tyr28. The NMR-derived model of the hBD6/CCR2 complex reveals a contiguous binding surface on hBD6, which comprises amino acid residues of the α-helix and ß2-ß3 loop. The microvesicle binding surface partially overlaps with the chemokine receptor interface. NMR spin relaxation suggests that free hBD6 and the hBD6/CCR2 complex exhibit microsecond-to-millisecond conformational dynamics encompassing the CCR2 binding site, which might facilitate selection of the molecular configuration optimal for binding. These data offer new insights into the structure-function relation of the hBD6-CCR2 interaction, which is a promising target for the design of novel anticancer agents.

Evolutionary relationship between defensins in the Poaceae family strengthened by the characterization of new sugarcane defensins.

Plant defensins are small (45-54 amino acids), highly basic, cysteine-rich peptides structurally related to defensins of other organisms, including insects and mammals. Small putative proteins (MW < 10 kDa) containing eight cysteines were screened based on the sugarcane expressed sequence tag (EST) database. We selected ORFs that exhibited 25-100% similarity in primary sequence with other defensins in the NCBI database and that contained eight cysteines. This similarity is sufficient for folding prediction, but not enough for biological activity inference. Six putative defensins (Sd1-6) were selected, and activity assays showed that recombinant Sd1, Sd3 and Sd5 are active against fungi, but not against bacteria. Structural characterization, based on circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy showed that the structures of these Sds were compatible with alpha/beta proteins, a feature expected for plant defensins. Phylogenetic analysis revealed that sugarcane defensins could clearly be grouped within defensins from Poaceae family and Andropogoneae tribe. Our work demonstrates that defensins show strong conservation in the Poaceae family and may indicate that the same conservation occurs in other families. We suggest that evolutionary relationships within plant families can be used as a procedure to predict and annotate new defensins in genomes and group them in evolutionary classes to help in the investigation of their biological function.

Molecular detection of hepatitis A virus in urban sewage in Rio de Janeiro, Brazil.

AIMS: A one-year survey was conducted to examine hepatitis A virus (HAV) prevalence, distribution of genotypes and their relationship to bacterial indicators in raw and treated sewage samples. METHODS AND RESULTS: Fifty sewage samples (raw = 25 and treated = 25) were collected twice monthly from one sewage treatment plant in Rio de Janeiro. Virus concentration was performed by adsorption to an electronegative membrane followed by ultrafiltration. Viral RNA was detected by nested reverse transcriptase-polymerase chain reaction (RT-PCR) and real-time PCR and positive products were directly sequenced. Total and faecal coliform concentrations were also determined. By nested RT-PCR, HAV RNA was detected in 16/50 (32%) and eight (16%) of them were found in treated sewage samples. By real-time PCR, HAV RNA was detected in 46/50 (92%) samples and 24 were from treated sewage. Phylogenetic analyses classified nine isolates (56%) as subgenotype IA and seven (44%) as IB. CONCLUSIONS: Real-time PCR was more sensitive than nested RT-PCR; the presence of subgenotypes IA and IB was described and bacterial indicators cannot be used to predict HAV presence in sewage. SIGNIFICANCE AND IMPACT OF THE STUDY: These results demonstrated that HAV still remains in the environment after sewage treatment and could play an important role in maintaining the endemicity of HAV infection.

Seroprevalence of viral hepatitis in riverine communities from the Western Region of the Brazilian Amazon Basin.

The western region of the Brazilian Amazon Basin has long been shown to be a highly endemic area for hepatitis B and hepatitis D viruses. Data concerning the prevalence of hepatitis C and E viruses in this region are still scarce. In this study we investigated the presence of hepatitis A, B, C, D and E viruses infection in communities that live along the Purus and Acre rivers in the states of Acre and Amazonas within the Amazon Basin. A total of 349 blood samples were collected and tested for hepatitis A-E serological markers (antibodies and/or antigens) using commercial enzyme linked immunosorbent assays. Anti-HCV positive sera were further assayed by an immunoblot. HBsAg positive sera were subtyped by immunodifusion. The overall prevalence for hepatitis A, B, C, and E were 93.7%, 66.1%, 1.7%, and 4%, respectively. A very high prevalence of delta hepatitis (66.6%) was found among HBsAg positive subjects. Hepatitis A, B and D viruses were shown to be largely disseminated in this population, while hepatitis C and E viruses infection presented low prevalence rates in this region. The analysis of risk factors for HBV infection demonstrated that transmission was closely associated with sexual activity.

Hepatitis E virus infection in selected Brazilian populations.

A retrospective study on the prevalence of hepatitis E virus (HEV) infection was conducted in selected populations in Rio de Janeiro, Brazil. A total of 1,115 subjects were tested including 146 patients with acute Non-A Non-B Non-C (NANBNC) viral hepatitis, 65 hemodialysis patients, 93 blood donors, 102 intravenous drug users (IVDUs), 304 pregnant women, 145 individuals living in the rural area and 260 individuals living in the urban area. In order to characterize a favorable epidemiological set for enterically transmitted infection in the studied populations we also evaluated the prevalence of anti-HAV IgG (hepatitis A virus) antibodies. Specific antibodies to HEV (anti-HEV IgG) were detected by a commercial EIA and specific antibodies to HAV (anti-HAV IgG) were detected using a competitive "in house" EIA. We found a high prevalence of anti-HAV IgG in these populations, that could indicate some risk for infections transmitted via the fecal-oral route. The anti-HEV IgG prevalence among the different groups were: 2.1% in patients with acute NANBNC viral hepatitis, 6.2% in hemodialysis patients, 4.3% in blood donors, 11.8% in IVDUs, 1% in pregnant women, and 2.1% in individuals form the rural area. Among individuals living in the urban area we did not find a single positive serum sample. Our results demonstrated the presence of anti-HEV IgG in almost all studied populations; however, further studies are necessary to establish the real situation of HEV epidemiology in Rio de Janeiro, Brazil.

Age-specific prevalence and transmission of TT virus.

TT virus (TTV) is an unenveloped, single-stranded DNA virus that was discovered recently in the sera of Japanese patients with posttransfusion hepatitis of unknown etiology. A high prevalence of TTV infection in blood donors of several countries, including Brazil, has been demonstrated. To study the variation in TTV prevalence between different age groups, sera from 223 individuals without liver disease, aged 0-80 years, were tested by the polymerase chain reaction for the presence of TTV DNA. All subjects were inhabitants of the city of Rio de Janeiro, Brazil. The prevalence increased continuously with age (P <.001), from 17% among children under the age of 11 years, to 57% in people older than 50 years. To assess vertical transmission, sera from 105 unselected, consecutive parturient women attending a public maternity hospital were paired with cord bloods and examined for the presence of TTV DNA. Thirty-seven (35%) mothers were found to be TTV infected. Seven cord bloods were also positive, suggesting the possible transplacental transmission of the virus. Furthermore, a direct correlation between TTV viremia and presence of antibodies to the enterically transmissible hepatitis A virus (HAV) was observed in this group of women, with a relative risk of TTV infection of 5.09 (95% confidence interval 0.76-34.03) for women with anti-HAV, compared with women without. This finding suggested that the fecal-oral route might be an important route of TTV transmission.