Characterisation of the translation efficiency and quasispecies composition of the 5'untranslated region of Hepatitis C virus in genotype 1 and 3 infected patients

Hepatitis C virus (HCV) infects over 170 million people worldwide. Chronic infection occurs in 50-80% of cases and eventually leads to cirrhosis and hepatocellular carcinoma. HCV can be classified into six genotypes. Genotypes 1, 2 and 3 have a world-wide distribution but their prevalence differs from one geographical area to another. In Scotland there is an approximate 50/50 split between patients infected with HCV genotype 1 and genotype 3. One difference which has been consistently demonstrated is the better response of patients infected with genotypes 2 and 3 to interferon treatment than those infected with genotype 1. The HCV lifecycle is only partly understood owing to the lack of a productive cell culture system. There is no vaccine to prevent infection by HCV. Given the predicted future impact of the disease, there is a great need to understand the molecular basis of the HCV life cycle. Protein translation is one of the important processes in HCV replication. It involves an internal ribosome entry site (IRES) in the 5'untranslated region (5'UTR). Comparison of the sequence and function of the 5'UTR from different genotypes might differentiate features essential to the virus life cycle in all genotypes from those relevant only to individual genotypes. In this study, the 5'UTR region of genotype 3 was compared with that of genotype 1 with respect to translation initiation and quasispecies composition. The association between translation efficiencies, serum viral loads and the histology of the liver was also investigated. (Abstract shortened by ProQuest.)

Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation

The HCV internal ribosome entry site (IRES) spans a region of ∼340 nt that encompasses most of the 5′ untranslated region (5′UTR) of the viral mRNA and the first 24–40 nt of the core-coding region. To investigate the implication of altering the primary sequence of the 5′UTR on IRES activity, naturally occurring variants of the 5′UTR were isolated from clinical samples and analyzed. The impact of the identified mutations on translation was evaluated in the context of RLuc/FLuc bicistronic RNAs. Results show that depending on their location within the RNA structure, these naturally occurring mutations cause a range of effects on IRES activity. However, mutations within subdomain IIId hinder HCV IRES-mediated translation. In an attempt to explain these data, the dynamic behavior of the subdomain IIId was analyzed by means of molecular dynamics (MD) simulations. Despite the loss of function, MD simulations predicted that mutant G266A/G268U possesses a structure similar to the wt-RNA. This prediction was validated by analyzing the secondary structure of the isolated IIId RNAs by circular dichroism spectroscopy in the presence or absence of Mg2+ ions. These data strongly suggest that the primary sequence of subdomain IIId plays a key role in HCV IRES-mediated translation

Evaluation of Cytogenetic Alterations in Peripheral Blood Lymphocytes of Esophageal Cancer Patients Treated with Radiotherapy or Chemoradiotherapy using Cytokinesis-Blocked Micronucleus Assay

The effects of combined radiotherapy (RT) and chemotherapy in the severity of cytogenetic alterations expressed as micronucleus (MN) in peripheral blood lymphocytes of patients treated for esophageal cancer was evaluated. To do this, blood was obtained from 23 and 15 esophageal cancer patients scheduled for chemo-radiotherapy and RT alone, respectively, before, during, and after treatment. Blood samples were cultured in RPMI-1640 complete medium containing 1% phytohemagglutinin and incubated in a CO2 incubator. Cytochalasin-B was added to the cultures at a final concentration of 5μg/ml. Finally, harvesting, slide making, and analysis were performed according to standard procedures. Results indicate that there was no significant difference between the frequencies of MN in lymphocytes of individuals before being treated with RT alone or chemo-radiotherapy. In the middle of treatment, (after 12 fractions of RT) the frequency of MN increased significantly compared with their concurrent pre-treatment samples in both groups (four-fold). However, the frequency of MN observed for RT patients was not significantly different with those received chemo- and radiotherapy. At the end of treatment, (after 24 fractions of radiotherapy) an increase in the MN frequency was observed for chemo-radiation group significantly higher than RT group (P=0.022). Mild increase in MN frequency in lymphocytes of patients receiving chemoradiation only after the completion of treatment course might be indicative of resistance induced by chemotherapeutics to the clastogenic effects of radiation. Therefore, using these agents repeatedly for cancer treatment in combination with radiation might not cause severe adverse biological effects in normal tissues

Cytokinesis blocked micronucleus assay for evaluation of chromosomal breaks in esophageal cancer

Background: Radiotherapy can cause DNA damage in normal cells, misrepaired or unrepaired double strand breaks in DNA lead to chromosomal breaks. As a result patient experience early and late effects in normal tissue during and after radiotherapy. Cytogenetic techniques can be used as a cancer predictive assay because there is an association between chromosome abnormalities and the risk of developing cancer. Also it can assess patient's complications during the therapy. The aim of the present study was evaluation of the cytogenetic alteration in peripheral blood lymphocytes of esophageal cancer patients treated with radiotherapy. Methods: The present study is an experimental and prospective research. It was done at radiotherapy department at Omid Center in Urmia from January to December 2012. Blood samples were obtained from 15 esophageal cancer patients, before (0 Gy), during (21.6 Gy), and after radiotherapy treatment (43.2 Gy). Blood samples were cultured in RPMI-1640 complete medium containing 1% phytohaemagglutinin and incubated in a CO2 incubator. Cytochalasin-B was added to the cultures at a final concentration of 5 µg/ml. Finally, harvesting, slide making, and analysis were performed according to standard procedures. Results: This study consisted of 15 patients, including 7 men and 8 women from 55 to 84 years old (70.07±11.548). Results indicate that, in the middle of treatment the average frequency of micronuclei increased significantly compared with their concurrent pre-treatment samples (greater than four-fold). Also, an increase in chromosome damage (MN frequency) proportional increasing radiation doses at the end of treatment was observed (P=0.001). Conclusion: Increasing in the MN frequency in the second and third stages is due to radiation effects. Thus, the use of the MN technique for assessing of the side effects in patients during the therapy is very helpful. Moreover, MN assay can be used as a predictive assay for detecting individuals (patient or healthy) with intrinsic radiosensitivity

Translation efficiencies of the 5 '-untranslated region of genotypes 1a and 3a in hepatitis C infected patients

Differences between the translation efficiencies mediated by the 5'-untranslated regions (5'UTR) of genotypes (gt) 1 and 3 of hepatitis C virus (HCV) have been reported but it is unknown if such differences are biologically significant. The 5'-UTR was sequenced from paired serum and liver samples from 26 patients with chronic HCV hepatitis (11 gt la, 15 gt 3a). To determine whether there is a consistent difference between gts 1a and 3a translation efficiency, 5'-UTR (nt 1-356) and 5'-UTR plus core (nt 1-914) sequences were cloned into bicistronic, luciferase-encoding constructs and relative translation efficiencies (RTE) measured in Huh7 cells and BHK cells. The relationships between viral load, liver biopsy Ishak scores, degree of steatosis and translational activity of the patient-derive nucleotide sequence were examined. There were no differences in 5'-UTR sequence between serum and corresponding liver samples. The mean RTE of 5'-UTR sequences from gt 3a isolates was not significantly different from gt la whether or not the core encoding sequence was included, although inclusion of core led to a reduction in RTE by 93-97% for both genotypes. No correlation was found between RTE and serum HCV RNA levels, liver steatosis, inflammation, or fibrosis. However, a significant correlation was found between the presence of steatosis and infection with HCV gt 3a. It is concluded that there was no difference in translation efficiencies of 5'-UTRs from patients infected with gts 1 a and 3a, and translation activity measured in vitro does not correlate with viral load or severity of liver disease

BK polyomavirus genotypes in renal transplant recipients in the United States: A meta‐analysis

Background: In the United States, increasing ethnic diversity has been apparent. However, the epidemiology and trends of BKV genotypes remain unclear. This meta-analysis was conducted with the aim to assess the prevalence of BKV genotypes among kidney transplant (KTx) recipients in the United States. Methods: A comprehensive literature review was conducted through October 2018 utilizing MEDLINE, Embase, and Cochrane Database to identify studies that reported the prevalence of BKV subtypes and/or subgroups in KTx recipients in the United States. Pooled prevalence rates were combined using random effects, generic inverse variance method. The protocol for this study is registered with PROSPERO (no. CRD42019134582). Results: A total of eight observational studies with a total of 193 samples (urine, blood, and kidney tissues) from 188 BKV-infected KTX recipients were enrolled. Overall, the pooled estimated prevalence rates of BKV subtypes were 72.2% (95% confidence of interval [CI]: 62.7-80.0%) for subtype I, 6.8% (95% CI: 2.5-16.9%) for subtype II, 8.3% (95% CI: 4.4-15.1%) for subtype III, and 16.1% (95% CI: 10.4-24.2%) for subtype IV, respectively. While metaregression analysis demonstrated a significant positive correlation between year of study and the prevalence of BKV subtype I (slopes = +0.1023, P =.01), there were no significant correlations between year of study and percentages of BKV subtype II-IV (P \u3e.05). Among KTx recipients with BKV subtype I, the pooled estimated percentages of BKV subgroups were 22.4% (95% CI: 13.7-34.5%) for subgroup Ia, 30.6% (95% CI: 17.7-47.5%) for subgroup Ib1, 47.7% (95% CI: 35.8-59.9%) for subgroup Ib2, and 4.1% (95% CI:1.2-13.3%) for subgroup Ic, respectively. Conclusion: BKV subtype I is the most prevalent subtype among KTx recipients in the United States and its prevalence seems to increasing overtime. Subgroup Ib2 is the most common subgroup among BKV subtype I

Epidemiology of hepatitis B in pregnant Iranian women: a systematic review and meta-analysis

Perinatal transmission is one of the most common routes of hepatitis B virus (HBV) transmission. This study aims to identify the epidemiological features of HBV among pregnant Iranian women. This study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Two authors independently searched several online databases without time limit until May 2017. The databases include Magiran, Iranmedex, SID, Medlib, IranDoc, Scopus, PubMed, Science Direct, Cochrane, Web of Science and Google Scholar. The data were analyzed based on a random-effects model using Comprehensive Meta-Analysis software version 2. Thirty-seven studies were included in the meta-analysis. The prevalence of HBV among pregnant Iranian women was 1.18 (95 CI: 0.09-1.53). The prevalence of HBV among pregnant women living in urban and rural areas was 1.60 (95 CI: 0.06-4.30) and 1.70 (95 CI: 0.09-3.2), respectively. The prevalence of HBV among housewives and working pregnant women was 4.3 (95 CI: 1.4-12.5) and 1.2 (95 CI: 0.02-5.8), respectively. The risk of developing an HBV infection was significantly associated with illiteracy (p = 0.013), abortion (p = 0.001), blood transfusion (p < 0.001) and addicted spouse (p = 0.045). However, no significant relationship was observed between HBV infection and urbanization (p = 0.65), occupation (p = 0.37), history of surgery (p = 0.32) or tattooing (p = 0.69). Vaccination coverage (receiving at least a single dose) in pregnant women was 9.8 (95 CI: 5.3-17.5). The prevalence of HBV among pregnant women is lower than in the general population of Iran. HBV vaccination coverage was low among pregnant Iranian women. Therefore, health policy-makers are recommended to enforce immunization programs for HBV vaccination among high-risk pregnant women