Engineered PUF proteins: New flexible toolkits to target the replication of RNA viruses

Aim: The RNA recognition code of an RNA-binding protein known as Pumilio/FBF (PUF) protein was reprogrammed in order to provide binding to internal ribosome entry site (IRES) of hepatitis C virus (HCV) genome. Materials & methods: The ability of the modified protein to repress IRES-dependent translation was analyzed by dual-luciferase reporter assay, cell viability assay, cell cytotoxicity assay and anti-HCV assay. Results: The modified protein was able to reduce reporter gene expression (>30) and HCV viral load (>98) and reduced HCV-induced cytotoxicity to the level observed in uninfected cells. Conclusion: Our results can set the stage for using modified PUFs for interfering with critical steps such as replication and translation in virus life cycle, especially RNA viruses. © 2021 Future Medicine Ltd

Nucleotide identity and variability among different Pakistani hepatitis C virus isolates

<p>Abstract</p> <p>Background</p> <p>The variability within the hepatitis C virus (HCV) genome has formed the basis for several genotyping methods and used widely for HCV genotyping worldwide.</p> <p>Aim</p> <p>The aim of the present study was to determine percent nucleotide identity and variability in HCV isolates prevalent in different geographical regions of Pakistan.</p> <p>Methods</p> <p>Sequencing analysis of the 5'noncoding region (5'-NCR) of 100 HCV RNA-positive patients representing all the four provinces of Pakistan were carried out using ABI PRISM 3100 Genetic Analyzer.</p> <p>Results</p> <p>The results showed that type 3 is the predominant genotypes circulating in Pakistan, with an overall prevalence of 50%. Types 1 and 4 viruses were 9% and 6% respectively. The overall nucleotide similarity among different Pakistani isolates was 92.50% ± 0.50%. Pakistani isolates from different areas showed 7.5% ± 0.50% nucleotide variability in 5'NCR region. The percent nucleotide identity (PNI) was 98.11% ± 0.50% within Pakistani type 1 sequences, 98.10% ± 0.60% for type 3 sequences, and 99.80% ± 0.20% for type 4 sequences. The PNI between different genotypes was 93.90% ± 0.20% for type 1 and type 3, 94.80% ± 0.12% for type 1 and type 4, and 94.40% ± 0.22% for type 3 and type 4.</p> <p>Conclusion</p> <p>Genotype 3 is the most prevalent HCV genotype in Pakistan. Minimum and maximum percent nucleotide divergences were noted between genotype 1 and 4 and 1 and 3 respectively.</p

Hepatitis C Virus Infection and HCV Genotypes of Hemodialysis Patients

&quot;nBackground: To evaluate the prevalence of hepatitis C by antibody testing, HCV-RNA detection by PCR and relative risk fac&amp;shy;tors of HCV infection among HD patients and staff members in Markazi Province/Iran. The other purpose was to deter&amp;shy;mine genotypes of HCV in this population.&quot;nMethods: The study group consisted of 204 HD patients and 47 staff members from all 9 dialysis centers in Markazi Prov&amp;shy;ince, Iran. Anti-HCV antibodies were tested using a third generation ELISA and confirmed by RIBA. HCV RNA was deter&amp;shy;mined by RT-PCR and genotyping was performed by a reverse hybridization assay (LiPA).&quot;nResults: The overall prevalence of HCV (HCV antibody and HCV-RNA) was 5.4%. Female sex (P= 0.019), duration of dialy&amp;shy;sis (P= 0.003) and kidney transplant (P= 0.049) were significantly correlated with HCV infection. The predominant sub&amp;shy;type was HCV-1a, detected in 4(50%) of the 8 HD patients. Genotype 4, 3a and 1b were found in 2(25%), 1(12.5%) and 1(12.5%) patients respectively. &amp;nbsp;The prevalence of anti-HCV among staff members of HD units was 0%.&quot;nConclusion: The presence of anti HCV positive patients who had never been transfused, high prevalence of genotype 4 in this population, duration of HD as a risk factor for HCV positivity and non significant association between blood transfu&amp;shy;sion and HCV infection suggest nosocomial transmission of the virus in dialysis units that needs to be confirmed by phyloge&amp;shy;netic analysis of subgenomic regions of HCV. HD staff members dose not seem to be at increased risk of hepatitis C de&amp;shy;spite the frequent blood exposure and lack of strict adherence to universal infection control precautions. &quot;n&amp;nbsp

Detection and molecular identification of leishmania RNA virus (LRV) in Iranian Leishmania species

Leishmania RNA virus (LRV) was first detected in members of the subgenus Leishmania (Viannia), and later, the virulence and metastasis of the New World species were attributed to this virus. The data on the presence of LRV in Old World species are confined to Leishmania major and a few Leishmania aethiopica isolates. The aim of this study was to survey the presence of LRV in various Iranian Leishmania species originating from patients and animal reservoir hosts. Genomic nucleic acids were extracted from 50 cultured isolates belonging to the species Leishmania major, Leishmania tropica, and Leishmania infantum. A partial sequence of the viral RNA-dependent RNA polymerase (RdRp) gene was amplified, sequenced and compared with appropriate sequences from the GenBank database. We detected the virus in two parasite specimens: an isolate of L. infantum derived from a visceral leishmaniasis (VL) patient who was unresponsive to meglumine antimoniate treatment, and an L. major isolate originating from a great gerbil, Rhombomys opimus. The Iranian LRV sequences showed the highest similarities to an Old World L. major LRV2 and were genetically distant from LRV1 isolates detected in New World Leishmania parasites. We could not attribute treatment failure in VL patient to the presence of LRV due to the limited number of specimens analyzed. Further studies with inclusion of more clinical samples are required to elucidate the potential role of LRVs in pathogenesis or treatment failure of Old World leishmaniasis. � 2016, Springer-Verlag Wien