Frequency distribution of hepatitis C virus genotypes in different geographical regions of Pakistan and their possible routes of transmission

<p>Abstract</p> <p>Background</p> <p>Information regarding hepatitis C virus genotypes and subtypes circulating in Pakistan and various risk factors for their transmission are not known well. The specific objective of this study was to find out the frequency of various HCV genotypes present in well-characterized Pakistani HCV isolates and their possible routes of transmission.</p> <p>Methods</p> <p>A total of 3351 serum samples were tested by type-specific genotyping assay. Out of 3351 HCV RNA positive patients, 2039 were males and 1312 were females. As regard as genotyped samples, 2165 belonged to Punjab region, 823 belonged to N.W.F.P., 239 to Sindh and 124 patients were from Balochistan.</p> <p>Results</p> <p>Out of the total 3351 tested serum samples, type-specific PCR fragments were observed in 3150 (94.00%) serum samples. The distribution of genotypes of the typeable samples as determined by this assay, was as follows: 1664 (49.05%) genotype 3a; 592 (17.66%) genotype 3b; 280 (8.35%) genotype 1a; 252 (7.52%) genotype 2a; 101 (3.01%) genotype 1b; 50 (1.49%) with genotype 4; 25 (0.75%) with 3c; 27 (0.80%) genotype 2b; 6 (0.18%) with subtype 5a; 5 (0.15%) genotype 1c; 4 (0.12%) with subtype 6a; 3 (0.09%) genotype 2c; and 161 (4.80%) patients were infected with mixed infection. Two hundred and one (5.99%) serum samples were found untypeable by the present genotyping system. More than 86% and 72% patients with genotypes 3a and 3b respectively had received multiple injections in past. For genotypes 1a and 1b the route of transmission was major/minor surgery along with unknown reasons. Majority of the cases with type 2a, 2b and indeterminate genotypes were sporadic. Mixed infections were common in thalassaemic patients.</p> <p>Conclusion</p> <p>The most common HCV genotype in Pakistan is type 3a. Regional difference in genotypes was observed only in Balochistan province of Pakistan. More than 70% of the cases were acquired in hospitals through reuse of needles/syringes and major/minor surgery that is very common in this country.</p

A study of best positive predictors for sustained virologic response to interferon alpha plus ribavirin therapy in naive chronic hepatitis C patients

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to determine the rate of sustained virological response (SVR) and various factors associated with response rates in chronic hepatitis C infected patients treated with interferon alpha and ribavirin combination therapy.</p> <p>Methods</p> <p>A retrospective review of patients data collected at this Centre from 2001 to 2007 was performed. Out of 731 consecutive patients 400 patients that fulfilled the study criteria were evaluated and subsequently treated with a combination of interferon alpha 2b (3 MU subcutaneously three injections weekly) and ribavirin (800–1200 mg orally daily). Treatment were administered for either 24 weeks or 48 weeks and patients were followed for an additional 6 months thereafter. End of the treatment response (ETR), SVR and side effects were recorded.</p> <p>Results</p> <p>Out of 400 patients, 394 completed the entire treatment course and six patients discontinued treatment at month 2. Over 67% responded at the end of treatment and 16% suffered relapse. Among all treated patients, 47.6% males and 56.7% females had sustained viral response with a total combined sustained viral response rate of 50.5%. Rapid response was seen in 46.5% patients. In a multivariate logistic regression analysis, slow virological responders (adjusted OR 2.6 [95% CI 1.9–3.7]), HCV genotype 1&4 (adjusted OR 2.4 [95% CI 1.7–3.5]), pre-treatment viral load > 0.2 MIU/mL (adjusted OR 2.2 [95% CI 1.8–4.2]), Panjabi ethnic group (adjusted OR 1.6 [95% CI 1.0–3.2]) and Age > 40 years (adjusted OR 1.5 [95% CI 0.9–2.4]) were independent risk factors for non response. Side effects were usual and tolerable and only 1.5% discontinued the treatment.</p> <p>Conclusion</p> <p>The best positive predictor for SVR in this country are: rapid virologic response, HCV genotype 2 & 3, age < 40 years, ethnic race Pashtoons and pre-treatment viral load < 0.2 million IU/mL.</p

Genetic polymorphism of milk protein variants and their association studies with milk yield in Sahiwal cattle

The objective of this study was to determine the allele and genotype frequencies of genetic variants in five milk protein genes and estimate the effect of these variants on milk yield in Sahiwal cattle. Genotypes of five milk protein genes (alpha s1 casein, beta casein, kappa casein, alpha lactalbumin and beta lactoglobulin) were detected using SNaPshot genotyping method. All the five milk protein genes studied exhibited polymorphism with high allele frequencies of 0.51 for alpha s1casein C, 0.93 for beta casein A2, 0.92 for kappa casein A, 0.93 for alpha lactalbumin B and 0.91 for beta lactoglobulin B. Statistically significant differences (p &gt; 0.05) were observed in kappa casein genotypes AA (AA) and AB (AC) that is, genotype AB had more milk yield in 1st lactation (422 kg) and 2nd lactation (612 kg), respectively. In conclusion, the AB genotype identified in kappa casein gene is associated with higher milk production therefore incorporation of AB and BB genotypes for kappa casein may help to improve the milk yield in Sahiwal cattle population of Pakistan. To the best of our knowledge, this is the first detailed study involving frequency distribution of genetic variants and their effects on milk yield in Bos indicus Sahiwal cattle of Pakistan.Keywords: Genetic variant, milk protein genes, Sahiwal cattleAfrican Journal of Biotechnology, Vol. 13(4), pp. 555-565, 22 January, 201

Immunoassay-based approach for detection of novel bacillus thuringiensis -endotoxins, entomocidal to cotton aphids (aphis gossypii) and whiteflies (bemisiatabaci

Abstract A new strategy, which is based on immunoassay, has been developed to screen locally isolated Bacillus thuringiensis (Bt). Delta endotoxins of three Bt strains (INS 2.13, HFZ 24.3 and GU 9.1) were prepared, electrophoresed on native PAGE and electroeluted the purified delta endotoxins from gels. Determined the toxicity of purified delta endotoxins against cotton aphids (Aphis gossypii) and whiteflies (B. tabaci). N-terminal sequences of the purified proteins (δ-endotoxins) of these three entomocidal Bt isolates showed no significant homology to protein sequences in the Gen bank (NCBI) protein database. The purified proteins having novelty in their sequences were used as antigens for the immunization of rabbits to raise polyclonal antibodies. The affinity purified antibodies were used in immunoassays to screen 170 Bt isolates for entomocidal activity and obtained promising results

Mutations in phosphodiesterase 6 identified in familial cases of retinitis pigmentosa.

To delineate the genetic determinants associated with retinitis pigmentosa (RP), a hereditary retinal disorder, we recruited four large families manifesting cardinal symptoms of RP. We localized these families to regions on the human genome harboring the α and β subunits of phosphodiesterase 6 and identified mutations that were absent in control chromosomes. Our data suggest that mutations in PDE6A and PDE6B are responsible for the retinal phenotype in these families

Loss of function mutations in RP1 are responsible for retinitis pigmentosa in consanguineous familial cases.

PurposeThis study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families.MethodsLarge consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon-intron boundaries of RP1 were sequenced to identify the causal mutation.ResultsThe ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G&gt;A (p.I263Nfs8*), a 2 bp duplication in exon 2: c.551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples.ConclusionsThese results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families

In-vitro antiviral activity of Solanum nigrum against Hepatitis C Virus

<p>Abstract</p> <p>Background</p> <p>Hepatitis C is a major health problem causes liver cirrhosis, hepatocellular carcinoma and death. The current treatment of standard interferon in combination with ribavirin, has limited benefits due to emergence of resistant mutations during long-term treatment, adverse side effects and high cost. Hence, there is a need for the development of more effective, less toxic antiviral agents.</p> <p>Results</p> <p>The present study was designed to search anti-HCV plants from different areas of Pakistan. Ten medicinal plants were collected and tested for anti-HCV activity by infecting the liver cells with HCV 3a innoculum. Methanol and chloroform extracts of <it>Solanum nigrum </it>(SN) seeds exhibited 37% and more than 50% inhibition of HCV respectively at non toxic concentration. Moreover, antiviral effect of SN seeds extract was also analyzed against HCV NS3 protease by transfecting HCV NS3 protease plasmid into liver cells. The results demonstrated that chloroform extract of SN decreased the expression or function of HCV NS3 protease in a dose- dependent manner and GAPDH remained constant.</p> <p>Conclusion</p> <p>These results suggest that SN extract contains potential antiviral agents against HCV and combination of SN extract with interferon will be better option to treat chronic HCV.</p