In silico approaches to study the human asparagine synthetase: An insight of the interaction between the enzyme active sites and its substrates.

Cancer is a leading concern and important cause of death worldwide. Cancer is a non-communicable illness defined as uncontrolled division of cells. It can develop into metastatic cancer when tumor cells migrate to other organs. In recent years evidence has emerged that the bioavailability of Asn play a crucial role in cancer metastasis. Asn is a non-essential amino acid formed from an ATP dependent catalyzed reaction by the enzyme asparagine synthetase (ASNS), where Asp and Gln are converted to Asn and Glu, respectively. The human ASNS enzyme consist of 561 amino acids, with a molecular weight of 64 KDa. ASNS governs the activation of transcriptional factors that regulate the process of metastasis. In this work the 3D model of ASNS in E. coli (AS-B) and the human ASNS docked with its different ligands have been used to study the 3D mechanism of the conversion of Asp and Gln to Asn and Glu, in human ASNS. The stability evaluation of the docked complexes was checked by molecular dynamic simulation through the bioinformatic tool Desmond. The binding residues and their interactions can be exploited for the development of inhibitors, as well as for finding new drug molecules against ASNS and prevention of metastatic cancer.

Phytochemical and antimicrobial properties of different plants and in silico investigation of their bioactive compounds in wound healing and rheumatism.

In the current study the assessment of the antimicrobial and phytochemical properties of Cassia fistula, Musa paradisiaca, Ficus religiosa and Murraya koenigii plants extracts was carried out. The antibacterial potential of these plants extracts was tested against S. aureus and E. coli. The Cassia fistula and Ficus religiosa leaves showed the larger zone of inhibition in aqueous and butanolic extract respectively against Escherichia coli. Musa paradisiaca and Murraya koenigii leaves showed larger zone of inhibition in ethanolic extract against S. aureus. Qualitative phytochemical analysis showed the presence of alkaloids, flavonoids, phenols, terpenoids, steroids, glycosides, saponins, carbohydrates, proteins and tannins in all extracts while phylobatannins, emodins, anthocyanins and leucoanthocyanins were not present in these extracts. Quantitative phytochemical analysis showed the highest alkaloid content in the Murraya koenigii leaves. Highest tannin content and flavonoid content was found in Ficus religiosa leaves, while highest phenolic content was found in case of Cassia fistula. In addition to this antioxidant potential of all the extracts was determined. Musa paradisiaca leaves showed highest antioxidant potential as compared to other plant extracts. In silico analysis of bioactive components present in plant extracts was performed by molecular docking. The rutin and Glu from Musa paradisiaca and Murraya koenigii respectively, were docked with Glycogen Synthase Kinase 3 beta (1GSK-3beta) protein. Quercetin and rutin from Cassia fistula and Ficus religiosa respectively, were docked with C- reactive protein (CRP). The tested bioactive compounds showed good binding affinity with significant number of hydrogen bonds and can be used as a good alternative of synthetic drugs to treat rheumatism and wounds.

Assessment of angiotensin converting enzyme inhibitory activity and quality attributes of yoghurt enriched with Cinnamomum verum, Elettaria cardamomum, Beta vulgaris and Brassica oleracea.

The new concept of functional foods has led to the varieties in the production of foods that provide not only basic nutrition, but can also warrant good health and longevity. This study deals with the production and evaluation of fortified yogurts' with Cinnamomum verum, Elettaria cardamomum, Beta vulgaris and Brassica oleracea. The qualitative and quantitative phytochemical analysis of above mentioned plant extracts before using them into the preparation of functional yoghurt was carried out. The sensory evaluation of enriched yogurts with plant extracts carried out using 9 point hedonic scale. Comparative analysis between enriched yogurts and plain yogurt was carried. The results indicated increase in ash contents, water holding capacity, titratable acidity, total soluble solids, total phenolic content, tannin content, and total flavonoid content in fortified yogurt as compared to plain yogurt. In addition to this fortified yogurts showed greater antioxidant and antibacterial activity in contrast to plain yogurt. However, moisture contents, pH and susceptibility to syneresis of yogurt decreases with the addition of plant extracts. Shelf life of plain and fortified yogurt was determined both at room and refrigerated temperature. The results revealed that shelf life of fortified yogurt was greater as compared to plain yogurt. In silico analysis was carried out by using the galaxy web software. The results indicated that bioactive compounds including ascorbic acid, sinapinic acid, cinnamaldehyde and linalool acetate present in the flavored yogurts binds with angiotensin converting enzyme. All enriched yogurts showed higher anti-Angiotensin converting enzyme activity as compared to plain-yogurt.

Purification, characterization and thermodynamic analysis of cellulases produced from Thermomyces dupontii and its industrial applications.

Cellulases involved in the hydrolysis of cellulose and plays a vital role in different industries like textile, detergent paper and Feed industry. Cellulases have been a prospective target for research by both the academic and industrial sectors because of the intricacy of the enzyme system and the enormous industrial potential. In the present work Thermomyces dupontii, which had previously been isolated and recorded as a promising cellulase producer were used. Both endoglucanases and betaglucosidases were purified to its homogeneity by ammonium sulfate followed by anion exchange and gel filtration chromatography. The recovery and purification fold for endoglucanases and betaglucosidases were 13.7, 10.7 % and 5.9, 2.7, respectively. The molecular weight of endoglucanases and betaglucosidases were estimated as 37 and 66 kDa on SDS-PAGE. Upon kinetic analysis the purified endoglucanases and betaglucosidases showed Km 0.63; 28.56 mg/ml and Vmax 82; 80 U/ml/min, respectively. Characterization revealed that enzyme was found to be acidophilic cellulase having optimal pH of 5.5 and 70 °C. Furthermore, cellulases were accelerated in the presence of Ca2+ and EDTA. The cellulases had activation energy (Ea) of -44.55; -50.02 kJ/mol for carboxy-methyl-cellulose hydrolysis and Enthalpy (ΔH) 42.20; 47.70 kJ/mol and entropy ΔS -5.1 and -5.7 kJ/mol for EG and BGL, respectively. In addition to this the enzyme had a secondary structure of protein as represented by FTIR spectrum The current study suggested that purified cellulases can be used as a detergent additive to improve washing. Furthermore, it shows the biostoning ability when applied on jean fabric.

Application of Synergistic Phenomena for Enhanced Production of Alpha 1,4 D- Glucan Glucanohydrolase Using Submerged Fermentation.

The study revealed enhanced production of α 1, 4 D glucan glucanohydrolase utilizing the synergistic phenomena of bacterial hetero-culture. For this purpose, 101 hetero-cultures were screened qualitatively and quantitatively. The bacterial hetero-culture showing the highest amylolytic potential was identified as Bacillus subtilis and Bacillus amyloliquefeciens by 16S rDNA sequencing technique. Different fermentation media were evaluated and M 5 gave maximum GGH production. Different physicochemical parameters like incubation time, temperature, initial pH and inoculum size was optimized. The optimal enzyme production was obtained at 24 h, 37oC, pH 7.0 and 3% inoculum size. Glucose (3%), ammonium sulphate (1.5%) and yeast extract (2.0%) was selected as best carbon and nitrogen source, respectively. The novelty of the present piece of research was the application of the hetero-culture technique for enhanced GGH production using submerged fermentation which was not experienced before with these strains.

Statistical optimization of cellulases by Talaromyces thermophilus utilizing Saccharum spontaneum, a novel substrate

BACKGROUND: At present, cellulases are the most important enzymes worldwide, and their demand has been increasing in the industrial sector owing to their notable hydrolysis capability. RESULTS: In the present study, contrary to conventional techniques, three physical parameters were statistically optimized for the production of cellulase by thermophilic fungi by using response surface methodology (RSM). Among all the tested thermophilic strains, the best cellulase producing fungus was identified as Talaromyces thermophilus ­ both morphologically and molecularly through 5.8S/ITS rDNA sequencing. The central composite design (CCD) was used to evaluate the interactive effect of the significant factors. The CCD was applied by considering incubation period, pH, and temperature as the model factors for the present investigation. A second-order quadratic model and response surface method revealed that the independent variables including pH 6, temperature 50 C, and incubation period 72 h significantly influenced the production of cellulases. The analysis of variance (ANOVA) indicated that the established model was significant (P 0.05) and showed the high adequacy of the model. The actual and predicted values of CMCase and FPase activity showed good agreement with each other and also confirmed the validity of the designed model. CONCLUSIONS: We believe the present findings to be the first report on cellulase production by exploiting Kans grass (Saccharum spontaneum) as a substrate through response surface methodology by using thermophilic fungus, Talaromyces thermophilus.

Bioethanol production from urban cellulosic waste employing Alcaligenes faecalis HI-1 isolated from gut of termite Heterotermes indicola

This study assessed the potential of termite gut inhabiting bacteria towards bioconversion of cellulosic waste into biofuel. Total seven bacterial isolates from the gut of Heterotermes indicola were isolated. Among all the isolates, HI-1 produced the largest zone upon primary screening. Untreated paper had more cellulose content (73.03%) than acid (0.5%) treated paper that was used as a lignocellulosic substrate for saccharification. Among all the isolates tested, glucose yield (1.08mg/mL) was high for HI-1 isolate. Several factors were considered for optimizing augmented glucose yield (8.57mg/mL) and growth (8.07×108cfu/mL), such as temperature 37°C, pH 4.5, 5% (w/v) substrate concentration, 6 % bacterial inoculum size, agitation 150 rpm with PEG 0.25 % and Ca2+ ions 0.002 g/L. Overall 8-fold increase in glucose yield was achieved. Enzyme activity of HI-1 showed higher endoglucanase 0.29 ± 0.01 (U/mL/min) and exoglucanase 0.15±0.01 (U/mL/min) activity under optimum conditions, mentioned above. temperature 37°C, pH 4.5, substrate concentration 5%, inoculum size 6%, surfactants PEG 0.01%, ions Ca2+(0.002g/L) and agitation (120 rpm). Simultaneous saccharification and fermentation (SSF) of hydrolyzed office paper yielded 5.43mg/mL bioethanol. According to 16S rRNA sequence homology, the bacterial isolate H1 was identified as Alcaligenes faecalis. Bioethanol production from office paper untreated waste proved an effective strategy. Bacteria having natural tendency towards cellulosic waste consumption are promising for bioconversion of cellulosic waste to valuable products.

Characterization of Hepatitis Delta Virus Among Pregnant Women of Pakistan.

Hepatitis delta virus (HDV) is a highly pathogenic virus and causes rapid disease progression from fulminant hepatitis to development of hepatocellular carcinoma in patients infected with hepatitis B virus (HBV). HDV is endemic in Pakistan; however, there are no available data on HDV prevalence among the high-risk group of HBV-infected pregnant women. A total of 1,394 pregnant women, visiting different public-sector hospitals in Lahore, were enrolled in this study. Their demographic data and blood samples were collected from May 2016 to July 2017. Samples were screened for both HBsAg and anti-HDV. Anti-HDV positive samples were tested for HDV RNA, and samples positive for HDV RNA were further sequenced to determine the HDV genotype. Of the 1,394 samples, HBsAg was positive in 63 (4.5%). Of these 63 HBsAg-positive samples, 13 (20.63%) were positive for anti-HDV. Of the 13 HBsAg/anti-HDV positive samples, HDV RNA was detected in 4 (30.8%) samples and all 4 carried HDV genotype 1. The age of enrolled women varied from 20 to 40 years, with most of the women living in urban areas, having education more than secondary school level, belonging to middle class, and being housewives. Majority of the tested women were of age from 25 to 30 years (39.2%); however, the prevalence of HBV was higher in age group 31-35 years (10.7%, confidence interval [CI]: 4.73-16.67); however, anti-HDV prevalence was 1.9% (CI: -0.7 to 4.7). This study is the first report on HDV prevalence among pregnant women in Pakistan. Our study showed a high predominance of HDV (20.63%) in HBV-infected pregnant women and the prevalence of HDV genotype 1 infection. The findings contribute to a better understanding of the HDV/HBV coinfection among pregnant women and circulating HDV genotypes in the country.

Molecular epidemiology of hepatitis delta and hepatitis B viruses circulating in two major provinces (East and North-West) of Pakistan.

OBJECTIVES: HBV and HDV are major public health problems with millions affected globally and Pakistan accounts for a significant proportion of the global Hepatitis burden. This cross sectional study was designed to assess the general epidemiological and virological features of HBV and HDV in the Punjab and Khyber Pakhtunkhawa (KP) provinces of Pakistan. METHODS: A total of 1890 HBV patients from March 2016 to May 2017 were recruited in the study and the presence of HDV was retrospectively evaluated in all participants. Most participants were young adults (from 21 to 30 years). Genotyping was based on PCR amplification using primers specific for HBV genotypes A-F, and HDV. 405 nucleotide fragments of HDV were sequenced. MEGA was used for phylogenetic analysis. RESULTS: Overall prevalence of HBV was 14.08% (266/1890). Higher prevalence was observed in males (66.85%) as compared to females (33.15%). Co-infection of HDV was found in 39 (14.66%) patients. HBV genotype-D was prevalent in dual infections followed by HDV/A (p < 0.05).While HDV genotype 1 was predominant in all HBV positive samples. Compared to Punjab, coinfection was higher in KP (14.3% versus15.2%; p < 0.05). CONCLUSION: The prevalence of HBV and HDV is high in Pakistan. The description of HBV and HDV genotypes circulating in East and North-West Pakistan can contribute to a better understanding of their relevance in regional epidemics. These infections are highly endemic in the KP, where their control is confounded by its vast territorial dimension with small, hard-to-reach municipalities and diverse ethnic populations.

Evaluation of microbial potential and ripening behavoiur of preclimacteric bananas following gamma irradiation / Avaliação do potencial microbiana e amadurecem comportamento de bananas preclimacteric seguinte irradiação gama

The current study was carried out to evaluate the effects of gamma irradiation on the epiphytic microflora and ripening process of the green Dwarf Cavendish bananas harvested at the three-quarter stage of the maturity. The mature green bananas were irradiated using Cobalt-60 as the source of irradiation at different dosages of 0.5, 0.75 and 1.0 kGy. The mean life of both the experimental and control group of fruits was analyzed under ambient conditions. For all the treatments the microbial potential, the decay percent and the ripening behavior of the fruits were recorded. Results revealed that the applied radiation doses reduced the decay incidence, delayed ripening process and greatly inhibit the microbial growth (total bacterial and fungal count) thereby enhancing the shelf life of bananas. Irradiation dose of 1.0 kGy was found to be the most effective dose to positively maintain the stored bananas under ambient conditions. The mean life of bananas was extended by 14 days. The identification of the enteric bacteriaeaceae through API 20 E strips revealed the presence of Shigella sonnie on the fruit surface along with Escherichia coli and a nonfermentor spp. The dominant spoilage causing fungi identified were Aspergillus niger, Aspergillus flavus, Collotrichum musae, Fusarium oxysporum,Mucor spp, Lasiodiplodia theobromea and Rhizopus stolonifer.

O Presente estudo foi realizado para investigar os efeitos da radiação gama sobre a microflora epífita e amadurecimento das bananas Cavendish Anão verde colhidas no estádio de três quartos da maturidade. As bananas verdes maduros foram irradiadas usando Cobalto-60 como fonte de irradiação a diferentes dosagens de 0,5, 0,75 e 1,0 kGy. A vida média de ambos os grupos experimental e de controlo de frutas foi analisada sob as condições ambientes. Para todos os tratamentos a potenciais microbiana, o percentual decadência e do comportamento do amadurecimento dos frutos foram recorded.Results revelou que as doses de radiação aplicadas reduziu a incidência de podridões, atrasou processo de amadurecimento e inibir significativamente o crescimento microbiano (contagem de bactérias e fungos total), assim aumentar a vida de prateleira das bananas. dose de irradiação de 1,0 kGy foi encontrada como sendo a dose mais eficaz para manter positivamente as bananas armazenada sob condições ambientes. A vida média de bananas foi prorrogado por 14 dias. A identificação do bacteriaeaceae entérico através de API 20 E tiras revelou a presença de Shigella sonnie sobre a superfície do fruto, juntamente com Escherichia coli e um nonfermentor spp. A deterioração dominante causando fungos identificados foram Aspergillus niger, Aspergillus flavus, Collotrichum musae, Fusarium oxysporum, Mucor spp, Lasiodiplodia theobromea e Rhizopus stolonifer.

Association of hepatitis C virus with insulin resistance: evidences from animal studies and clinical studies.

CONTEXT: HCV infection is strongly associated with development of insulin resistance and type-2 diabetes, however molecular mechanism of these associations is not known. The aim of this review was to conduct a comprehensive literature search to understand the nature of the association between hepatitis C virus (HCV) infection and insulin resistance (IR). We also explored the role of HCV core protein and NS5a in modulating the course of the insulin-signaling pathway. EVIDENCE ACQUISITIONS: We searched Directory of Open Access Journals (DOAJ) Google Scholar, Pubmed (NLM), LISTA (EBSCO), Web of Science (TS and PakMediNet). RESULTS: Emerging evidence suggests an association between HCV infection and carotid/coronary vascular disease. IR appears to be a dominant underlying cause of accelerated atherosclerosis in patients with chronic hepatitis C (CHC). HCV can induce IR directly through the stimulation of SOCS3 and PPA2, and both of these molecules have been shown to inhibit interferon-α signaling. Improvement of insulin sensitivity may increase the response rate to antiviral treatment and prevent IR complications, including vascular diseases. The results of several clinical trials that have used insulin sensitizers (metformin and PPAR-γ agonists) have been inconclusive. CONCLUSIONS: Beside the association between HCV and IR, the published data also have showed the possible association of HCV core and NS5A protein with IR.

Serotype and genotype analysis of dengue virus by sequencing followed by phylogenetic analysis using samples from three mini outbreaks-2007-2009 in Pakistan.

BACKGROUND: Since the first reported outbreak of dengue hemorrhagic fever in Pakistan, several mini outbreaks have erupted in the region. Dengue virus serotype 3 (DEN-3) was first documented in 2005 outbreak in Karachi. Reports show that serotype 3 is prevalent in Lahore since 2008. Serotype 2 (DEN-2) is the major circulating serotype in Pakistan as it is documented since 1994. We have conducted a detailed study of three outbreaks of dengue virus infection that occurred in years 2007, 2008 and 2009 in Lahore by using molecular techniques such as PCR and nucleotide sequencing of the C-prM gene junction of Dengue virus. RESULTS: Through the analysis of 114 serum samples collected over the period of three years (2007-2009), total 20 patients were found to be infected with dengue virus. In year 2007, four were positive for serotype 2 and one sample was positive for serotype DEN-3. In 2008, five samples had concurrent infection with serotypes DEN-2 and DEN-3 while three samples were infected only with serotype DEN-2. In year 2009, one sample had concurrent infection with serotypes DEN-2 and DEN-3 while six were positive for serotype DEN-2 only. CONCLUSIONS: Our study showed that serotype DEN-2 was dominant in positive samples of dengue virus infection collected during the period of three years (2007-2009). The other serotype present was serotype DEN-3. Genotypes of serotype DEN-2 and serotype DEN-3 were subtype IV and subtype III, respectively.

Characterization of hepatitis C Virus genotype 3a hypervariable region 1 in patients achieved rapid virological response to alpha interferon and ribavirin combination therapy.

BACKGROUND: Hepatitis C virus roots a chronic liver disease. Currently approved treatment strategy includes administration of alpha interferon and ribavirin combined therapy for 24-48 weeks. One of the predictor of sustained virological response is an early virological response to treatment characterized as rapid response. Hyper variable region 1 (HVR1) of E2 protein is responsible for viral entry and acts as a target for neutralizing antibodies. Any mutation in this region would effect virus interaction with target cell and viral persistence. METHODS: Thirty one clones of six pre-treatment samples subjected to combination therapy were investigated. Three of the patients were rapid responders (R1, R2 and R3) and two were breakthrough responders (BT1 and BT2). Envelope 2 gene was amplified, cloned and sequenced. Amino acid substitution, frequency, composition and antigenic properties of HVR 1 of E2 protein were studied. RESULTS: In both rapid responders (R.R) (14 amino acid sites) and breakthrough responders (BT.R) (13 amino acid sites) half of the amino acid sites were either conserved or resistant to any physiochemical change due to amino acid substitution. It also indicated that average composition of hydrophilic and basic amino acids were comparatively lower in rapid responders than other samples affecting probable interaction of virus with target cells. A central non antigenic region was constant among the breakthrough responders but differed in length significantly among rapid responders reflecting the adaptive nature of HVR1 to the immune response. CONCLUSIONS: We observed that although HVR1is quite variable region in HCV 3a patients responding differently to treatment it still maintains its physiochemical properties for its proper functioning and viability.

Hepatitis C treatment: current and future perspectives.

Hepatitis C virus (HCV) is a member of Flaviviridae family and one of the major causes of liver disease. There are about 175 million HCV infected patients worldwide that constitute 3% of world's population. The main route of HCV transmission is parental however 90% intravenous drug users are at highest risk. Standard interferon and ribavirin remained a gold standard of chronic HCV treatment having 38-43% sustained virological response rates. Currently the standard therapy for HCV is pegylated interferon (PEG-INF) with ribavirin. This therapy achieves 50% sustained virological response (SVR) for genotype 1 and 80% for genotype 2 & 3. As pegylated interferon is expensive, standard interferon is still the main therapy for HCV treatment in under developed countries. On the other hand, studies showed that pegylated IFN and RBV therapy has severe side effects like hematological complications. Herbal medicines (laccase, proanthocyandin, Rhodiola kirilowii) are also being in use as a natural and alternative way for treatment of HCV but there is not a single significant report documented yet. Best SVR indicators are genotype 3 and 2, < 0.2 million IU/mL pretreatment viral load, rapid virological response (RVR) rate and age <40 years. New therapeutic approaches are under study like interferon related systems, modified forms of ribavirin, internal ribosome entry site (HCV IRES) inhibitors, NS3 and NS5a inhibitors, novel immunomodulators and specifically targeted anti-viral therapy for hepatitis C compounds. More remedial therapies include caspase inhibitors, anti-fibrotic agents, antibody treatment and vaccines.

Mutations in the E2-PePHD region of hepatitis C virus genotype-3a and correlation with response to interferon and ribavirin combination therapy in Pakistani patients.

Hepatitis C is a major health problem affecting more than 200 million individuals in the world. Current treatment regimen consisting of interferon alpha and ribavirin does not always succeed in eliminating the virus completely from patient's body. One of the mechanisms by which virus evades the antiviral effect of interferon alpha involves protein kinase (PKR) eukaryotic initiation factor 2 alpha (eIF2a) phosphorylation homology domain (PePHD). This domain in genotype 1 strains is reportedly homologous to PKR and its target eIF2a. By binding to PKR, PePHD inhibits its activity and therefore cause virus to evade antiviral activity of interferon (IFN). Many studies have correlated substitutions in this domain to the treatment response and lead to inconclusive results. Some studies suggested that substitutions favor response while others emphasized that no correlation exists. In the present study we therefore compared sequences of PePHD domain of thirty one variants of six hepatitis C virus patients of genotype 3. Three of our HCV 3a infected patients showed rapid virological response to interferon alpha and ribavirin combination therapy whereas the remaining three had breakthrough to the same combination therapy. It is found that PePHD domain is not entirely conserved and has substitutions in some isolates irrespective of the treatment response. However substitution of glutamine (Q) with Leucine (L) in one of the breakthrough responders made it more identical to HCV genotype 1a. These substitutions in the breakthrough responders also tended to increase average hydrophilic activity thus making binding of PePHD to PKR and inhibition of PKR more favorable.

Hepatitis C virus genotype 3a infection and hepatocellular carcinoma: Pakistan experience.

AIM: To assess the association between chronic hepatitis C virus (HCV) infection and hepatocellular carcinoma (HCC) in Pakistan, and the genotype distribution among these HCC patients. METHODS: One hundred and sixty-one subjects with HCC were included in this study. Liver biopsy was performed on 145 of the patients; sixteen were excluded because they failed to fulfill the inclusion criteria. Qualitative polymerase chain reaction (PCR) was performed for hepatitis B virus and HCV. Samples positive for HCV RNA were genotyped using genotype-specific PCR and confirmed by HCV 5' noncoding region sequencing analysis. RESULTS: Chronic HCV infection was identified a major risk factor (63.44% of tested HCC patients) for the development of HCC. The time from HCV infection to appearance of cancer was 10-50 years. In the HCC patient population, broader distributions of genotypes were present with genotype 3a as the predominant genotype. Using the type-specific genotyping method, we found HCV genotype 3a in 40.96%, 3b in 15.66%, 1a in 9.63%, and 1b in 2.40% of HCC tissue samples. About 28% of cases were found with mixed genotypes. Two cases were unable to be genotyped because of low viral load. Sixty-six percent of treated patients with cirrhosis had an end of treatment response, but unfortunately they relapsed quickly when the treatment was discontinued, and HCC developed during a median 3.8 years. CONCLUSION: There was a strong association between chronic HCV infection and HCC in Pakistan, and between HCV genotype 3a and HCC.

Nucleotide identity and variability among different Pakistani hepatitis C virus isolates.

BACKGROUND: The variability within the hepatitis C virus (HCV) genome has formed the basis for several genotyping methods and used widely for HCV genotyping worldwide. AIM: The aim of the present study was to determine percent nucleotide identity and variability in HCV isolates prevalent in different geographical regions of Pakistan. METHODS: 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. RESULTS: 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. CONCLUSION: 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.