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1.  Genotyping of HCV RNA Reveals That 3a Is the Most Prevalent Genotype in Mardan, Pakistan 
Advances in Virology  2014;2014:606201.
The clinical outcomes of patients infected with hepatitis C virus (HCV) range from acute resolving hepatitis to chronic liver diseases such as liver cirrhosis or hepatocellular carcinoma. Identification of the infecting virus genotype is indispensable for the exploration of many aspects of HCV infection, including epidemiology, pathogenesis, and response to antiviral therapy. 1419 individuals were screened for anti-HCV in this study, of which 166 (11.7%) were found reactive by ICT (Immunochromatographic test). These 166 anti-HCV positive and 26 normal individuals were further analyzed. RNA was extracted from serum and reverse-transcribed to cDNA and the core region of HCV genome was targeted and amplified by multiplex PCR. HCV RNA was detected in 121 individuals, of which 87 were male and 34 were female. Genotype 3a was the most prevalent among all the genotypes observed followed by 3b. Genotypes 1a, 2a, and 2b were found in 10.89%, 13.22%, and 6.61% patients, respectively. 25.41% of the HCV RNA positive samples were not typed. 6.05% of patients were found having mixed genotypes. These findings will not only help the physicians to prescribe more appropriate treatment for the HCV infection but will also draw the attention of health-related policy makers to devise strategies to curb the disease more effectively.
doi:10.1155/2014/606201
PMCID: PMC3955652  PMID: 24715902
2.  Molecular Interactions between Complement Factor H and Its Heparin and Heparan Sulfate Ligands 
Complement factor H (CFH) is the major regulator of the central complement protein C3b in the alternative pathway of complement activation. A molecular view of the CFH interaction with native heparan sulfate (HS) is central for understanding the mechanism of how surface-bound CFH interacts with C3b bound to host cell surfaces. HS is composed of sulfated heparin-like S-regions that alternate with desulfated NA-regions. Solution structural studies of heparin (equivalent to the S-regions) and desulfated HS (the NA-regions) by scattering and ultracentrifugation showed that each structure was mostly extended and partially bent, but with greater bending and flexibility in the NA-regions compared to the S-regions. Their solution structures have been deposited in the Protein Data Bank. The largest HS oligosaccharides showed more bent and flexible structures than those for heparin. A folded-back domain structure for the solution structure of the 20 domains in CFH was determined likewise. CFH binds to the S-regions but less so to the NA-regions of HS. The bivalent interaction of CFH–heparin was observed by ultracentrifugation, and binding studies of CFH fragments with heparin-coated sensor chips. In common with other CFH interactions with its physiological and pathophysiological ligands, the CFH–heparin and CFH–C3b interactions have moderate micromolar dissociation constants KD, meaning that these complexes do not fully form in vivo. The combination of the solution structures and binding studies indicated a two-site interaction model of CFH with heparin at cell surfaces. By this, the bivalent binding of CFH to a cell surface is co-operative. Defective interactions at either of the two independent CFH–heparin sites reduce the CFH interaction with surface-bound C3b and lead to immune disorders.
doi:10.3389/fimmu.2014.00126
PMCID: PMC3978290  PMID: 24744754
analytical ultracentrifugation; surface plasmon resonance; X-ray scattering; complement factor H; heparin; heparan sulfate
3.  The Solution Structure of Heparan Sulfate Differs from That of Heparin 
The Journal of Biological Chemistry  2013;288(39):27737-27751.
Background: The polysaccharide heparan sulfate (HS) exhibits key physiological roles.
Results: Analytical ultracentrifugation and x-ray scattering revealed extended but bent HS solution structures.
Conclusion: Scattering fits resulted in molecular models for HS in solution with glycosidic angles in good accord with a HS crystal structure.
Significance: These bent HS models clarify how HS interacts with its ligands.
The highly sulfated polysaccharides heparin and heparan sulfate (HS) play key roles in the regulation of physiological and pathophysiological processes. Despite its importance, no molecular structures of free HS have been reported up to now. By combining analytical ultracentrifugation, small angle x-ray scattering, and constrained scattering modeling recently used for heparin, we have analyzed the solution structures for eight purified HS fragments dp6–dp24 corresponding to the predominantly unsulfated GlcA-GlcNAc domains of heparan sulfate. Unlike heparin, the sedimentation coefficient s20,w of HS dp6–dp24 showed a small rotor speed dependence, where similar s20,w values of 0.82–1.26 S (absorbance optics) and 1.05–1.34 S (interference optics) were determined. The corresponding x-ray scattering measurements of HS dp6–dp24 gave radii of gyration RG values from 1.03 to 2.82 nm, cross-sectional radii of gyration RXS values from 0.31 to 0.65 nm, and maximum lengths L from 3.0 to 10.0 nm. These data showed that HS has a longer and more bent structure than heparin. Constrained scattering modeling starting from 5,000 to 12,000 conformationally randomized HS structures gave best fit dp6–dp24 molecular structures that were longer and more bent than their equivalents in heparin. Alternative fits were obtained for HS dp18 and dp24, indicating their higher bending and flexibility. We conclude that HS displays bent conformations that are significantly distinct from that for heparin. The difference is attributed to the different predominant monosaccharide sequence and reduced sulfation of HS, indicating that HS may interact differently with proteins compared with heparin.
doi:10.1074/jbc.M113.492223
PMCID: PMC3784691  PMID: 23921391
Analytical Ultracentrifugation; Heparan Sulfate; Heparin; Heparin-binding Protein; Molecular Modeling; X-ray Scattering
4.  Application of DNA comet assay for detection of radiation treatment of grams and pulses 
Several types of whole pulses (green lentils, red lentils, yellow lentils, chickpeas, green peas, cowpeas and yellow peas) and grams (black grams, red grams and white grams) have been investigated for the identification of radiation treatment using microgel electrophoresis of single cells (DNA comet assay). Pulses and grams were exposed to the radiation doses of 0.5, 1.0 and 5 kGy covering the legalized commercial dose range for protection from insect/pest infestations. All irradiated samples showed comet like stretching of fragmented DNA toward anode, which is expected for irradiated samples. Unirradiated samples showed many intact cells/nuclei in form of round stains or with short faint tails, which is typical for unirradiated food samples. The study shows that DNA comet assay can be used as a rapid, inexpensive and highly effective screening test for the detection of radiation treatment of foods, like pulses and grams.
doi:10.1007/s13197-010-0169-z
PMCID: PMC3551050  PMID: 23572810
Food irradiation; Pulses; Grams; Irradiation identification; DNA comet assay
5.  Retraction: Aurora kinase-C-T191D is constitutively active mutant 
BMC Cell Biology  2012;13:17.
doi:10.1186/1471-2121-13-17
PMCID: PMC3418155  PMID: 22734616
6.  Aurora kinase-C-T191D is constitutively active mutant 
BMC Cell Biology  2012;13:8.
Background
Aurora kinases (Aurora-A, B and C) belong to a family of conserved serine/threonine kinases which are key regulators of cell cycle progression. Aurora-A and Aurora-B are expressed in somatic cells and involved in cell cycle regulation while aurora-C is meiotic chromosome passenger protein. As Aurora kinase C is rarely expressed in normal somatic cells and has been found over expressed in many cancer lines. It is suggested that Aurora-C-T191D is not hyperactive mutant.
Result
Aurora-C-T191D variant form was investigated and compared with wild type. The overexpression of Aurora-C-T191D was observed that it behaves like Aurora-C wild type (aurC-WT). Both Aurora-C-T191D and aurC-WT induce abnormal cell division resulting in centrosome amplification and multinucleation in transiently transfected cells as well as in stable cell lines. Similarly, Aurora-C-T191D and aurC-WT formed foci of colonies when grown on soft agar, indicating that a gain of Aurora-C activity is sufficient to transform cells. Furthermore, we reported that NIH-3 T3 stable cell lines overexpressing Aurora-C-T191D and its wild type partner induced tumour formation when injected into nude mice, demonstrating the oncogenic activity of enzymatically active Aurora kinase C. Interestingly enough tumour aggressiveness was positively correlated with the rate of kinase activity, making Aurora-C a potential anti-cancer therapeutic target.
Conclusion
These findings proved that Aurora C-T191D is not hyperactive but is constitutively active mutant.
doi:10.1186/1471-2121-13-8
PMCID: PMC3324370  PMID: 22443468
Aurora-C; Oncogene; Centrosome; Multinucleation; Tumour
7.  Rabies molecular virology, diagnosis, prevention and treatment 
Virology Journal  2012;9:50.
Rabies is an avertable viral disease caused by the rabid animal to the warm blooded animals (zoonotic) especially human. Rabies occurs in more than 150 countries and territories. According to an estimation by WHO, almost 55,000 people die because of rabies every year. The Dogs are the major reason behind this, approximately 99% human deaths caused by dog's bites. Developing and under developing countries, both are the victims of rabies. With the post-exposure preventive regimes, 327,000 people can prevent this disease annually.
The current article mainly covers the genome, virology, symptoms, epidemiology, diagnostic methods, and the high risk countries around the globe.
doi:10.1186/1743-422X-9-50
PMCID: PMC3307483  PMID: 22348291
Rabies; Zoonosis; Vaccine; Prevention
8.  Trend of transfusion transmitted infections frequency in blood donors: provide a road map for its prevention and control 
Background
Transfusion transmitted infections create significant burden on health care system. Donor selection is of paramount importance because infected individuals serve as an asymptomatic reservoir and a potential source of transmission.
Methods
A retrospective study was carried out in healthy blood donors in the Lady Reading Hospital Peshawar, Pakistan over a period of three and a half years i.e., from January 2008 to June 2011, to determine the prevalence of HBV, HCV, HIV and syphilis in order to provide information for relevant polices.
Results
Out of 1,27,828 sample of blood donors, recorded mean prevalence for HBs Ag, anti-HCV, anti-HIV and syphilis was 2.68%, 2.46%, 0.06% and 0.43%, respectively, with an increasing trend in frequencies of transfusion transmitted infections (TTIs).
Conclusions
This study reflects that blood transfusion is one of the leading risk factor of spread of the TTIs, which showed the need and importance of the mandatory screening of these infectious markers in blood donations.
doi:10.1186/1479-5876-10-20
PMCID: PMC3286364  PMID: 22293125
TTIs; HBV; HCV; HIV; Syphilis; Blood donor
9.  Rising burden of Hepatitis C Virus in hemodialysis patients 
Virology Journal  2011;8:438.
Aim
High prevalence of Hepatitis C virus (HCV) has been reported among the dialysis patients throughout the world. No serious efforts were taken to investigate HCV in patients undergoing hemodialysis (HD) treatment who are at great increased risk to HCV. HCV genotypes are important in the study of epidemiology, pathogenesis and reaction to antiviral therapy. This study was performed to investigate the prevalence of active HCV infection, HCV genotypes and to assess risk factors associated with HCV genotype infection in HD patients of Khyber Pakhtunkhwa as well as comparing this prevalence data with past studies in Pakistan.
Methods
Polymerase chain reaction was performed for HCV RNA detection and genotyping in 384 HD patients. The data obtained was compared with available past studies from Pakistan.
Results
Anti HCV antibodies were observed in 112 (29.2%), of whom 90 (80.4%) were HCV RNA positive. In rest of the anti HCV negative patients, HCV RNA was detected in 16 (5.9%) patients. The dominant HCV genotypes in HCV infected HD patients were found to be 3a (n = 36), 3b (n = 20), 1a (n = 16), 2a (n = 10), 2b (n = 2), 1b (n = 4), 4a (n = 2), untypeable (n = 10) and mixed (n = 12) genotype.
Conclusion
This study suggesting that i) the prevalence of HCV does not differentiate between past and present infection and continued to be elevated ii) HD patients may be a risk for HCV due to the involvement of multiple routes of infections especially poor blood screening of transfused blood and low standard of dialysis procedures in Pakistan and iii) need to apply infection control practice.
doi:10.1186/1743-422X-8-438
PMCID: PMC3180426  PMID: 21920054
Dialysis patients; HCV; HCV Genotype; Epidemiology; Pakistan
10.  Hepatitis C virus genotypes in Pakistan: a systemic review 
Virology Journal  2011;8:433.
Background and aim
Phylogenetic analysis has led to the classification of hepatitis C virus (HCV) into 1-6 major genotypes. HCV genotypes have different biological properties, clinical outcome and response to antiviral treatment and provide important clues for studying the epidemiology, transmission and pathogenesis. This article deepens the current molecular information about the geographical distribution of HCV genotypes and subgenotypes in population of four provinces of Pakistan. 34 published papers (1996-2011) related to prevalence of HCV genotypes/serotypes and subgenotypes in Pakistan were searched.
Result
HCV genotype/s distribution from all 34 studies was observed in 28,400 HCV infected individuals in the following pattern: 1,999 (7.03%) cases of genotype 1; 1,085 (3.81%) cases of genotype 2; 22,429 (78.96%) cases of genotype 3; 453 (1.59%) cases of genotype 4; 29 (0.10%) cases of genotype 5; 37 (0.13%) cases of genotype 6; 1,429 (5.03%) cases of mixed genotypes, and 939 (3.30%) cases of untypeable genotypes. Overall, genotype 3a was the predominant genotype with a rate of 55.10%, followed by genotype 1a, 3b and mixed genotype with a rate of 10.25%, 8.20%, and 5.08%, respectively; and genotypes 4, 5 and 6 were rare. Genotype 3 occurred predominately in all the provinces of Pakistan. Second more frequently genotype was genotype 1 in Punjab province and untypeable genotypes in Sindh, Khyber Pakhtunkhwa and Balochistan provinces.
doi:10.1186/1743-422X-8-433
PMCID: PMC3178528  PMID: 21902822
HCV; Genotypes; Prevalence; Pakistan
11.  Active hepatitis C infection and HCV genotypes prevalent among the IDUs of Khyber Pakhtunkhwa 
Virology Journal  2011;8:327.
Injection drug users (IDUs) are considered as a high risk group to develop hepatitis C due to needle sharing. In this study we have examined 200 injection drug users from various regions of the Khyber Pakhtunkhwa province for the prevalence of active HCV infection and HCV genotypes by Immunochromatographic assays, RT-PCR and Type-specific PCR. Our results indicated that 24% of the IDUs were actively infected with HCV while anti HCV was detected among 31.5% cases. Prevalent HCV genotypes were HCV 2a, 3a, 4 and 1a. Majority of the IDUs were married and had attained primary or middle school education. 95% of the IDUs had a previous history of needle sharing. Our study indicates that the rate of active HCV infection among the IDUs is higher with comparatively more prevalence of the rarely found HCV types in KPK. The predominant mode of HCV transmission turned out to be needle sharing among the IDUs.
doi:10.1186/1743-422X-8-327
PMCID: PMC3148566  PMID: 21711541
IDUs; HCV; Genotype; RT-PCR; KPK
12.  Prevalence of Hepatitis B virus genotypes in HBsAg positive individuals of Afghanistan 
Virology Journal  2011;8:281.
Background
The structural and functional differences between hepatitis B virus (HBV) genotypes are the mainstay to severity, complications, treatment and possibly vaccination against the virus. This study was conducted to determine the HBV genotypes in HBsAg positive patients of Afghanistan as no such large scale data available previously.
Methods
Two hundred and fourteen HBsAg-positive patients were included in this study. All patients were anti-HCV and anti-HIV negative. All the samples were confirmed for HBV DNA with nested PCR while HBV DNA positive samples were subjected to type specific PCR for HBV genotyping (A-F).
Results
Of the total samples, 168 (78.5%) were males and 46 (21.49%) females, aged ranged between 18 to 71 years. This study demonstrated that genotype D (35.67%) is the predominant genotype circulating in Afghani's population. Genotype C was observed in 32.16% followed by genotype A (19.30%), and genotype B (7.02%) while 6.07% of the individuals were not typed.
Conclusion
This study has shown a heterogeneous distribution of HBV genotypes. Further more, extensive studies are required to investigate genetic and geographical divergence and characteristics of the virus in the country, as no such large sample sized study has been carried out so far in this country.
doi:10.1186/1743-422X-8-281
PMCID: PMC3118365  PMID: 21649888
13.  Prevalence of HBV and HBV vaccination coverage in health care workers of tertiary hospitals of Peshawar, Pakistan 
Virology Journal  2011;8:275.
Background
Hepatitis B Virus (HBV) may progress to serious consequences and increase dramatically beyond endemic dimensions that transmits to or from health care workers (HCWs) during routine investigation in their work places. Basic aim of this study was to canvass the safety of HCWs and determine the prevalence of HBV and its possible association with occupational and non-occupational risk factors. Hepatitis B vaccination coverage level and main barriers to vaccination were also taken in account.
Results
A total of 824 health care workers were randomly selected from three major hospitals of Peshawar, Khyber Pakhtunkhwa. Blood samples were analyzed in Department of Zoology, Kohat University of Science and Technology Kohat, and relevant information was obtained by means of preset questionnaire. HCWs in the studied hospitals showed 2.18% prevalence of positive HBV. Nurses and technicians were more prone to occupational exposure and to HBV infection. There was significant difference between vaccinated and non-vaccinated HCWs as well as between the doctors and all other categories. Barriers to complete vaccination, in spite of good knowledge of subjects in this regard were work pressure (39.8%), negligence (38.8%) un-affordability (20.9%), and unavailability (0.5%).
Conclusions
Special preventive measures (universal precaution and vaccination), which are fundamental way to protect HCW against HBV infection should be adopted.
doi:10.1186/1743-422X-8-275
PMCID: PMC3121707  PMID: 21645287
14.  Response to combination therapy of HCV 3a infected Pakistani patients and the role of NS5A protein 
Virology Journal  2011;8:258.
Background
Hepatitis C virus (HCV) genotype 3a is known to show comparatively better response to combination therapy than genotype 1 and 4. Mutations within NS5A gene of HCV have earlier been implicated with response to interferon (IFN) therapies in chronic HCV patients among various populations. As response to therapy are available in different populations because of the ethnic and viral factors and there was no study available on the phenomenon of resistivity to IFN.
Results
Chronic HCV 3a infected Pakistani patients were kept on IFN-α and ribavirin therapy for six months. NS5A gene of HCV was amplified and sequenced in the case of all the patients prior to therapy and the sequences were analysed for mutations. Out of the total 27 patients, 20 (74.07%) were observed with sustained virological response (SVR), 4 (14.81%) patients were non responder (NR) while 3 (11.11%) patients exhibited in end of treatment response (ETR). Three (3/20) (15%) SVR patients and two (2/3) ETR patients had mutations (ranging from I-V amino acids) within the NS5A ISDR regions. While the rest of the SVR patients (85%) and the NR had no mutations at ISDR region when compared with HCV K3a ISDR.
Conclusions
Mutations within the NS5A gene of HCV 3a genotype may not influence the outcome of combination therapy in Pakistani populations.
doi:10.1186/1743-422X-8-258
PMCID: PMC3118205  PMID: 21609495
HCV; genotype 3a; IFN; NS5A gene
15.  Share of afghanistan populace in hepatitis B and hepatitis C infection's pool: is it worthwhile? 
Virology Journal  2011;8:216.
There is a notable dearth of data about Hepatitis B Virus (HBV) and Hepatitis C Virus(HCV) prevalence in Afghanistan. Awareness program and research capacity in the field of hepatitis are very limited in Afghanistan. Number of vulnerabilities and patterns of risk behaviors signal the need to take action now.
Thirty one studies dating from October 2003 to 2011 were included, consisting the data of 1,32,981 individuals for HBV and 1,32,500 individuals for HCV. Percentage prevalence was 1.9% for HBV and 1.1% for HCV in all available Afghanistan population. Most at risk population to hepatitis include injecting drug users who share needles and female sex workers, while truck drivers, prisoners and homosexual men needs attention, as their statistical figure are missing. Data suggests that high incidence of intravenous drug use, sexual activities, unsafe blood transfusion procedures and mobility are major risk factors for hepatitis transmission.
This review is based on analysis of the limited available data in Afghanistan. Although there are many underlying vulnerability factors, it appears that Afghanistan remains at an early epidemic phase. Further research is required to determine the seroprevalence and prevalent genotype(s) of HBV and HCV in all provinces in Afghanistan. This article provides some key insights into the potential and likely future transmission dynamics of Hepatitis which will serve as a guide in the identification of priority areas in term of high risk groups and risk behaviours in the country and will assist to develop urgent strategic plans to combat the future burden of Hepatitis in Afghanistan.
doi:10.1186/1743-422X-8-216
PMCID: PMC3125356  PMID: 21569317
Hepatitis B virus; Hepatitis C virus; Epidemiology; Risk behaviours; Risk groups; Afghanistan
16.  Prevalence of active HCV infection among the blood donors of Khyber Pakhtunkwa and FATA region of Pakistan and evaluation of the screening tests for anti-HCV 
Virology Journal  2011;8:154.
Hepatitis C is a fatal liver disease caused by the hepatitis C virus. In this study, blood donors, from various districts of the KPK province and the federally administered tribal area (FATA) of Pakistan were tested for anti-HCV antibodies and HCV RNA by ICT (Immuno-chromatographic test), ELISA and RT-PCR. Out of the 7148 blood donors, 224 (3.13%) were positive for anti-HCV antibodies by ICT, 135 (1.89%) by ELISA while 118 (1.65%) blood donors had active HCV infection as detected by RT-PCR. We suggest that ELISA should be used for anti-HCV screening in public sector hospitals and health care units.
doi:10.1186/1743-422X-8-154
PMCID: PMC3080828  PMID: 21457531
anti HCV; immunochromatography; ELISA; RT-PCR; Pakistan
17.  Molecular epidemiology of hcv among health care workers of khyber pakhtunkhwa 
Virology Journal  2011;8:105.
Background
Studies of the molecular epidemiology and risk factors for hepatitis C virus (HCV) in health care workers (HCWs) of Peshawar, Khyber Pakhtunkhwa region are scarce. Lack of awareness about the transmission of HCV and regular blood screening is contributing a great deal towards the spread of hepatitis C. This study is an attempt to investigate the prevalence of HCV and its possible association with both occupational and non-occupational risk factors among the HCWs of Peshawar.
Results
Blood samples of 824 HCWs, aged between 20-59 years were analysed for anti-HCV antibodies, HCV RNA and HCV genotypes by Immunochromatographic tests and PCR. All relevant information was obtained from the HCWs with the help of a questionnaire. The study revealed that 4.13% of the HCWs were positive for HCV antibodies, while HCV RNA was detected in 2.79% of the individuals. The most predominant HCV genotype was 3a and 2a.
Conclusion
A program for education about occupational risk factors and regular blood screening must be implemented in all healthcare setups of Khyber Pakhtunkhwa province in order to help reduce the burden of HCV infection.
doi:10.1186/1743-422X-8-105
PMCID: PMC3060846  PMID: 21385397

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