101
|
Affiliation(s)
- Y Waheed
- Foundation University Medical College, Foundation University Islamabad, Pakistan.
| |
Collapse
|
102
|
Iqbal K, Imran M, Ullah S, Jamal M, Waheed Y, Ali Q. Correlation of Apolipoprotein B mRNA-editing Enzyme, Catalytic Polypeptide- like 3G Genetic Variant rs8177832 with HIV-1 Predisposition in Pakistani Population. Curr HIV Res 2018; 16:297-301. [PMID: 30338740 PMCID: PMC6416456 DOI: 10.2174/1570162x16666181018155827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/08/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human immunodeficiency virus (HIV) infection is a global health burden which ultimately results in acquired immune deficiency syndrome (AIDS). There are multiple host factors which are capable of limiting HIV-1 replication. One of the most important host factors which inhibit HIV-1 DNA synthesis is the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide- like 3G (APOBEC3G). Any genetic variation of this important host factor may influence the host susceptibility to viral infection. OBJECTIVE The aim of the current study was to evaluate any correlation of APOBEC3G genetic variation rs8177832 with HIV-1 infection. METHODS The study involved 142 healthy control and 100 HIV-1 infected subjects. The genetic variation rs8177832 of all studied subjects was determined by allele-specific polymerase chain reaction (AS-PCR). RESULTS The results showed that the distribution of rs8177832 genotypes AA, AG and GG in healthy subjects and HIV-1 subjects was; 42.253%, 42.957%, 14.788% and 66%, 27%, 7% respectively. Statistical analyses of data showed that there was a significant variation in rs8177832 genotype AA in healthy control and HIV-1 infected subjects (42.257% vs 66%; p-value<0.001). CONCLUSION Thus it was concluded that APOBEC3G rs8177832 AA genotype contributes in genetic predisposition to HIV-1 infection in Pakistani population.
Collapse
Affiliation(s)
- Khurshid Iqbal
- Address correspondence to this author at the Department of Medical Laboratory Sciences, Imperial College of Business Studies, Lahore, Pakistan; Tel: 00923028051657; E-mail:
| | | | | | | | | | | |
Collapse
|
103
|
Naeem A, Waheed Y. Sequence analysis of hepatitis C virus nonstructural protein 3-4A serine protease and prediction of conserved B and T cell epitopes. Biomed Rep 2017; 7:563-566. [PMID: 29250328 PMCID: PMC5727757 DOI: 10.3892/br.2017.1007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023] Open
Abstract
The hepatitis C virus (HCV) is a global health issue. The nonstructural protein 3 (NS3)-4Agene of HCV is responsible for serine protease activity. The aim of the present study was to develop a global consensus sequence of HCV serine protease, analyze conserved residues, and predict highly conserved B- and T-cell binding epitopes in the NS3-4A protein. A total of 160 NS3-4A sequences from the six genotypes of HCV were refracted in the current study. The amino acid sequences were aligned to obtain a global consensus sequence. The location of possible B- and T-cell epitopes were predicted in the HCV NS3-4A consensus sequence by employing bioinformatics tools. Despite the high mutation rate of HCV, the functionally important residues are highly conserved. These include residues that form the catalytic triad (His57, Asp81 and Ser139), the S1 and S6 pocket, zinc-binding site (Cys97, Cys99, Cys145 and His149) and the substrate binding groove. The epitopes B1, B8 and B9 are predicted to be ideal candidates for B-cell-based vaccine and are >95% conserved across six major HCV genotypes. The major histocompatibility complex (MHC) class I epitopes, M4, M5, M7 and M10, and MHC class II epitopes, T5, T7 and T10 are ideal epitopes for vaccine development with high antigenicity scores and high conservancy across major HCV genotypes. The predicted B- and T-cell epitopes are ideal targets for vaccine development, and are capable of producing a strong immune response for all major genotypes of HCV.
Collapse
Affiliation(s)
- Ayesha Naeem
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, DHA-I, Islamabad 44000, Pakistan
| | - Yasir Waheed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, DHA-I, Islamabad 44000, Pakistan
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan
- Correspondence to: Dr Yasir Waheed, Foundation University Medical College, Foundation University Islamabad, Defence Avenue, DHA-I, Islamabad 44000, Pakistan, E-mail:
| |
Collapse
|
104
|
Imran M, Waheed Y, Ghazal A, Ullah S, Safi SZ, Jamal M, Ali M, Atif M, Imran M, Ullah F. Modern biotechnology-based therapeutic approaches against HIV infection. Biomed Rep 2017; 7:504-507. [PMID: 29250325 PMCID: PMC5727756 DOI: 10.3892/br.2017.1006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/27/2017] [Indexed: 02/07/2023] Open
Abstract
The causative agent of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus (HIV). Since its discovery before 30 years, a number of drugs known as highly active antiretroviral therapy have been developed to suppress the life cycle of the virus at different stages. With the current therapeutic approaches, ending AIDS means providing treatment to 35 million individuals living with HIV for the rest of their lives or until a cure is developed. Additionally, therapy is associated with various other challenges such as potential of drug resistance, toxicity and presence of latent viral reservoir. Therefore, it is imperative to search for treatments and to identify new therapeutic approaches against HIV infection to avoid daily intake of drugs. The aim of the current review was to summarize different therapeutic strategies against HIV infection, including stem cell therapy, RNA interference, CRISPR/Cas9 pathways, antibodies, intrabodies and nanotechnology. Silencing RNA against chemokine receptor 5 and other HIV RNAs have been tested and found to elicit homology-based, post-transcriptional silencing. The CRISPR/Cas9 is a gene editing technology that produces a double-stranded nick in the virus DNA, which is repaired by the host machinery either by non-homology end joining mechanism or via homology recombination leading to insertion, deletion mutation which further leads to frame shift mutation and non-functional products. Intrabodies are intracellular-expressed antibodies that are directed towards the targets inside the cell unlike the naturally expressed antibodies which target outside the cell. Different nanotechnology-based therapeutic approaches are also in progress against HIV. HIV eradication is not feasible without deploying a cure or vaccine alongside the treatment.
Collapse
Affiliation(s)
- Muhammad Imran
- Department of Microbiology, University of Health Sciences, Lahore 54600, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University, Islamabad 44000, Pakistan
| | - Ayesha Ghazal
- Department of Microbiology, University of Health Sciences, Lahore 54600, Pakistan
| | - Sajjad Ullah
- Department of Medical Laboratory Sciences, Imperial College of Business Studies, Lahore 53720, Pakistan
| | - Sher Zaman Safi
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology, Lahore 54000, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan 23200, Pakistan
| | - Muhammad Ali
- Department of Life Sciences, University of Management Technology, Lahore 54600, Pakistan
| | - Muhammad Atif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Aljouf University, Sakaka, Saudi Arabia
| | - Muhammad Imran
- Department of Diet and Nutrition, Imperial College of Business Studies, Lahore 54600, Pakistan
- Correspondence to: Dr Muhammad Imran, Department of Microbiology, University of Health Sciences, Khayaban-e-Jamia Punjab, Lahore 54600, Pakistan, E-mail:
| | - Farman Ullah
- Department of Physiology, Shaheed Zulfiqar Ali Bhutto Medical university Islamabad, Islamabad 44000, Pakistan
| |
Collapse
|
105
|
Waheed Y, Najmi MH, Aziz H, Waheed H, Imran M, Safi SZ. Prevalence of hepatitis C in people who inject drugs in the cities of Rawalpindi and Islamabad, Pakistan. Biomed Rep 2017; 7:263-266. [PMID: 28894573 PMCID: PMC5582579 DOI: 10.3892/br.2017.959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 08/01/2017] [Indexed: 02/07/2023] Open
Abstract
Pakistan has the second highest burden of hepatitis C (HCV) in the world. The major route of HCV transmission is contaminated blood or needle sharing. Seventy percent of people who inject drugs (PWIDs) shared needles at some time in their addiction history. The aim of the present study was to estimate the prevalence of HCV in PWIDs in cities of Pakistan. We enrolled 100 PWIDs from the Rawalpindi and Islamabad cities of Pakistan. Blood samples were taken in collection tubes and were subjected to HCV screening by using three rapid HCV screening kits including one step anti-HCV test, onsite HCV Ab rapid test and advance quality rapid anti-HCV test. All 100 blood samples were also subjected to HCV detection by using Elecsys anti-HCV II performed on the Roche Cobas 601 platform based on the ECLIA principle. Seventy-two percent of PWIDs showed the presence of HCV antibodies using the Roche anti-HCV II ECLIA test. We also compared the performance of different rapid kits in comparison with the anti-HCV II by Roche. The sensitivity of CTK kit was 84.72%, which was almost equal to the sensitivity by the SD Bioline HCV and Advanced Quality Rapid HCV tests, which was 83.33%. All three kits showed 100% specificity and positive predictive values. The results showed that the three market competitors of HCV rapid test showed almost equal results. The prevalence of HCV is very high in PWIDs in the capital twin cities of Pakistan. There is dire need to initiate the administration of a hepatitis test and treatment program for both high-risk and the general HCV-positive population. This is the optimal way to achieve HCV control targets established by the United Nations Sustainable Development Goals and Global Health Sector Strategy by WHO.
Collapse
Affiliation(s)
- Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
- Correspondence to: Dr Yasir Waheed, Foundation University Medical College, Foundation University Islamabad, Defence Avenue, Phase-I, DHA, Islamabad 44000, Pakistan, E-mail:
| | - Muzammil Hasan Najmi
- Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan
| | - Hafsa Aziz
- Nuclear Medicine Oncology and Radiotherapy Institute Islamabad, Islamabad 44000, Pakistan
| | | | - Muhammad Imran
- Department of Microbiology, University of Health Sciences, Lahore 54600, Pakistan
| | - Sher Zaman Safi
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology, Lahore Campus, Lahore 54000, Pakistan
| |
Collapse
|
106
|
Waheed Y, Safi SZ, Najmi MH, Aziz H, Imran M. Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus. ASIAN PAC J TROP MED 2017; 10:760-764. [PMID: 28942824 DOI: 10.1016/j.apjtm.2017.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To explore RNA dependent RNA polymerase of Chikungunya virus (CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen (HLA) classes as targets for epitopes based CHIKV vaccine. METHODS In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases (NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. Propred I and Propred software were used to predict HLA I and HLA II binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLA I binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database (IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. RESULTS Twenty two HLA class II epitopes and eight HLA class I epitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486-494 and VRRLNAVLL at 331-339 were found to bind with 37 and 36 of the 51 HLA class II alleles respectively. Epitope MANRSRYQS at position 58-66 and epitopes YQSRKVENM at positions 64-72 were predicted to bind with 12 and 9 HLA II alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLA I alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. CONCLUSIONS Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development of efficacious vaccine for CHIKV.
Collapse
Affiliation(s)
- Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan.
| | - Sher Zaman Safi
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology, Lahore Campus, Lahore, Pakistan
| | - Muzammil Hasan Najmi
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan
| | - Hafsa Aziz
- Nuclear Medicine Oncology and Radiotherapy Institute Islamabad, Islamabad 44000, Pakistan
| | - Muhammad Imran
- Department of Medical Laboratory Sciences (DMLS), Faculty of Health and Allied Sciences (FHAS), Imperial College of Business Studies (ICBS), Lahore, Pakistan; Department of Microbiology, University of Health Sciences, Lahore, Pakistan
| |
Collapse
|
107
|
Waheed Y, Waheed H. Pakistan needs to speed up its human immunodeficiency virus control strategy to achieve targets in fast-track acquired immune deficiency syndrome response. World J Virol 2017; 6:46-48. [PMID: 28573089 PMCID: PMC5437383 DOI: 10.5501/wjv.v6.i2.46] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/17/2017] [Accepted: 04/10/2017] [Indexed: 02/05/2023] Open
Abstract
In last fifteen years remarkable success in the fight against human immunodeficiency virus (HIV) is achieved globally. The number of HIV infections has decreased and the number of people on antiretroviral therapy is increased. This all is possible by strong political commitments and heavy investments in the fight against HIV. Pakistan is among few Asian countries in which HIV cases are increasing year by year since 1990. There are 94000 cases of HIV in Pakistan and only 14000 are registered with government. The main source of HIV infection in Pakistan is the use of contaminated injection equipment among people who inject drugs (PWID). The overall prevalence of HIV among PWID in Pakistan is 27.2%. There are five cities in Pakistan in which HIV prevalence is above 40% in PWIDs. In June 2016, United Nations political declaration on acquired immune deficiency syndrome (AIDS) provided a global mandate to fast-track the AIDS response over the next five years to achieve the targets in Sustainable Development Goals. To achieve the targets in fast-track AIDS response, the global leaders showed strong commitments to invest $ 26 billion per year by 2020. Pakistan needs to speed up its HIV control program. There is a dire need to locate all HIV positive people and enroll them in the treatment program. Pakistan also needs to calculate exact number of people living with HIV, increase HIV treatment centers and increase HIV awareness. Recently, Global Fund invested handsome money in the fight against HIV. Let’s hope the country will have effective HIV control strategy to achieve the HIV elimination target by 2030.
Collapse
|
108
|
Waheed Y, Tahir M, Waheed H, Safi SZ. Recent advances on Ebola virus. Asian Pac J Trop Dis 2017. [DOI: 10.12980/apjtd.7.2017d6-390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
109
|
Dar H, Zaheer T, Rehman MT, Ali A, Javed A, Khan GA, Babar MM, Waheed Y. Prediction of promiscuous T-cell epitopes in the Zika virus polyprotein: An in silico approach. ASIAN PAC J TROP MED 2016; 9:844-850. [PMID: 27633296 DOI: 10.1016/j.apjtm.2016.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/16/2016] [Accepted: 07/01/2016] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To predict immunogenic promiscuous T cell epitopes from the polyprotein of the Zika virus using a range of bioinformatics tools. To date, no epitope data are available for the Zika virus in the IEDB database. METHODS We retrieved nearly 54 full length polyprotein sequences of the Zika virus from the NCBI database belonging to different outbreaks. A consensus sequence was then used to predict the promiscuous T cell epitopes that bind MHC 1 and MHC II alleles using PorPred1 and ProPred immunoinformatic algorithms respectively. The antigenicity predicted score was also calculated for each predicted epitope using the VaxiJen 2.0 tool. RESULTS By using ProPred1, 23 antigenic epitopes for HLA class I and 48 antigenic epitopes for HLA class II were predicted from the consensus polyprotein sequence of Zika virus. The greatest number of MHC class I binding epitopes were projected within the NS5 (21%), followed by Envelope (17%). For MHC class II, greatest number of predicted epitopes were in NS5 (19%) followed by the Envelope, NS1 and NS2 (17% each). A variety of epitopes with good binding affinity, promiscuity and antigenicity were predicted for both the HLA classes. CONCLUSION The predicted conserved promiscuous T-cell epitopes examined in this study were reported for the first time and will contribute to the imminent design of Zika virus vaccine candidates, which will be able to induce a broad range of immune responses in a heterogeneous HLA population. However, our results can be verified and employed in future efficacious vaccine formulations only after successful experimental studies.
Collapse
Affiliation(s)
- Hamza Dar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Tahreem Zaheer
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Muhammad Talha Rehman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad 44000, Pakistan.
| | - Gohar Ayub Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Mustafeez Mujtaba Babar
- Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan.
| |
Collapse
|
110
|
Jamil Z, Waheed Y, Durrani TZ. Zika virus, a pathway to new challenges. ASIAN PAC J TROP MED 2016; 9:626-9. [PMID: 27393088 DOI: 10.1016/j.apjtm.2016.05.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 02/07/2023] Open
Abstract
The current Zika outbreak is largest of its kind with 1.4 million cases in Brazil alone. World Health Organization declared the current outbreak as the public health emergency of international concerns. The major route of Zika virus transmission is mosquito bites. Sexual transmission and monkey bites are also observed in few cases. There is dire need to evaluate the other routes of transmission like blood transfusion, lactation and contact with body fluids. Zika virus is infecting infants, not only causing microcephaly but also creating number of complications resulting in bad outcomes of pregnancy. In Brazil alone, 4000 cases of microcephaly have observed during the current outbreak. The incidence of Guillain-Barre (GB) syndrome is also observed during the current Zika virus outbreak. GB syndrome is acute medical condition leading the patients to death due to weakness of respiratory muscles or can cause the life time disability. There is no anti-viral drug or vaccine available for Zika virus. Zika infection can be prevented by using mosquito repellents, mosquito nets, cooling rooms by air conditions and wearing full sleeves or permethrin-treated clothes. The current outbreak of Zika has not only affected the health care but also caused great economic loss. Estimated loss in Latin America and Caribbean is US$3.5 billion. United Nation's sustainable development goal 3.d stresses the strengthening of early warning, risk reduction and management of national and global health risks. The world will keep on facing new challenges in the form of Ebola or Zika; there is strong need to prepare ourselves for any disease outbreak.
Collapse
Affiliation(s)
- Zubia Jamil
- Fauji Foundation Hospital, Rawalpindi 46000, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA Phase I, Islamabad 44000, Pakistan.
| | | |
Collapse
|
111
|
Rana A, Sattar SS, Shahzad A, Ali GM, Waheed Y. Scavenger receptor class-A plays diverse role in innate immunity, cell signaling and different pathologies. Asian Pacific Journal of Tropical Disease 2016; 6:567-72. [DOI: 10.1016/s2222-1808(16)61088-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
112
|
Ayub G, Waheed Y. Sequence analysis of the L protein of the Ebola 2014 outbreak: Insight into conserved regions and mutations. Mol Med Rep 2016; 13:4821-6. [PMID: 27082438 DOI: 10.3892/mmr.2016.5145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023] Open
Abstract
The 2014 Ebola outbreak was one of the largest that have occurred; it started in Guinea and spread to Nigeria, Liberia and Sierra Leone. Phylogenetic analysis of the current virus species indicated that this outbreak is the result of a divergent lineage of the Zaire ebolavirus. The L protein of Ebola virus (EBOV) is the catalytic subunit of the RNA‑dependent RNA polymerase complex, which, with VP35, is key for the replication and transcription of viral RNA. Earlier sequence analysis demonstrated that the L protein of all non‑segmented negative‑sense (NNS) RNA viruses consists of six domains containing conserved functional motifs. The aim of the present study was to analyze the presence of these motifs in 2014 EBOV isolates, highlight their function and how they may contribute to the overall pathogenicity of the isolates. For this purpose, 81 2014 EBOV L protein sequences were aligned with 475 other NNS RNA viruses, including Paramyxoviridae and Rhabdoviridae viruses. Phylogenetic analysis of all EBOV outbreak L protein sequences was also performed. Analysis of the amino acid substitutions in the 2014 EBOV outbreak was conducted using sequence analysis. The alignment demonstrated the presence of previously conserved motifs in the 2014 EBOV isolates and novel residues. Notably, all the mutations identified in the 2014 EBOV isolates were tolerant, they were pathogenic with certain examples occurring within previously determined functional conserved motifs, possibly altering viral pathogenicity, replication and virulence. The phylogenetic analysis demonstrated that all sequences with the exception of the 2014 EBOV sequences were clustered together. The 2014 EBOV outbreak has acquired a great number of mutations, which may explain the reasons behind this unprecedented outbreak. Certain residues critical to the function of the polymerase remain conserved and may be targets for the development of antiviral therapeutic agents.
Collapse
Affiliation(s)
- Gohar Ayub
- Department of Health Biotechnology, Atta‑ur‑Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Yasir Waheed
- Department of Health Biotechnology, Atta‑ur‑Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| |
Collapse
|
113
|
Ayub G, Waheed Y, Najmi MH. Prediction and conservancy analysis of promiscuous T-cell binding epitopes of Ebola virus L protein: An in silico approach. Asian Pacific Journal of Tropical Disease 2016. [DOI: 10.1016/s2222-1808(15)61007-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
114
|
Abstract
Hepatitis C virus (HCV) is a major global health problem with high morbidity and mortality. About 185 million people are living with HCV, of which 80% are living in low and middle income countries. With the development of new highly effective treatments for HCV, it is considered that the eradication of HCV may only be one step away. The major problem with new treatment options is its high price. The price of sofosbuvir-based treatment for one patient in the United States is US$85000-110000, while the actual production cost of a 12 wk direct-acting antiviral regimen is less than US$250. Another major hindrance in HCV eradication is the lack of quality management of blood transfusion screens. Due to the lack of HCV screening, 75% of people in the United States with HCV infection are unaware of their positive HCV status. The control of massive HCV pandemic will require a significant financial investment, political will, and support from medical, pharmaceutical, and civil organizations around the globe.
Collapse
|
115
|
Waheed Y. Ledipasvir and sofosbuvir: Interferon free therapy for hepatitis C virus genotype 1 infection. World J Virol 2015; 4:33-35. [PMID: 25674516 PMCID: PMC4308526 DOI: 10.5501/wjv.v4.i1.33] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/03/2014] [Accepted: 12/17/2014] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) has infected more than 200 million people around the globe. From 2001-2011, interferon plus ribavirin remained the standard of care for patients with HCV infection. The therapy had a limited response with a number of side effects. Recently, results for phase III trials of ledipasvir and sofosbuvir combination therapy have been announced. In treatment naïve patients, 12 wk of therapy with ledipasvir and sofosbuvir showed a sustained virological response (SVR) rate of 99%. In treatment experienced patients, 12-24 wk of therapy with ledipasvir and sofosbuvir in the absence or presence of ribavirin showed an SVR rate of 94%-99%. In cirrhotic patients the rate of SVR was 86% and 99% for 12 and 24 wk of therapy, respectively. The ledipasvir and sofosbuvir therapy showed very good results in different subgroups of patients regardless of patient’s race, alanine aminotransferase levels, sex and host genetic factors. The combination therapy was well tolerated with no emergence of resistant mutants. The most common adverse effects were nausea, headache and fatigue. With the availability of interferon free therapy with minimal adverse effects, it will be easy to decrease the future morbidity and mortality caused by HCV infection.
Collapse
|
116
|
Waheed Y. Effect of interferon plus ribavirin therapy on hepatitis C virus genotype 3 patients from Pakistan: Treatment response, side effects and future prospective. ASIAN PAC J TROP MED 2015; 8:85-9. [PMID: 25902019 DOI: 10.1016/s1995-7645(14)60193-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/15/2014] [Accepted: 01/15/2015] [Indexed: 02/07/2023] Open
Abstract
More than 10 million people are suffering from hepatitis C virus (HCV) in Pakistan. The available treatment option is a combination of interferon and ribavirin. Treatment response is linked with several factors and also induces a number of side effects. We searched in Pubmed, Pak Medi Net and Google Scholar for the articles presenting the effect of interferon plus ribavirin therapy on HCV patients from Pakistan, their side effects and future prospects. The major prevalent HCV genotype in Pakistan is 3. Conventional interferon alpha plus ribavirin showed sustained virological response of 54%-64% while pegylated interferon alpha plus ribavirin showed sustained virological response of 58%-75%. IL-28B CC genotype is linked with better sustained virological response. Studies on patients with HCV genotype 3 infections showed no correlation between treatment response and interferon sensitivity determining region mutations. Interferon therapy is linked with a number of side effects like thyroid dysfuncton, haematological disorders, weight loss, gastrointestinal tract side effects and neuropsychiatric side effects. Unusual side effects of clubbing of fingers and seizures were also observed in a couple of patients. Interferon alpha plus ribavirin therapy showed better response rate in HCV genotype 3 patients from Pakistan with number of side effects. A couple of interferon free therapies are light of hope for the patients living with HCV.
Collapse
Affiliation(s)
- Yasir Waheed
- Atta ur Rahman School of Applied Biosciences, National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan; Foundation University Medical College, Foundation University Islamabad, DHA Phase 1, Islamabad 44000, Pakistan.
| |
Collapse
|
117
|
Affiliation(s)
- Yasir Waheed
- Correspondence to: Yasir Waheed, Foundation University Medical College, Foundation University Islamabad, DHA Phase I, Islamabad 46000, Pakistan. ;
| |
Collapse
|
118
|
Saeed U, Waheed Y, Ashraf M, Waheed U, Anjum S, Afzal MS. Estimation of Hepatitis B Virus, Hepatitis C Virus, and Different Clinical Parameters in the Thalassemic Population of Capital Twin Cities of Pakistan. Virology (Auckl) 2015; 6:11-6. [PMID: 26568681 PMCID: PMC4636113 DOI: 10.4137/vrt.s31744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/01/2015] [Accepted: 10/06/2015] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B and C are serious public health problems worldwide. Thalassemia patients are dependent on blood transfusions throughout their life and are at high risk of viral infections. The aim of this study was to estimate the prevalence of hepatitis B/C infections and different clinical parameters in multitransfused thalassemia population. In this study, 262 multitransfused β-thalassemia patients were enrolled from the capital twin cities of Pakistan. The presence of hepatitis B virus (HBV)/hepatitis C virus (HCV), alanine aminotransferase (ALT) level, serum creatinine, serum ferritin, hepatomegaly, splenomegaly, and splenectomy were analyzed. The overall prevalence of HBV and HCV was 3.08% and 55.73%, respectively, with 100% of patients older than 20 years had HCV infection. The ALT levels among HBV- and HCV-positive thalassemia patients were 92.62 ± 41.57 U/L and 98 ± 63.65 U/L, respectively; creatinine values observed were 0.4 ± 0.35 mg/dL (for HBV) and 0.39 ± 0.24 mg/dL (for HCV), while serum ferritin levels were 6865.87 ± 1649.13 ng/dL (for HBV) and 5445.95 ± 3059.28 ng/dL (for HCV). A total of 74.8% and 82.20% of HBV- and HCV-positive patients had hepatomegaly with an average increase in liver size of 4.17 and 4.33 cm, respectively. Splenomegaly was observed in 64.9% and 67.12% of HBV- and HCV-positive patients with an average increase in spleen size of 4 and 4.46 cm, respectively. Splenectomy was observed among 14.50% and 15.75% of HBV- and HCV-infected thalassemia patients. There is a strong need to properly screen blood before transfusions to reduce the future load of viral hepatitis from Pakistan.
Collapse
Affiliation(s)
- Umar Saeed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Yasir Waheed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Foundation University Medical College, Foundation University Islamabad, DHA Phase I, Islamabad, Pakistan
- CORRESPONDENCE:
| | - Muhammad Ashraf
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Usman Waheed
- Safe Blood Transfusion Programme, Ministry of National Health Services, Government of Pakistan
| | - Sadia Anjum
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Sohail Afzal
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Department of Chemistry, School of Sciences, University of Management and Technology (UMT), Lahore, Pakistan
| |
Collapse
|
119
|
Affiliation(s)
- Fatima Riaz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Yasir Waheed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
| |
Collapse
|
120
|
|
121
|
Saeed U, Waheed Y, Ashraf M. Hepatitis B and hepatitis C viruses: a review of viral genomes, viral induced host immune responses, genotypic distributions and worldwide epidemiology. Asian Pac J Trop Dis 2014; 4. [PMCID: PMC4032054 DOI: 10.1016/s2222-1808(14)60322-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatitis B and hepatitis C viruses (HCV) are frequently propagating blood borne pathogens in global community. Viral hepatitis is primarily associated with severe health complications, such as liver cirrhosis, hepatocellular carcinoma, hepatic fibrosis and steatosis. A literature review was conducted on hepatitis B virus (HBV), HBV genome, genotypic distribution and global epidemiology of HBV, HCV, HCV genome, HCV and host immune responses, HCV genotypic distribution and global epidemiology. The valued information was subjected for review. HBV has strict tissue tropism to liver. The virus infecting hepatocytes produces large amount of hepatitis B surface antigen particles which lack the DNA. It has capability to integrate into host genome. It has been found that genotype C is most emerging genotype associated with more severe liver diseases (cirrhosis). The approximate prevalence rate of genotype C is 27.7% which represents a major threat to future generations. Approximately 8% of population is chronic carrier of HBV in developing countries. The chronic carrier rate of HBV is 2%-7% in Middle East, Eastern and Southern Europe, South America and Japan. Among HCV infected individuals, 15% usually have natural tendency to overcome acute viral infection, where as 85% of individuals were unable to control HCV infection. The internal ribosomal entry site contains highly conserved structures important for binding and appropriate positioning of viral genome inside the host cell. HCV infects only in 1%-10% of hepatocytes, but production of tumor necrosis factor alpha (from CD8+ cells) and interferon-gamma cause destruction of both infected cells and non-infected surrounding cells. Almost 11 genotypes and above 100 subtypes of HCV exists worldwide with different geographical distribution. Many efforts are still needed to minimize global burden of these infections. For the complete eradication of HBV (just like small pox and polio) via vaccination strategies, sincere efforts would be required from government and nongovernmental organizations.
Collapse
Affiliation(s)
- Umar Saeed
- *Corresponding author: Umar Saeed, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad (44000) Pakistan. Tel: +92-323-5338544. E-mail:
| | | | | |
Collapse
|
122
|
Waheed Y, Bhatti A, Anjum S, Ashraf M. Sequence comparison and phylogenetic analysis of hepatitis C virus genotype 3 polymerase. Mol Med Rep 2014; 9:1266-70. [PMID: 24481933 DOI: 10.3892/mmr.2014.1926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 07/04/2013] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is a worldwide health problem with high morbidity and mortality. HCV polymerase is an attractive target for the development of antiviral strategies. The aim of the present study was to report the sequence variation in the HCV NS5B gene from genotype 3 patient samples. The gene was amplified, cloned and sequenced. A nucleotide and amino acid sequence comparison of conserved motifs of HCV NS5B from the current reported sequences and previously reported genotype 3 sequences was performed. The sequence comparison indicated that the motifs A, B, C and F and β loop sequences are conserved in the reported sequences, while sequence variation was observed in motifs D and E. Amino acids E18, Y191, C274, Y276 and H502, which are involved in the interaction between template and primer, are highly conserved in the reported sequences. R48, R158, D225, S367, R386 and R394 amino acids interact with initiating GTP, and are also highly conserved in the reported sequences. A phylogenetic tree revealed that the sequences are clustered with sequences from India. HCV polymerase lacks proofreading ability and has high error rates. The present study revealed that the residues that form the important motifs of HCV NS5B remain conserved. However, it was observed that numerous place changes in the nucleotide sequences did not affect the amino acid sequences of HCV NS5B. The conserved motifs are strong targets for the development of peptide vaccines against HCV.
Collapse
Affiliation(s)
- Yasir Waheed
- Atta‑ur‑Rahman School of Applied BioSciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Attya Bhatti
- Atta‑ur‑Rahman School of Applied BioSciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Sadia Anjum
- Atta‑ur‑Rahman School of Applied BioSciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Muhammad Ashraf
- Atta‑ur‑Rahman School of Applied BioSciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| |
Collapse
|
123
|
Saeed U, Waheed Y, Manzoor S, Ashraf M. Identification of novel silent HIV propagation routes in Pakistan. World J Virol 2013; 2:136-138. [PMID: 24255884 PMCID: PMC3832857 DOI: 10.5501/wjv.v2.i3.136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/19/2013] [Accepted: 07/25/2013] [Indexed: 02/05/2023] Open
Abstract
Human immunodeficiency virus (HIV) is rapidly increasing in both high risk groups and the general population. In this study, silent routes of propagation in teenaged Pakistanis are discussed. In order to promote sexual activity in youths, regular clients write contact details of sex workers on the doors of public washrooms. HIV prevalence is much higher among Hijra sex workers. Hijra sex workers have apparently stepped into the profession of begging at public places, where they earn money by both begging and distributing visiting cards offering unsafe sex. In many educational institutes, sex education is lacking or absent; if delivered via teachers, government agencies and nongovernmental organizations this could prevent a future epidemic of sexually transmitted infections in Pakistan.
Collapse
|
124
|
Anjum S, Afzal MS, Ahmad T, Aslam B, Waheed Y, Shafi T, Qadri I. Mutations in the STAT1‑interacting domain of the hepatitis C virus core protein modulate the response to antiviral therapy. Mol Med Rep 2013; 8:487-92. [PMID: 23799612 DOI: 10.3892/mmr.2013.1541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/31/2013] [Indexed: 02/07/2023] Open
Abstract
RNA viruses, such as hepatitis C virus (HCV), have markedly error-prone replication, resulting in high rates of mutagenesis. In addition, the standard treatment includes ribavirin, a base analog that is likely to cause mutations in different regions of the HCV genome, resulting in deleterious effects on HCV itself. The N-terminal region of the core protein is reported to block interferon (IFN) signaling by interaction with the STAT1‑SH2 domain, resulting in HCV resistance to IFN therapy. In this study, mutations in the HCV core protein from IFN/ribavirin‑treated patients were analyzed, with particular focus on the N‑terminal domain of the HCV core which is reported to interact with STAT1. HCV PCR positive patients enrolled in this study were either undergoing pegylated IFN/ribavirin bitherapy and had completed 12 weeks of initial treatment or were treatment‑naïve patients. The HCV core protein was cloned and sequenced from these patients and mutations observed in the STAT1‑interacting domain of the core protein from treated patients were characterized using in silico interaction to depict the role of these mutations in disease outcomes. Our results suggest that the amino acids at positions 2, 3, 8, 16 and 23 of the HCV core protein are critical for core-STAT1 interaction and ribavirin-induced mutations at these positions interfere with the interaction, resulting in a better response of the treated patients. In conclusion, this study anticipates that HCV core residues 2, 3, 8, 16 and 23 directly interact with STAT1. We propose that IFN/ribavirin bitherapy‑induced mutations in the STAT1‑interacting domain of the HCV core protein may be responsible for the improved therapeutic response and viral clearance, thus amino acids 1-23 of the N-terminus of the core protein are an ideal antiviral target. However, this treatment may give rise to resistant variants that are able to escape the current therapy. We propose similar studies in responsive and non-responsive genotypes in order to gain a broader picture of this proposed mechanism of viral clearance.
Collapse
Affiliation(s)
- Sadia Anjum
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan.
| | | | | | | | | | | | | |
Collapse
|
125
|
Anjum S, Ali S, Ahmad T, Afzal MS, Waheed Y, Shafi T, Ashraf M, Andleeb S. Sequence and structural analysis of 3' untranslated region of hepatitis C virus, genotype 3a, from pakistani isolates. Hepat Mon 2013; 13:e8390. [PMID: 23922562 PMCID: PMC3732663 DOI: 10.5812/hepatmon.8390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 02/07/2013] [Accepted: 03/05/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) is the cause of high morbidity and mortality worldwide, inflicting around one million people in Pakistan alone. The HCV genomic RNA harbors conserved structural elements that are indispensable for its replication. The 3' untranslated region (UTR) contains several of these elements essentially involved in regulating the major steps of the viral life cycle. OBJECTIVES Differences in regulatory elements of HCV may contribute towards differential infectivity of local isolates. The present study explicates sequence analysis and secondary structure prediction of HCV 3'UTR region of subtype 3a from Pakistan to characterize this particular region. PATIENTS AND METHODS HCV 3'UTR region was amplified, cloned and sequenced from five different patients. Sequence and structural analysis was performed and phylogenetic analysis was carried out using the 3'UTR sequence reported in NCBI nucleotide data base (http://www.ncbi.nlm.nih.gov/nuccore) by other studies. RESULTS Sequence analysis of the amplified fragment from five patients indicated that the 3'UTR is composed of 214-235 nts. Its sequence contains a type-specific variable region followed by a poly U/UC region and a highly conserved X-tail of 98 nts. The variable region reported here has 26 nts and one stem loop at the secondary structure that differentiate it from HCV genotype 1a ( GT1a) 3'UTR which contains additional 14 nts and two stem loops. The poly U/UC region varied in length (100-79 nts) and nucleotide sequence within the Pakistani isolates, and among different genotypes. Some substitutions found in the X-tail do not affect secondary structure of this element suggesting that this region might play an important role in replication, stabilization and packaging of HCV genome. Additionally, U residues are not present at the end of the X-tail in Pakistani 3a isolates as otherwise reported for the variants of genotype 1b. CONCLUSIONS Sequence and structural diversity of the 3'UTR variable region and Poly U/UC region found in the local isolates indicate specificity in the regulating elements of 3'UTR that might be associated with differential replication efficacy of the HCV Pakistani isolates. The study necessitates functional characterization of these regulating elements to elucidate variable viral efficiency and pathogenicity associated with inter-geographical isolates.
Collapse
Affiliation(s)
- Sadia Anjum
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Corresponding author: Sadia Anjum, Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, H-12 Sector, Islamabad, Pakistan. Tel: +92-5190856152, Fax: +92-5190856102, E-mail:
| | - Sidra Ali
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tahir Ahmad
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Sohail Afzal
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yasir Waheed
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Talha Shafi
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Ashraf
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| |
Collapse
|
126
|
Aziz H, Raza A, Murtaza S, Waheed Y, Khalid A, Irfan J, Samra Z, Athar MA. Molecular epidemiology of hepatitis C virus genotypes in different geographical regions of Punjab Province in Pakistan and a phylogenetic analysis. Int J Infect Dis 2013. [PMID: 23183233 DOI: 10.1016/j.ijid.2012.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) is a causative agent of chronic liver disease, cirrhosis, and hepatocellular carcinoma. In Pakistan, more than 10 million people are living with HCV. Very little is known about the genotype distribution in Punjab Province, the largest province of Pakistan. Pretreatment genotype identification is very important, as different HCV genotypes respond differently to interferon therapy. METHODS In this study we performed HCV genotyping for 1537 HCV-infected patients from different districts of Punjab Province, Pakistan. Sequencing of partial HCV NS5B sequences from 14 samples belonging to genotypes 3 and 1 was also done. A sequence comparison was made of our reported sequences with those reported in the National Center for Biotechnology Information (NCBI), and a phylogenetic tree was constructed. RESULTS Our study showed that the most frequent HCV genotype was 3a (in 88.1% of infected individuals), followed by 1a (3.5%), 3b (3.0%), 1b (0.8%), and 2a (1.0%). A mixed genotype infection was found in 3.6% of infected individuals, with 0.3% living with 1a + 1b co-infection, 3.1% with 3a+3b, and 0.2% suffering from 3a+1b co-infection. The sequence comparison showed that HCV NS5B motif B residues G283, T287, and N291 were highly conserved in both genotype 1 and genotype 3 sequences, while the motif B residue T286 was mutated to proline in all the genotype 3 sequences. The GDD motif, which forms the catalytic pocket and binding site for the divalent cations, was highly conserved in all the reported sequences. The phylogenetic tree suggests clustering of genotype 1 sequences with sequences from the USA, UK, Germany, and France, while genotype 3 sequences are clustered with sequences from Japan and the UK. CONCLUSIONS The major prevalent genotype in Punjab Province of Pakistan was genotype 3a, followed by genotype 1a, and only 3.6% of infected individuals had a mixed genotype infection. Sequencing of the HCV NS5B gene suggested that the active site residues were highly conserved in all the reported sequences. Our sequences, which are clustered with sequences from the USA, UK, France, and Japan, show the diversity in origin of the different genotypes prevalent in Pakistan.
Collapse
Affiliation(s)
- Hafsa Aziz
- Diagnostic Laboratories, Nuclear Medicine Oncology and Radiotherapy Institute, Hanna Road, G-8/3, Islamabad, Pakistan.
| | | | | | | | | | | | | | | |
Collapse
|
127
|
Waheed U, Hayat K, Ahmad B, Waheed Y, Zaheer HA. Evaluation of HIV/AIDS diagnostics kits and formulation of a testing strategy for Pakistan. J Clin Virol 2013; 56:367-9. [PMID: 23298517 DOI: 10.1016/j.jcv.2012.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 12/03/2012] [Accepted: 12/10/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Rapid diagnosis of HIV/AIDS enables the development of prevention and treatment programmes but accurate, reliable and cost effective testing strategies should be used for testing of HIV/AIDS from a large population. OBJECTIVE To evaluate the performance and effectiveness of three assays for the diagnosis of HIV in comparison with Western blot and to formulate an alternative cost-effective confirmatory approach for HIV diagnosis. STUDY DESIGN 472 specimens (serum) from a Pakistani population were evaluated. Two rapid HIV testing kits (Capillus, SD Bioline) and one ELISA (Vironostika Ag/Ab) kit were used to detect HIV. Results were compared with Western blot against which sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of all HIV assays were assessed. RESULTS 280/472 (59.3%) of the samples were positive for antibodies against purified HIV-1 viral proteins. The sensitivity of SD Bioline and Vironostika ELISA was 100% (95% CI; 98-100) while that of anti-HIV Capillus™ kit was 94.6% (95% CI; 91-96.8). The specificity of the Vironostika ELISA and anti-HIV Capillus™ kit was 100% (95% CI; 97-100) while specificity of SD Bioline was 98.4% (95% CI; 95-99). PPV was 100% (95% CI; 98-100%) for the anti-HIV Capillus™ and Vironostika ELISA and 98.9% (95% CI; 96-99%) for SD Bioline. NPV for SD Bioline and Vironostika ELISA was 100% (95% CI; 98-100%) and 92.7% for anti-HIV Capillus™ (95% CI; 88-96%). CONCLUSION The sensitivity and specificity of all three kits were satisfactory compared to Western blot and could be used for effective diagnosis of HIV/AIDS in Pakistani population.
Collapse
Affiliation(s)
- Usman Waheed
- National HIV/STI Referral Laboratory, National AIDS Control Programme, Ministry of Health, Government of Pakistan, Pakistan.
| | | | | | | | | |
Collapse
|
128
|
Waheed Y, Bhatti A, Ashraf M. RNA dependent RNA polymerase of HCV: a potential target for the development of antiviral drugs. Infect Genet Evol 2013; 14:247-57. [PMID: 23291407 DOI: 10.1016/j.meegid.2012.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/07/2012] [Accepted: 12/11/2012] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma, cirrhosis and end stage liver disease. More than 200million people are living with HCV worldwide with high morbidity and mortality. There is no vaccine available for this virus; the approved treatment option for the majority of HCV genotypes is the combination of pegylated (Peg) interferon and ribavirin. The therapy has a different response rate on different HCV genotypes and has a number of side effects. Recently, as well as Peg interferon and ribavirin, two protease inhibitors have been introduced to treat patients with HCV genotype 1 infection. The protease inhibitors have rapid onset of resistance and are not approved for use for infections with other HCV genotypes. The HCV NS5B gene encodes RNA dependent RNA polymerase (RdRp), which is the key player in viral replication and is a promising target for the development of antiviral drugs. HCV NS5B has been studied in various biochemical assays, cell based assays and animal model systems. So far, a number of nucleoside and non-nucleoside inhibitors have been screened for effects on viral replication. This review presents a deep insight into the structure and function of HCV polymerase and the effect of various nucleoside and non-nucleoside inhibitors on viral replication.
Collapse
Affiliation(s)
- Yasir Waheed
- Atta ur Rahman School of Applied Biosciences, National University of Sciences & Technology (NUST), Islamabad 44000, Pakistan.
| | | | | |
Collapse
|
129
|
Hussain T, Manzoor S, Waheed Y, Tariq H, Hanif K. Phylogenetic analysis of Torque Teno Virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients. Virol J 2012; 9:320. [PMID: 23270330 PMCID: PMC3573928 DOI: 10.1186/1743-422x-9-320] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/05/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the present study compiles the first indigenous report to comprehensively illustrate the incidence of the virus in uninfected and hepatitis infected population from Pakistan. Another aim of the study was to present the sequence of full length TTV genome from a local isolate and compare it with the already reported genome sequences from other parts of the world. METHODS TTV DNA was screened in the serum of 116, 100 and 40 HBV infected, HCV infected and uninfected individuals respectively. Nearly full length genome of TTV was cloned from a HBV patient. The genome sequence was subjected to in-silico analysis using CLC Workbench, ClustalW, ClustalX and TreeView. Statistical analysis was carried out in SPSS v17.0. RESULTS Our results report that 89.7%, 90.0% and 92.5% of HBV, HCV patients and healthy control population were positive for TTV infection. TTV genome of 3603 bp was also cloned from a local isolate and given the identity of TPK01. The TTV genome sequence mentioned in this paper is submitted in the GenBank/EMBL/DDBJ under the accession number JN980171. Phylogenetic analysis of TPK01 revealed that the Pakistani isolate has sequence similarities with genotype 23 and 22 (Genogroup 2). CONCLUSION The results of the current study indicate that the high frequency of TTV viremia in Pakistan conforms to the reports from other areas of the world, wherever screening of TTV DNA was performed against 5'-UTR of the genome. The high sequence diversity among TTV genome sequences and the high frequency of prevalence makes it harder to study this virus in cellular systems.
Collapse
Affiliation(s)
- Tabinda Hussain
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Sobia Manzoor
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Yasir Waheed
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Huma Tariq
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Khushbakht Hanif
- Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan
| |
Collapse
|
130
|
Waheed Y, Saeed U, Anjum S, Afzal MS, Ashraf M. Development of Global Consensus Sequence and Analysis of Highly Conserved Domains of the HCV NS5B Prote in. Hepat Mon 2012; 12:e6142. [PMID: 23087757 PMCID: PMC3475062 DOI: 10.5812/hepatmon.6142] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 07/31/2012] [Accepted: 08/14/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) is a plus stranded RNA virus which encodes 10 different genes. The HCV NS5B gene encodes a polymerase, which is responsible for the replication of the virus and is a potential target for the development of antiviral agents. HCV has a high mutation rate and is classified into six major genotypes. OBJECTIVES The aim of this study was to draw a representing consensus sequence of each HCV genotype, align all six consensus sequences to draw a global consensus sequence and also study the highly conserved residues. MATERIALS AND METHODS 236 HCV NS5B sequences, belonging to all six genotypes, reported from all over the world were aligned then a representing phylogenetic tree wasdrawn. RESULTS The active site residues D220, D225, D318 and D319, which bind the divalent cations, are highly conserved among all the HCV genotypes. The other catalytic pocket residues, R158, S367, R386, and T390 and R394, which interact with the triphosphate of NTPs, are also highly conserved while T390 is mutated to valine in the genotype 5. The motif B residues G283, T286, T287 and N291, which take part in sugar selection by RdRp, are also highly conserved except for T286 which is mutated to proline in the genotypes 3 and 6. The residues E18, Y191, C274, Y276 and H502, which take part in primer/template interaction, are also high conserved except for H502 which is mutated to serine in genotype 2. High variation in all the six consensus sequences was observed in a 12 amino acid beta hairpin loop, which interacts with the double stranded RNA. Nine different peptides from the highly conserved regions of HCV NS5B protein were drawn which can be used as a peptide vaccine. The HCV NS5B phylogenetic tree shows the clusters of different genotypes and their evolutionary association. CONCLUSIONS In spite of a high mutation rate in HCV, the residues which are present in the catalytic pocket, sugar selection and template/primer interaction are highly conserved. These are target sites for the development of antiviral agents or peptide vaccines. The phylogenetic analysis suggests that different HCV genotypes have been evolved from the genotype 1a.
Collapse
Affiliation(s)
- Yasir Waheed
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Corresponding author: Yasir Waheed, Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, (44000), Pakistan. Tel.: +92-3005338171, Fax: +92-5190856102, E-mail:
| | - Umar Saeed
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sadia Anjum
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Mohammad Sohail Afzal
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Ashraf
- Atta-ur-Rehman School of Applied BioSciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| |
Collapse
|
131
|
Aziz H, Raza A, Waheed Y, Gill U, Gill ML. Analysis of variables and interactions among variables associated with a sustained virological response to pegylated interferon alfa-2a plus ribavirin in hepatitis C virus genotype 3-infected patients. Int J Infect Dis 2012; 16:e597-602. [PMID: 22658873 DOI: 10.1016/j.ijid.2012.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/17/2012] [Accepted: 03/23/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The recommended standard therapeutic regimen for chronic hepatitis patients with hepatitis C virus (HCV) genotype 3 is pegylated interferon plus ribavirin for 24 weeks. The aim of the present study was to evaluate treatment efficacy and variables predictive of treatment success, interactions among variables contributing to a response to therapy, and the utility of the rapid virological response (RVR; week 4 virological response) to predict treatment outcomes in HCV genotype 3-infected patients in routine clinical practice. METHODS We prospectively studied baseline and during-treatment factors associated with a sustained virological response (SVR) in HCV genotype 3-infected patients who received pegylated interferon alfa-2a (PEG-IFN α2a) 180 μg/week plus ribavirin 800 mg daily for 24 weeks and who were followed for 24 weeks after the completion of treatment. RESULTS Four hundred and twenty-six treated patients were included in the analysis; 320 (75.1%) showed an SVR. The following factors were assessed for their ability to predict SVR by means of univariable and multivariable logistic regression analysis: patient age, sex, pre-treatment viral load, pre-treatment alanine aminotransferase (ALT), body mass index (BMI), and RVR. Four factors - age, pre-treatment viral load, pre-treatment ALT, and RVR - were statistically significant predictors of SVR (p<0.05) in the univariable analysis. Factors showing a significant association with SVR were assessed by multivariable logistic regression analysis. In the multivariable analysis, independent factors associated with SVR were the attainment of RVR (odds ratio (OR) 11, 95% confidence interval (CI) 6.15-20.69; p<0.0001), patient age ≤40 years (OR 4.2, 95% CI 2.30-7.96, p<0.0001), and a low pre-treatment viral load (≤8 × 10(5) IU/ml; OR 3.4, 95% CI 1.87-6.25; p<0.0001). The effect of RVR in patients aged >40 years was more pronounced than in those aged ≤40 years: 81.1% of patients aged >40 years who achieved an RVR had an SVR, whereas only 7.5% of patients aged >40 years who did not achieve an RVR had an SVR (p<0.05). CONCLUSIONS RVR is an independent variable that is predictive of SVR. Moreover older patients (>40 years) who achieve an RVR are likely to have an SVR, while patients who do not achieve an RVR and who have a high pre-treatment viral load (>8 × 10(5) IU/ml) are unlikely to have an SVR.
Collapse
Affiliation(s)
- Hafsa Aziz
- Diagnostic Department, Nuclear Medicine Oncology and Radiotherapy Institute, Hanna Road, Islamabad, 44000 Pakistan.
| | | | | | | | | |
Collapse
|
132
|
Safi SZ, Waheed Y, Sadat J, Solat-Ul-Islam, Salahuddin S, Saeed U, Ashraf M. Molecular study of HCV detection, genotypes and their routes of transmission in North West Frontier Province, Pakistan. Asian Pac J Trop Biomed 2012; 2:532-6. [PMID: 23569965 PMCID: PMC3609335 DOI: 10.1016/s2221-1691(12)60091-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/27/2011] [Accepted: 12/28/2011] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE To determine hepatitis C virus (HCV) genotypes and explore the associated risk factors in chronic HCV patients. METHODS A total of 116 patients with chronic hepatitis C were subjected to polymerase chain reaction (PCR) based detection out of which 112 chronic HCV patients [53 male (47.32%), 59 female (52.68%); mean age (43.76±16.40) years; mean BMI (23.8±3.9) kg] were enrolled in this study. The frequency of 6 HCV genotypes and associated risk factors were evaluated from five districts of North West Frontier Province (NWFP). RESULTS Genotype 3 was the most prevalent in 73 samples (65.17%) followed by genotype 1 in 24 (21.42%) and genotype 2 in 13 (11.60%) samples. Genotype 3 had significantly high prevalence (P=0.000 2). The results showed that 48 (42.85%) samples were infected with HCV 3a; 25 (22.32%) with 3b; 14 (12.50%) with 1a; 10 (8.92%) with 1b; 11 (9.82%) with 2a; 2 (1.78%) with 2b; and 2 were untypable. The distribution of HCV genotypes in Mardan, Charsadda, Peshawar, Sawabi and Nowshehra districts was different. Use of unsterile equipment for medication, barbers and previous history of hospitalization were the main risk factors for HCV transmission. CONCLUSIONS Genotype 3a and 3b, 1a, 1b and 2a are the common genotypes in NWFP. Genotype 4, 5, and 6 can not be found in a single sample. The level of awareness about various modes of transmission of HCV among the population is found to be very low.
Collapse
Affiliation(s)
- Sher Zaman Safi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
- *Corresponding author: Mr. Sher Zaman Safi, PhD Scholar, NUST Center of Virology and Immunology, National University of Sciences & Technology, H-12 Islamabad Pakistan. Tel: +92-313-5393030 Fax: +92-51-9271593 E-mail:
| | - Yasir Waheed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Joharia Sadat
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | | | - Sadia Salahuddin
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Umar Saeed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| | - Muhammad Ashraf
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science and Technology (NUST), Islamabad, Pakistan
| |
Collapse
|
133
|
Imran M, Waheed Y, Manzoor S, Bilal M, Ashraf W, Ali M, Ashraf M. Interaction of Hepatitis C virus proteins with pattern recognition receptors. Virol J 2012; 9:126. [PMID: 22726246 PMCID: PMC3538621 DOI: 10.1186/1743-422x-9-126] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 06/11/2012] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is an important human pathogen that causes acute and chronic hepatitis, cirrhosis and hepatocellular carcinoma worldwide. This positive stranded RNA virus is extremely efficient in establishing persistent infection by escaping immune detection or hindering the host immune responses. Recent studies have discovered two important signaling pathways that activate the host innate immunity against viral infection. One of these pathways utilizes members of Toll-like receptor (TLR) family and the other uses the RNA helicase retinoic acid inducible gene I (RIG-I) as the receptors for intracellular viral double stranded RNA (dsRNA), and activation of transcription factors. In this review article, we summarize the interaction of HCV proteins with various host receptors/sensors through one of these two pathways or both, and how they exploit these interactions to escape from host defense mechanisms. For this purpose, we searched data from Pubmed and Google Scholar. We found that three HCV proteins; Core (C), non structural 3/4 A (NS3/4A) and non structural 5A (NS5A) have direct interactions with these two pathways. Core protein only in the monomeric form stimulates TLR2 pathway assisting the virus to evade from the innate immune system. NS3/4A disrupts TLR3 and RIG-1 signaling pathways by cleaving Toll/IL-1 receptor domain-containing adapter inducing IFN-beta (TRIF) and Cardif, the two important adapter proteins of these signaling cascades respectively, thus halting the defense against HCV. NS5A downmodulates the expressions of NKG2D on natural killer cells (NK cells) via TLR4 pathway and impairs the functional ability of these cells. TLRs and RIG-1 pathways have a central role in innate immunity and despite their opposing natures to HCV proteins, when exploited together, HCV as an ever developing virus against host immunity is able to accumulate these mechanisms for near unbeatable survival.
Collapse
Affiliation(s)
- Muhammad Imran
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Yasir Waheed
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Sobia Manzoor
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Muhammad Bilal
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Waseem Ashraf
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Muhammad Ali
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Muhammad Ashraf
- Atta Ur Rahman school of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| |
Collapse
|
134
|
Afzal. Interleukin-10 gene promoter polymorphism as a potential host susceptibility factor in Pakistani patients with pulmonary tuberculosis. ACTA ACUST UNITED AC 2011. [DOI: 10.5897/ajb10.2288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
135
|
Abstract
Hepatitis C virus (HCV) is the main cause of severe liver disease, including hepatocellular carcinoma, cirrhosis and end stage liver disease. In Pakistan most of HCV positive patients have history of facial/armpit shaving from barbers. 79% of barbers are rubbing Potash Alum stone on facial shaving cuts. Dark blood spots are analyzed on Potash Alum stones being used at different barber shops. The aim of the study was to check the viability of hepatitis C virus on potash alum stone being used at barber shops. Blood samples from HCV positive patients were taken and treated with 0.1, 0.2, 0.3, 0.4 and 0.5 molar concentrations of Potash Alum for different periods of time. Blood was centrifuged to isolate the serum; HCV RNA was extracted from serum and subjected to first strand synthesis and PCR. PCR fragments were confirmed by sequencing. PCR amplification was observed in all the samples, treated with different concentrations of Potash Alum, indicated that the virus remains alive on Potash Alum stone for a long period of time. Potash Alum being used by barbers on facial shaving cuts has definite role in HCV transmission in Pakistani population. Therefore use of Potash Alum stone should be banned on facial shaving cuts at barber shops.
Collapse
Affiliation(s)
- Yasir Waheed
- NUST Center of Virology and Immunology, National University of Sciences and Technology, H-12 Sector, Islamabad, Pakistan
| | - Sher Zaman Safi
- NUST Center of Virology and Immunology, National University of Sciences and Technology, H-12 Sector, Islamabad, Pakistan
| | - Ishtiaq Qadri
- NUST Center of Virology and Immunology, National University of Sciences and Technology, H-12 Sector, Islamabad, Pakistan
| |
Collapse
|
136
|
Aziz H, Athar MA, Murtaza S, Irfan J, Waheed Y, Bilal I, Raza A. Predictors of response to antiviral therapy in patients with chronic hepatitis C from Pakistani population. Chin Med J (Engl) 2011. [PMID: 21740743 DOI: 10.3760/cma.j.issn.0366-6999.2011.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) constitutes a major public health issue around the world, especially in developing countries like Pakistan. In this study, we assessed outcome of interferon (INF) treatment in chronic hepatitis C patients categorized by gender, age, and viral load. METHODS In this study, 750 HCV positive patients with genotype 3 were selected, out of which 616 completed the entire treatment. Their personal history, pre-treatment HCV RNA and serum alanine transaminase (ALT) was quantified. Patients were treated with combination therapy of INF-α 2b three million units (thrice a week) plus ribavirin (1000 - 1200 mg per day) for 24 weeks. After 24 weeks their HCV RNA and serum ALT level was quantified. RESULTS Out of the 616 patients, 391 (63.5%) responded to therapeutic regimen (INF-α 2b plus ribavirin). Among the responders, 27.1% were men and 36.4% were women. Best treatment response was observed in patients having low viral load < 8 × 10(5) IU/ml and age ≤ 40 years than patients having low viral load and age > 40 years (73.2% vs. 60.3%, P = 0.05). CONCLUSIONS Better response to IFN-α 2b plus ribavirin was observed in patients with lower viral RNA and younger age. It suggests that all patients considered for treatment should have quantification of serum HCV RNA level. The result can be used to counsel patients on the likelihood of response and may influence the patient's decision on treatment.
Collapse
Affiliation(s)
- Hafsa Aziz
- Nuclear Medicine Oncology and Radiotherapy Institute Islamabad, Punjab University, Lahore, Pakistan.
| | | | | | | | | | | | | |
Collapse
|
137
|
Aziz H, Gil ML, Waheed Y, Adeeb U, Raza A, Bilal I, Athar MA. Evaluation of prognostic factors for Peg Interferon alfa-2b plus ribavirin treatment on HCV infected patients in Pakistan. Infect Genet Evol 2011; 11:640-5. [PMID: 21316487 DOI: 10.1016/j.meegid.2011.01.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 01/27/2011] [Accepted: 01/27/2011] [Indexed: 02/06/2023]
Abstract
The effective standard therapeutic regimen for patients with chronic hepatitis C is pegylated interferon plus ribavirin. The efficacy of treatment in chronic hepatitis C is defined as absence of detectable virus at six months after treatment. Analysis of patient dependent and virus related factors that enable us to predict the response to antiviral treatment is very important. We prospectively studied 403 patients who received PEG-IFN alpha-2b 1.5 μg/kg/body weight plus ribavirin. Treatment was administrated for 24 weeks and 48 weeks for hepatitis C virus (HCV) genotypes 3 and 1, respectively. Out of 403 treated patients, 301 patients (74.7%) showed a sustained virologic response (SVR). Seven variables (age, sex, ethnic group, pretreatment viral load, HCV genotyping and pretreatment ALT) were chosen as possible predictors of SVR and were analysed by means of univariable and multivariable logistic regression analysis. Five variables were statistically significant (p<0.005) on univariable analysis: age, ethnic group, pretreatment viral load, response rate at week 4, and HCV genotype. In multivariable analysis independent factors associated with SVR were low pretreatment viral load (1.97; 95%CI, 1.06-3.66; p=0.03) and attainment of rapid virological response (RVR) (7.19; 95%CI, 4.15-12.45; p<0.001). Our findings support the association between viral load and SVR to PEG-IFN-alpha-2b plus ribavirin therapy. No achievement of RVR is an unfavorable marker for SVR. These findings suggest that all patients considered for treatment should have quantification of serum HCV RNA levels. The result can be used to counsel patients on the likelihood of achieving SVR and may influence the patient's decision on treatment. Future studies should confirm and explore this observation in other ethnic groups and in relation to HCV genotypes 1 and 3.
Collapse
Affiliation(s)
- Hafsa Aziz
- Nuclear Medicine Oncology and Radiotherapy Institute, Islamabad, Pakistan.
| | | | | | | | | | | | | |
Collapse
|
138
|
Ahmad T, Waheed Y, Tahir S, Safi SZ, Fatima K, Afzal MS, Farooqi ZUR, Qadri I. Frequency of HEV contamination in sewerage waters in Pakistan. J Infect Dev Ctries 2010; 4:842-5. [PMID: 21252466 DOI: 10.3855/jidc.612] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Revised: 07/05/2010] [Accepted: 04/07/2010] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Enteric viruses, including Hepatitis E virus (HEV), are able to persist under environmental conditions and may cause public health problems by contaminating natural and drinking water resources. Routine procedures for monitoring viruses in water samples have not been established for the water microbiology screening panel. METHODOLOGY Eighty-six raw sewerage samples were collected from the different regions of Islamabad and Rawalpindi, the twin cities of Pakistan. Samples were concentrated for HEV, using a polyethylene glycol-based method followed by viral RNA extraction using a commercial kit-based method. Reverse transcription polymerase chain reaction (RT-PCR) with HEV specific primers was used for the detection of HEV. RESULTS The present investigation focused on 86 raw sewerage water samples taken from different locations of drainage outlets of Islamabad and Rawalpindi. After careful experimentation, 35 samples were found to be RT-PCR positive. Nineteen (44.7%) out of 47 samples from Rawalpindi city were HEV positive while 16 (41.02%) out of 39 samples from Islamabad were HEV positive. All positive samples were found in the highly congested areas. CONCLUSIONS The high detection rate of HEV in this study shows that HEV circulates at a relatively high frequency in the sewerage waters in Pakistan. This study is the first report on detection of HEV from sewerage waste water from Pakistan and suggests that HEV might be a potent indicator of viral pollution in environmental specimens.
Collapse
Affiliation(s)
- Tahir Ahmad
- NUST Center of Virology and immunology, National University of Sciences and Technology, Islamabad, Pakistan.
| | | | | | | | | | | | | | | |
Collapse
|
139
|
Abstract
In Pakistan more than 10 million people are living with Hepatitis C virus (HCV), with high morbidity and mortality. This article reviews the prevalence, genotypes and factors associated with HCV infection in the Pakistani population. A literature search was performed by using the keywords; HCV prevalence, genotypes and risk factors in a Pakistani population, in Pubmed, PakMediNet and Google scholar. Ninety-one different studies dating from 1994 to May 2009 were included in this study, and weighted mean and standard error of each population group was calculated. Percentage prevalence of HCV was 4.95% +/- 0.53% in the general adult population, 1.72% +/- 0.24% in the pediatric population and 3.64% +/- 0.31% in a young population applying for recruitment, whereas a very high 57% +/- 17.7% prevalence was observed in injecting drug users and 48.67% +/- 1.75% in a multi-transfused population. Most prevalent genotype of HCV was 3a. HCV prevalence was moderate in the general population but very high in injecting drug users and multi-transfused populations. This data suggests that the major contributing factors towards increased HCV prevalence include unchecked blood transfusions and reuse of injection syringes. Awareness programs are required to decrease the future burden of HCV in the Pakistani population.
Collapse
Affiliation(s)
- Yasir Waheed
- NUST Center of Virology and Immunology, National University of Sciences & Technology, Sector H-12 Islamabad, Pakistan.
| | | | | | | |
Collapse
|