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Habib A, Habib N, Anjum KM, Iqbal R, Ashraf Z, Taj MU, Asim M, Javid K, Idoon F, Dashti S, Medeiros CR, Gurgel APAD, Coutinho HDM. Molecular evolution, virology and spatial distribution of HCV genotypes in Pakistan: A meta-analysis. INFECTIOUS MEDICINE 2023; 2:324-333. [PMID: 38205178 PMCID: PMC10774773 DOI: 10.1016/j.imj.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024]
Abstract
Background Hepatitis C, caused by the Hepatitis C Virus (HCV), is the second most common form of viral hepatitis. The geographical distribution of HCV genotypes can be quite complex, making it challenging to ascertain the most prevalent genotype in a specific area. Methods To address this, a review was conducted to determine the prevalence of HCV genotypes across various provinces and as a whole in Pakistan. The scientific literature regarding the prevalence, distribution, genotyping, and epidemiology of HCV was gathered from published articles spanning the years 1996-2020. Results Genotype 1 accounted for 5.1% of the patients, with its predominant subtype being 1a at 4.38%. The frequencies of its other subtypes, 1b and 1c, were observed to be 1.0% and 0.31% respectively. Genotype 2 had a frequency of 2.66%, with the most widely distributed subtype being 2a at 2.11% of the patients. Its other subtypes, 2b and 2c, had frequencies of 0.17% and 0.36% respectively. The most prevalent genotype among all isolates was 3 (65.35%), with the most frequent subtype being 3a (55.15%), followed by 3b (7.18%). The prevalence of genotypes 4, 5, and 6 were scarce in Pakistan, with frequencies of 0.97%, 0.08%, and 0.32% respectively. The prevalence of untypeable and mixed genotypes was 21.34% and 3.53% respectively. Estimating genotypes proves to be a productive method in assisting with the duration and selection of antiviral treatment. Different HCV genotypes can exhibit variations in their response to specific antiviral treatments. Different genotypes may have distinct natural histories, including variations in disease progression and severity. Some genotypes may lead to more rapid liver damage, while others progress more slowly. Conclusions This information can guide screening and testing strategies, helping to identify individuals at higher risk of developing severe complications. Studying the distribution of HCV genotypes in a population can provide valuable insights into the transmission dynamics of the virus.
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Affiliation(s)
- Arslan Habib
- Laboratory of Molecular Immunology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Nadiya Habib
- Department of Zoology, University of Gujrat, Gujrat, Punjab 50700, Pakistan
| | - Khalid Mahmood Anjum
- Department of Zoology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Riffat Iqbal
- Department of Zoology, Government College University, Lahore 54000, Pakistan
| | - Zeeshan Ashraf
- Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Muhammad Usman Taj
- Department of Fisheries and Aquaculture, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Muhammad Asim
- Department of Zoology, University of Narowal, Narowal 51600, Pakistan
| | - Kanwal Javid
- Department of Geography, Government College University, Lahore 54000, Pakistan
| | - Faezeh Idoon
- Department of Surgical Technology, Ferdows School of Allied Medicine and Public Health, Birjand University of Medical Sciences, Birjand 97178, Iran
| | - Saeid Dashti
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 97178, Iran
| | | | | | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry, Regional University of Cariri, Crato 63105-000, Brazil
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Khan A, Nawaz M, Ullah S, Rehman IU, Khan A, Saleem S, Zaman N, Shinwari ZK, Ali M, Wei DQ. Core amino acid substitutions in HCV-3a isolates from Pakistan and opportunities for multi-epitopic vaccines. J Biomol Struct Dyn 2022; 40:3753-3768. [PMID: 33246391 DOI: 10.1080/07391102.2020.1850353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV), which infected 71 million worldwide and about 5%-6% are from Pakistan, is an ssRNA virus, responsible for end-stage liver disease. To date, no effective therapy is available to cure this disease. Hence, it is important to study the most prevalent genotypes infecting human population and design novel vaccine or small molecule inhibitors to control the infections associated with HCV. Therefore, in this study clinical samples (n = 35; HCV-3a) from HCV patients were subjected to Sanger sequencing method. The sequencing of the core gene, which is generally considered as conserved, involved in the detection, quantitation and genotyping of HCV was performed. Multiple mutations, that is, R46C, R70Q, L91C, G60E, N/S105A, P108A, N110I, S116V, G90S, A77G and G145R that could be linked with response to antiviral therapies were detected. Phylogenetic analysis suggests emerging viral isolates are circulating in Pakistan. Using ab initio modelling technique, we predicted the 3D structure of core protein and subjected to molecular dynamics simulation to extract the most stable conformation of the structure for further analysis. Immunoinformatic approaches were used to propose a multi-epitopes vaccine against HCV by using core protein. The vaccine constructs consist of nine CTL and three HTL epitopes joined by different linkers were docked against the two reported Toll-like receptors (TLR-3 and TLR-8). Docking of vaccine construct with TLR-3 and TLR-8 shows proper binding and in silico expression of the vaccine resulted in a CAI value of 0.93. These analyses suggest that specific immune responses may be produced by the proposed vaccine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayyaz Khan
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Mehboob Nawaz
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Saeed Ullah
- Saidu Group of Teaching Hospital, Swat, Pakistan
| | - Irshad Ur Rehman
- Center of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Shoaib Saleem
- National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Nasib Zaman
- Center of Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China
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3
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Kaur D, Prabhakar K, Das S. Distribution of HCV genotypes and HCV RNA viral load in hepatitis infected patients of Kolar region, Karnataka, India. Bioinformation 2022; 18:387-391. [PMID: 36909692 PMCID: PMC9997504 DOI: 10.6026/97320630018387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/30/2022] [Accepted: 04/30/2022] [Indexed: 11/23/2022] Open
Abstract
Decisions and disease progression prediction, understanding the distribution of the hepatitis C virus (HCV) genotype and its association with viral load is significant for treatment. Therefore, it is of interest to document the distribution pattern of HCV genotypes and their association with viral load among HCV infected patients in Kolar, Karnataka. Seventy-four HCV-positive patients and not on antiviral therapy were enrolled from R.L. Jalappa hospital in Kolar, Karnataka. Blood samples were taken and demographics were recorded. HCV RNA was isolated after plasma was separated. qPCR was performed to measure the viral load, and RT-PCR was performed to determine the genotype. Genotype 3 was the prevalent (n=11, 40.7%) followed by genotype 4 (n=8, 29.6%), 2 (n=6, 22.2%), 1 (n= 13.7%), and mix (n=1, 13.7%). The median viral load of genotype 3 was a 2,87,835 IU/mL (IQR 10, 780-3, 71, 66) , genotype 2 was 81,030 IU/mL (IQR 66,495-95,565), genotype 4 was 43, 410 IU/mL (IQR 38, 355-48, 465) belongs to viral load less than 8,00,000 IU/mL. The median viral load genotype 3 was a 1, 05, 19, 500 IU/mL (IQR 49, 37, 250-2, 36, 71, 500), genotype 2 was 2,55,99,000 IU/mL (IQR 2,00,10,000-32,725,500), genotype 4 was 1,67,40,000 IU/mL (IQR 1,45,50,000-17,493,000) belonging to viral load more than 8,00,000 IU/mL category. A correlation between genotype and viral load was observed (p =1.5x10-12), of which genotype 3 showed a high viral load. Thus, HCV genotypes 1 2, 3, 4, and mixed genotype was observed in the patients studied. HCV genotype was associated with viral load in patient plasma. This data finds use in the treatment and prevention of hepatitis C in Kolar, Karnataka.
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Affiliation(s)
- Devinder Kaur
- Sri. Devaraj Urs Medical College, SDUMC, Kolar, Karnataka, India
| | - K Prabhakar
- Sri. Devaraj Urs Medical College, SDUMC, Kolar, Karnataka, India
| | - Subhashis Das
- Sri. Devaraj Urs Medical College, SDUMC, Kolar, Karnataka, India
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4
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Qamar Z, Anwar F, Ahmad R, Haq I, haq M, Kashif Khan AM, Hussain R, ullah A, Shahzad Z, Ahmad I, Munir Malik MS, Kamran khan M, Khan J. Prevalence of Hepatitis C virus and determination of its genotypes in subjects of Tehsil Daggar District Buner, KP, Pakistan. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2021. [DOI: 10.1016/j.cegh.2021.100809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Distribution of hepatitis C virus genotypes in Punjab region, Pakistan, based on a study of 4177 specimens. INFECTION GENETICS AND EVOLUTION 2021; 91:104811. [PMID: 33741510 DOI: 10.1016/j.meegid.2021.104811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 12/21/2022]
Abstract
Hepatitis C virus (HCV) is a heterogenetic infectious agent that affects a huge proportion of population around the globe. Diverse distribution of multiple subtypes of HCV makes it mandatory and remarkably imperative to understand the genotypic distribution in target population. It could serve as an indictive guideline for the improvement of diagnostic methodologies, and development of effective therapies against this viral infection, in order to improve the infected patients' quality of life. This study included HCV infected patients presented to the diagnostic facility of the Centre for Applied Molecular Biology, University of Punjab, Lahore, between 2016 and 2019. During the 4 years of study, samples were collected from 4177 subjects. Our data revealed no significant differences regarding the prevalence of various genotypes between genders in the adult population. Genotyping was carried out by following the Ohno protocol. The obtained results shown that genotype 3a is the most frequent genotype and accounts for 66.29% of cases. Among other genotypes, 1a is 2.11%, 1b is 0.07%, 3b is 1.89%, 5a is 0.02%, while genome of 28.23% patients was untypable; 1.22% of the samples were non-detectable as viremic. An important concern is that this untypable genome in HCV infected patients may indicate possible mutation of HCV.
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6
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Molecular Epidemiology of Hepatitis C Virus Genotypes Among Chronically Infected Patients in Pakistan. Jundishapur J Microbiol 2019. [DOI: 10.5812/jjm.86428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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7
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Wahid B, Waqar M, Rasool N, Rehman Z, Saeed J, Wasim M, Khan MA, Ali A, Rafique S, Sajjad, Idrees M. Recent trends in molecular epidemiology of Hepatitis C virus in Mardan, KPK Pakistan. INFECTION GENETICS AND EVOLUTION 2018; 66:66-71. [PMID: 30201500 DOI: 10.1016/j.meegid.2018.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023]
Abstract
To determine the genotypic distribution of HCV, frequency of risk factors involved in its transmission, and correlation of genotype with viral load in Mardan population which is the second largest city of Khyber Pakhtunkhwa (KPK), Pakistan. Blood samples of 1140 were collected from different regions of Mardan and major proportion of recruited patients were internally displaced people (IDPs), refugees, and slum dwellers. Complete patient's history was analyzed to assess the possible risks involved in HCV transmission. Viral genotype was determined by PCR (polymerase chain reaction) whereas, HCV RNA was measured by qRT-PCR. Data was analyzed using SPSS statistical software. Our results indicate 3a as the most abundant subtype in Mardan population followed by 3b, 2a, 2b, 4a, untypeable, mixed, 1a, and 1b. In contrast to previous findings, genotype 1 was the least prevalent genotype and the overall prevalence of HCV in Mardan population was significantly higher in females (n = 687, 60.2%) than males (n = 453, 39.7%). Significant difference between-genotypes and gender was observed in genotype 1 (p < .034) and genotype 3 (p < .004). The mean age was 44 (SD ± 9.51). The most frequently found mixed genotype was 3a + 1b and mixed genotype was more prevalent in males. The proportion of middle-aged people (41-49 years) was higher whereas, older and younger people were least infected with HCV. This is the first study that showed substantial correlation of genotype 3 with low and intermediate viral load in Mardan population. Moreover, high and extremely high viral load was associated with other genotypes. Our findings showed that most of the patients who experienced high and extremely high viremia in their blood were males and belonged to Takhat Bhai and Mardaan regions. There were significant difference in the prevalence of HCV genotype 3a (p = .001) and genotype 3b (p = .005) in different regions of Mardan. Pre-treatment viral load is significantly high (p 0.001) in tehsil Mardan patients infected with HCV genotype 3 as compared to other genotypes. Unsafe medical practices such as medical and dental surgeries, intravenous drug use, and blood transfusions were the main risk factors for HCV transmission in Mardan, KPK Pakistan. This study gives clear insights into the epidemiological status of HCV in Mardan population. Genotype 3 is correlated with low and intermediate viral load whereas high viral loads were revealed among patients infected with genotypes other than genotype 3. In the absence of better data and robust epidemiological information, this detailed analysis of HCV genotypes with special reference to risk factors, pretreatment viral load, gender, and age will provide the baseline data for development of optimal HCV eradication and preventive strategies.
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Affiliation(s)
- Braira Wahid
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan.
| | - Muhammad Waqar
- Genome Centre for Molecular Based Diagnostics and Research, Cl-25 Block B Al-Sudais Plaza, Abdalian Cooperative Society, Lahore, Pakistan
| | - Nouman Rasool
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan
| | - Zobaria Rehman
- Genome Centre for Molecular Based Diagnostics and Research, Cl-25 Block B Al-Sudais Plaza, Abdalian Cooperative Society, Lahore, Pakistan
| | - Jamaluddin Saeed
- Department of Medicine, Khyber Teaching Hospital, Peshawar, KPK, Pakistan
| | - Muhammad Wasim
- Department of Medicine, Khyber Teaching Hospital, Peshawar, KPK, Pakistan
| | - Muhammad Arif Khan
- Departments of Medicine, District Head Quarter Hospital, Mardan, Khyber Paktunkhwa, Pakistan
| | - Amjad Ali
- Centre for Applied Molecular Biology (CAMB), 87-West Canal Bank Road, Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Division of Molecular Virology and Diagnostics, Center of Excellence in Molecular Biology (CEMB), 87-West Canal Bank Road, Thokar Niaz Baig, University of the Punjab, Lahore, Pakistan
| | - Sajjad
- Genome Centre for Molecular Based Diagnostics and Research, Cl-25 Block B Al-Sudais Plaza, Abdalian Cooperative Society, Lahore, Pakistan
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8
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Zafar A, Imran M, Zahoor S, Shah ZH, Ali M, Afzal MS. Prevalence and Treatment of Untypable HCV Variants in Different Districts of Punjab, Pakistan. Viral Immunol 2018; 31:426-432. [PMID: 29920175 DOI: 10.1089/vim.2017.0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In Pakistan, around 11 million people are infected with, at least, six circulating genotypes and subtypes of hepatitis C virus (HCV). The viral burden is still on rise. HCV genotype determination is necessary to devise appropriate antiviral therapy. Previous reports highlight the prevalence circulating untypable (in diagnostic perspectives) HCV subtype in local Pakistani patients. Present study was designed to investigate the epidemiological distribution of genotypes in different districts of Punjab, Pakistan and focuses on prevalence of diagnostically untypable subtype and its possible antiviral therapy. A total of 8,353 HCV patients were included through 2011 to 2016 for determination of HCV prevalent genotypes in the local community. HCV genotyping was carried out using Ohno et al. method, and five cases of diagnostically untypable patients were treated with interferon-based antiviral regimen to find the possible treatment strategy. Of the 8,353 patients, the genotype 3a (n = 6,650, 79.6%) was most significantly prevalent throughout the study period followed by undetermined genotype that is, untypable (n = 1,377, 16.5%). The presence of untypable variants suggested that there are some novel or quasi species prevailing among HCV patients in local community. Five HCV patients infected with untypable genotype had been treated effectively with interferon alpha plus ribavirin therapy for 24 weeks at standard doses and achieved sustained virological response. This study highlighted an important aspect of HCV treatment for local Pakistani HCV patients. Untypable HCV variants could be treated with interferon-based antiviral regimens such as 3a genotype. The study raises the need of characterization of diagnostically untypable HCV variant. On the basis of these results, it can be proposed that until the availability of pangenotypic direct-acting antiviral for HCV treatment in Pakistan, interferon-based antiviral regimens will be of choice for majority of patients infected with 3a or untypable genotypes.
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Affiliation(s)
- Ayesha Zafar
- 1 Department of Life Sciences, School of Science, University of Management and Technology , Lahore, Pakistan
| | - Muhammad Imran
- 1 Department of Life Sciences, School of Science, University of Management and Technology , Lahore, Pakistan .,2 Department of Molecular Biology, Lahore Clinical Laboratory and Research Center , Lahore, Pakistan
| | - Sarmad Zahoor
- 3 Department of Internal Medicine, Mayo Hospital , Lahore, Pakistan
| | - Zaheer Hussain Shah
- 1 Department of Life Sciences, School of Science, University of Management and Technology , Lahore, Pakistan
| | - Muhammad Ali
- 1 Department of Life Sciences, School of Science, University of Management and Technology , Lahore, Pakistan
| | - Muhammad Sohail Afzal
- 1 Department of Life Sciences, School of Science, University of Management and Technology , Lahore, Pakistan
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9
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Pattern of hepatitis C virus genotypes and subtypes circulating in war-stricken Khyber Pakhtunkhwa, Pakistan: Review of published literature. ASIAN PAC J TROP MED 2017; 10:1037-1042. [DOI: 10.1016/j.apjtm.2017.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 02/07/2023] Open
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10
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Nazir N, Jan MR, Ali A, Asif M, Idrees M, Nisar M, Zahoor M, Abd El-Salam NM. Prevalence of hepatitis-C virus genotypes and potential transmission risks in Malakand Khyber Pakhtunkhwa, Pakistan. Virol J 2017; 14:160. [PMID: 28830526 PMCID: PMC5568223 DOI: 10.1186/s12985-017-0829-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 08/14/2017] [Indexed: 12/24/2022] Open
Abstract
Background Hepatitis C virus (HCV) is a leading cause of chronic liver disease and frequently progresses towards liver cirrhosis and Hepatocellular Carcinoma (HCC). This study aimed to determine the prevalence of HCV genotypes and their association with possible transmission risks in the general population of Malakand Division. Methodology Sum of 570 serum samples were collected during March 2011 to January 2012 from suspected patients visited to different hospitals of Malakand. The suspected sera were tested using qualitative PCR and were then subjected to molecular genotype specific assay. Quantitative PCR was also performed for determination of pre-treatment viral load in confirmed positive patients. Results Out of 570 serum samples 316 sera were seen positive while 254 sera were found negative using qualitative PCR. The positive samples were then subjected to genotyping assay out of 316, type-specific PCR fragments were seen in 271 sera while 45 samples were found untypable genotypes. Genotype 3a was seen as a predominant genotype (63.3%) with a standard error of ±2.7%. Cramer’s V statistic and Liklihood-Ratio statistical procedures are used to measure the strength and to test the association, respectively, between the dependent variable, genotype, and explanatory variables (e.g. gender, risk, age and area/districts). The dependent variable, genotype, is observed statistically significant association with variable risk factors. This implies that the genotype is highly dependent on how the patient was infected. In contrast, the other covariates, for example, gender, age, and district (area) no statistical significant association are observed. The association between gender-age indicates that the mean age of female was older by 10.5 ± 2.3 years with 95% confidence level using t-statistic. Conclusion It was concluded from the present study that the predominant genotype was 3a in the infected population of Malakand. This study also highlights the high prevalence rate of untypable genotypes which an important issue of health care setup in Malakand and create complications in therapy of infected patients. Major mode of HCV transmission is multiple uses and re-uses of needles/injections. Trial registration ISRCTN ISRCTN73824458. Registered: 28 September 2014
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Affiliation(s)
- Nausheen Nazir
- Department of Botany, University of Malakand, Chakdara Dir (L), Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Rasul Jan
- Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Amjad Ali
- Centre for Applied Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, Pakistan.
| | - Muhammad Asif
- Department of Statistics, University of Malakand, Chakdara Dir (L), Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Idrees
- Centre for Applied Molecular Biology, University of the Punjab, 87-West Canal Bank Road Thokar Niaz Baig, Lahore, Pakistan.,Vice Chancellor Hazara University, Mansehra, Pakistan
| | - Mohammad Nisar
- Department of Botany, University of Malakand, Chakdara Dir (L), Khyber Pakhtunkhwa, Pakistan.
| | - Muhammad Zahoor
- Department of Chemistry, University of Malakand, Khyber Pakhtunkhwa, Chakdara Dir (L), Pakistan
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Afzal MS, Iqbal MA. Hepatitis C Virus in Pakistan: Community Education Is an Effective Weapon Against the Killer. Viral Immunol 2017. [PMID: 28622101 DOI: 10.1089/vim.2016.0171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Muhammad Sohail Afzal
- Department of Life Sciences, School of Science, University of Management and Technology (UMT) , Lahore, Pakistan
| | - Muhammad Azhar Iqbal
- Department of Life Sciences, School of Science, University of Management and Technology (UMT) , Lahore, Pakistan
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12
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Afzal MS. Hepatitis C Virus and Interferon-Free Antiviral Therapeutics Revolution: Implications for Pakistan. Viral Immunol 2017; 30:252-257. [PMID: 28118096 DOI: 10.1089/vim.2016.0164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hepatitis C virus (HCV) is a major health concern worldwide as a leading cause of liver-related mortalities and morbidities. Pakistan ranks second among countries with endemic HCV infection; ∼11 million cases are reported so far. HCV burden is continuously rising in Pakistan, mainly because of unsafe blood transfusions, surgical procedures, dental procedures, untrained clinicians, reuse of syringes, barbers, and ear/nose piercing tools. Lack of awareness about HCV transmission routes among the general and high-risk population is a major hurdle in disease management. HCV prevalence in the general population and healthy blood donors ranges from 3.13% to 23.83% and from 1.05% to 20.8%, respectively; whereas in the high-risk groups, HCV prevalence is up to 66%. Genotype 3 is most prevalent in Pakistan followed by genotypes 1 and 2 along with an alarming number of untypable viral genotypes in the local community. Mainly interferon-based antiviral regimens are used in Pakistan and are quite effective, because the major prevalent genotype (genotype 3) showed the best sustained virological response (SVR) with it. But a large number of individuals did not show SVR either because of infection with nonresponder genotypes or because of side effects. Due to these reasons, there was a need for interferon-free direct acting antivirals (DAAs). Recently, Sovaldi (Sofosbuvir: NS5B inhibitor) is approved on a heavy discounted rate for Pakistan; it is currently in effective use and showed good SVR. Sovaldi plus ribavirin is used alone or along with interferon to treat different viral genotypes. Sovaldi will be the future treatment regime for Pakistan, because genotype 2 and genotype 3 infected individuals achieve the best SVR with it. For the treatment of other prevalent viral genotypes, approval of some other DAAs such as Ledipasvir on discounted price is required for better disease management.
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Affiliation(s)
- Muhammad Sohail Afzal
- Department of Chemistry, School of Science, University of Management and Technology (UMT) , Lahore, Pakistan
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13
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Khan AW, Nasim Z, Zahir F, Ali S, Ali A, Iqbal A, Munir I. Untypeable hepatitis C virus subtypes in Pakistan: A neglected section. Acta Microbiol Immunol Hung 2016; 63:427-431. [PMID: 28033725 DOI: 10.1556/030.63.2016.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Diagnostically untypeable subtypes contribute a considerable percent of hepatitis C virus (HCV) subtypes in Pakistan. In the present study, chronically infected HCV patients with known viremia were subjected to HCV genotyping. Among the total retrieved samples, 92.7% (64/69) were found typeable while 7.24% (5/69) were diagnostically untypeable. In conclusion, the presence of large number of untypeable HCV subtypes emphasizes the need of an updated type-specific genotyping assay and consideration of primers for proportionally rare subtypes to minimize the number of untypeable HCV subtypes.
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Affiliation(s)
- Abdul Waheed Khan
- 1 Institute of Biotechnology and Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
- 2 Center for Biotechnology and Microbiology, University of Swat , Odigram, Pakistan
| | - Zeeshan Nasim
- 1 Institute of Biotechnology and Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
| | - Fazli Zahir
- 1 Institute of Biotechnology and Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
| | - Shahid Ali
- 2 Center for Biotechnology and Microbiology, University of Swat , Odigram, Pakistan
| | - Abid Ali
- 1 Institute of Biotechnology and Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
| | - Aqib Iqbal
- 1 Institute of Biotechnology and Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
| | - Iqbal Munir
- 1 Institute of Biotechnology and Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
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Riaz S, Bashir MF, Haider S, Rahid N. Association of genotypes with viral load and biochemical markers in HCV-infected Sindhi patients. Braz J Microbiol 2016; 47:980-986. [PMID: 27528079 PMCID: PMC5052380 DOI: 10.1016/j.bjm.2016.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/05/2016] [Indexed: 12/16/2022] Open
Abstract
The presented study had two objectives. The first was to examine distributions of Hepatitis C Virus (HCV) genotypes in Sindh, Pakistan, where HCV is prevalent. The other was to explore clinically relevant relationships between the genotypes, viral load (measured by real-time polymerase chain reaction assays) and biochemical markers. For this, 1471 HCV-infected patients in six cities in Sindh were recruited and sampled. HCV genotype distributions varied among the cities, but genotype 3a was most prevalent, followed by 3b, 1a and 1b (detected in 51.5, 22.7. 9.25 and 3.2% of the cases, respectively). No type-specific sequences were detected in serum samples from 189 (12.8%) of the 1471 patients. Frequencies of low (<200,000IU/mL serum), intermediate (200,000-600,000IU/mL serum) and high (>600,000IU/mL serum) viral loads were respectively 45.4, 16.5 and 38.1% for patients infected with genotype 3, and 16.9, 36.9 and 46.2%, respectively, for patients with other genotypes. Infection with genotype 1a was associated with significantly higher (p<0.005) alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase titers than infection with genotype 3a. The results will help in the formulation of treatment strategies.
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Affiliation(s)
- Saba Riaz
- Citilab and Research Centre, Division of Molecular Pathology, Lahore, Pakistan; University of the Punjab, Department of Microbiology and Molecular Genetics, Lahore, Pakistan.
| | - Muhammad Faisal Bashir
- University of the Punjab, School of Biological Sciences, Lahore, Pakistan; Citilab and Research Centre, Division of Molecular Pathology, Lahore, Pakistan
| | - Saleem Haider
- University of the Punjab, School of Biological Sciences, Lahore, Pakistan; University of the Punjab, Institute of Agricultural Sciences, Lahore, Pakistan.
| | - Naeem Rahid
- University of the Punjab, School of Biological Sciences, Lahore, Pakistan
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Afzal MS. Predictive potential of IL-28B genetic testing for interferon based hepatitis C virus therapy in Pakistan: Current scenario and future perspective. World J Hepatol 2016; 8:1116-1118. [PMID: 27660680 PMCID: PMC5026995 DOI: 10.4254/wjh.v8.i26.1116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/29/2016] [Accepted: 07/22/2016] [Indexed: 02/06/2023] Open
Abstract
In Pakistan which ranked second in terms of hepatitis C virus (HCV) infection, it is highly needed to have an established diagnostic test for antiviral therapy response prediction. Interleukin 28B (IL-28B) genetic testing is widely used throughout the world for interferon based therapy prediction for HCV patients and is quite helpful not only for health care workers but also for the patients. There is a strong relationship between single nucleotide polymorphisms at or near the IL-28B gene and the sustained virological response with pegylated interferon plus ribavirin treatment for chronic hepatitis C. Pakistan is a resource limited country, with very low per capita income and there is no proper social security (health insurance) system. The allocated health budget by the government is very low and is used on other health emergencies like polio virus and dengue virus infection. Therefore it is proposed that there should be a well established diagnostic test on the basis of IL-28B which can predict the antiviral therapy response to strengthen health care set-up of Pakistan. This test once established will help in better management of HCV infected patients.
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Afzal MS. Are efforts up to the mark? A cirrhotic state and knowledge about HCV prevalence in general population of Pakistan. ASIAN PAC J TROP MED 2016; 9:616-8. [PMID: 27262079 DOI: 10.1016/j.apjtm.2016.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Accepted: 04/08/2016] [Indexed: 02/07/2023] Open
Affiliation(s)
- Muhammad Sohail Afzal
- Department of Chemistry, School of Science, University of Management and Technology (UMT), Lahore, Pakistan.
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Afzal MS, Shah ZH, Ahmed H. Recent HCV genotype changing pattern in the Khyber Pakhtunkhwa province of Pakistan; is it pointing out a forthcoming problem? Braz J Infect Dis 2016; 20:312-3. [PMID: 26963150 PMCID: PMC9425352 DOI: 10.1016/j.bjid.2015.12.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022] Open
Affiliation(s)
- Muhammad Sohail Afzal
- Department of Chemistry, School of Science, University of Management and Technology (UMT), Lahore, Pakistan.
| | - Zaheer Hussain Shah
- Department of Physics, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Haroon Ahmed
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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Umer M, Iqbal M. Hepatitis C virus prevalence and genotype distribution in Pakistan: Comprehensive review of recent data. World J Gastroenterol 2016; 22:1684-1700. [PMID: 26819533 PMCID: PMC4721999 DOI: 10.3748/wjg.v22.i4.1684] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/11/2015] [Accepted: 12/14/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is endemic in Pakistan and its burden is expected to increase in coming decades owing mainly to widespread use of unsafe medical procedures. The prevalence of HCV in Pakistan has previously been reviewed. However, the literature search conducted here revealed that at least 86 relevant studies have been produced since the publication of these systematic reviews. A revised updated analysis was therefore needed in order to integrate the fresh data. A systematic review of data published between 2010 and 2015 showed that HCV seroprevalence among the general adult Pakistani population is 6.8%, while active HCV infection was found in approximately 6% of the population. Studies included in this review have also shown extremely high HCV prevalence in rural and underdeveloped peri-urban areas (up to 25%), highlighting the need for an increased focus on this previously neglected socioeconomic stratum of the population. While a 2.45% seroprevalence among blood donors demands immediate measures to curtail the risk of transfusion transmitted HCV, a very high prevalence in patients attending hospitals with various non-liver disease related complaints (up to 30%) suggests a rise in the incidence of nosocomial HCV spread. HCV genotype 3a continues to be the most prevalent subtype infecting people in Pakistan (61.3%). However, recent years have witnessed an increase in the frequency of subtype 2a in certain geographical sub-regions within Pakistan. In Khyber Pakhtunkhwa and Sindh provinces, 2a was the second most prevalent genotype (17.3% and 11.3% respectively). While the changing frequency distribution of various genotypes demands an increased emphasis on research for novel therapeutic regimens, evidence of high nosocomial transmission calls for immediate measures aimed at ensuring safe medical practices.
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Villar LM, Cruz HM, Barbosa JR, Bezerra CS, Portilho MM, Scalioni LDP. Update on hepatitis B and C virus diagnosis. World J Virol 2015; 4:323-42. [PMID: 26568915 PMCID: PMC4641225 DOI: 10.5501/wjv.v4.i4.323] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/25/2015] [Accepted: 10/23/2015] [Indexed: 02/05/2023] Open
Abstract
Viral hepatitis B and C virus (HBV and HCV) are responsible for the most of chronic liver disease worldwide and are transmitted by parenteral route, sexual and vertical transmission. One important measure to reduce the burden of these infections is the diagnosis of acute and chronic cases of HBV and HCV. In order to provide an effective diagnosis and monitoring of antiviral treatment, it is important to choose sensitive, rapid, inexpensive, and robust analytical methods. Primary diagnosis of HBV and HCV infection is made by using serological tests for detecting antigens and antibodies against these viruses. In order to confirm primary diagnosis, to quantify viral load, to determine genotypes and resistance mutants for antiviral treatment, qualitative and quantitative molecular tests are used. In this manuscript, we review the current serological and molecular methods for the diagnosis of hepatitis B and C.
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Raza H, Ahmad T, Afzal MS. HCV, Interferon Therapy Response, Direct Acting Antiviral Therapy Revolution and Pakistan: Future Perspectives. Asian Pac J Cancer Prev 2015. [DOI: 10.7314/apjcp.2015.16.13.5583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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