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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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Ullah A, Yu X, Odenthal M, Meemboor S, Ahmad B, Rehman IU, Ahmad J, Ali Q, Nadeem T. Circulating microRNA-122 in HCV cirrhotic patients with high frequency of genotype 3. PLoS One 2022; 17:e0268526. [PMID: 35617369 PMCID: PMC9135289 DOI: 10.1371/journal.pone.0268526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 05/02/2022] [Indexed: 11/18/2022] Open
Abstract
MicroRNA-122 (miR-122) is a liver abundant microRNA that is released upon liver injury. In the present study, we investigated the circulating miR-122 profiles in a Pakistani patients´ cohort with HCV chronic liver disease that was mainly based on HCV genotype 3 infections. From 222 patients with chronic HCV liver disease, classified as mild, moderate, or severe, serum samples were collected. Cell-free RNA was isolated and used for miR-122 quantification by qPCR. More than 60% of 222 patients were infected with HCV genotype 3. ALT values and HCV viral load showed no correlation with the HCV genotype. Circulating miR-122 levels were significantly upregulated in patients with cirrhosis. Notably, HCV patients with mild cirrhosis showed the most marked increase in serum miR-122 levels (p = 0.0001). Furthermore, we proved a positive correlation (r = 0.46) of miR-122 with the ALT values in patients with mild cirrhosis. Importantly, our data of increased miR-122 levels in serum samples obtained from a patient cohort with a high prevalence of chronic genotype 3 HCV infection confirmed the previous findings collected from cohorts with a high prevalence of genotype 1. Therefore, we suggest that miR-122 increase after HCV infection does not depend on the HCV genotype. In conclusion, our findings confirm that serum miR-122 levels are significantly upregulated in the HCV cirrhotic patients serving in particular as a biomarker for the non-advanced stages of cirrhosis, independently of the HCV genotype.
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Affiliation(s)
- Amin Ullah
- Centre of Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Pakistan
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Xiaojie Yu
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Margarete Odenthal
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
- * E-mail: (MO); (QA)
| | - Sonja Meemboor
- Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Bashir Ahmad
- Centre of Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Pakistan
| | - Irshad ur Rehman
- Centre of Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Pakistan
| | - Jamshaid Ahmad
- Centre of Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Pakistan
| | - Qurban Ali
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
- Department of Plant Breeding and Genetics, Faculty of Agriculture, University of the Punjab, Lahore, Pakistan
- * E-mail: (MO); (QA)
| | - Tariq Nadeem
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Khan A, Nadir A, Mushtaq MH, Junaid K, Khan AM, Ali H, Waqar F, Khan TA, Khan AA. Molecular epidemiology and genotype distribution of hepatitis C in Pakistan; a multicenter cross-sectional study. INFECTION GENETICS AND EVOLUTION 2020; 84:104372. [PMID: 32454246 DOI: 10.1016/j.meegid.2020.104372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/13/2020] [Accepted: 05/19/2020] [Indexed: 11/30/2022]
Abstract
Pakistan has second highest burden of hepatitis C virus (HCV) infected patients in the World. Little is known about the molecular epidemiology and risk factors for prevailing HCV genotypes in Pakistan. Considering this a multicenter cross-sectional study was conducted at 23different viral hepatitis control and prevention centers. A total of 175,897 patients were registered and screened for HCV, out of which 73,180 (41.6%) were found positive on Architect screening test. The screened positive patients were sequentially tested on RT-PCR; where 41,241 (56.35%) were detected positive. Molecular characterization results showed genotype 3 (73.9%) as the most prevalent type, followed by genotype 1 (9.7%), and genotype 4 (0.3%) was isolated for the first time in Pakistan. On regression analysis; risk factors associated with genotype 3 and 1 included; age group of 30-50 years, rural residence, exposure to >10 injections, barber shaving, circumcision by barbers, and low literacy rate. Phylogenetic analysis based on genotypes identified in this study and sequences isolated from Pakistan in last 10 years demonstrated that genotype 3 and 1 are endemic locally in Punjab province. The high prevalence rate of HCV is a threat for a generalized epidemic and genetic recombination with such variability of genotypes identified here is an alarming condition. More focused attention and resources should be spent in awareness of the population to prevent the spread of HCV among high risk population.
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Affiliation(s)
- Amjad Khan
- Department of Community Medicine, King Edward Medical University, Lahore 75500, Pakistan.
| | - Abdul Nadir
- Pakistan Kidney and liver institute and research center, Lahore, Pakistan
| | | | - Khunsa Junaid
- Department of Public Health, Institute of Social and Cultural Studies, University of Punjab, Lahore 75500, Pakistan
| | - Aabish Mehreen Khan
- Department of Community Medicine, King Edward Medical University, Lahore 75500, Pakistan
| | - Hassan Ali
- Department of Public Health, Institute of Social and Cultural Studies, University of Punjab, Lahore 75500, Pakistan
| | - Fatmee Waqar
- Department of Community Medicine, King Edward Medical University, Lahore 75500, Pakistan
| | - Taimoor Akram Khan
- Department of Community Medicine, King Edward Medical University, Lahore 75500, Pakistan
| | - Ali Akram Khan
- Department of Community Medicine, King Edward Medical University, Lahore 75500, Pakistan
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Ullah A, Rehman IU, Ahmad J, Gohar M, Ahmad S, Ahmad B. Hepatitis-C Virus and Cirrhosis: An Overview from Khyber Pakhtunkhwa Province of Pakistan. Viral Immunol 2020; 33:396-403. [PMID: 32109202 DOI: 10.1089/vim.2019.0176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Hepatitis C virus (HCV) leads to liver cirrhosis and carcinoma worldwide. The data of HCV cirrhotic patients were collected from hospitals of Peshawar in the period from 2015 to 2018. A total sample of 267 patients, in the age limit (>19 and <87 years) were found to be cirrhotic and HCV positive. The samples were analyzed through different tests, that is, raised alkaline phosphatase (410 IU/L), aspartate aminotransferase (209 U/L), and reverse transcription-polymerase chain reaction (PCR) viral load (>5,000,000 IU/mL). The mean and standard deviation (SD) of alanine transaminase and alpha fetoprotein were noted, (121.46 ± 29.23) and (43.09 ± 28.08), respectively. Samples of HCV cirrhotic patients (59.6% males and 40.4% females) were included and their mean age and SD of the patients was 49.62 ± 12.65 years. The Child-Turcotte-Pugh Score system was assessed on the base of liver disease. High blood pressure was observed in 26.2%, low in 40.8%, and normal in 33% of patients. The ascites was recorded high in 59% patients (male 38.6%, female 20.6%) and the level of albumin was abnormal in 64.5% patients. Furthermore, multiplex PCR was run to determine HCV genotypes. The frequency of HCV genotype 3a was 47.9%, 2a and 3b was 11%, 1a was 6%, and 1b was 1%; 4.1% were mixed genotypes and 18.7% were untypable genotypes in these patients. The HCV genotype 3a was found a major prevalent genotype in Khyber Pakhtunkhwa patients and it was observed that the HCV cirrhosis issue was significantly increased in the province.
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Affiliation(s)
- Amin Ullah
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Irshad Ur Rehman
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Jamshaid Ahmad
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Maryam Gohar
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Saeed Ahmad
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Bashir Ahmad
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
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Haqqi A, Munir R, Khalid M, Khurram M, Zaid M, Ali M, Shah ZH, Ahmed H, Afzal MS. Prevalence of Hepatitis C Virus Genotypes in Pakistan: Current Scenario and Review of Literature. Viral Immunol 2019; 32:402-413. [PMID: 31556811 DOI: 10.1089/vim.2019.0058] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a major public health concern globally, resulting in liver-related complications. Approximately 6% population of Pakistan is infected with HCV. HCV is error prone, due to which it is classified into 7 genotypes and 67 subtypes. HCV genotype determination is critical for treatment and therapy response. In this study, 3,539 samples were collected from 2015 to 2019 from all over Punjab. RNA was extracted from samples using QIA Amp Viral RNA MINI kit (Qiagen, Germany) and viral genotyping was performed. Furthermore, a systemized literature search (2009-2018) was done to analyze the HCV genotype distribution pattern in Pakistan. In Punjab, genotype 3a (86.46%) is most prevalent, followed by untypable (7.17%) and genotype 1a (3.84%) and 3b (1.04%). Mixed genotype constitutes only 0.67% of total infections. Genotype 2a, 2b, 3c, and 4 were found to be rare. Data available from literature review when compiled showed that HCV genotype 3a (58.16%) was predominant in Pakistan, followed by genotypes 3b (9.05%), 2a (6.70%), 1a (6.22%), and 1b (2.39%). The frequency of mixed genotypes was found to be 4% and 12% of untypable HCV variants. This study highlights the HCV genotype distribution pattern in different regions of Pakistan. Therapy response and disease management depend on genotype, so HCV genotype determination is crucial. In Pakistan, the most prevalent genotype is 3a, followed by untypable genotype. Both interferon and sofosbuvir are effective against genotype 3a, but treatment with sofosbuvir has comparatively high sustained virological response, less adverse effects, and more tolerability.
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Affiliation(s)
- Aleena Haqqi
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Rimsha Munir
- Cancer Biology Lab, MMG, University of the Punjab, Lahore, Pakistan.,Hormone Lab, Lahore, Pakistan
| | | | - Muhammad Khurram
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Muhammad Zaid
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Muhammad Ali
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Zaheer Hussain Shah
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Haroon Ahmed
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad Sohail Afzal
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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6
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National prevalence rate of hepatitis B and C in Pakistan and its risk factors. J Public Health (Oxf) 2019. [DOI: 10.1007/s10389-019-01081-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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7
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Real Time PCR Based Detection of Hepatitis C Virus Major Genotypes in Chronic HCV Patients in Khyber Pakhtunkhwa. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.80931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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8
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Molecular characterization and clinical epidemiology of HCV in District Dir (Lower), Pakistan. Virusdisease 2018; 29:369-374. [PMID: 30159373 DOI: 10.1007/s13337-018-0457-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022] Open
Abstract
With about 200 million infections globally, Hepatitis C virus (HCV) infection is a major global health threat. The relative prevalence of hepatitis and HCV genotypes/subtypes varies among different geographic regions. Therefore, the present study was conducted to determine the prevalence of hepatitis C and HCV genotypes/subtypes in District Dir (Lower), Pakistan. Blood samples from HCV positive patients were genotyped through multiplex PCR using specific primers for HCV core region. A structured questionnaire was used to obtain information from the patients and data was statistically analyzed for different epidemiological parameters. The molecular evaluation results suggested the prevalence of genotype 3 in this study. The frequency of hepatitis C was found higher in males (P < 0.01). Present study suggests injections received at local clinics as a highly significant mode of HCV transmission to these patients (P < 0.002). These findings might be helpful for clinicians and related health care personnel to assess status of this important disease and highlight the need for more detailed evaluation of this devastating disease in order to frame better treatment strategies.
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Maryam M, Idrees M. Study of promoter hypomethylation profiles ofRASoncogenes in hepatocellular carcinoma derived from hepatitis C virus genotype 3a in Pakistani population. J Med Virol 2018; 90:1516-1523. [DOI: 10.1002/jmv.25221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Maryam
- National Centre of Excellence in Molecular Biology; University of the Punjab; Lahore Pakistan
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology; University of the Punjab; Lahore Pakistan
- Vice Chancellor Office, Hazara University; Mansehra Pakistan
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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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Rising relapse rate in hepatitis C virus type 3a-infected patients against sofosbuvir and ribavirin combination therapy: a Pakistani experience. Eur J Gastroenterol Hepatol 2017; 29:979-980. [PMID: 28471832 DOI: 10.1097/meg.0000000000000895] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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The p7 viroporin of the hepatitis C virus contributes to liver inflammation by stimulating production of Interleukin-1β. Biochim Biophys Acta Mol Basis Dis 2017; 1863:712-720. [DOI: 10.1016/j.bbadis.2016.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022]
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Kumar T, Ahmad N, Hayat MK, Gao BX, Faisal S, Ilahi N, Ali B, Zada S, Sajjad W. Prevalence and Genotypic Distribution of Hepatitis C Virus in Peshawar KPK, Pakistan. HAYATI JOURNAL OF BIOSCIENCES 2017. [DOI: 10.1016/j.hjb.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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14
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Prevalence of HCV Infection in General Population of District Malakand, Pakistan: A Comparative Analysis of the Diagnostic Techniques. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2337-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Prevalence of Blood-Borne Viruses in Health Care Workers of a Northern District in Pakistan: Risk Factors and Preventive Behaviors. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2016; 2016:2393942. [PMID: 27525015 PMCID: PMC4976191 DOI: 10.1155/2016/2393942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/20/2016] [Accepted: 06/19/2016] [Indexed: 11/20/2022]
Abstract
Background. Blood-borne viral infections like viral hepatitis are highly prevalent in Pakistan. There is also a potential threat of human immunodeficiency virus (HIV) spread in the country. Health care workers (HCWs) are a high risk population for acquiring such viral infections and potential spread to the patients. This study aimed to determine the frequency of three blood-borne viruses: HCV, HBV, and HIV in HCWs of district Malakand in northern Khyber Pakhtunkhwa (KPK) province of Pakistan. Moreover, risk factors and preventive behaviors among HCWs were investigated in detail. Materials and Methods. Prevalence was investigated using serological assays followed by real time polymerase chain reaction (RT-PCR) based characterization. A total of 626 health care workers working at 17 different health care units, belonging to 6 different job categories, were included in this study. Results. HIV was not detected in the HCWs while rate of prevalence of HCV and HBV was far less (0.8 % and 0.64 %, resp.) as compared to general population (4.7%–38%). The majority of HCWs were aware of the mode of spread of these viruses and associated risk factors. Needle stick injury was found to be the most important risk factor for possible acquisition of these infections.
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Sadeghi F, Salehi-Vaziri M, Almasi-Hashiani A, Gholami-Fesharaki M, Pakzad R, Alavian SM. Prevalence of Hepatitis C Virus Genotypes Among Patients in Countries of the Eastern Mediterranean Regional Office of WHO (EMRO): A Systematic Review and Meta-Analysis. HEPATITIS MONTHLY 2016; 16:e35558. [PMID: 27274353 PMCID: PMC4894080 DOI: 10.5812/hepatmon.35558] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 12/11/2022]
Abstract
CONTEXT Hepatitis C virus (HCV) infection is a major global public health issue. The Eastern Mediterranean regional office (EMRO) of the world health organization (WHO) seems to have one of the highest prevalence rates worldwide, with at least 21.3 million HCV-infected patients. OBJECTIVES The aim of the present study was to review systematically all epidemiological data related to the prevalence of HCV genotypes in infected patients in EMRO countries. DATA SOURCES A systematic search was conducted of peer-reviewed journals indexed in electronic databases (PubMed, Scopus, ISI, PakMediNet, and IMEMR, and Persian-specific databases including SID, Iran Medex, and MagIran). STUDY SELECTION A systematic search was performed with temporal limits (papers published between January 2000 up to June 2015), regarding the prevalence and distribution of HCV genotypes in EMRO countries. DATA EXTRACTION The prevalence rates of HCV genotypes were pooled by metan command in Stata 14. Statistical heterogeneity was explored using the I-square at the 5% significance level. Publication bias was assessed, graphically and statistically, by funnel plot and Begg and Egger tests. RESULTS A total of 563 records were identified through the electronic search. Of these records, 134 studies comprising 67681 HCV-infected individuals were included in the meta-analysis. In Iran, subtype 1a was the predominant subtype with a rate of 42% (95% CI, 39 - 46), followed by subtype 3a, 35% (95% CI, 31 - 38). In Pakistan, Subtype 3a was the most common subtype with a rate of 56% (95% CI, 49 - 62), followed by subtype 3b, 10% (95% CI, 7 - 12). In Saudi Arabia and Egypt, genotype 4 was the most prevalent genotype with a rate of 65% (95% CI, 59 - 72) and 69% (95% CI, 36 - 100) respectively. In Tunisia and Morocco, subtype 1b was the most common subtype with a rate of 69% (95% CI, 50 - 88) and 32% (95% CI, 7 - 56) respectively. CONCLUSIONS The genotype distribution of HCV takes diverse patterns in EMRO countries. Genotypes 1 and 3 were predominant in Iran and Pakistan, while genotype 4 and 1 were the most common genotypes in the Middle East Arab countries and North African Arab countries. Understanding the genotypes of HCV can help policy makers in designing good strategies for treatment.
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Affiliation(s)
- Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, IR Iran
| | - Mostafa Salehi-Vaziri
- Department of Arboviruses and Viral Hemorrhagic Fevers, Institute Pasteur of Iran, Tehran, IR Iran
| | - Amir Almasi-Hashiani
- Medical Ethics and Law Research Center, Shahid Beheshti University of Medical Sciences, Tehran, IR Iran
| | | | - Reza Pakzad
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Seyed Moayed Alavian, Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran, E-mail:
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17
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Gul A, Zahid N, Ahmed J, Zahir F, Khan IA, Ali I. Molecular characterization of Hepatitis C virus 3a in Peshawar. BMC Infect Dis 2016; 16:163. [PMID: 27090517 PMCID: PMC4836082 DOI: 10.1186/s12879-016-1488-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/29/2016] [Indexed: 01/17/2023] Open
Abstract
Background The purpose of this study was to explore molecular epidemiology of HCV genotype 3a in Peshawar based on sequencing and phylogenetic analysis of Core region of HCV genome. Methods Chronically infected Hepatitis C virus infected patients enrolled under the Prime Minister Hepatitis C control program at three Tertiary care units of Peshawar [Khyber Teaching Hospital Peshawar, Lady Reading Hospital Peshawar, Hayat Abad Medical Complex Peshawar] were included in this cross sectional observational study. Qualitative detection of HCV and HCV genotyping was carried out by a modified reverse transcription-polymerase chain reaction (RT-PCR) and type specific genotyping assay. The Core gene of HCV genotype 3a was amplified, cloned and sequenced. The sequences obtained were used for phylogenetic analysis using MEGA 6 software. Results Among the 422 (82.75 %) PCR positive samples, 192 (45.5 %) were identified as having HCV genotype 3a infection. HCV Core gene sequencing was carried out randomly for the characterization of HCV 3a. Nucleotide sequence analysis of the obtained viral genomic sequences based on partial HCV 3a Core gene sequences with reference sequences from different countries showed that our sequences clustered with some local and regional sequences with high bootstrap values. Conclusion HCV 3a is highly prevalent in Peshawar, Pakistan and its phylogenetics based on Core gene sequences indicate the prevalence of different lineages of HCV 3a in Peshawar which may have consequences for disease management strategies causing more economic pressure on the impoverished population due to possible antiviral resistance.
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Affiliation(s)
- Amina Gul
- Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.,Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Islamabad, Pakistan
| | - Nabeela Zahid
- IBGE, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Jawad Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan
| | - Fazli Zahir
- IBGE, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Imtiaz Ali Khan
- Department of Entomology, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Ijaz Ali
- Department of Biosciences, COMSATS Institute of Information Technology Islamabad, 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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New patterns of HCV subtypes distribution in the Khyber Pakhtunkhwa province of Pakistan. Braz J Infect Dis 2016; 20:107-8. [PMID: 26626168 PMCID: PMC9425417 DOI: 10.1016/j.bjid.2015.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 09/27/2015] [Accepted: 09/29/2015] [Indexed: 12/04/2022] Open
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Kramer M, Halleran D, Rahman M, Iqbal M, Anwar MI, Sabet S, Ackad E, Yousef M. Comparative molecular dynamics simulation of Hepatitis C Virus NS3/4A protease (Genotypes 1b, 3a and 4b) predicts conformational instability of the catalytic triad in drug resistant strains. PLoS One 2014; 9:e104425. [PMID: 25111232 PMCID: PMC4128671 DOI: 10.1371/journal.pone.0104425] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/08/2014] [Indexed: 02/06/2023] Open
Abstract
The protease domain of the Hepatitis C Virus (HCV) nonstructural protein 3 (NS3) has been targeted for inhibition by several direct-acting antiviral drugs. This approach has had marked success to treat infections caused by HCV genotype 1 predominant in the USA, Europe, and Japan. However, genotypes 3 and 4, dominant in developing countries, are resistant to a number of these drugs and little progress has been made towards understanding the structural basis of their drug resistivity. We have previously developed a 4D computational methodology, based on 3D structure modeling and molecular dynamics simulation, to analyze the active sites of the NS3 proteases of HCV-1b and 4a in relation to their catalytic activity and drug susceptibility. Here, we improved the methodology, extended the analysis to include genotype 3a (predominant in South Asia including Pakistan), and compared the results of the three genotypes (1b, 3a and 4a). The 4D analyses of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) indicate conformational instability of the catalytic site in HCV-3a and 4a compared to that of HCV-1b NS3 protease. The divergence is gradual and genotype-dependent, with HCV-1b being the most stable, HCV-4a being the most unstable and HCV-3a representing an intermediate state. These results suggest that the structural dynamics behavior, more than the rigid structure, could be related to the altered catalytic activity and drug susceptibility seen in NS3 proteases of HCV-3a and 4a.
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Affiliation(s)
- Mitchell Kramer
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
| | - Daniel Halleran
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
| | - Moazur Rahman
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Mazhar Iqbal
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Ikram Anwar
- Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Salwa Sabet
- Department of Zoology, Faculty of Science, Cairo University, Giza, Egypt
| | - Edward Ackad
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
| | - Mohammad Yousef
- Department of Physics, College of Arts and Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois, United States of America
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- * E-mail:
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Prevalence of hepatitis C virus genotypes in district bannu, khyber pakhtunkhwa, pakistan. HEPATITIS RESEARCH AND TREATMENT 2014; 2014:165826. [PMID: 25093120 PMCID: PMC4100271 DOI: 10.1155/2014/165826] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 06/09/2014] [Indexed: 12/17/2022]
Abstract
Determination of an individual's hepatitis C virus (HCV) genotypes prior to antiviral therapy has become increasingly important for the clinical management and prognosis of HCV infection. Therefore, this study was conducted to investigate the prevalence of HCV genotypes in HCV infected patients of district Bannu in Khyber Pakhtunkhwa region of Pakistan. Serum samples of 117 seropositive patients were screened for HCV-RNA by using reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) and then PCR positive samples were subjected to HCV genotyping. Out of 117 seropositive samples, 110 samples were found positive by PCR analysis. Genotype 3a was the most prevalent one detected in 38% of patients, followed by genotype 3b in 21% of patients, and then genotype 2a in 12% of patients. However 21% of HCV-PCR positive samples could not be genotyped by method used in this study. Genotype 3a was the most prevalent genotype in patients of all age groups and its prevalence was found high among patients with increasing age (>34 years). Moreover, genotypes 3a and 3b were found to be the most prevalent genotypes in patients with history of shaving by barbers, receiving multiple injections, and dental procedures. In conclusion there is need of further investigation of genotypes of HCV by using more sensitive assays and considering large sample size in district Bannu.
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Ali M, Rehman IU, Idrees M. Emergence of genetically variant Hepatitis C virus population in response to increased antiviral drug pressure, Pakistan. Virus Genes 2014; 48:543-9. [PMID: 24532035 DOI: 10.1007/s11262-014-1047-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/30/2014] [Indexed: 01/06/2023]
Abstract
Mutations in NS5B gene of Hepatitis C virus (HCV) have been reported in patients undergoing antiviral therapy. In the present study, we report emerging clade of HCV-3a in patients administered with IFN plus ribavirin therapy for 24 weeks and having low viral loads (<250 IU/mL). Mutations D/N244E, K304R, N/K307G, Q/T329V, and A338V were found associated with these emerging strains. This distinct HCV could be associated with the increased antiviral drug pressure.
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Affiliation(s)
- Muhammad Ali
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal bank Road, Thokar Niaz baig, Lahore, 53700, Pakistan,
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Determination of hepatitis C virus genotypes circulating in different districts of Punjab (Pakistan). Eur J Gastroenterol Hepatol 2014; 26:59-64. [PMID: 23743560 DOI: 10.1097/meg.0b013e328362dc3f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Hepatitis C virus (HCV) is a principal cause of severe liver diseases worldwide and a possible source of significant morbidity and fatality in the long term. Information on the genotype is more significant because it has prognostic value in the response to antiviral therapy. OBJECTIVES This study aimed to determine the frequency of various HCV genotypes circulating in the different districts of Punjab and to show the pattern distribution of HCV genotypes in different age groups and sexes. MATERIALS AND METHODS A total of 542 HCV-positive patients were selected from various districts of the province and were subjected to an HCV genotype-specific assay. Among 542 positive patients, 300 (55.35%) were men and 242 (44.65%) were women. There were 245 (45.20%), 61 (11.25%), 56 (10.33%), 56 (10.33%), 53 (9.77%), 27 (5%), 20 (3.69%), 16 (3%), and eight (1.47%) HCV-positive patients from Lahore, Sargodha, Multan, Toba Tek Singh, Faisalabad, Rawalpindi, Mandi Bahauddin Gujranwala, and Sahiwal districts, respectively. RESULTS Of a total of 542 serum samples analyzed, 476 (88%) were successfully genotyped whereas 66 (12%) samples were undetermined genotypes. Among the typable genotypes, 1a was found in 37 (7%), 1b in 18 (3%), 3a in 386 (71%), and genotype 3b in five (1%) patients. Thirty patients (6%) were identified to be infected with mixed HCV genotypes. Genotypes 3a (P=0.0001), 1a (P=0.001), and untypable genotypes (P=0.03) were circulating significantly in all the studied districts. All the genotypes were distributed evenly in male and female patients. The most affected age range of patients was 21-40 years as compared with teenage and older age groups. CONCLUSION The study found a significantly high prevalence of HCV among the patients of Punjab. In addition, genotype 1a was found to be a significantly and rapidly increasing genotype in the study area. It appears that HCV-3a (the most prevalent genotype) may be replaced by genotype 1a. If this occurs, it will make the present scenario more complex in terms of response to therapy and economic burden on the health sector of Pakistan. HCV infection is more common in the age group of 21-40 years. All the genotypes were distributed at the same frequency in men and women.
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Rimmert B, Sabet S, Ackad E, Yousef MS. A 3D structural model and dynamics of hepatitis C virus NS3/4A protease (genotype 4a, strain ED43) suggest conformational instability of the catalytic triad: implications in catalysis and drug resistivity. J Biomol Struct Dyn 2013; 32:950-8. [PMID: 23768174 PMCID: PMC3956140 DOI: 10.1080/07391102.2013.800001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Egypt has the highest prevalence of hepatitis C virus (HCV) infection worldwide with a frequency of 15%. More than 90% of these infections are due to genotype 4, and the subtype 4a (HCV-4a) predominates. Moreover, due to the increased mobility of people, HCV-4a has recently spread to several European countries. The protease domain of the HCV nonstructural protein 3 (NS3) has been targeted for inhibition by several drugs. This approach has had marked success in inhibiting genotype 1 (HCV-1), the predominant genotype in the USA, Europe, and Japan. However, HCV-4a was found to resist inhibition by a number of these drugs, and little progress has been made to understand the structural basis of its drug resistivity. As a step forward, we sequenced the NS3 HCV-4a protease gene (strain ED43) and subsequently built a 3D structural model threaded through a template crystal structure of HCV-1b NS3 protease. The model protease, HCV-4a, shares 83% sequence identity with the template protease, HCV-1b, and has nearly identical rigid structural features. Molecular dynamics simulations predict similar overall dynamics of the two proteases. However, local dynamics and 4D analysis of the interactions between the catalytic triad residues (His57, Asp81, and Ser139) indicate conformational instability of the catalytic site in HCV-4a NS3 protease. These results suggest that the divergent dynamics behavior, more than the rigid structure, could be related to the altered catalytic activity and drug resistivity seen in HCV-4a.
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Affiliation(s)
- Bradley Rimmert
- a Department of Physics , College of Arts and Sciences, Southern Illinois University Edwardsville , Edwardsville , IL , 62026-1654 , USA
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Afridi SQ, Zahid MN, Shabbir MZ, Hussain Z, Mukhtar N, Tipu MY, Akhtar F, Yaqub T. Prevalence of HCV genotypes in district Mardan. Virol J 2013; 10:90. [PMID: 23514695 PMCID: PMC3616848 DOI: 10.1186/1743-422x-10-90] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 03/18/2013] [Indexed: 12/12/2022] Open
Abstract
Background Approximately 170 million people are infected with Hepatitis C virus (HCV) worldwide. The prevalence of chronic HCV infections in Pakistan is about 5%, with most individuals being infected with HCV genotype 3a. Data on HCV genotypes distribution across various districts of the country are scarce. One example is district Mardan from where such data is available only from 17 individuals. Accordingly, the present study aimed at determining HCV genotypes distribution among 177 HCV RNA positive individuals from district Mardan. Findings Serum samples (n = 215) from patients suspected of hepatitis C were collected and processed for Nested PCR based detection and subsequent genotyping. Gender-wise and age-wise differences in HCV prevalence and HCV genotypes distribution were determined by χ2 test. Out of the total 215 serum samples, 177 were found to be positive for HCV RNA. The genotype 3a was the most predominant genotype among HCV RNA positive samples with a prevalence of 90.3%, followed by genotype 1a (5.6%), mixed genotypes (2.8%), genotype 3b (0.6%) and genotype 4 (0.6%). The HCV prevalence was higher in young individuals than old people and was indicative of reduced survival rate beyond 40 years. Conclusion HCV genotype 3a is the most predominant genotype in district Mardan. The state of the art preventive and therapeutic strategies should be implemented to control the spread of HCV infections. Further temporal studies involving different geographical areas of Pakistan, are required to improve the control measures for HCV infection.
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Ali A, Nisar M, Ahmad H, Saif N, Idrees M, Bajwa MA. Determination of HCV genotypes and viral loads in chronic HCV infected patients of Hazara Pakistan. Virol J 2011; 8:466. [PMID: 21982599 PMCID: PMC3198714 DOI: 10.1186/1743-422x-8-466] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 10/09/2011] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C Virus (HCV) genotype and viral load are two significant predictive variables knowledge of which might persuade treatment decisions. The objective of the present study was to identify the distribution of different HCV genotypes circulating in the study area and to estimate viral load in chronically HCV infected patients. Out of total 305 HCV positive patients, 177 (58%) were males and 128 (42%) were females. Frequency breakup of the HCV positive patients was 169, 69, 38 and 29 from Abbottabad, Mansehra, Haripur and Battagram districts respectively. Out of the total 305 tested serum samples, 255 (83.06%) were successfully genotyped whereas 50 (16.4%) samples were found with unclassified genotypes. Among typable genotypes, 1a accounted for 21 (6.8%) 1b for 14 (4.6%), 2a for 4 (1.31%) 3a for 166 (54.42%) and genotype 3b for (8.19%). Twenty five (8.19%) patients were infected with mixed HCV genotypes. Viral load distribution was classified into three categories based on its viral load levels such as low (< 60, 0000 IU/mL), intermediate (60,0000-80,0000 IU/mL) and high (> 80,0000 IU/mL). The baseline HCV RNA Viral load in HCV genotype 3 infected patients was 50 (26.17%), 46 (24.08%) and 95 (49.73%) for low, intermediate and high categories respectively. For genotypes other than 3, these values for low, intermediate and high viral load categories were 50 (43.85), 35 (30.70) and 29 (25.43) respectively. Pre-treatment viral load in patients with untypable genotype was 19 (38.00%), 5 (20.00%) and 11 (44.00%) for low, intermediate and high viral load categories. Viral load distribution was also categorized sex wise; for males it was 58 (32.76%), 26 (14.68%) and 93 (52.54%) whereas for females it was 40 (31.25%), 34 (26.56%) and 54 (42.18%) for low, intermediate and high viral load respectively. In conclusion HCV genotype 3a is the most prevalent genotype circulating in Hazara Division like other parts of pakistan. Pre-treatment viral load is significantly high (p 0.014) in patients infected with HCV genotype 3 as compared to other genotypes.
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Affiliation(s)
- Amjad Ali
- 1Department of Biotechnology University of Malakand, Chakdara, Khyber Pakhtoonkhaw, Pakistan
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Attaullah S, Khan S, Ali I. Hepatitis C virus genotypes in Pakistan: a systemic review. Virol J 2011; 8:433. [PMID: 21902822 PMCID: PMC3178528 DOI: 10.1186/1743-422x-8-433] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 09/08/2011] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND AND AIM Phylogenetic analysis has led to the classification of hepatitis C virus (HCV) into 1-6 major genotypes. HCV genotypes have different biological properties, clinical outcome and response to antiviral treatment and provide important clues for studying the epidemiology, transmission and pathogenesis. This article deepens the current molecular information about the geographical distribution of HCV genotypes and subgenotypes in population of four provinces of Pakistan. 34 published papers (1996-2011) related to prevalence of HCV genotypes/serotypes and subgenotypes in Pakistan were searched. RESULT HCV genotype/s distribution from all 34 studies was observed in 28,400 HCV infected individuals in the following pattern: 1,999 (7.03%) cases of genotype 1; 1,085 (3.81%) cases of genotype 2; 22,429 (78.96%) cases of genotype 3; 453 (1.59%) cases of genotype 4; 29 (0.10%) cases of genotype 5; 37 (0.13%) cases of genotype 6; 1,429 (5.03%) cases of mixed genotypes, and 939 (3.30%) cases of untypeable genotypes. Overall, genotype 3a was the predominant genotype with a rate of 55.10%, followed by genotype 1a, 3b and mixed genotype with a rate of 10.25%, 8.20%, and 5.08%, respectively; and genotypes 4, 5 and 6 were rare. Genotype 3 occurred predominately in all the provinces of Pakistan. Second more frequently genotype was genotype 1 in Punjab province and untypeable genotypes in Sindh, Khyber Pakhtunkhwa and Balochistan provinces.
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Affiliation(s)
- Sobia Attaullah
- Department of Zoology, Islamia College (Public Sector University) Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sanaullah Khan
- Kohat University of Science and Technology, Kohat Khyber Pakhtunkhwa, Pakistan
| | - Ijaz Ali
- Institution of Biotechnology and Genetic Engineering, KPK Agricultural University Peshawar, Pakistan
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Yousaf MZ, Idrees M, Saleem Z, Rehman IU, Ali M. Expression of core antigen of HCV genotype 3a and its evaluation as screening agent for HCV infection in Pakistan. Virol J 2011; 8:364. [PMID: 21787436 PMCID: PMC3152539 DOI: 10.1186/1743-422x-8-364] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 07/26/2011] [Indexed: 11/16/2022] Open
Abstract
Background Pakistan is facing a threat from hepatitis C infection which is increasing at an alarming rate throughout the country. More specific and sensitive screening assays are needed to timely and correctly diagnose this infection. Methods After RNA extraction from specimen (HCV-3a), cDNA was synthesized that was used to amplify full length core gene of HCV 3a. After verification through PCR, DNA sequencing and BLAST, a properly oriented positive recombinant plasmid for core gene was digested with proper restriction enzymes to release the target gene which was then inserted downstream of GST encoding DNA in the same open reading frame at proper restriction sites in multiple cloning site of pGEX4t2 expression vector. Recombinant expression vector for each gene was transformed in E. coli BL21 (DE3) and induced with IPTG for recombinant fusion protein production that was then purified through affinity chromatography. Western blot and Enzyme Linked Immunosorbant Assay (ELISA) were used to detect immuno-reactivity of the recombinant protein. Results The HCV core antigen produced in prokaryotic expression system was reactive and used to develop a screening assay. After validating the positivity (100%) and negativity (100%) of in-house anti-HCV screening assay through a standardized panel of 200 HCV positive and 200 HCV negative sera, a group of 120 serum specimens of suspected HCV infection were subjected to comparative analysis of our method with commercially available assay. The comparison confirmed that our method is more specific than the commercially available assays for HCV strains circulating in this specific geographical region of the world and could thus be used for HCV screening in Pakistan. Conclusion In this study, we devised a screening assay after successful PCR amplification, isolation, sequencing, expression and purification of core antigen of HCV genotype 3a. Our developed screening assay is more sensitive, specific and reproducible than the commercially available screening assays in Pakistan.
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Affiliation(s)
- Muhammad Z Yousaf
- Division of Molecular Virology & Molecular Diagnostics, National Centre of Excellence in Molecular Biology, University of the Punjab, Pakistan.
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Swellam M, Mahmoud MS, Ali AAF. Diagnosis of hepatitis C virus infection by enzyme-linked immunosorbent assay and reverse transcriptase-nested polymerase chain reaction: A comparative evaluation. IUBMB Life 2011; 63:430-434. [DOI: 10.1002/iub.469] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Shehzadi A, Ur Rehman S, Idrees M. Promiscuous prediction and conservancy analysis of CTL binding epitopes of HCV 3a viral proteome from Punjab Pakistan: an in silico approach. Virol J 2011; 8:55. [PMID: 21303499 PMCID: PMC3042956 DOI: 10.1186/1743-422x-8-55] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 02/08/2011] [Indexed: 12/17/2022] Open
Abstract
Background HCV is a positive sense RNA virus affecting approximately 180 million people world wide and about 10 million Pakistani populations. HCV genotype 3a is the major cause of infection in Pakistani population. One of the major problems of HCV infection especially in the developing countries that limits the limits the antiviral therapy is the long term treatment, high dosage and side effects. Studies of antigenic epitopes of viral sequences of a specific origin can provide an effective way to overcome the mutation rate and to determine the promiscuous binders to be used for epitope based subunit vaccine design. An in silico approach was applied for the analysis of entire HCV proteome of Pakistani origin, aimed to identify the viral epitopes and their conservancy in HCV genotypes 1, 2 and 3 of diverse origin. Results Immunoinformatic tools were applied for the predictive analysis of HCV 3a antigenic epitopes of Pakistani origin. All the predicted epitopes were then subjected for their conservancy analysis in HCV genotypes 1, 2 and 3 of diverse origin (worldwide). Using freely available web servers, 150 MHC II epitopes were predicted as promiscuous binders against 51 subjected alleles. E2 protein represented the 20% of all the predicted MHC II epitopes. 75.33% of the predicted MHC II epitopes were (77-100%) conserve in genotype 3; 47.33% and 40.66% in genotype 1 and 2 respectively. 69 MHC I epitopes were predicted as promiscuous binders against 47 subjected alleles. NS4b represented 26% of all the MHC I predicted epitopes. Significantly higher epitope conservancy was represented by genotype 3 i.e. 78.26% and 21.05% for genotype 1 and 2. Conclusions The study revealed comprehensive catalogue of potential HCV derived CTL epitopes from viral proteome of Pakistan origin. A considerable number of predicted epitopes were found to be conserved in different HCV genotype. However, the number of conserved epitopes in HCV genotype 3 was significantly higher in contrast to its conservancy in HCV genotype 1 and 2. Despite of the lower conservancy in genotype 1 and 2, all the predicted epitopes have important implications in diagnostics as well as CTL-based rational vaccine design, effective for most population of the world and especially the Pakistani Population.
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Affiliation(s)
- Abida Shehzadi
- Bioinformatics Division, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
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Detection of hepatitis C virus and antibodies in postmortem blood and bloodstains. J Clin Microbiol 2011; 49:1122-3. [PMID: 21248094 DOI: 10.1128/jcm.01887-10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To evaluate the risk of accidental hepatitis C virus (HCV) infection, we examined whether anti-HCV antibodies and HCV RNA were detectable in HCV-infected blood samples from living donors, cadavers, and bloodstains. We showed that even after blood has left the body for several days, anti-HCV antibodies and HCV RNA may persist in it.
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Inamullah, Idrees M, Ahmed H, Sajid-ul-Ghafoor, Ali M, Ali L, Ahmed A. Hepatitis C virus genotypes circulating in district Swat of Khyber Pakhtoonkhaw, Pakistan. Virol J 2011; 8:16. [PMID: 21235746 PMCID: PMC3027131 DOI: 10.1186/1743-422x-8-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 01/14/2011] [Indexed: 12/15/2022] Open
Abstract
Hepatitis C virus (HCV) is the leading cause of chronic hepatitis worldwide and its subtypes/genotypes are clinically important for clinical management and vaccine development. The present study describes frequency distribution of different HCV genotypes and their treatment status in HCV RNA positive patients from district Swat. A total of 185 HCV infected sera were analyzed by molecular genotyping assay. The most prevalent genotype was 3a (34.1%), followed by 2a (8.1%), 3b (7%) and 1a (5.4%). The samples found untypable by the present method of genotypes was 37.8% while, patients with mixed genotype infections were 7.6%. More than 80% of untypable cases were from those HCV patients who had received interferon plus ribavirin standard therapy in the past and either were non-responders and were relapsed thereafter or were under treatment. In conclusion, genotype 3a is the most prevalent HCV genotype in the region. A high prevalence rate of untypable genotypes is present in treated patients that need further investigation for the successful genotyping by developing new assays or using viral sequencing method.
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Affiliation(s)
- Inamullah
- Department of Genetics, Hazara University Mansehra, Pakistan
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Division of Molecular Virology, National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Habib Ahmed
- Department of Genetics, Hazara University Mansehra, Pakistan
| | | | - Muhammad Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Liaqat Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aziz Ahmed
- Department of Medicine, Saidu Teaching Hospital, Saidu Sharif, Swat, Pakistan
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Ali A, Ahmad H, Ali I, Khan S, Zaidi G, Idrees M. Prevalence of active hepatitis c virus infection in district Mansehra Pakistan. Virol J 2010; 7:334. [PMID: 21092143 PMCID: PMC2996369 DOI: 10.1186/1743-422x-7-334] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/22/2010] [Indexed: 12/17/2022] Open
Abstract
Prevalence of active hepatitis C virus (HCV) infection in apparently healthy inhabitants of District Mansehra, Pakistan was surveyed during September, 2009 to May, 2010. Subjects of different age and gender groups were analyzed through random blood sampling from people of three areas viz; Tehsil Mansehra, Tehsil Balakot and Tehsil Oghi. Sum of 400 individuals, 300 male and 100 females with age groups from 10 years to 50 and above were included in the study. All the individuals were screened for antibodies against HCV. The positive samples thus screened, were subjected to polymerase chain reaction (PCR) analysis for detection of HCV-RNA. The results showed that 3.5% of the people of District Mansehra are actively infected with HCV whereas 7% of the population in general, has the presence of antibodies against HCV in their blood. It was also concluded that the prevalence of active HCV infection was high 4% in males as compared to females (2%). The prevalence of HCV proportionality increases with the increase in age of the people. Its incidence was highest (7.69%) in the people of the age group of 51 years and above, whereas no sign of infection was recorded for the age group of 10-20 years.
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Affiliation(s)
- Amjad Ali
- Department of Genetics, Hazara University Mansehra, Pakistan
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