Cover Image

Identification of hepatitis C virus genotypes and subtypes in patients from Maharashtra based on 5’UTR sequencing and analysis: a retrospective study

Ushanandini Mohanraj*, Yashwant G. Chavan, Sharad R. Pawar


The clinical importance of HCV genotypes lies in its persistence and ability to cause chronic liver disease. Knowledge of HCV genotype distribution periodically is now essential for the clinical management of infected patients. The current study was designed to genotype and subtype HCV isolates in patients from Pune, Mumbai and Nashik districts of Maharashtra, determine association of HCV genotypes between both sexes and different age groups and perform phylogenetic analysis of the study isolates. Eighty HCV RNA positive patients were genotyped and subtyped in the study.  Primers targeting 5’untranslated region (UTR) were designed for both amplification and sequencing of all isolates. All HCV isolates were characterized by direct sequencing of 5’ UTR followed by analysis with NCBI genotyping tool and in-silico BLAST analysis. The results were correlated with the Los Alamos Hepatitis C sequence and immunology database’s sequence alignment tool HCVAlign and phylogenetic analysis. Most of HCV isolates in this study belonged to genotype 3(56.25%) followed by genotype 1(35%) and genotype 4(7.5%). A rare genotype 5(1.25%) was identified in one of the patients. Prevalent subtypes were: subtype 3a (42.5%), subtype 1a (21.25%) and subtype 1b (13.75%). No notable association of age and gender with respect to genotypes was observed except for genotype 1a which showed an overrepresentation in males. Compared with phylogenetic analysis, NCBI genotyping tool was simpler for genotyping and subtyping HCV isolates. The present study revealed that HCV genotypes 3 and 1 were prevalent in Pune, Mumbai and Nashik districts of Maharashtra. With rare genotype (genotype 5) being identified and due to very few genotyping studies carried out in this region, this study aims at contributing towards monitoring the distribution of HCV genotypes among studied regions of Maharashtra.  


HCV genotypes; 5’UTR; primers; sequencing; phylogenetic analysis; age; gender; Maharashtra

Full Text:



Messina, Jane P., Isla Humphreys, Abraham Flaxman, Anthony Brown, Graham S. Cooke, Oliver G. Pybus, and Eleanor Barnes. "Global distribution and prevalence of hepatitis C virus genotypes." Hepatology 61.1 (2015): 77-87.

Kar, Premashis. "Risk factors for hepatocellular carcinoma in India." Journal of clinical and experimental hepatology 4 (2014): S34-S42.

Lindenbach, Brett D., and Charles M. Rice. "Unravelling hepatitis C virus replication from genome to function." Nature 436.7053 (2005): 933-938.

Foy, Eileen, Kui Li, Chunfu Wang, Rhea Sumpter, Masanori Ikeda, Stanley M. Lemon, and Michael Gale. "Regulation of interferon regulatory factor-3 by the hepatitis C virus serine protease." Science 300.5622 (2003): 1145-1148.

Drazan, K. "Molecular biology of hepatitis C infection." Liver Transplantation 6. 4 (2000): 396-406.

Smith, Donald B., Jens Bukh, Carla Kuiken, A. Scott Muerhoff, Charles M. Rice, Jack T. Stapleton, and Peter Simmonds. "Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource." Hepatology 59.1 (2014): 318-327.

Davis, Gary L. "Hepatitis C virus genotypes and quasispecies." The American journal of medicine 107.6 (1999): 21-26.

El-Serag, Hashem B. "Epidemiology of viral hepatitis and hepatocellular carcinoma." Gastroenterology 142.6 (2012): 1264-1273.

McOmish, F., P. L. Yap, B. C. Dow, E. A. Follett, C. Seed, A. J. Keller, T. J. Cobain, T. Krusius, E. Kolho, and R. Naukkarinen. "Geographical distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey." Journal of Clinical Microbiology 32.4 (1994): 884-892.

Al Naamani, Khalid, Siham Al Sinani, and Marc Deschênes. "Epidemiology and treatment of hepatitis C genotypes 5 and 6." Canadian Journal of Gastroenterology 27.1 (2013): 8.

Aziz, Hafsa, Abida Raza, Shahnaz Murtaza, Yasir Waheed, Ali Khalid, Javaid Irfan, Zahoor Samra, and Muhammad Amin Athar. "Molecular epidemiology of hepatitis C virus genotypes in different geographical regions of Punjab Province in Pakistan and a phylogenetic analysis." International Journal of Infectious Diseases 17.4 (2013): 247-253.

Petruzziello, Arnolfo, Nicola Coppola, Anna Maria Diodato, Vincenzo Iervolino, Rosa Azzaro, Gaetano Di Costanzo, Catia Addolorata Di Macchia et al. "Age and gender distribution of hepatitis C virus genotypes in the metropolitan area of Naples." Intervirology 56. 3 (2013): 206-212.

Zein, Nizar N. "Clinical significance of hepatitis C virus genotypes." Clinical microbiology reviews 13.2 (2000): 223-235.

Arens, Max. "Methods for subtyping and molecular comparison of human viral genomes." Clinical microbiology reviews 12.4 (1999): 612-626.

Weck, Karen. "Molecular methods of hepatitis C genotyping." Expert Review of Molecular Diagnostics 5.4 (2005): 507-520.

Ohno, Tomoyoshi, and J. Y. Lau. "The “gold‐standard,” accuracy, and the current concepts: Hepatitis C virus genotype and viremia." Hepatology 24.5 (1996): 1312-1315.

Halfon, P., P. Trimoulet, M. Bourliere, H. Khiri, V. De Ledinghen, P. Couzigou, J. M. Feryn et al. "Hepatitis C virus genotyping based on 5′ noncoding sequence analysis (Trugene)." Journal of clinical microbiology 39. 5 (2001): 1771-1773.

Rozanov, Mikhail, Uwe Plikat, Colombe Chappey, Andrey Kochergin, and Tatiana Tatusova. "A web-based genotyping resource for viral sequences."Nucleic acids research 32. 2 (2004): 654-659.

Kuiken, Carla, Peter Hraber, James Thurmond, and Karina Yusim. "The hepatitis C sequence database in Los Alamos." Nucleic acids research 36. 1 (2008): 512-516.

Tamura, Koichiro, Glen Stecher, Daniel Peterson, Alan Filipski, and Sudhir Kumar. "MEGA6: molecular evolutionary genetics analysis version 6.0."Molecular biology and evolution 30.12 (2013): 2725-2729.

Sneath, Peter HA, and Robert R. Sokal. "Numerical taxonomy." Nature 193.4818 (1962): 855-860.

Nei, Masatoshi, and Sudhir Kumar. Molecular evolution and phylogenetics. Oxford University Press, 2000.

Cai, Qingxian, Zhixin Zhao, Ying Liu, Xiaoqiong Shao, and Zhiliang Gao. "Comparison of three different HCV genotyping methods: core, NS5B sequence analysis and line probe assay." International journal of molecular medicine 31.2 (2013): 347-352.

Chakravarti, Anita, Gaurav Dogra, Vikas Verma, and Amit Parkash Srivastava. "Distribution pattern of HCV genotypes & its association with viral load." The Indian journal of medical research 133.3 (2011): 326.

Hissar, Syed S., Ankur Goyal, Manoj Kumar, Chandana Pandey, P. V. Suneetha, Ajit Sood, Vandana Midha, Puja Sakhuja, Veena Malhotra, and Shiv K. Sarin. "Hepatitis C virus genotype 3 predominates in North and Central India and is associated with significant histopathologic liver disease." Journal of medical virology 78.4 (2006): 452-458.

Narahari, Shobha, Abida Juwle, Subhankar Basak, and Dhananjaya Saranath. "Prevalence and geographic distribution of Hepatitis C Virus genotypes in Indian patient cohort." Infection, Genetics and Evolution 9.4 (2009): 643-645.

Choudhary, Manish Chandra, Vidhya Natarajan, Priyanka Pandey, Ekta Gupta, Shvetank Sharma, Rachana Tripathi, M. Shesheer Kumar, Syed N. Kazim, and Shiv K. Sarin. "Identification of Indian sub-continent as hotspot for HCV genotype 3a origin by Bayesian evolutionary reconstruction." Infection, Genetics and Evolution 28 (2014): 87-94.

Raghuraman, Sukanya, Priya Abraham, Gopalan Sridharan, Hubert Darius Daniel, B. S. Ramakrishna, and R. V. Shaji. "HCV genotype 4—an emerging threat as a cause of chronic liver disease in Indian (south) patients." Journal of clinical virology 31.4 (2004): 253-258.

Ramia, S., and J. Eid-Fares. "Distribution of hepatitis C virus genotypes in the Middle East." International Journal of Infectious Diseases 10.4 (2006): 272-277.

Valliammai, T., S. P. Thyagarajan, Arie J. Zuckerman, and Tim J. Harrison. "Diversity of genotypes of hepatitis C virus in southern India." Journal of general virology 76. 3 (1995): 711-716.

Raghuraman, Sukanya, and Priya Abraham. "HCV genotyping in India--quo vadis?." The Indian journal of medical research 119. 4 (2004): ix.

Birks, J. S., Ian J. Seccombe, and C. A. Sinclair. "Labour Migration in the Arab Gulf States: Patterns, Trends and Prospects*." International Migration 26. 3 (1988): 267-286.

Gededzha, Maemu P., Selokela G. Selabe, Jason T. Blackard, Thanda Kyaw, and M. Jeffrey Mphahlele. "Near full-length genome analysis of HCV genotype 5 strains from South Africa." Infection, Genetics and Evolution 21 (2014): 118-123.

Das, B. R., Biduth Kundu, Rashmi Khandapkar, and Sumedha Sahni. "Geographical distribution of hepatitis C virus genotypes in India." Indian journal of pathology & microbiology 45.3 (2002): 323-328.

Christdas, J., J. Sivakumar, J. David, H. Daniel, S. Raghuraman, and P. Abraham. "Genotypes of hepatitis C virus in the Indian sub-continent: A decade-long experience from a tertiary care hospital in South India." Indian journal of medical microbiology 31.4 (2013): 349.

Cantaloube, Jean-François, Pierre Gallian, Houssam Attoui, Philippe Biagini, Philippe De Micco, and Xavier de Lamballerie. "Genotype distribution and molecular epidemiology of hepatitis C virus in blood donors from southeast France." Journal of clinical microbiology 43.8 (2005): 3624-3629.

Khan, Nasar, Muhammad Akmal, Muhammad Hayat, Muhammad Umar, Atta Ullah, Iqbal Ahmed, Kashif Rahim, Sadar Ali, Sulaiman Bahadar, and Shamim Saleha. "Geographic distribution of hepatitis C virus genotypes in pakistan."Hepatitis monthly 14.10 (2014).

Altuglu, Imre, Ilknur Soyler, Tijen Ozacar, and Selda Erensoy. "Distribution of hepatitis C virus genotypes in patients with chronic hepatitis C infection in Western Turkey." International Journal of Infectious Diseases 12. 3 (2008): 239-244.

Hraber, Peter T., William Fischer, William J. Bruno, Thomas Leitner, and Carla Kuiken. "Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5'untranslated region (UTR) fails to classify subtypes."Virology Journal 3.1 (2006): 103.



  • There are currently no refbacks.

Copyright (c) 2015 International Journal of Bioassays

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

International Journal of Bioassays is a member of the Publishers International Linking Association, Inc. (PILA), CROSSREF and CROSSMARK (USA). Digital Object Identifier (DOI) will be assigned to all its published content.