title: Recombination in hepatitis C virus is not uncommon among people who inject drugs in Kolkata, India.
abstract: Recombination in RNA virus is a rare event in the survival and evolution to evade host immune system. This is increasing within high risk group population (HRG) due to super infection that occurs by continuous sharing of common drug equipment by HCV infected or HIV-HCV co-infected recurrent drug users. Recombination causes impediment to vaccine development and therapeutic intervention as standard HCV treatment is still genotype specific. Blood samples of 194 people who inject drugs (PWID) were collected from an Opioid Substitution Therapy Centre in Kolkata, India. HCV sero-reactivity was checked by ELISA. Detection of HCV RNA by nested RT-PCR and genotyping by DNA sequencing were done. Phylogenetic analysis, Simplot, Bootscan plot, Recombination Detection Program were used for recombinant strain identification. Out of 80 HCV sero-reactive samples, 77 were RNA positive (96.25%). Out of 74 HIV mono-infected individuals, 12 HCV sero-nonreactive samples were HCV RNA positive. Out of total 89 RNA positive samples, 64 paired partial core and NS5B region (71.9%) were sequenced by Sanger's method. Two major genotypes (1 and 3), four subtypes and an inter-genotype recombinant strain (3a/1a) with a novel breakpoint in the NS4B coding region were found.
authors.affiliation: ICMR Virus Unit, 57, Dr. Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, West Bengal, India.
authors.forename: Debanjali
authors.initials: D
authors.lastname: Gupta
authors.affiliation: ICMR Virus Unit, 57, Dr. Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, West Bengal, India.
authors.forename: Kallol
authors.initials: K
authors.lastname: Saha
authors.affiliation: ICMR Virus Unit, 57, Dr. Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, West Bengal, India.
authors.forename: Aritra
authors.initials: A
authors.lastname: Biswas
authors.affiliation: ICMR Virus Unit, 57, Dr. Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, West Bengal, India.
authors.forename: Rushna
authors.initials: R
authors.lastname: Firdaus
authors.affiliation: ICMR Virus Unit, 57, Dr. Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, West Bengal, India.
authors.forename: Monika
authors.initials: M
authors.lastname: Ghosh
authors.affiliation: ICMR Virus Unit, 57, Dr. Suresh Chandra Banerjee Road, Beliaghata, Kolkata 700010, West Bengal, India. Electronic address: provash2000@gmail.com.
authors.forename: Provash Chandra
authors.initials: PC
authors.lastname: Sadhukhan
mesh_terms: D000328:Adult; D060085:Coinfection / Q000821:virology*; D055030:Drug Users; D019143:Evolution, Molecular; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D007194:India / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D015819:Substance Abuse, Intravenous / Q000453:epidemiology / Q000821:virology*; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D017361:Viral Nonstructural Proteins
keywords: Genotype; HIV infection; Hepatitis C virus; High risk group population; People who inject drugs; Phylogenetic analysis; RNA virus; Recombination