title: Molecular characterization of Hepatitis C virus 3a in Peshawar.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.|Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Islamabad, Pakistan.
authors.forename: Amina
authors.initials: A
authors.lastname: Gul
authors.affiliation: IBGE, The University of Agriculture Peshawar, Peshawar, Pakistan.
authors.forename: Nabeela
authors.initials: N
authors.lastname: Zahid
authors.affiliation: Institute of Basic Medical Sciences, Khyber Medical University Peshawar, Peshawar, Pakistan.
authors.forename: Jawad
authors.initials: J
authors.lastname: Ahmed
authors.affiliation: IBGE, The University of Agriculture Peshawar, Peshawar, Pakistan.
authors.forename: Fazli
authors.initials: F
authors.lastname: Zahir
authors.affiliation: Department of Entomology, The University of Agriculture Peshawar, Peshawar, Pakistan.
authors.forename: Imtiaz Ali
authors.initials: IA
authors.lastname: Khan
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Islamabad, Pakistan. ijaz.ali@fulbrightmail.org.
authors.forename: Ijaz
authors.initials: I
authors.lastname: Ali
mesh_terms: D000328:Adult; D003430:Cross-Sectional Studies; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000175:diagnosis / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D008297:Male; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D015995:Prevalence; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins
keywords: HCV 3a; Hepatitis C; Pakistan; Peshawar KP