title: Phylogenetic analysis of Torque Teno Virus genome from Pakistani isolate and incidence of co-infection among HBV/HCV infected patients.
abstract: BACKGROUND
  Torque Teno Virus (TTV) was the first single stranded circular DNA virus to be discovered that infects humans. Although there have been numerous reports regarding the prevalence of TTV from other countries of South Asia, there is severe lack of information regarding its prevalence in Pakistan. Thus the present study compiles the first indigenous report to comprehensively illustrate the incidence of the virus in uninfected and hepatitis infected population from Pakistan. Another aim of the study was to present the sequence of full length TTV genome from a local isolate and compare it with the already reported genome sequences from other parts of the world.
  
  
  METHODS
  TTV DNA was screened in the serum of 116, 100 and 40 HBV infected, HCV infected and uninfected individuals respectively. Nearly full length genome of TTV was cloned from a HBV patient. The genome sequence was subjected to in-silico analysis using CLC Workbench, ClustalW, ClustalX and TreeView. Statistical analysis was carried out in SPSS v17.0.
  
  
  RESULTS
  Our results report that 89.7%, 90.0% and 92.5% of HBV, HCV patients and healthy control population were positive for TTV infection. TTV genome of 3603 bp was also cloned from a local isolate and given the identity of TPK01. The TTV genome sequence mentioned in this paper is submitted in the GenBank/EMBL/DDBJ under the accession number JN980171. Phylogenetic analysis of TPK01 revealed that the Pakistani isolate has sequence similarities with genotype 23 and 22 (Genogroup 2).
  
  
  CONCLUSIONS
  The results of the current study indicate that the high frequency of TTV viremia in Pakistan conforms to the reports from other areas of the world, wherever screening of TTV DNA was performed against 5'-UTR of the genome. The high sequence diversity among TTV genome sequences and the high frequency of prevalence makes it harder to study this virus in cellular systems.
authors.affiliation: Atta-ur-Rehman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44000, Pakistan.
authors.forename: Tabinda
authors.initials: T
authors.lastname: Hussain
authors.forename: Sobia
authors.initials: S
authors.lastname: Manzoor
authors.forename: Yasir
authors.initials: Y
authors.lastname: Waheed
authors.forename: Huma
authors.initials: H
authors.lastname: Tariq
authors.forename: Khushbakht
authors.initials: K
authors.lastname: Hanif
mesh_terms: D000328:Adult; D000368:Aged; D060085:Coinfection / Q000821:virology*; D004266:DNA Virus Infections / Q000821:virology*; D005260:Female; D016679:Genome, Viral; D016174:Hepacivirus / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D006509:Hepatitis B / Q000821:virology*; D006515:Hepatitis B virus / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010154:Pakistan; D010802:Phylogeny; D022783:Torque teno virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D055815:Young Adult