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Genetic variations in a well conserved 5-untranslated region of hepatitis C virus genome isolated in Pakistan
Journal of Virological Methods
  • Anila Yasmeen, Aga Khan University
  • Anwar Ali Siddiqui, Aga Khan University
  • Saeed Hamidb, Aga Khan University
  • Taranum Sultana, Aga Khan University
  • Wasim Jafri, Aga Khan University
  • Mats A.A. Perssonc, Karolinska Institutet,
Publication Date
Document Type
The diversity and extent of sequence variations between hepatitis C virus (HCV) isolates from Pakistan were studied and the probable effects of these variations were assessed on secondary viral structures. Sequencing and phylogenetic analysis was performed on 33 samples, of which 25 were typed as genotype 3 by RFLP (restriction fragment length polymorphism) and 8 remained unresolved. Rooted neighbour-joining (NJ) tree revealed that 28 isolates were HCV type 3a and 5 isolates were typed as 3b. The majority of unresolved samples clustered in a different branch of genotype 3, supported by a bootstrap value of 71%. Another, cluster, cluster I, was found to have a bootstrap value of 81%. Genetic distance values showed significant diversity of isolates in these two clusters compared to the reference sequences. Pair-wise comparison showed the presence of additional restriction sites of HaeIII and RsaI in unresolved isolates. In conclusion, unique sequence variability was observed in the 5′-UTR of HCV type 3 isolates from Pakistan. One of the reasons for this sequence variability is the presence of mutations, which are additional restriction sites in the 5′-UTR. These mutations were also responsible for failure of conventional RFLP to type some of the HCV isolates.
Citation Information
Anila Yasmeen, Anwar Ali Siddiqui, Saeed Hamidb, Taranum Sultana, et al.. "Genetic variations in a well conserved 5-untranslated region of hepatitis C virus genome isolated in Pakistan" Journal of Virological Methods Vol. 160 Iss. 1-2 (2009) p. 38 - 47
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