TY - JOUR
T1 - Genetic variations in a well conserved 5′-untranslated region of hepatitis C virus genome isolated in Pakistan
AU - Yasmeen, Anila
AU - Siddiqui, Anwar Ali
AU - Hamid, Saeed
AU - Sultana, Taranum
AU - Jafri, Wasim
AU - Persson, Mats A.A.
N1 - Funding Information:
We acknowledge the valuable support of Dr. Thomas Leitner in terms of suggestions, guidance to A.Y. and critical reading of the manuscript. We would like to thank Dr. Kulsoom Ghias for critical reading of the manuscript. This work was supported by the University Research Council, AKU and Swedish Institute fellowship awarded to A.Y.
PY - 2009/9
Y1 - 2009/9
N2 - 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.
AB - 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.
KW - Genotype 3
KW - Hepatitis C virus
KW - Neighbour-joining tree
KW - Pakistan
KW - Phylogenetic analysis
UR - http://www.scopus.com/inward/record.url?scp=67649249799&partnerID=8YFLogxK
U2 - 10.1016/j.jviromet.2009.04.007
DO - 10.1016/j.jviromet.2009.04.007
M3 - Article
C2 - 19406160
AN - SCOPUS:67649249799
SN - 0166-0934
VL - 160
SP - 38
EP - 47
JO - Journal of Virological Methods
JF - Journal of Virological Methods
IS - 1-2
ER -
