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Occurrence of genetic modifications in core, 5'UTR and NS5b of HCV associated with viral response to treatment.

Kanwal S, Mahmood T - Virol. J. (2014)

Bottom Line: At nucleotide and amino acid level, the genetic distance and mutation, number of predicted N-phosphorylation and N-glycosylation sites was higher in group 2 as compared to group 1.It can be concluded that heterogeneity both at nucleotide and amino acid level contributed in developing drug resistant phenotype.Furthermore, prediction of phosphorylation and glycosylation sites could help in targeting the proper sites for drug designing.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. tmahmood.qau@gmail.com.

ABSTRACT

Background: It is becoming progressively more understandable that genetic variability of viruses is a major challenge in translating the laboratory findings to clinic. Genetic variability is the underlying cause of variant viral proteins which are not targetable by host immunological machinery.

Methods: 500 patients were enrolled in study and amongst them, 451 patients were followed and categorized into two groups on the basis of their treatment response. Group 1 consisting of the 376 patients exhibited SVR while group 2 comprised 75 patients who were non-responders on the basis of viral load as evidenced by Real-Time PCR. Comparative sequence analysis was done between 75 non-responders and 75 responders (randomly picked from 376) by targeting three genomic regions, 5'UTR, core and NS5B and amplified products were directly sequenced and obtained sequences were cleaned, aligned and submitted to GenBank. Maximum Parsimony (MP) method was used for phylogenetic analysis and dendrograms were dragged using MEGA 5. Heterogeneity at nucleotide and amino acid level was determined using software BioEdit and DNAman while phosphorylation and N-linked glycosylation sites were determined using NetPhos 2.0 and SignalP-NN.

Results: Genotype 3 was prevalent in group 1 whereas non-responders indicated rare genotypes of Pakistan i.e. 4 and 5, genotype 6q and 6v were reported first time from Pakistan in this study. At nucleotide and amino acid level, the genetic distance and mutation, number of predicted N-phosphorylation and N-glycosylation sites was higher in group 2 as compared to group 1. Difference in percentage composition of individual amino acids was noted to be different between the two groups.

Conclusions: It can be concluded that heterogeneity both at nucleotide and amino acid level contributed in developing drug resistant phenotype. Moreover, occurrence of rare genotypes might hurdle the way to positive response of conventional treatment. Furthermore, prediction of phosphorylation and glycosylation sites could help in targeting the proper sites for drug designing.

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Related in: MedlinePlus

Potential N-glycosylation sites in core protein sequence predicted from SignalP-NN: (A) group I (with SVR); (B) group 2 (non-responders).
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Fig12: Potential N-glycosylation sites in core protein sequence predicted from SignalP-NN: (A) group I (with SVR); (B) group 2 (non-responders).

Mentions: Increase in N-linked glycosylation sites was observed in core and NS5b protein sequences in patients who did not respond to the therapy (group 2) as compared to those who showed SVR (group 1) (FigureĀ 12 and 13).Figure 12


Occurrence of genetic modifications in core, 5'UTR and NS5b of HCV associated with viral response to treatment.

Kanwal S, Mahmood T - Virol. J. (2014)

Potential N-glycosylation sites in core protein sequence predicted from SignalP-NN: (A) group I (with SVR); (B) group 2 (non-responders).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289283&req=5

Fig12: Potential N-glycosylation sites in core protein sequence predicted from SignalP-NN: (A) group I (with SVR); (B) group 2 (non-responders).
Mentions: Increase in N-linked glycosylation sites was observed in core and NS5b protein sequences in patients who did not respond to the therapy (group 2) as compared to those who showed SVR (group 1) (FigureĀ 12 and 13).Figure 12

Bottom Line: At nucleotide and amino acid level, the genetic distance and mutation, number of predicted N-phosphorylation and N-glycosylation sites was higher in group 2 as compared to group 1.It can be concluded that heterogeneity both at nucleotide and amino acid level contributed in developing drug resistant phenotype.Furthermore, prediction of phosphorylation and glycosylation sites could help in targeting the proper sites for drug designing.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan. tmahmood.qau@gmail.com.

ABSTRACT

Background: It is becoming progressively more understandable that genetic variability of viruses is a major challenge in translating the laboratory findings to clinic. Genetic variability is the underlying cause of variant viral proteins which are not targetable by host immunological machinery.

Methods: 500 patients were enrolled in study and amongst them, 451 patients were followed and categorized into two groups on the basis of their treatment response. Group 1 consisting of the 376 patients exhibited SVR while group 2 comprised 75 patients who were non-responders on the basis of viral load as evidenced by Real-Time PCR. Comparative sequence analysis was done between 75 non-responders and 75 responders (randomly picked from 376) by targeting three genomic regions, 5'UTR, core and NS5B and amplified products were directly sequenced and obtained sequences were cleaned, aligned and submitted to GenBank. Maximum Parsimony (MP) method was used for phylogenetic analysis and dendrograms were dragged using MEGA 5. Heterogeneity at nucleotide and amino acid level was determined using software BioEdit and DNAman while phosphorylation and N-linked glycosylation sites were determined using NetPhos 2.0 and SignalP-NN.

Results: Genotype 3 was prevalent in group 1 whereas non-responders indicated rare genotypes of Pakistan i.e. 4 and 5, genotype 6q and 6v were reported first time from Pakistan in this study. At nucleotide and amino acid level, the genetic distance and mutation, number of predicted N-phosphorylation and N-glycosylation sites was higher in group 2 as compared to group 1. Difference in percentage composition of individual amino acids was noted to be different between the two groups.

Conclusions: It can be concluded that heterogeneity both at nucleotide and amino acid level contributed in developing drug resistant phenotype. Moreover, occurrence of rare genotypes might hurdle the way to positive response of conventional treatment. Furthermore, prediction of phosphorylation and glycosylation sites could help in targeting the proper sites for drug designing.

Show MeSH
Related in: MedlinePlus