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Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment
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. METH...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289283/ https://www.ncbi.nlm.nih.gov/pubmed/25270660 http://dx.doi.org/10.1186/1743-422X-11-171 |
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author | Kanwal, Sobia Mahmood, Tariq |
author_facet | Kanwal, Sobia Mahmood, Tariq |
author_sort | Kanwal, Sobia |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4289283 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42892832015-01-11 Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment Kanwal, Sobia Mahmood, Tariq Virol J Research 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. BioMed Central 2014-09-30 /pmc/articles/PMC4289283/ /pubmed/25270660 http://dx.doi.org/10.1186/1743-422X-11-171 Text en © Kanwal and Mahmood; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Kanwal, Sobia Mahmood, Tariq Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment |
title | Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment |
title_full | Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment |
title_fullStr | Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment |
title_full_unstemmed | Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment |
title_short | Occurrence of genetic modifications in core, 5′UTR and NS5b of HCV associated with viral response to treatment |
title_sort | occurrence of genetic modifications in core, 5′utr and ns5b of hcv associated with viral response to treatment |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289283/ https://www.ncbi.nlm.nih.gov/pubmed/25270660 http://dx.doi.org/10.1186/1743-422X-11-171 |
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