Sequence and genome analysis of hepatitis C virus

Studying the molecular features of hepatitis C virus (HCV) throws light on its epidemiology and behavior. In this study, HCV infecting a high risk group patient were characterized. The prevalence of the various genotypes and subtypes were determined and the full-length genome of the most prevalent g...

Full description

Bibliographic Details
Main Author:	Hamzah, Hairul Aini
Format:	Book
Language:	English
Published:	IIUM Press, International Islamic University Malaysia 2017
Subjects:	QR Microbiology QR355 Virology
Online Access:	http://irep.iium.edu.my/63742/ http://irep.iium.edu.my/63742/1/63742_Sequence%20and%20%20genome%20analysis%20of.pdf

id	iium-63742
recordtype	eprints
spelling	iium-637422019-10-14T06:58:43Z http://irep.iium.edu.my/63742/ Sequence and genome analysis of hepatitis C virus Hamzah, Hairul Aini QR Microbiology QR355 Virology Studying the molecular features of hepatitis C virus (HCV) throws light on its epidemiology and behavior. In this study, HCV infecting a high risk group patient were characterized. The prevalence of the various genotypes and subtypes were determined and the full-length genome of the most prevalent genotype was elucidated. Viral RNA was extracted from sera of 40 HD patients. The molecular technique of reverse-transcription polymerase chain reaction (RT-PCR) was used to detect and amplify segments of the viral genomic RNA at the 5’untranslated region (UTR) and the nonstructural 5B region (NS5B). The base sequences of the amplicons were determined and later employed in phylogenetic analysis for genotype assignment of the isolates. The sequence pattern (SP) and the conformational features of domain III 5’UTR were also evaluated. The overall prevalence of HCV viremia in HD centres was 8.3 %, including one acute infection that occured during the course of study. For 33 of the 40 viremic patients, the HCV 5’UTR and NS5B base sequences were successfully determined. Five patients (15.2 %) were shown to be infected by more than one genotype. In the remaining 28 patients, genotypes 3, 1, 4, and 6 occurred in 19 (67.9 %), seven (25.0 %), one (3.6 %), and one (3.6 %) of them respectively. Four sequence patterns (SPs) were determined in domain III 5’UTR of genotype 3, a finding unique to this genotype. Overall, the secondary structure of the domain was not affected by nucleotide changes in the SP region. The complete base sequence of two genomes of the predominant subtype 3a isolates (MAL 22 & MAL 43) were elucidated and found to be consisting of 9430 and 9429 nucleotides. Genotype 3a HCV genome contained a long open reading frame capable of encoding a sequence of 3010 amino acid residues. In the phylogenetic analysis, both isolates clustered with known HCV-3a isolates (NZL1, K3a & CB), while it diverged from other genotypes by 47.1 - 41.8 %. Three hypervariable regions of the isolates were also revealed and described. The predominance of genotypes 3 and 1 was not unique to HD centres in Pahang as it was reported in normal population in Malaysia. Both the complete viral nucleotide sequence and the amino acid sequence of the coding region of the HCV genome provided the foundation data for future HCV studies in Malaysia including studies on epidemiology, novel diagnostic approaches and antiviral therapies. Despite the known high risk of chronic hepatitis C infection in HD patients, these infections, whether overt or occult and of single or mixed genotypes, were usually clinically silent. Thus, investigational viral nucleic acid based tests on HCV patients was recommended to be done periodically to monitor for the occurrence of these asymptomatic and sometimes even sero-negative infections. IIUM Press, International Islamic University Malaysia 2017 Book PeerReviewed application/pdf en http://irep.iium.edu.my/63742/1/63742_Sequence%20and%20%20genome%20analysis%20of.pdf Hamzah, Hairul Aini (2017) Sequence and genome analysis of hepatitis C virus. IIUM Press, International Islamic University Malaysia, Kuala Lumpur, Malaysia. ISBN 978-967-418-716-3
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	QR Microbiology QR355 Virology
spellingShingle	QR Microbiology QR355 Virology Hamzah, Hairul Aini Sequence and genome analysis of hepatitis C virus
description	Studying the molecular features of hepatitis C virus (HCV) throws light on its epidemiology and behavior. In this study, HCV infecting a high risk group patient were characterized. The prevalence of the various genotypes and subtypes were determined and the full-length genome of the most prevalent genotype was elucidated. Viral RNA was extracted from sera of 40 HD patients. The molecular technique of reverse-transcription polymerase chain reaction (RT-PCR) was used to detect and amplify segments of the viral genomic RNA at the 5’untranslated region (UTR) and the nonstructural 5B region (NS5B). The base sequences of the amplicons were determined and later employed in phylogenetic analysis for genotype assignment of the isolates. The sequence pattern (SP) and the conformational features of domain III 5’UTR were also evaluated. The overall prevalence of HCV viremia in HD centres was 8.3 %, including one acute infection that occured during the course of study. For 33 of the 40 viremic patients, the HCV 5’UTR and NS5B base sequences were successfully determined. Five patients (15.2 %) were shown to be infected by more than one genotype. In the remaining 28 patients, genotypes 3, 1, 4, and 6 occurred in 19 (67.9 %), seven (25.0 %), one (3.6 %), and one (3.6 %) of them respectively. Four sequence patterns (SPs) were determined in domain III 5’UTR of genotype 3, a finding unique to this genotype. Overall, the secondary structure of the domain was not affected by nucleotide changes in the SP region. The complete base sequence of two genomes of the predominant subtype 3a isolates (MAL 22 & MAL 43) were elucidated and found to be consisting of 9430 and 9429 nucleotides. Genotype 3a HCV genome contained a long open reading frame capable of encoding a sequence of 3010 amino acid residues. In the phylogenetic analysis, both isolates clustered with known HCV-3a isolates (NZL1, K3a & CB), while it diverged from other genotypes by 47.1 - 41.8 %. Three hypervariable regions of the isolates were also revealed and described. The predominance of genotypes 3 and 1 was not unique to HD centres in Pahang as it was reported in normal population in Malaysia. Both the complete viral nucleotide sequence and the amino acid sequence of the coding region of the HCV genome provided the foundation data for future HCV studies in Malaysia including studies on epidemiology, novel diagnostic approaches and antiviral therapies. Despite the known high risk of chronic hepatitis C infection in HD patients, these infections, whether overt or occult and of single or mixed genotypes, were usually clinically silent. Thus, investigational viral nucleic acid based tests on HCV patients was recommended to be done periodically to monitor for the occurrence of these asymptomatic and sometimes even sero-negative infections.
format	Book
author	Hamzah, Hairul Aini
author_facet	Hamzah, Hairul Aini
author_sort	Hamzah, Hairul Aini
title	Sequence and genome analysis of hepatitis C virus
title_short	Sequence and genome analysis of hepatitis C virus
title_full	Sequence and genome analysis of hepatitis C virus
title_fullStr	Sequence and genome analysis of hepatitis C virus
title_full_unstemmed	Sequence and genome analysis of hepatitis C virus
title_sort	sequence and genome analysis of hepatitis c virus
publisher	IIUM Press, International Islamic University Malaysia
publishDate	2017
url	http://irep.iium.edu.my/63742/ http://irep.iium.edu.my/63742/1/63742_Sequence%20and%20%20genome%20analysis%20of.pdf
first_indexed	2023-09-18T21:30:23Z
last_indexed	2023-09-18T21:30:23Z
_version_	1777412471375527936

Sequence and genome analysis of hepatitis C virus

Similar Items