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Phylogenetic analysis of hepatitis C virus among HIV/ HCV co-infected patients in Nigeria
research-article
Publication date (Electronic):
6 February 2019
Journal:
PLoS ONE
Publisher:
Public Library of Science
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Abstract
Hepatitis C virus (HCV) infection has been associated with liver disease including liver cirrhosis and hepatocellular carcinoma (HCC) in chronically-infected persons. However, in HIV/HCV co-infected patients, increased rate of progression to cirrhosis and HCC has been reported. Limited information exists regarding genetic variants of HCV circulating among co-infected patients, which could be important in the design of broadly protective vaccine and management of the disease. Here, we determined the genotypes of HCV isolates circulating among HIV/HCV co-infected patients in Ibadan, southwestern Nigeria. One hundred and twenty-five HIV/HCV IgM positive samples obtained from HIV laboratory, University of Ibadan were used for this study. HCV NS5B gene was amplified using polymerase chain reaction (PCR). The amplified NS5B gene was sequenced using gene specific primers. Twenty isolates were amplified, out of which 13 were successfully sequenced. Phylogenetic analysis of the 13 sequenced isolates showed three HCV subtypes 1a, 3a and 5a belonging to genotypes 1, 3 and 5 respectively. Ten isolates (77%) belong to subtype 5a, followed by 2 isolates (15%) subtype 1a and 1 isolate (8%) was subtype 3a. The predominant HCV genotype was 5, followed by genotype 1 (subtype 1a). The findings, as well as the observed mutations in NS5B gene, indicate the need for screening and monitoring of HIV/HCV co-infected patients. Further study to determine the phylogeny of isolates circulating in other parts of Nigeria will be carried out.
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Most cited references34
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Diagnosis, management, and treatment of hepatitis C: an update.
Marc G Ghany, Doris B Strader, David Thomas … (2009)
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Genetic diversity and evolution of hepatitis C virus--15 years on.
Peter Simmonds (2004)
In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus-host interactions may represent key components in establishing its 'ecological niche' in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.
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The increasing burden of mortality from viral hepatitis in the United States between 1999 and 2007.
Jian Xing, Kathleen Ly, John Ward … (2012)
The increasing health burden and mortality from hepatitis B virus (HBV) and hepatitis C virus (HCV) in the United States are underappreciated. To examine mortality from HBV; HCV; and, for comparison, HIV. Analysis of U.S. multiple-cause mortality data from 1999 to 2007 from the National Center for Health Statistics. All U.S. states and the District of Columbia. Approximately 22 million decedents. Age-adjusted mortality rates from HBV, HCV, and HIV. Logistic regression analyses of 2007 data generated 4 independent models per outcome (HCV- or HBV-related deaths) that each included 1 of 4 comorbid conditions and all sociodemographic characteristics. Between 1999 and 2007, recorded deaths from HCV [corrected] increased significantly to 15,106, whereas deaths from HIV declined to 12,734 by 2007. Factors associated with HCV-related deaths included chronic liver disease, HBV co-infection, alcohol-related conditions, minority status, and HIV co-infection. Factors that increased odds of HBV-related death included chronic liver disease, HCV co-infection, Asian or Pacific Islander descent, HIV co-infection, and alcohol-related conditions. Most deaths from HBV and HCV occurred in middle-aged persons. A person other than the primary physician of the decedent frequently completed the death certificate, and HCV and HBV often were not detected and thus not reported as causes of death. By 2007, HCV had superseded HIV as a cause of death in the United States, and deaths from HCV and HBV disproportionately occurred in middle-aged persons. To achieve decreases in mortality similar to those seen with HIV requires new policy initiatives to detect patients with chronic hepatitis and link them to care and treatment. Centers for Disease Control and Prevention.
Author and article information
Contributors
Juliet A. Shenge:
ORCID: http://orcid.org/0000-0003-1298-8522
Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole:
InvestigationRole: MethodologyRole: Writing – original draft
Georgina N. Odaibo: Role: Writing – review & editing
David O. Olaleye: Role: Funding acquisitionRole: SupervisionRole: Writing – review & editing
Jason Blackard: Role: Editor
Journal
Journal ID (nlm-ta): PLoS One
Journal ID (iso-abbrev): PLoS ONE
Journal ID (publisher-id): plos
Journal ID (pmc): plosone
Title:
PLoS ONE
Publisher:
Public Library of Science
(San Francisco, CA USA
)
ISSN
(Electronic):
1932-6203
Publication date
(Electronic):
6
February
2019
Publication date Collection: 2019
Volume: 14
Issue: 2
Electronic Location Identifier: e0210724
Affiliations
Author notes
* E-mail:
jadamma@
123456yahoo.com
Author information
Juliet A. Shenge
http://orcid.org/0000-0003-1298-8522
Article
Publisher ID: PONE-D-18-19874DOI: 10.1371/journal.pone.0210724
PMC ID: 6364902
PubMed ID: 30726229
SO-VID: bb61e160-39bf-4d26-939a-867d99db54c3
Copyright © © 2019 Shenge et al
License:
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
History
Date
received
: 4
July
2018
Date
accepted
: 31
December
2018
Page count
Figures: 2,
Tables: 0,
Pages: 10
Funding
Funded by: Medical Education Partnership Initiaves AWard
Award ID: R24TW008878
Award Recipient
:
ORCID: http://orcid.org/0000-0003-1298-8522
Juliet A. Shenge
This study was supported by Medical Education Partnership Initiative Nigeria (MEPIN)
through National Institute of Health (NIH) USA grant funded by Fogarty International
Centre, the office of AIDS Research and National Human Genome Research Institute of
NIH, the Health Resources and Services Administration (HRSA) and the Office of the
U.S. Global AIDS Coordinator under award number R24TW008878’ to JAS. The funders had
no role in study design, data collection and analysis, decision to publish, or preparation
of the manuscript.
Categories
Subject:
Research Article
Subject:
Biology and life sciences
Subject:
Organisms
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Viruses
Subject:
RNA viruses
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Flaviviruses
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Hepacivirus
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Hepatitis C virus
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Biology and life sciences
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Microbiology
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Custom metadata
Data Availability All relevant data are within the manuscript and its supporting files. NS5B sequences
available at Doi:
10.6084/m9.figshare.7471454.
ScienceOpen disciplines: Uncategorized
Data availability:
ScienceOpen disciplines: Uncategorized