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Next-generation sequencing studies on the E1-HVR1 region of hepatitis C virus (HCV) from non-high-risk HCV patients living in Punjab and Khyber Pakhtunkhwa, Pakistan. Arch Virol 2021; 166:3049-3059. [PMID: 34448937 DOI: 10.1007/s00705-021-05203-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022]
Abstract
The incidence rate of hepatitis C virus (HCV) infection in Pakistan is very high. In this study, we evaluated the genetic heterogeneity of HCV hypervariable region 1 (HVR1) from the HCV-infected Pakistani population and compare the isolated genotypes with representative sequences from internationally diverse geographic regions. We also investigated potential transmission events in non-high-risk HCV patients. Next-generation sequencing (NGS) data from the E1-HVR1 region from 30 HCV patients were used for phylogenetic analysis. Reference sequences were retrieved from the Los Alamos HCV and GenBank databases. NGS data were analyzed to examine HCV HVR1 sequence diversity and identify transmission links among HCV-infected individuals using Global Hepatitis Outbreak and Surveillance Technology (GHOST). Phylogenetic analysis showed the predominance of HCV genotype 3a (86.6%), followed by 1a (6.6%), 1b (3.3%), and 3b (3.3%). NGS of HVR1 displayed significant genetic heterogeneity of HCV populations within each patient. The average nucleotide sequence diversity for HVR1 was 0.055. JR781281 was found to be the most diverse (0.14) of the specimens. Phylogenetic analysis demonstrated that all HCV specimens sequenced in this study were more similar to each other and showed variations from the representative sequences. The GHOST results suggested genetic relatedness between two (6.6%) HCV cases, possibly defining an incipient outbreak in a non-high-risk population. We urge rigorous countrywide investigation of outbreaks to identify transmission clusters and their sources to incorporate preventive measures for disease control.
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Shared HCV Transmission Networks Among HIV-1-Positive and HIV-1-Negative Men Having Sex With Men by Ultradeep Sequencing. J Acquir Immune Defic Syndr 2020; 82:105-110. [PMID: 31169768 DOI: 10.1097/qai.0000000000002099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Several studies reported hepatitis C virus (HCV) transmission networks among men having sex with men (MSM) in Europe and the spread of HCV strains from HIV-HCV coinfected toward HCV monoinfected MSM. We aimed to investigate HCV transmission dynamics among HIV-positive and HIV-negative MSM by ultradeep sequencing (UDS). DESIGN AND METHODS NS5B fragment (388 bp) was sequenced from virus of 50 HIV-positive and 18 HIV-negative patients diagnosed with recent HCV infection. UDS data were analyzed by Geneious (version 10.3.2). Phylogenetic trees were constructed by FastTree (version 2.1) and submitted to ClusterPicker (version 1.2.3) for transmission chain detection at different thresholds of maximum genetic distance (MGD) (3% for Sanger, 3% and 4.5% for UDS). RESULTS Ten, 17, and 18 HCV transmission chains were identified by Sanger at 3%, UDS at 3% and at 4.5% of MGD, respectively. Of 68 subjects enrolled, 38 (55.9%), 38 (55.9%), and 43 (65.3%) individuals were involved in transmission networks found by Sanger at 3%, UDS at 3%, and at 4.5% of MGD, respectively. Mixed transmission chains including HIV-positive and HIV-negative subjects were detected for 8/10 chains by Sanger at 3%, for 9/17 by UDS at 3%, and for 10/18 by UDS at 4.5% of MGD. Overall, the number of HIV-negative individuals clustering with HIV-positive ones was 9/18 by Sanger, 9/18 by UDS at 3%, and 10/18 by UDS at 4.5% of MGD. CONCLUSIONS HIV-positive and HIV-negative MSM shared HCV transmission networks, which emphasizes the need for HCV surveillance and prevention measures in these communities regardless of the HIV status.
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Caro-Pérez N, Martínez-Rebollar M, Gregori J, Quer J, González P, Gambato M, García-González N, González-Candelas F, Costa J, Esteban JI, Mallolas J, Forns X, Laguno M, Pérez-Del-Pulgar S. Phylogenetic analysis of an epidemic outbreak of acute hepatitis C in HIV-infected patients by ultra-deep pyrosequencing. J Clin Virol 2017; 92:42-47. [PMID: 28521213 DOI: 10.1016/j.jcv.2017.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/29/2017] [Accepted: 05/06/2017] [Indexed: 01/18/2023]
Abstract
BACKGROUND The incidence of acute hepatitis C (AHC) among HIV-infected men who have sex with men (MSM) has increased significantly in the last 10 years. Several studies point to a social and sexual network of HIV-positive MSM that extends internationally. OBJECTIVES The aim of our study was to investigate the dynamics of HCV transmission in an outbreak of AHC in HIV-infected MSM in Barcelona by ultra-deep pyrosequencing. STUDY DESIGN Between 2008 and 2013, 113 cases of AHC in HIV-infected MSM were diagnosed in the Infectious Diseases Unit, Hospital Clínic, Barcelona. Massive sequencing was performed using the Roche 454 GS Junior platform. To define possible transmission networks, maximum likelihood phylogenetic trees were constructed, and levels of genetic diversity within and among patients were compared. RESULTS Among the 70 cases analyzed, we have identified 16 potential clusters of transmission: 8 for genotype 1a (23 cases involved), 1 for genotype 1b (3 cases) and 7 for genotype 4d (27 cases). Although the initial phylogenetic reconstruction suggested a local transmission cluster of HCV gt4d, our approach based on low genetic differentiation did not corroborate it. Indeed, gt4d strains formed 4 independent groups related to patients from other countries. CONCLUSIONS Frequent clustering of HIV-positive MSM shows that HCV infection has spread through a local network in Barcelona. This outbreak is related to a large international HCV transmission network among MSM. Public health efforts are needed to reduce HCV transmission among this high-risk group.
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Affiliation(s)
- Noelia Caro-Pérez
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | | | - Josep Gregori
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Patricia González
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Martina Gambato
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Neris García-González
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain.
| | - Josep Costa
- Microbiology Department, Centre Diagnòstic Biomèdic, Hospital Clínic, CIBERehd, Barcelona, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron, CIBERehd, Barcelona, Spain.
| | - Josep Mallolas
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
| | - Montse Laguno
- Infectious Diseases Unit, Hospital Clínic, IDIBAPS, Barcelona, Spain.
| | - Sofía Pérez-Del-Pulgar
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Universitat de Barcelona, Barcelona, Spain.
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Leung P, Eltahla AA, Lloyd AR, Bull RA, Luciani F. Understanding the complex evolution of rapidly mutating viruses with deep sequencing: Beyond the analysis of viral diversity. Virus Res 2016; 239:43-54. [PMID: 27888126 DOI: 10.1016/j.virusres.2016.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts. These analyses are revealing more accurate descriptions of the evolutionary dynamics that underpin the rapid adaptation of these viruses to the host response, and to drug therapies. This review assesses recent developments in methods and provide informative research examples using deep sequencing data generated from rapidly mutating viruses infecting humans, particularly hepatitis C virus (HCV), human immunodeficiency virus (HIV), Ebola virus and influenza virus, to understand the evolution of viral genomes and to explore the relationship between viral mutations and the host adaptive immune response. Finally, we discuss limitations in current technologies, and future directions that take advantage of publically available large deep sequencing datasets.
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Affiliation(s)
- Preston Leung
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Andrew R Lloyd
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia.
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Wu Z, Cui L, Zhao W, Yang D, Chen H, Wang R, Wang X, Zhang L, He T. Molecular epidemiology of hepatitis C infections in Ningxia, China: genotype, phylogeny and mutation analysis. Virol J 2016; 13:172. [PMID: 27756381 PMCID: PMC5070218 DOI: 10.1186/s12985-016-0635-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/12/2016] [Indexed: 02/07/2023] Open
Abstract
Background Current prevalence and genotype distribution of hepatitis C virus (HCV) infection remain unknown in Ningxia, northwest China. Methods From June to December 2013, 13,022 individuals were screened in Ningxia HIV/AIDS Sentinel Surveillance System, with their demographic features collected and serum samples tested for HCV antibody. Sero-positive drug users were further subjected to sequencing of NS5B and Core regions of HCV. Results The anti-HCV prevalence was 0.34 % among individuals without history of drug use, while it was 15.80 % among drug users. Of 79 NS5B sequences amplified from drug users, 64 (81.0 %) were male and 51 (64.0 %) were injection drug users (IDUs). Subtype 3a (40.5 %) and 1b (25.3 %) were the most predominant subtypes, followed in frequency by 3b (10.1 %) and 2a (7.6 %). Subtype distribution has no significant difference between injection and non-injection drug users. Based on phylogeographic analysis, HCV strains in Ningxia IDUs were mainly originated from two sites, Yunnan province (in southwest China bordering Myanmar, also known as Burma) and Xinjiang Autonomous Region (in northwest China on the border of Central Asia), which are the two major drug trafficking originates in China. Previously reported drug-resistance mutations were also scanned in this treatment-naïve population. Amino acid substitutions (C316N) associated with direct anti-viral agents (DAA) resistance were identified in the NS5B region in seven samples. Conclusion This study is the first to reveal the existence of multiple genotypes of HCV in Ningxia, an inland province in northwest China, suggesting the rapid spreading of the virus. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0635-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhonglan Wu
- Ningxia Center for Disease Control and Prevention, Ningxia, 750001, China
| | - Lijia Cui
- Tsinghua University School of Medicine, Beijing, 100084, China
| | - Weiming Zhao
- Ningxia Medical University School of Public Health and Management, Ningxia, 750001, China
| | - Dongzhi Yang
- Ningxia Center for Disease Control and Prevention, Ningxia, 750001, China
| | - Hui Chen
- Ningxia Center for Disease Control and Prevention, Ningxia, 750001, China
| | - Ruiqing Wang
- Wuzhong Center of Disease Control and Prevention, Ningxia, 751100, China
| | - Xuemin Wang
- Ningxia Center for Disease Control and Prevention, Ningxia, 750001, China
| | - Linqi Zhang
- Comprehensive AIDS Research Center, and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Tianhua He
- Tsinghua University School of Medicine, Beijing, 100084, China.
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Montoya V, Olmstead A, Tang P, Cook D, Janjua N, Grebely J, Jacka B, Poon AFY, Krajden M. Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing. INFECTION GENETICS AND EVOLUTION 2016; 43:329-37. [PMID: 27282472 DOI: 10.1016/j.meegid.2016.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 01/17/2023]
Abstract
Effective surveillance and treatment strategies are required to control the hepatitis C virus (HCV) epidemic. Phylogenetic analyses are powerful tools for reconstructing the evolutionary history of viral outbreaks and identifying transmission clusters. These studies often rely on Sanger sequencing which typically generates a single consensus sequence for each infected individual. For rapidly mutating viruses such as HCV, consensus sequencing underestimates the complexity of the viral quasispecies population and could therefore generate different phylogenetic tree topologies. Although deep sequencing provides a more detailed quasispecies characterization, in-depth phylogenetic analyses are challenging due to dataset complexity and computational limitations. Here, we apply deep sequencing to a characterized population to assess its ability to identify phylogenetic clusters compared with consensus Sanger sequencing. For deep sequencing, a sample specific threshold determined by the 50th percentile of the patristic distance distribution for all variants within each individual was used to identify clusters. Among seven patristic distance thresholds tested for the Sanger sequence phylogeny ranging from 0.005-0.06, a threshold of 0.03 was found to provide the maximum balance between positive agreement (samples in a cluster) and negative agreement (samples not in a cluster) relative to the deep sequencing dataset. From 77 HCV seroconverters, 10 individuals were identified in phylogenetic clusters using both methods. Deep sequencing analysis identified an additional 4 individuals and excluded 8 other individuals relative to Sanger sequencing. The application of this deep sequencing approach could be a more effective tool to understand onward HCV transmission dynamics compared with Sanger sequencing, since the incorporation of minority sequence variants improves the discrimination of phylogenetically linked clusters.
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Affiliation(s)
- Vincent Montoya
- BC Centre for Disease Control, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrea Olmstead
- BC Centre for Disease Control, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Darrel Cook
- BC Centre for Disease Control, Vancouver, BC, Canada
| | - Naveed Janjua
- BC Centre for Disease Control, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jason Grebely
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - Brendan Jacka
- The Kirby Institute, UNSW Australia, Sydney, NSW, Australia
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, BC, Canada
| | - Mel Krajden
- BC Centre for Disease Control, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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