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Coffin CS, Fung SK, Alvarez F, Cooper CL, Doucette KE, Fournier C, Kelly E, Ko HH, Ma MM, Martin SR, Osiowy C, Ramji A, Tam E, Villeneuve JP. Management of Hepatitis B Virus Infection: 2018 Guidelines from the Canadian Association for the Study of Liver Disease and Association of Medical Microbiology and Infectious Disease Canada. CANADIAN LIVER JOURNAL 2018; 1:156-217. [PMID: 35992619 PMCID: PMC9202759 DOI: 10.3138/canlivj.2018-0008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 08/01/2023]
Abstract
Hepatitis B virus (HBV) infection is an important public health problem in Canada. In keeping with evolving evidence and understanding of HBV pathogenesis, the Canadian Association for the Study of Liver Disease periodically publishes HBV management guidelines. The goals of the 2018 guidelines are to (1) highlight the public health impact of HBV infection in Canada and the need to improve diagnosis and linkage to care, (2) recommend current best-practice guidelines for treatment of HBV, (3) summarize the key HBV laboratory diagnostic tests, and (4) review evidence on HBV management in special patient populations and include more detail on management of HBV in pediatric populations. An overview of novel HBV tests and therapies for HBV in development is provided to highlight the recent advances in HBV clinical research. The aim and scope of these guidelines are to serve as an up-to-date, comprehensive resource for Canadian health care providers in the management of HBV infection.
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Affiliation(s)
- Carla S. Coffin
- Cumming School of Medicine, University of Calgary, Calgary, Alberta
| | - Scott K. Fung
- Faculty of Medicine, University of Toronto, Toronto, Ontario
| | - Fernando Alvarez
- Centre hospitalier de l’université de Montréal (CHUM)—CHU Sainte-Justine, Montreal, Québec
| | - Curtis L. Cooper
- Division of Infectious Diseases, Department of Medicine, University of Ottawa, Ottawa, Ontario
| | - Karen E. Doucette
- Division of Infectious Diseases, University of Alberta, Edmonton, Alberta
| | - Claire Fournier
- Department of Medicine, Université de Montréal, Montreal, Québec
| | - Erin Kelly
- Division of Gastroenterology, Department of Medicine, University of Ottawa, Ottawa, Ontario
| | - Hin Hin Ko
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia
| | - Mang M Ma
- Division of Gastroenterology, University of Alberta, Edmonton, Alberta
| | | | - Carla Osiowy
- Viral Hepatitis and Bloodborne Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
| | - Alnoor Ramji
- St. Paul’s Hospital, Vancouver, British Columbia
| | - Edward Tam
- LAIR Centre, Vancouver, British Columbia
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Kou R, Lam H, Duan H, Ye L, Jongkam N, Chen W, Zhang S, Li S. Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations. PLoS One 2016; 11:e0146638. [PMID: 26752634 PMCID: PMC4709065 DOI: 10.1371/journal.pone.0146638] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/21/2015] [Indexed: 11/18/2022] Open
Abstract
Indexing individual template molecules with a unique identifier (UID) before PCR and deep sequencing is promising for detecting low frequency mutations, as true mutations could be distinguished from PCR errors or sequencing errors based on consensus among reads sharing same index. In an effort to develop a robust assay to detect from urine low-abundant bladder cancer cells carrying well-documented mutations, we have tested the idea first on a set of mock templates, with wild type and known mutants mixed at defined ratios. We have measured the combined error rate for PCR and Illumina sequencing at each nucleotide position of three exons, and demonstrated the power of a UID in distinguishing and correcting errors. In addition, we have demonstrated that PCR sampling bias, rather than PCR errors, challenges the UID-deep sequencing method in faithfully detecting low frequency mutation.
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Affiliation(s)
- Ruqin Kou
- Department of Development, GENEWIZ LLC, 115 Corporate Blvd., South Plainfield, NJ, 07080, United States of America
| | - Ham Lam
- Department of Development, GENEWIZ LLC, 115 Corporate Blvd., South Plainfield, NJ, 07080, United States of America
| | - Hairong Duan
- Department of Bioinformatics, GENEWIZ CN, 218 Xinghu Street, Suzhou, Jiangsu, 215123, China
| | - Li Ye
- Department of Bioinformatics, GENEWIZ CN, 218 Xinghu Street, Suzhou, Jiangsu, 215123, China
| | - Narisra Jongkam
- Department of Development, GENEWIZ LLC, 115 Corporate Blvd., South Plainfield, NJ, 07080, United States of America
| | - Weizhi Chen
- Department of Bioinformatics, GENEWIZ CN, 218 Xinghu Street, Suzhou, Jiangsu, 215123, China
| | - Shifang Zhang
- Department of Development, GENEWIZ LLC, 115 Corporate Blvd., South Plainfield, NJ, 07080, United States of America
| | - Shihong Li
- Department of Development, GENEWIZ LLC, 115 Corporate Blvd., South Plainfield, NJ, 07080, United States of America
- * E-mail:
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Li F, Zhang D, Li Y, Jiang D, Luo S, Du N, Chen W, Deng L, Zeng C. Whole genome characterization of hepatitis B virus quasispecies with massively parallel pyrosequencing. Clin Microbiol Infect 2015; 21:280-7. [DOI: 10.1016/j.cmi.2014.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/04/2014] [Accepted: 10/10/2014] [Indexed: 01/19/2023]
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Capobianchi MR, Giombini E, Rozera G. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 2013; 19:15-22. [PMID: 23279287 DOI: 10.1111/1469-0691.12056] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/17/2012] [Accepted: 09/22/2012] [Indexed: 12/18/2022]
Abstract
Recent advances in nucleic acid sequencing technologies, referred to as 'next-generation' sequencing (NGS), have produced a true revolution and opened new perspectives for research and diagnostic applications, owing to the high speed and throughput of data generation. So far, NGS has been applied to metagenomics-based strategies for the discovery of novel viruses and the characterization of viral communities. Additional applications include whole viral genome sequencing, detection of viral genome variability, and the study of viral dynamics. These applications are particularly suitable for viruses such as human immunodeficiency virus, hepatitis B virus, and hepatitis C virus, whose error-prone replication machinery, combined with the high replication rate, results, in each infected individual, in the formation of many genetically related viral variants referred to as quasi-species. The viral quasi-species, in turn, represents the substrate for the selective pressure exerted by the immune system or by antiviral drugs. With traditional approaches, it is difficult to detect and quantify minority genomes present in viral quasi-species that, in fact, may have biological and clinical relevance. NGS provides, for each patient, a dataset of clonal sequences that is some order of magnitude higher than those obtained with conventional approaches. Hence, NGS is an extremely powerful tool with which to investigate previously inaccessible aspects of viral dynamics, such as the contribution of different viral reservoirs to replicating virus in the course of the natural history of the infection, co-receptor usage in minority viral populations harboured by different cell lineages, the dynamics of development of drug resistance, and the re-emergence of hidden genomes after treatment interruptions. The diagnostic application of NGS is just around the corner.
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Affiliation(s)
- M R Capobianchi
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy.
| | - E Giombini
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy
| | - G Rozera
- National Institute for Infectious Diseases 'L. Spallanzani', Rome, Italy
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Ma J, Zhang Y, Chen X, Jin Y, Chen D, Wu Y, Cui J, Wang H, Liu J, Li N, Gao F. Association of preexisting drug-resistance mutations and treatment failure in hepatitis B patients. PLoS One 2013; 8:e67606. [PMID: 23935839 PMCID: PMC3728369 DOI: 10.1371/journal.pone.0067606] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 05/19/2013] [Indexed: 12/18/2022] Open
Abstract
The role of preexisting minority drug-resistance mutations in treatment failure has not been fully understood in chronic hepatitis B patients. To understand mechanisms of drug resistance, we analyzed drug-resistance mutations in 46 treatment-failure patients and in 29 treatment-naïve patients and determined linkage patterns of the drug-resistance mutations in individual viral genomes using a highly sensitive parallel allele-specific sequencing (PASS) method. Lamivudine resistance (LAMr) mutations were predominant in treatment-failure patients, irrespective of the inclusion of LAM in the regimen. The primary LAMr mutations M204V and M204I were detected in 100% and 30% of the treatment-failure patients, respectively. Two secondary LAMr mutations (L180M and V173L) were also found in most treatment-failure patients (87% and 78%, respectively). The linkages containing these three mutations dominated the resistant viruses. Importantly, minority LAMr mutations present in <2% of the viral population were detected in 83% of the treatment-naïve patients. Moreover, the low-frequency same linked LAMr mutations (<0.15%) were detected in 24% of the treatment-naïve patients. Our results demonstrate that the selection of preexisting minority linked LAMr mutations may be an important mechanism for the rapid development of LAM resistance, caution the continuous use of LAM to treat drug-experienced and -naïve hepatitis B patients, and underline the importance of the detection of minority single and linked drug-resistance mutations before initiating antiviral therapy.
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Affiliation(s)
- Jie Ma
- Beijing Institute of Liver Disease, Beijing, China
- Beijing Baihuirui Bio-Technologies Inc, Beijing, China
| | | | - Xinyue Chen
- Department of Medicine, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Yi Jin
- Department of Medicine, Beijing You'an Hospital, Capital Medical University, Beijing, China
| | - Dexi Chen
- Beijing Institute of Liver Disease, Beijing, China
| | - Yun Wu
- Beijing Baihuirui Bio-Technologies Inc, Beijing, China
| | - Jing Cui
- Beijing Baihuirui Bio-Technologies Inc, Beijing, China
| | - Haitao Wang
- Beijing Baihuirui Bio-Technologies Inc, Beijing, China
| | - Jia Liu
- Department of Microbiology, Peking University Health Science Center, Beijing, China
| | - Ning Li
- Beijing Institute of Liver Disease, Beijing, China
- Department of Medicine, Beijing You'an Hospital, Capital Medical University, Beijing, China
- Department of Surgery, Beijing You'an Hospital, Capital Medical University, Beijing, China
- * E-mail: (NL); (FG)
| | - Feng Gao
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (NL); (FG)
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Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol 2011; 12:R59. [PMID: 21699709 PMCID: PMC3218847 DOI: 10.1186/gb-2011-12-6-r59] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 05/30/2011] [Accepted: 06/23/2011] [Indexed: 12/19/2022] Open
Abstract
Background Originally believed to be a rare phenomenon, heteroplasmy - the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual - is emerging as an important component of eukaryotic genetic diversity. Heteroplasmies can be used as genetic markers in applications ranging from forensics to cancer diagnostics. Yet the frequency of heteroplasmic alleles may vary from generation to generation due to the bottleneck occurring during oogenesis. Therefore, to understand the alterations in allele frequencies at heteroplasmic sites, it is of critical importance to investigate the dynamics of maternal mtDNA transmission. Results Here we sequenced, at high coverage, mtDNA from blood and buccal tissues of nine individuals from three families with a total of six maternal transmission events. Using simulations and re-sequencing of clonal DNA, we devised a set of criteria for detecting polymorphic sites in heterogeneous genetic samples that is resistant to the noise originating from massively parallel sequencing technologies. Application of these criteria to nine human mtDNA samples revealed four heteroplasmic sites. Conclusions Our results suggest that the incidence of heteroplasmy may be lower than estimated in some other recent re-sequencing studies, and that mtDNA allelic frequencies differ significantly both between tissues of the same individual and between a mother and her offspring. We designed our study in such a way that the complete analysis described here can be repeated by anyone either at our site or directly on the Amazon Cloud. Our computational pipeline can be easily modified to accommodate other applications, such as viral re-sequencing.
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Affiliation(s)
- Hiroki Goto
- The Huck Institutes of Life Sciences and Department of Biology, Penn State University, 305 Wartik Lab, University Park, PA 16802, USA
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