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Wade KE, Chen L, Deng C, Zhou G, Hu P. Investigating alignment-free machine learning methods for HIV-1 subtype classification. BIOINFORMATICS ADVANCES 2024; 4:vbae108. [PMID: 39228995 PMCID: PMC11371153 DOI: 10.1093/bioadv/vbae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/26/2024] [Indexed: 09/05/2024]
Abstract
Motivation Many viruses are organized into taxonomies of subtypes based on their genetic similarities. For human immunodeficiency virus 1 (HIV-1), subtype classification plays a crucial role in infection management. Sequence alignment-based methods for subtype classification are impractical for large datasets because they are costly and time-consuming. Alignment-free methods involve creating numerical representations for genetic sequences and applying statistical or machine learning methods. Despite their high overall accuracy, existing models perform poorly on less common subtypes. Furthermore, there is limited work investigating the impact of sequence vectorization methods, in particular natural language-inspired embedding methods, on HIV-1 subtype classification. Results We present a comprehensive analysis of sequence vectorization methods across machine learning methods. We report a k-mer-based XGBoost model with a balanced accuracy of 0.84, indicating that it has good overall performance for both common and uncommon HIV-1 subtypes. We also report a Word2Vec-based support vector machine that achieves promising results on precision and balanced accuracy. Our study sheds light on the effect of sequence vectorization methods on HIV-1 subtype classification and suggests that natural language-inspired encoding methods show promise. Our results could help to develop improved HIV-1 subtype classification methods, leading to improved individual patient outcomes, and the development of subtype-specific treatments. Availability and implementation Source code is available at https://www.github.com/kwade4/HIV_Subtypes.
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Affiliation(s)
- Kaitlyn E Wade
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Lianghong Chen
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Chutong Deng
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Gen Zhou
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Pingzhao Hu
- Department of Computer Science, University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
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Fahmy AM, Hammad MS, Mabrouk MS, Al-Atabany WI. On leveraging self-supervised learning for accurate HCV genotyping. Sci Rep 2024; 14:15463. [PMID: 38965254 PMCID: PMC11224313 DOI: 10.1038/s41598-024-64209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/06/2024] [Indexed: 07/06/2024] Open
Abstract
Hepatitis C virus (HCV) is a major global health concern, affecting millions of individuals worldwide. While existing literature predominantly focuses on disease classification using clinical data, there exists a critical research gap concerning HCV genotyping based on genomic sequences. Accurate HCV genotyping is essential for patient management and treatment decisions. While the neural models excel at capturing complex patterns, they still face challenges, such as data scarcity, that exist a lot in computational genomics. To overcome this challenges, this paper introduces an advanced deep learning approach for HCV genotyping based on the graphical representation of nucleotide sequences that outperforms classical approaches. Notably, it is effective for both partial and complete HCV genomes and addresses challenges associated with imbalanced datasets. In this work, ten HCV genotypes: 1a, 1b, 2a, 2b, 2c, 3a, 3b, 4, 5, and 6 were used in the analysis. This study utilizes Chaos Game Representation for 2D mapping of genomic sequences, employing self-supervised learning using convolutional autoencoder for deep feature extraction, resulting in an outstanding performance for HCV genotyping compared to various machine learning and deep learning models. This baseline provides a benchmark against which the performance of the proposed approach and other models can be evaluated. The experimental results showcase a remarkable classification accuracy of over 99%, outperforming traditional deep learning models. This performance demonstrates the capability of the proposed model to accurately identify HCV genotypes in both partial and complete sequences and in dealing with data scarcity for certain genotypes. The results of the proposed model are compared to NCBI genotyping tool.
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Affiliation(s)
- Ahmed M Fahmy
- Computer Science program, School of Information Technology and Computer Science (ITCS), Nile University, Sheikh Zayed City, Egypt.
| | - Muhammed S Hammad
- Biomedical Engineering Department, Faculty of Engineering, Helwan University, Cairo, Egypt
| | - Mai S Mabrouk
- Biomedical informatics program, School of Information Technology and Computer Science (ITCS), Nile University, Sheikh Zayed City, Egypt
| | - Walid I Al-Atabany
- Biomedical informatics program, School of Information Technology and Computer Science (ITCS), Nile University, Sheikh Zayed City, Egypt
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3
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Guo X, Yu D, Liu M, Li H, Chen M, Wang X, Zhai X, Zhang B, Wang Y, Yang C, Wang C, Liu Y, Han J, Wang X, Li J, Jia L, Li L. A unified classification system for HIV-1 5' long terminal repeats. PLoS One 2024; 19:e0301809. [PMID: 38696412 PMCID: PMC11065288 DOI: 10.1371/journal.pone.0301809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024] Open
Abstract
The HIV-1 provirus mainly consists of internal coding region flanked by 1 long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic and phylogenetic classifications for HIV-1 5' LTRs, which hinders our elaboration on 5' LTR and a better understanding of the viral origin, spread and therapy. Here, by analyzing all available resources of 5' LTR sequences in public databases following 4 recognized principles for the reference classification, 83 representatives and 14 consensus sequences were identified as representatives of 2 groups, 6 subtypes, 6 sub-subtypes, and 9 CRFs. To test the reliability of the supplemented classification system, the constructed references were applied to identify the 5' LTR assignment of the 22 clinical isolates in China. The results revealed that 16 out of 22 tested strains showed a consistent subtype classification with the previous LTR-independent classification system. However, 6 strains, for which recombination events within 5' LTR were demonstrated, unexpectedly showed a different subtype classification, leading a significant change of binding sites for important transcription factors including SP1, p53, and NF-κB. The binding change of these transcriptional factors would probably affect the transcriptional activity of 5' LTR. This study supplemented a unified classification system for HIV-1 5' LTRs, which will facilitate HIV-1 characterization and be helpful for both basic and clinical research fields.
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Affiliation(s)
- Xing Guo
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Dan Yu
- Laboratory of Dermatology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Mengying Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Xinyu Wang
- Laboratory of Dermatology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children’s Hospital, National Center for Children’s Health, Capital Medical University, Beijing, China
| | - Xiuli Zhai
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanglan Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Caiqing Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Chunlei Wang
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Teiti I, Aubry M, Glaziou P, Mendiboure V, Teissier A, Paoaafaite T, Simon A, Chung K, Dian L, Olivier S, Pineau P, Fontanet A, Condat B, Madec Y, Lastère S, Cao-Lormeau VM. Towards elimination of chronic viral hepatitis in French Polynesia: results from a national population-based survey. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 45:101035. [PMID: 38445260 PMCID: PMC10914476 DOI: 10.1016/j.lanwpc.2024.101035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/25/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
Abstract
Background In French Polynesia, hepatitis B virus (HBV) infection appears as a major risk factor for hepatocellular carcinoma (HCC), which detection rate in the Austral archipelago is among the highest in the world. Through a nationally representative cross-sectional survey of the adult population, this study aimed at assessing the prevalence of HBV, but also hepatitis C virus (HCV), and hepatitis delta virus (HDV). Methods A total of 1942 blood samples from participants aged 18-69 years were tested for anti-HBc, anti-HBs, HBsAg, anti-HCV IgG, and HDV RNA. Complete genome sequencing of detected HBV strains was performed. Findings Among participants, 315/1834, 582/1834, 33/1834, 0/1857, and 0/33 tested positive for anti-HBc, anti-HBs, HBsAg, anti-HCV IgG, and HDV RNA, respectively. The population prevalence of HBsAg was estimated at 1.0% (95% CI: 0.6-1.7). All HBsAg carriers were born in French Polynesia before vaccination at birth became mandatory. In multivariate analyses, identified factors associated with HBsAg carriage included: the archipelago of residence (p < 0.0001), age (p < 0.0001), and education level (p = 0.0077). HBV genotypes B, C, and F were detected. Interpretation French Polynesia has a low endemicity level of HBV and its population may be considered at low risk for HCV and HDV infection. However, prevalence of HBsAg was found concerning in Austral (3.8%; 95% CI: 1.9-7.5) and Marquesas (6.5%; 95% CI: 3.8-11) archipelagoes. In the Austral archipelago, the presence of genotype C may account for the elevated rate of HCC. Our findings warrant more efforts to improve access to detection, prevention and care to people born before the systematic vaccination policy application, and residing in higher-risk areas, to achieve HBV elimination in French Polynesia. Funding Research Delegation of French Polynesia.
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Affiliation(s)
- Iotefa Teiti
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Maite Aubry
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Philippe Glaziou
- Non-communicable Diseases Laboratory, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Vincent Mendiboure
- Institut Pasteur, Université Paris Cité, Epidemiology of Emerging Diseases Unit, Paris 75015, France
| | - Anita Teissier
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Tuterarii Paoaafaite
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Aurélie Simon
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Kiyojiken Chung
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Lisa Dian
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Sophie Olivier
- Clinical Laboratory, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Pascal Pineau
- Institut Pasteur, Université Paris Cité, Unité“Organisation Nucléaire et Oncogenèse”, INSERM U993, Paris 75015, France
| | - Arnaud Fontanet
- Institut Pasteur, Université Paris Cité, Epidemiology of Emerging Diseases Unit, Paris 75015, France
- PACRI Unit, Conservatoire National des Arts et Métiers, Paris, France
| | - Bertrand Condat
- Department of Gastroenterology, Centre Hospitalier de la Polynésie Française, Pirae, Tahiti, French Polynesia
| | - Yoann Madec
- Institut Pasteur, Université Paris Cité, Epidemiology of Emerging Diseases Unit, Paris 75015, France
| | - Stéphane Lastère
- Clinical Laboratory, Centre Hospitalier de la Polynésie Française, Pirae, Tahiti, French Polynesia
| | - Van-Mai Cao-Lormeau
- Laboratory of Research on Emerging Viral Diseases, Institut Louis Malardé, Papeete, Tahiti, French Polynesia
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Osiowy C, Giles E, Lowe CF, Matic N, Murphy DG, Uzicanin S, Drews SJ, O'Brien SF. Hepatitis B virus genotype surveillance in Canadian blood donors and a referred patient population, 2016-2021. Vox Sang 2024; 119:232-241. [PMID: 38141175 DOI: 10.1111/vox.13568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/06/2023] [Accepted: 11/05/2023] [Indexed: 12/25/2023]
Abstract
BACKGROUND AND OBJECTIVES Hepatitis B virus (HBV) genotypes (A-H) have a distinct geographic distribution and are highly associated with the country of birth. Canada has experienced increased immigration over the past decade, primarily from regions where HBV is endemic. This study investigated the proportions and trends of HBV genotypes within blood donor and clinical populations of Canada over the period 2016-2021. MATERIALS AND METHODS Study samples involved two cohorts: (1) Canadian blood donors (n = 246) deferred from donation due to HBV test positivity and (2) chronic HBV patients from across Canada (clinically referred population, n = 3539). Plasma or serum was extracted, and the surface antigen and/or polymerase-coding region was amplified and sequenced to determine genotype by phylogenetic analysis. RESULTS Six (A-E, G) and eight (A-H) HBV genotypes were detected among deferred blood donors and the clinically referred population, respectively. Differences in HBV genotype proportions between the two cohorts were observed across Canada. Males comprised most of the referred population among genotypes A-E (p < 0.0001), except for genotypes B and C. The median age was younger among blood donors (36 years [range 17-72]) compared with the referred population (41 years [range 0-99]). Distinct trends of increasing (E, referred; B, blood donor) and decreasing genotype prevalence were observed over the study period. CONCLUSION HBV genotypes in Canada are highly diverse, suggesting a large immigrant population. Observed trends in genotype prevalence and proportional differences among cohorts imply shifts among the HBV-infected population of Canada, which warrants continued surveillance.
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Affiliation(s)
- Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Elizabeth Giles
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Christopher F Lowe
- St. Paul's Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nancy Matic
- St. Paul's Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Donald G Murphy
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | | | - Steven J Drews
- Canadian Blood Services, Edmonton, Alberta, Canada
- Division of Diagnostic and Applied Microbiology, Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sheila F O'Brien
- Canadian Blood Services, Ottawa, Ontario, Canada
- School of Epidemiology & Public Health, University of Ottawa, Ottawa, Ontario, Canada
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Kim SC, Wallin JJ, Ghosheh Y, Zahoor MA, Sanchez Vasquez JD, Nkongolo S, Fung S, Mendez P, Feld JJ, Janssen HL, Gehring AJ. Efficacy of antiviral therapy and host-virus interactions visualised using serial liver sampling with fine-needle aspirates. JHEP Rep 2023; 5:100817. [PMID: 37600958 PMCID: PMC10432215 DOI: 10.1016/j.jhepr.2023.100817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/09/2023] [Indexed: 08/22/2023] Open
Abstract
Background & Aims Novel therapies for chronic hepatitis B (CHB), such as RNA interference, target all viral RNAs for degradation, whereas nucleoside analogues are thought to block reverse transcription with minimal impact on viral transcripts. However, limitations in technology and sampling frequency have been obstacles to measuring actual changes in HBV transcription in the liver of patients starting therapy. Methods We used elective liver sampling with fine-needle aspirates (FNAs) to investigate the impact of treatment on viral replication in patients with CHB. Liver FNAs were collected from patients with CHB at baseline and 12 and 24 weeks after starting tenofovir alafenamide treatment. Liver FNAs were subjected to single-cell RNA sequencing and analysed using the Viral-Track method. Results HBV was the only viral genome detected and was enriched within hepatocytes. The 5' sequencing technology identified protein-specific HBV transcripts and showed that tenofovir alafenamide therapy specifically reduced pre-genomic RNA transcripts with little impact on HBsAg or HBx transcripts. Infected hepatocytes displayed unique gene signatures associated with an immunological response to viral infection. Conclusions Longitudinal liver sampling, combined with single-cell RNA sequencing, captured the dynamic impact of antiviral therapy on the replication status of HBV and revealed host-pathogen interactions at the transcriptional level in infected hepatocytes. This sequencing-based approach is applicable to early-stage clinical studies, enabling mechanistic studies of immunopathology and the effect of novel therapeutic interventions. Impact and Implications Infection-dependent transcriptional changes and the impact of antiviral therapy on viral replication can be measured in longitudinal human liver biopsies using single-cell RNA sequencing data.
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Affiliation(s)
| | | | - Yanal Ghosheh
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Muhammad Atif Zahoor
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Juan Diego Sanchez Vasquez
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Shirin Nkongolo
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Internal Medicine IV (Gastroenterology, Hepatology, Infectious Diseases), University Hospital Heidelberg, Heidelberg, Germany
| | - Scott Fung
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Jordan J. Feld
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Harry L.A. Janssen
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Erasmus Medical Center, Division of Gastroenterology and Hepatology, Rotterdam, The Netherlands
| | - Adam J. Gehring
- Toronto Centre for Liver Disease, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
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Athamneh RY, Abudalo R, Sallam M, Alqudah A, Alquran H, Amawi KF, Abu-Harirah HA. Sub-genotypes of hepatitis C virus in the Middle East and North Africa: Patterns of distribution and temporal changes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 109:105412. [PMID: 36791585 DOI: 10.1016/j.meegid.2023.105412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Infection with the hepatitis C virus (HCV) remains a considerable public health concern in the Middle East and North Africa (MENA). The objectives of this study were to analyze the HCV genotype (GT) and sub-genotype (SGT) distribution in the MENA region and to assess the temporal change in the number of sequences within the MENA region. All HCV molecular sequences collected in the MENA region had been retrieved from GenBank as of 1 August 2022. The number of HCV sequences retrieved was 6740 representing sequences from a total of 17 MENA countries with a majority from Iran (n = 1969, 29.2%), Egypt (n = 1591, 23.6%), Tunisia (n = 1305, 19.4%) and Saudi Arabia (n = 1085, 16.1%). The determination of GT/SGT was based on the NCBI genotyping and Blast tool. Genotype 1 (GT1) dominated infections in the MENA (n = 2777, 41.2%), followed by GT4 (n = 2566, 39.0%). Additionally, SGT4a (1515/6393, 23.7%) was the most common SGT in the MENA, and SGT4a was dominant in Egypt and Saudi Arabia, followed by SGT1b (n = 1308, 20.5%), which was dominant in Morocco and Tunisia, while SGT1a (n = 1275, 19.9%) was common in Iran, Iraq and Palestine. Furthermore, significant temporal increase in the number of HCV MENA sequences was observed. On the SGT level, specific patterns of HCV genetic diversity were seen in the MENA region, with the most common SGT being 4a, in addition to increasing the availability of HCV sequences in the MENA region.
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Affiliation(s)
- Rabaa Y Athamneh
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan.
| | - Rawan Abudalo
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan; Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman, Jordan
| | - Abdelrahim Alqudah
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, Zarqa, Jordan
| | - Hasan Alquran
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Kawther Faisal Amawi
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
| | - Hashem A Abu-Harirah
- Department of Medical Laboratories Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa, Jordan
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8
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Khan T, Raza S. Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review. Curr Top Med Chem 2023; 23:1640-1663. [PMID: 36725827 DOI: 10.2174/1568026623666230201144522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
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9
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Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022; 23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Several new viral infections have emerged in the human population and establishing as global pandemics. With advancements in translation research, the scientific community has developed potential therapeutics to eradicate or control certain viral infections, such as smallpox and polio, responsible for billions of disabilities and deaths in the past. Unfortunately, some viral infections, such as dengue virus (DENV) and human immunodeficiency virus-1 (HIV-1), are still prevailing due to a lack of specific therapeutics, while new pathogenic viral strains or variants are emerging because of high genetic recombination or cross-species transmission. Consequently, to combat the emerging viral infections, bioinformatics-based potential strategies have been developed for viral characterization and developing new effective therapeutics for their eradication or management. This review attempts to provide a single platform for the available wide range of bioinformatics-based approaches, including bioinformatics methods for the identification and management of emerging or evolved viral strains, genome analysis concerning the pathogenicity and epidemiological analysis, computational methods for designing the viral therapeutics, and consolidated information in the form of databases against the known pathogenic viruses. This enriched review of the generally applicable viral informatics approaches aims to provide an overview of available resources capable of carrying out the desired task and may be utilized to expand additional strategies to improve the quality of translation viral informatics research.
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Affiliation(s)
- Sanjay Kumar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Geethu S Kumar
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India.,Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | | | - Petr Malý
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Shiv Bharadwaj
- Laboratory of Ligand Engineering, Institute of Biotechnology of the Czech Academy of Sciences v.v.i., BIOCEV Research Center, Vestec, Czech Republic
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India.,Institute of Advanced Materials, IAAM, 59053 Ulrika, Sweden
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10
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Cakal B, Atasoy A, Cavus B, Poda M, Bulakci M, Gulluoglu M, Demirci M, Akyuz F. Prevalence of occult hepatitis B infection in liver biopsy sample of patients with nonviral liver disease. Future Virol 2022. [DOI: 10.2217/fvl-2021-0316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To determine the prevalence of occult hepatitis B (HBV) infection (OBI) in patients with nonviral liver disease. Materials & methods: This study included 83 HBsAg-negative patients followed up at a gastroenterohepatology clinic. The presence of HBV DNA was investigated by using an in-house nested-PCR method applied to liver parenchymal biopsy samples obtained from patients who underwent due nonviral chronic liver disease. Results: OBI was detected in 19 (22.9%) of the 83 cases, in 11 (44%) of 25 anti-HBc-positive patients, and 15 (31.9%) of 47 anti-HBc and/or anti-HBs antibodies-positive patients. Conclusion: There is a considerable prevalence of OBI among patients with nonviral chronic liver disease. Therefore, it is suggested that closely monitoring HBV can be useful to prevent or more effectively manage possible OBI-related complications among patients with nonviral chronic liver disease, especially those who are HBsAg seronegative or anti-HBV antibody seropositive.
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Affiliation(s)
- Bulent Cakal
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Alp Atasoy
- Division of Gastroenterohepatology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Bilger Cavus
- Division of Gastroenterohepatology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mehves Poda
- Department of Genetics, Aziz Sancar Institute for Experimental Medical Research, Istanbul University, Istanbul, Turkey
| | - Mesut Bulakci
- Department of Radiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mine Gulluoglu
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mehmet Demirci
- Department of Medical Microbiology, Faculty of Medicine, Kirklareli University, Kirklareli, Turkey
| | - Filiz Akyuz
- Division of Gastroenterohepatology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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11
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Nishizawa T, Takahashi M, Matsuoka H, Nishizono A, Yamamoto S, Fukui E, Mizuo H, Kawakami M, Murata K, Okamoto H. Genomic characterization and the prevalence of a novel copiparvovirus in wild sika deer (Cervus nippon) in Japan. Virus Res 2022; 314:198749. [PMID: 35344744 DOI: 10.1016/j.virusres.2022.198749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 11/19/2022]
Abstract
A preliminary metagenomic analysis of the virome of wild sika deer (Cervus nippon) blood in Japan resulted in the identification of a novel parvovirus. The virus was closest, but only 44.7-60.7% identical to 17 reported strains belonging to the genus Copiparvovirus within the subfamily Parvovirinae, over the near-entire genomic sequence. The sika deer copiparvovirus DNA was detected in 15% (31/206) of sika deer captured in 7 prefectures of Japan, and a region-dependent prevalence of 0-66.7% was noted, with a biased distribution in the southern part of Japan. The observed biased distribution of sika deer copiparvovirus may be due to the habitat density of deer and the number of ticks, which might play a role in the transmission of the virus.
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Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan
| | | | - Akira Nishizono
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu, Oita 879-5593, Japan
| | - Seigo Yamamoto
- Miyazaki Prefectural Institute for Public Health and Environment, Miyazaki, Miyazaki 889-2155, Japan
| | - Emiko Fukui
- Laboratory of Animal Breeding and Reproduction, School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Hitoshi Mizuo
- Department of Internal Medicine, Kin-ikyo Chuo Hospital, Sapporo, Hokkaido 007-8505, Japan
| | - Manri Kawakami
- Center for Liver Disease, Okayama Saiseikai General Hospital, Okayama, Okayama 700-8511, Japan
| | - Kazumoto Murata
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi 329-0498, Japan.
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12
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Discrepant results of hepatitis B virus genotype determination by PCR and DNA sequencing. J Virol Methods 2022; 303:114503. [DOI: 10.1016/j.jviromet.2022.114503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/25/2022]
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13
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Oluniyi PE, Ajogbasile FV, Zhou S, Fred-Akintunwa I, Polyak CS, Ake JA, Tovanabutra S, Iroezindu M, Rolland M, Happi CT. HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria. AIDS 2022; 36:137-146. [PMID: 34628443 PMCID: PMC8654252 DOI: 10.1097/qad.0000000000003098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/13/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country. METHODS We used an advanced next-generation sequencing platform, Primer ID, to: investigate the presence of high and low abundance drug resistance mutations; characterize preexisting Integrase Strand Transfer Inhibitor (INSTI) mutations in antiretroviral therapy (ART)-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people with HIV-1 (PWH). RESULTS HIV-1 subtype analysis revealed the predominance of CRF02_AG and subtype G in our study population. At detection sensitivity of 30% abundance, drug resistance mutations (DRMs) were identified in 3% of samples. At a sensitivity level of 10%, DRMs were identified in 27.3% of samples. We did not detect any major INSTI mutation associated with dolutegravir-resistance. Only one recent infection was detected in our study population. CONCLUSION Our study suggests that dolutegravir-containing antiretroviral regimens will be effective in Nigeria. Our study also further emphasizes the high genetic diversity of HIV-1 in Nigeria and that CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria. These two circulating forms of the virus are largely driving the epidemic in the country.
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Affiliation(s)
- Paul E. Oluniyi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Fehintola V. Ajogbasile
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Iyanuoluwa Fred-Akintunwa
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Christina S. Polyak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- HJF Medical Research International, Abuja, Nigeria
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, Maryland, USA
| | - Christian T. Happi
- Department of Biological Sciences, Faculty of Natural Sciences
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
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14
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Bradshaw D, Bibby DF, Manso CF, Piorkowska R, Mohamed H, Ledesma J, Bubba L, Chan YT, Ngui SL, Carne S, Mbisa JL. Clinical evaluation of a Hepatitis C Virus whole-genome sequencing pipeline for genotyping and resistance testing. Clin Microbiol Infect 2021; 28:405-409. [PMID: 34245902 DOI: 10.1016/j.cmi.2021.06.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022]
Abstract
OBJECTIVES We sought to evaluate clinically a hepatitis C virus (HCV) whole-genome, next-generation sequencing (NGS) pipeline that is agnostic to viral genotype. METHODS Performance of the NGS pipeline was assessed through comparison of results with Sanger sequencing (SS) of partial HCV genomes. RESULTS There was 98.7% (376/381) concordance for viral subtype between SS and NGS. The positive and negative per cent agreements for determination of resistance-associated substitutions were 97.8% (95% CI 92.5-99.4%) and 99.9% (95% CI 99.5-100.0%), respectively. The NGS pipeline was also able to detect novel subtypes, mixtures, recombinants, transiently occurring resistance mutations and distinguish re-infection with the same subtype from relapse. DISCUSSION Particular scenarios where NGS may be used include settings without universal access to pan-genotypic antiviral regimens, those infected with a 'rare' subtype or who have been failed by first-line therapy, and in cases of suspected re-infection.
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Affiliation(s)
- Daniel Bradshaw
- National Infection Service, Public Health England, London, UK.
| | - David F Bibby
- National Infection Service, Public Health England, London, UK
| | - Carmen F Manso
- National Infection Service, Public Health England, London, UK
| | | | - Hodan Mohamed
- National Infection Service, Public Health England, London, UK
| | - Juan Ledesma
- National Infection Service, Public Health England, London, UK
| | - Laura Bubba
- National Infection Service, Public Health England, London, UK
| | - Yuen T Chan
- National Infection Service, Public Health England, London, UK
| | - Siew Lin Ngui
- National Infection Service, Public Health England, London, UK
| | - Simon Carne
- National Infection Service, Public Health England, London, UK
| | - Jean L Mbisa
- National Infection Service, Public Health England, London, UK
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- National Infection Service, Public Health England, London, UK
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15
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Phan NMH, Faddy HM, Flower RL, Dimech WJ, Spann KM, Roulis EV. Low Genetic Diversity of Hepatitis B Virus Surface Gene amongst Australian Blood Donors. Viruses 2021; 13:1275. [PMID: 34208852 PMCID: PMC8310342 DOI: 10.3390/v13071275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022] Open
Abstract
Variants in the small surface gene of hepatitis B virus (HBV), which codes for viral surface antigen (HBsAg), can affect the efficacy of HBsAg screening assays and can be associated with occult HBV infection (OBI). This study aimed to characterise the molecular diversity of the HBV small surface gene from HBV-reactive Australian blood donors. HBV isolates from 16 HBsAg-positive Australian blood donors' plasma were sequenced and genotyped by phylogenies of viral coding genes and/or whole genomes. An analysis of the genetic diversity of eight HBV small surface genes from our 16 samples was conducted and compared with HBV sequences from NCBI of 164 international (non-Australian) blood donors. Genotypes A-D were identified in our samples. The region of HBV small surface gene that contained the sequence encoding the 'a' determinant had a greater genetic diversity than the remaining part of the gene. No escape mutants or OBI-related variants were observed in our samples. Variant call analysis revealed two samples with a nucleotide deletion leading to truncation of polymerase and/or large/middle surface amino acid sequences. Overall, we found that HBV small surface gene sequences from Australian donors demonstrated a lower level of genetic diversity than those from non-Australian donor population included in the study.
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Affiliation(s)
- Ngoc Minh Hien Phan
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia; (H.M.F.); (R.L.F.); (K.M.S.); (E.V.R.)
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland 4059, Australia
| | - Helen M. Faddy
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia; (H.M.F.); (R.L.F.); (K.M.S.); (E.V.R.)
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland 4059, Australia
- School of Health and Behavioural Sciences, University of Sunshine Coast, Petrie, Queensland 4502, Australia
| | - Robert L. Flower
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia; (H.M.F.); (R.L.F.); (K.M.S.); (E.V.R.)
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland 4059, Australia
| | - Wayne J. Dimech
- Scientific & Business Relations, National Serology Reference Laboratory, Fitzroy, Victoria 3065, Australia;
| | - Kirsten M. Spann
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia; (H.M.F.); (R.L.F.); (K.M.S.); (E.V.R.)
| | - Eileen V. Roulis
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, Queensland 4059, Australia; (H.M.F.); (R.L.F.); (K.M.S.); (E.V.R.)
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland 4059, Australia
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16
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Nishizawa T, Takahashi M, Tsatsralt-Od B, Nyamdavaa K, Dulmaa N, Osorjin B, Tseren-Ochir EO, Sharav T, Bayasgalan C, Sukhbaatar B, Nagashima S, Murata K, Okamoto H. Identification and a full genome analysis of novel camel hepatitis E virus strains obtained from Bactrian camels in Mongolia. Virus Res 2021; 299:198355. [PMID: 33662492 DOI: 10.1016/j.virusres.2021.198355] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus (HEV) infects humans and a wide variety of other mammalian hosts. Recently, HEV strains belonging to genotype 8 (G8) within the Orthohepevirus A species of the Hepeviridae family, were identified in Bactrian camels (Camelus bactrianus) in China. The Bactrian camel (also known as the Mongolian camel) is native to the steppes of Central Asia. However, the HEV strains of Mongolian camels have not been examined. Among 200 serum samples from domestic Bactrian camels raised on 6 farms, in 6 soums in 3 provinces; 71 (35.5 %) were positive for anti-HEV IgG, with prevalence differing by farm (soum) (4.2-75.0 %); and 2 camels (1.0 %) that had been raised in Bogd, Bayankhongor Province, which had the highest seroprevalence among the six studied areas, were positive for HEV RNA. The two HEV strains (BcHEV-MNG140 and BcHEV-MNG146) obtained from the viremic camels in the present study shared 97.7 % nucleotide identity. They were closest to the reported G8 Chinese camel HEV strains but differed from them by 13.9-14.3 % over the entire genome, with a nucleotide difference of 24.0-26.5 % from the reported G1-G7 HEV strains. A phylogenetic tree indicated that the BcHEV-MNG140 and BcHEV-MNG146 strains were located upstream of a clade consisting of the Chinese camel HEV strains and formed a cluster with them, with a bootstrap value of 100 %, suggesting that they may represent a novel subtype within G8. These results indicate a high prevalence of HEV infection in Mongolian camels and suggest that the variability of camel HEV genomes is markedly high.
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Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Bira Tsatsralt-Od
- National Center for Communicable Diseases, Ministry of Health Mongolia, Ulaanbaatar, 210648, Mongolia
| | | | - Nyamkhuu Dulmaa
- National Center for Communicable Diseases, Ministry of Health Mongolia, Ulaanbaatar, 210648, Mongolia
| | | | - Erdene-Ochir Tseren-Ochir
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, 17024, Mongolia
| | - Tumenjargal Sharav
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, 17024, Mongolia
| | - Chimedtseren Bayasgalan
- Department of Infectious Diseases and Microbiology, School of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar, 17024, Mongolia
| | - Boldbaatar Sukhbaatar
- Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory, Ulaanbaatar, 17024, Mongolia
| | - Shigeo Nagashima
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Kazumoto Murata
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan.
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17
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Guvenir M, Arikan A. Hepatitis B Virus: From Diagnosis to Treatment. Pol J Microbiol 2020; 69:391-399. [PMID: 33574867 PMCID: PMC7812357 DOI: 10.33073/pjm-2020-044] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B infection is still a global concern progressing as acute-chronic hepatitis, severe liver failure, and death. The infection is most widely transmitted from the infected mother to a child, with infected blood and body fluids. Pregnant women, adolescents, and all adults at high risk of chronic infection are recommended to be screened for hepatitis B infection. The initial analysis includes serological tests that allow differentiation of acute and chronic hepatitis. Molecular assays performed provide detection and quantification of viral DNA, genotyping, drug resistance, and precore/core mutation analysis to confirm infection and monitor disease progression in chronic hepatitis B patients. All patients with chronic hepatitis B should be treated with antiviral medications and regularly monitored for efficient treatment. The current treatment is based on nucleos(t)ide analogs and pegylated interferons that save lives by decreasing liver cancer death, liver transplant, slow or reverse the progression of liver disease as well as the virus infectivity.
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Affiliation(s)
- Meryem Guvenir
- Near East University, Vocational School of Health Services, Nicosia, Northern Cyprus
| | - Ayse Arikan
- Near East University, Faculty of Medicine, Department of Medical Microbiology, Nicosia, Northern Cyprus
- Near East University, DESAM Institute, Nicosia, Northern Cyprus
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18
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Prevalence and genotype/subtype distribution of hepatitis E virus (HEV) among wild boars in Japan: Identification of a genotype 5 HEV strain. Virus Res 2020; 287:198106. [PMID: 32777387 DOI: 10.1016/j.virusres.2020.198106] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
To further investigate the prevalence of hepatitis E virus (HEV) infection and characterize HEV genomes among Japanese wild boars (Sus scrofa leucomystax), 1880 boars captured in 17 prefectures in Japan from 2013 to 2019 were studied. Overall, anti-HEV IgG was detected in 8.9 % and HEV RNA was detected in 3.9 % of boars, which was comparable with our previous studies during 2003-2013 (10.3 % and 3.5 %, respectively). Among 74 boar HEV strains obtained from infected boars in the present study, 50 (68 %) were classified into genotype 3 (3a and 3b), 23 (31 %) were classified into genotype 4 (4i), and the remaining strain (wbJGF_19-1) was classified into genotype 5. The wbGF_19-1 strain shared 92.7 % identity over the entire genome with the prototype genotype 5 strain (JBOAR135-Shiz09). The identification of the second genotype 5 HEV strain in a place that is located only 100 km from the site at which JBOAR135-Shiz09 was identified, suggests that genotype 5 HEV circulates within a relatively close range in Japan. Genetically similar HEV strains forming a clade were identified from wild boars living in each area during the observation period of 11-13 years, although the nucleotide sequence changed gradually, accounting for up to 3.4-3.6 % within the 412-nucleotide ORF2 sequence. Eight groups of boars with a cluster of HEV infections were observed, consisting of two, three or four infected offspring, presumably born to the same mother or offspring with their mother. These results suggest that wild boars continue to be important reservoirs for HEV infection in humans in Japan.
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19
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Kyaw YY, Lwin AA, Aye KS, Thu HM, Htun MM, Soe HO, Aye KT, Thant KZ, Hwang HJ, Cheong J. Distribution of hepatitis B virus genotypes in the general population of Myanmar via nationwide study. BMC Infect Dis 2020; 20:552. [PMID: 32727389 PMCID: PMC7392661 DOI: 10.1186/s12879-020-05269-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/16/2020] [Indexed: 12/12/2022] Open
Abstract
Background Hepatitis B virus (HBV) infections are a severe health concern worldwide. HBV is a DNA virus with a rapid rate of mutation. Based on heterogeneity of the nucleotide sequence, the HBV strains are divided into nine genotypes, each with a characteristic geographical distribution. Identifying and tracking alterations of HBV genotypes is important in epidemiological and transmission studies, and contributes to predicting the risk for development of severe liver disease and response to antiviral treatment. The present study was undertaken to detect HBV genotypes and sub-genotypes in the general population of different states and regions in Myanmar. Methods In 2015, a total of 5547 adults of the general population, residing in seven states, seven regions and the Nay Pyi Taw Union Territory, were screened for Hepatitis B Surface antigen (HBsAg) by the immunochromatographic test (ICT). Of the 353 HBsAg positive samples, the HBVDNA was identified using polymerase chain reactions (PCR) targeting the DNA sequences encoding the Pre-S region. A total of 153 PCR positive samples were subsequently subjected to genotyping by partial genome sequencing in both directions. The resulting sequences were then edited, aligned, and compared with reference sequences using the National Centre for Biotechnology Information (NCBI) web-based genotyping tool. Results Three HBV genotypes (HBV genotype B, genotype C and genotype D) were detected in Myanmar, of which genotype HBV genotype C (66.7%) was the most prevalent, followed by HBV genotype D (32%) and HBV genotype B (1.3%). Sub-genotyping revealed a total of 7 variants within the B, C and D genotypes: 2 (B4 and B5) in HBV genotype B, 3 (C1, C5 and C7) in HBV genotype C, and 2 (D3 and D6) in HBV genotype D. Conclusion HBV genotype C, sub-genotype C1 was predominantly distributed in all states and regions of Myanmar. This study is the first report on the nationwide distribution of HBV genotypes and sub-genotypes in Myanmar. We believe our findings will enable huge support for the hepatitis disease surveillance program, since HBV infection is one of the National Priority Diseases in Myanmar.
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Affiliation(s)
- Yi Yi Kyaw
- Advanced Molecular Research Centre, Department of Medical Research, Republic of Union of Myanmar, Yangon, Myanmar.,Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Aye Aye Lwin
- Department of Medical Research, Republic of Union of Myanmar, Yangon, Republic of the Union of Myanmar
| | - Khin Saw Aye
- Department of Medical Research, Republic of Union of Myanmar, Yangon, Republic of the Union of Myanmar
| | - Hlaing Myat Thu
- Department of Medical Research, Republic of Union of Myanmar, Yangon, Republic of the Union of Myanmar
| | - Moh Moh Htun
- Department of Medical Research, Republic of Union of Myanmar, Yangon, Republic of the Union of Myanmar
| | - Hnin Ohmar Soe
- Advanced Molecular Research Centre, Department of Medical Research, Republic of Union of Myanmar, Yangon, Myanmar
| | - Kay Thi Aye
- Advanced Molecular Research Centre, Department of Medical Research, Republic of Union of Myanmar, Yangon, Myanmar
| | - Kyaw Zin Thant
- Department of Medical Research, Republic of Union of Myanmar, Yangon, Republic of the Union of Myanmar
| | - Hyeon Jeong Hwang
- Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - JaeHun Cheong
- Department of Molecular Biology, Pusan National University, Busan, 46241, Republic of Korea.
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20
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Ostankova YV, Semenov AV, Zueva EB, Nogoybaeva KA, Kasymbekova KT, Tobokalova ST, Totolian AA. [The prevalence clinically significant virus mutations among patients with chronic viral hepatitis B.]. Klin Lab Diagn 2020; 65:61-66. [PMID: 32155009 DOI: 10.18821/0869-2084-2020-65-1-61-66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/16/2019] [Indexed: 11/17/2022]
Abstract
The prevalence of clinically significant virus mutations in patients with chronic viral hepatitis B from the Kyrgyz Republic was analyzed. Blood plasma samples of 64 patients with verified chronic viral hepatitis B obtained from Kyrgyzstan indigenous people were used in the work. Asymmetric PCR was carried out with extended oligonucleotides and the first reaction amplification product was further used in a new PCR with one of the nested pairs overlapping primers that flanked the entire HBV genome together, followed by sequencing. Based on the phylogenetic analysis of 64 HBV isolates obtained from patients from the Kyrgyz Republic, it was shown that only the genotype D virus was present in the examined group, the HBV subgenotype D1 (68.75%) prevailed compared with the HBV subgenotype D2 (18.75%) and subgenotype D3 (12.5%). For all subgenotypes, several independent infection sources are obvious, subclusters that include isolates from Kyrgyzstan, Kazakhstan and Uzbekistan are distinguished, as well as subclusters that include isolates only from Kyrgyzstan, which are less similar to isolates previously deposited in the international database, which probably indicates an independent HBV homologous evolution in the region. Clinically significant mutations were identified in 26.5% of patients. Including 12.5% with escape mutations that prevent the virus detection and / or allow the virus to replicate despite the vaccine (122K, 128V, 133I, 134N). Another 12.5% of the isolates are characterized by mutations that are independently associated with the liver cirrhosis and hepatocellular carcinoma development, including 21, 24, 27 nucleotides deletions in the Pre-S2 region and the S11F mutation in the PreCore region. In one case, unusual 236S and 250P mutations were found in the positions described as drug resistance sites of the P region associated with the resistance development to adefovir, tenofovir, and entecavir. The hepatitis B virus genetic structure analysis, early virus mutations detection in patients with chronic hepatitis B virus can help to choose the right vaccination strategy, antiviral and immunosuppressive therapy, as well as predict the clinical course and disease progression.
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Affiliation(s)
- Y V Ostankova
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia
| | - A V Semenov
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia.,Saint-Petersburg State Medical University n.a. acad. I.P. Pavlov, 197022, Saint Petersburg, Russia.,North-West State Medical University n.a. I.I. Mechnikov, 191015, Saint Petersburg, Russia
| | - E B Zueva
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia
| | - K A Nogoybaeva
- Kyrgyz State Medical Institute of Retraining and Skill, 720040, Bishkek, Kyrgyz Republic
| | - K T Kasymbekova
- Kyrgyz State Medical Institute of Retraining and Skill, 720040, Bishkek, Kyrgyz Republic
| | - S T Tobokalova
- Kyrgyz State Medical Institute of Retraining and Skill, 720040, Bishkek, Kyrgyz Republic
| | - A A Totolian
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia.,Saint-Petersburg State Medical University n.a. acad. I.P. Pavlov, 197022, Saint Petersburg, Russia
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21
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Bradshaw D, Vasylyeva TI, Davis C, Pybus OG, Thézé J, Thomson EC, Martinello M, Matthews GV, Burholt R, Gilleece Y, Cooke GS, Page EE, Waters L, Nelson M. Transmission of hepatitis C virus in HIV-positive and PrEP-using MSM in England. J Viral Hepat 2020; 27:721-730. [PMID: 32115809 DOI: 10.1111/jvh.13286] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/12/2019] [Accepted: 02/18/2020] [Indexed: 12/14/2022]
Abstract
We sought to characterize risk factors and patterns of HCV transmission amongst men who have sex with men (MSM). MSM with recently acquired HCV (AHCV) were prospectively recruited ('clinic cohort') between January and September 2017. Clinical data and risk behaviours were identified and blood obtained for HCV whole genome sequencing. Phylogenetic analyses were performed, using sequences from this cohort and two other AHCV cohorts, to identify transmission clusters. Sixteen (40.0%) men in the clinic cohort were HIV-negative MSM. HIV-negative MSM were younger than HIV-positive MSM; most (81.3%) had taken HIV PrEP in the preceding year. Eighteen men (45.0%) reported injection drug use; most (34, 85.0%) reported noninjection drug use in the last year. Most in both groups reported condomless anal sex, fisting and sex in a group environment. Few (7, 17.5%) men thought partners may have had HCV. There were 52 sequences in the HCV genotype 1a phylogeny, 18 from the clinic cohort and 34 from other AHCV cohorts; 47 (90.4%) clustered with ≥1 other sequence. There were 7 clusters of 2-27 sequences; 6 clusters contained HIV-negative and HIV-positive MSM and 1 cluster only HIV-positive MSM. Four of these clusters were part of larger clusters first described in 2007. PrEP-using MSM are at risk of HCV, sharing similar risk factors to HIV-positive MSM. Phylogenetics highlights that PrEP-using and HIV-positive MSM are involved in the same HCV transmission networks. Few men demonstrated HCV awareness and risk reduction strategies should be expanded.
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Affiliation(s)
- Daniel Bradshaw
- Department of HIV and Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | | | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Gail V Matthews
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Ruth Burholt
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Yvonne Gilleece
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | | | - Emma E Page
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Mark Nelson
- Department of HIV and Sexual Health, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
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22
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New Subtype B Containing HIV-1 Circulating Recombinant of sub-Saharan Africa Origin in Nigerian Men Who Have Sex With Men. J Acquir Immune Defic Syndr 2020; 81:578-584. [PMID: 31107298 DOI: 10.1097/qai.0000000000002076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND HIV-1 circulating recombinant forms (CRF) containing subtype B are uncommon in sub-Saharan Africa. Prevalent infections observed during enrollment of a prospective study of men who have sex with men (MSM) from Lagos, Nigeria, revealed the presence of a family of subtype B and CRF02_AG recombinants. This report describes the HIV-1 genetic diversity within a high-risk, high-prevalence, and previously undersampled cohort of Nigerian MSM. METHODS Between 2013 and 2016, 672 MSM were enrolled at the Lagos site of the TRUST/RV368 study. Prevalent HIV-1 infections were initially characterized by pol sequencing and phylogenetic subtyping analysis. Samples demonstrating the presence of subtype B were further characterized by near full-length sequencing, phylogenetic, and Bayesian analyses. RESULTS Within this cohort, HIV-1 prevalence was 59%. The major subtype was CRF02_AG (57%), followed by CRF02/B recombinants (15%), subtype G (13%), and smaller amounts of A1, B, and other recombinants. Nine clusters of closely related pol sequences indicate ongoing transmission events within this cohort. Among the CRF02_AG/B, a new CRF was identified and termed CRF95_02B. Shared risk factors and Bayesian phylogenetic inference of the new CRF95_02B and the similarly structured CRF56_cpx indicate a Nigerian or West African origin of CRF56_cpx before its observation in France. CONCLUSION With high HIV-1 prevalence, new strains, and multiple transmission networks, this cohort of Nigerian MSM represents a previously hidden reservoir of HIV-1 strains, including the newly identified CRF95_02B and closely related CRF56_cpx. These strains will need to be considered during vaccine selection and development to optimize the design of a globally effective HIV-1 vaccine.
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23
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In silico Analysis of Genetic Diversity of Human Hepatitis B Virus in Southeast Asia, Australia and New Zealand. Viruses 2020; 12:v12040427. [PMID: 32283837 PMCID: PMC7232418 DOI: 10.3390/v12040427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023] Open
Abstract
The extent of whole genome diversity amongst hepatitis B virus (HBV) genotypes is not well described. This study aimed to update the current distribution of HBV types and to investigate mutation rates and nucleotide diversity between genotypes in Southeast Asia, Australia and New Zealand. We retrieved 930 human HBV complete genomes from these regions from the NCBI nucleotide database for genotyping, detection of potential recombination, serotype prediction, mutation identification and comparative genome analyses. Overall, HBV genotypes B (44.1%) and C (46.2%) together with predicted serotypes adr (36%), adw2 (29%) and ayw1 (19.9%) were the most commonly circulating HBV types in the studied region. The three HBV variants identified most frequently were p.V5L, c.1896G>A and double mutation c.1762A>T/c.1764G>A, while genotypes B and C had the widest range of mutation types. The study also highlighted the distinct nucleotide diversity of HBV genotypes for whole genome and along the genome length. Therefore, this study provided a robust update to HBV currently circulating in Southeast Asia, Australia and New Zealand as well as an insight into the association of HBV genetic hypervariability and prevalence of well reported mutations.
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24
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Zhang M, Li G, Shang J, Pan C, Zhang M, Yin Z, Xie Q, Peng Y, Mao Q, Xiao X, Jiang Y, Luo K, Xu Y, Ding H, Fan W, Diego V, Pourkarim MR, De Clercq E, Wang G, Gong G. Rapidly decreased HBV RNA predicts responses of pegylated interferons in HBeAg-positive patients: a longitudinal cohort study. Hepatol Int 2020; 14:212-224. [PMID: 32100261 PMCID: PMC7136184 DOI: 10.1007/s12072-020-10015-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/18/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND As an important anti-HBV drug, pegylated interferon α (PegIFNα) offers promising clinical efficacy, but biomarkers that accurately forecast treatment responses are yet to be elucidated. Here, we evaluated whether HBV RNA could act as an early monitor of pegylated interferon responses. METHODS We analyzed a phase 3, multicenter, randomized cohort of 727 HBeAg-positive non-cirrhotic patients receiving a 48-week treatment of PegIFNα-2a or PegIFNα-2b and a 24-week treatment-free follow-up. Serum levels of HBV RNA, HBV DNA, HBeAg, and HBsAg were measured at weeks 0, 12, 24, 48, and 72. RESULTS HBeAg seroconversion and HBsAg loss at week 72 were observed in 217 (29.8%) and 21 (2.9%) patients, respectively. During the 48-week treatment, HBV RNA decreased more rapidly than HBV DNA and HBsAg, but HBV RNA and HBeAg shared similar dynamics with positive correlations. Multivariate regression analyses consistently revealed the significance of HBV RNA at weeks 0, 12, 24, and 48 to monitor HBeAg seroconversion but not HBsAg loss. Although baseline HBV RNA only showed a modest AUC performance, HBV RNA with a significant increase of AUC at week 12 outperformed other HBV biomarkers to forecast HBeAg seroconversion (p value < 0.05). HBV RNA ≤ 1000 copies/mL was an optimized cutoff at week 12 that offered better prediction than other HBV biomarkers. This optimized cutoff plus patient age, HBV genotype B, and HBeAg offered a strong estimation of HBeAg seroconversion (accuracy 95.2%, true negative rate 99.8%). CONCLUSION HBV RNA at week 12 is an effective monitor of HBeAg seroconversion in HBeAg-positive patients treated with pegylated interferons.
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Affiliation(s)
- Min Zhang
- Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Guangdi Li
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, 410078, Hunan, China
| | - Jia Shang
- Department of Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
| | - Chen Pan
- Department of Gastroenterology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, 350025, Fujian, China
| | - Minxiang Zhang
- Department of Infectious Diseases, The Sixth People's Hospital of Shengyang, Shengyang, 110006, Liaoning, China
| | - Zhibiao Yin
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, 510260, Guangdong, China
| | - Qing Xie
- Department of Infectious Diseases, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanzhong Peng
- Department of Infectious Diseases, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Qing Mao
- Chongqing Key Laboratory for Research of Infectious Diseases, Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Xinqiang Xiao
- Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yongfang Jiang
- Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Kaizhong Luo
- Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yun Xu
- Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Hai Ding
- Hunan Sansure Biotech Incorporation, Changsha, 410205, Hunan, China
| | - Wenzhou Fan
- Hunan Sansure Biotech Incorporation, Changsha, 410205, Hunan, China
| | - Vidaurre Diego
- Oxford Centre for Human Brain Activity, University of Oxford, Oxford, OX3 7JX, UK
| | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, Division of Clinical and Epidemiological Virology, KU Leuven, 3000, Leuven, Belgium
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Erik De Clercq
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Guiqiang Wang
- Department of Infectious Diseases, The Center for Liver Diseases, Peking University First Hospital, Beijing, 100034, China.
| | - Guozhong Gong
- Institute of Hepatology and Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
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25
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Lorenzin G, Gargiulo F, Caruso A, Caccuri F, Focà E, Celotti A, Quiros-Roldan E, Izzo I, Castelli F, De Francesco MA. Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis. Microorganisms 2019; 8:microorganisms8010036. [PMID: 31878069 PMCID: PMC7022943 DOI: 10.3390/microorganisms8010036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms; subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included >10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.
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Affiliation(s)
- Giovanni Lorenzin
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
- Institute of Microbiology and Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy
| | - Franco Gargiulo
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
| | - Arnaldo Caruso
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
| | - Francesca Caccuri
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
| | - Emanuele Focà
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Anna Celotti
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Ilaria Izzo
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (E.F.); (A.C.); (E.Q.-R.); (I.I.); (F.C.)
| | - Maria A. De Francesco
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia-Spedali Civili, 25123 Brescia, Italy; (G.L.); (F.G.); (A.C.); (F.C.)
- Correspondence: ; Tel.: +39-030-399-5860
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26
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Araújo PMM, Martins JS, Osório NS. SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. Virus Evol 2019; 5:vez050. [PMID: 31768265 PMCID: PMC6863187 DOI: 10.1093/ve/vez050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy/releases.
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Affiliation(s)
- Pedro M M Araújo
- Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Joana S Martins
- Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
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27
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Kafando A, Serhir B, Doualla-Bell F, Fournier E, Sangaré MN, Martineau C, Sylla M, Chamberland A, El-Far M, Charest H, Tremblay CL. A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses. AIDS Res Hum Retroviruses 2019; 35:906-919. [PMID: 31407606 PMCID: PMC6806616 DOI: 10.1089/aid.2019.0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.
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Affiliation(s)
- Alexis Kafando
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Bouchra Serhir
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Florence Doualla-Bell
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Mohamed Ndongo Sangaré
- Département de Médecine Sociale et Préventive, École de Santé Publique, Université de Montréal, Montréal, Canada
| | - Christine Martineau
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Mohamed Sylla
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Annie Chamberland
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Mohamed El-Far
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
| | - Hugues Charest
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
| | - Cécile L. Tremblay
- Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Canada
- Laboratoire de Santé Publique du Québec, Institut National de Santé publique du Québec, Sainte-Anne-de-Bellevue, Canada
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada
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28
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Uribe-Noguez LA, Mata-Marín JA, Ocaña-Mondragón A, Pompa-Mera EN, Ribas-Aparicio RM, Arroyo-Anduiza CI, Gomez-Torres ME, Chaparro-Sánchez A, Gaytán-Martínez J, Mauss S. Comparison of direct sequencing of the NS5B region with the Versant HCV genotype 2.0 assay for genotyping of viral isolates in Mexico. J Infect Chemother 2019; 26:205-210. [PMID: 31537472 DOI: 10.1016/j.jiac.2019.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
Hepatitis C virus (HCV) infection affects an estimated 71 million people worldwide. HCV is classified into eight genotypes and >70 subtypes. Determination of HCV genotype is important for selection of type and duration of antiviral therapy, and genotype is also a predictor of treatment response. The most commonly used HCV genotyping method in clinical laboratories is a hybridization-based line probe assay (LiPA; Versant HCV Genotype 2.0). However, these methods have a lack of specificity in genotype identification and subtype assignment. Here, we compared the performance of Versant HCV Genotype 2.0 with the gold standard direct sequencing of the NS5B region, in 97 samples from Mexican patients. We found a genotypic concordance of 63.9% between these methods. While 68 samples (70%) were classified into HCV genotype 1 (GT1) by NS5B sequencing, it was not true for 17 samples (17.5%), which were not match HCV subtype by LiPA. Furthermore, nine of the 33 samples classified by NS5B sequencing as GT1a were not identified by LiPA. Use of direct sequencing could improve selection of the optimal therapy, avoid possible failures of therapy and avoid high costs resulting from incorrect genotyping tests in settings without broad access to pangenotypic regimens.
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Affiliation(s)
- Luis Antonio Uribe-Noguez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico; Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico; Centro de Simulación Médica, Facultad Mexicana de Medicina, Universidad La Salle, Mexico City, Mexico.
| | - José Antonio Mata-Marín
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alicia Ocaña-Mondragón
- Laboratorio Central de Epidemiología, División de Laboratorios de Vigilancia e Investigación Epidemiológica, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Ericka Nelly Pompa-Mera
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, IPN, Mexico City, Mexico
| | - Carla Ileana Arroyo-Anduiza
- Departamento de Patología Clínica, Banco Central de Sangre, CMN "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - María Elena Gomez-Torres
- Laboratorio de Urgencias, Hospital de Infectología, Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Alberto Chaparro-Sánchez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Jesus Gaytán-Martínez
- Departamento de Enfermedades Infecciosas, Hospital de Infectología, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social, IMSS, Mexico City, Mexico
| | - Stefan Mauss
- Center for HIV and Hepatogastroenterology, Duesseldorf, Germany
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Tovanabutra S, Sirijatuphat R, Pham PT, Bonar L, Harbolick EA, Bose M, Song H, Chang D, Oropeza C, O'Sullivan AM, Balinang J, Kroon E, Colby DJ, Sacdalan C, Hellmuth J, Chan P, Prueksakaew P, Pinyakorn S, Jagodzinski LL, Sutthichom D, Pattamaswin S, de Souza M, Gramzinski RA, Kim JH, Michael NL, Robb ML, Phanuphak N, Ananworanich J, Valcour V, Kijak GH, Sanders-Buell E, Spudich S. Deep Sequencing Reveals Central Nervous System Compartmentalization in Multiple Transmitted/Founder Virus Acute HIV-1 Infection. Cells 2019; 8:E902. [PMID: 31443253 PMCID: PMC6721674 DOI: 10.3390/cells8080902] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/10/2019] [Accepted: 08/11/2019] [Indexed: 01/31/2023] Open
Abstract
HIV-1 disseminates to a broad range of tissue compartments during acute HIV-1 infection (AHI). The central nervous system (CNS) can serve as an early and persistent site of viral replication, which poses a potential challenge for HIV-1 remission strategies that target the HIV reservoir. CNS compartmentalization is a key feature of HIV-1 neuropathogenesis. Thus far, the timing of how early CNS compartmentalization develops after infection is unknown. We examined whether HIV-1 transmitted/founder (T/F) viruses differ between CNS and blood during AHI using single-genome sequencing of envelope gene and further examined subregions in pol and env using next-generation sequencing in paired plasma and cerebrospinal fluid (CSF) from 18 individuals. Different proportions of mostly minor variants were found in six of the eight multiple T/F-infected individuals, indicating enrichment of some variants in CSF that may lead to significant compartmentalization in the later stages of infection. This study provides evidence for the first time that HIV-1 compartmentalization in the CNS can occur within days of HIV-1 exposure in multiple T/F infections. Further understanding of factors that determine enrichment of T/F variants in the CNS, as well as potential long-term implications of these findings for persistence of HIV-1 reservoirs and neurological impairment in HIV, is needed.
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Affiliation(s)
- Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.
| | - Rujipas Sirijatuphat
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Phuc T Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Lydia Bonar
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Elizabeth A Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Hongshuo Song
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - David Chang
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Celina Oropeza
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Anne Marie O'Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Joyce Balinang
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Eugene Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Donn J Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Joanna Hellmuth
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Phillip Chan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | | | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Linda L Jagodzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | | | | | - Mark de Souza
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Robert A Gramzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- International Vaccine Institute, Seoul 08826, Korea
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
- Academic Medical Center, Department of Global Health, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Serena Spudich
- Department of Neurology, Yale University; New Haven, CT 06510, USA
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Rezanezhadi M, Mohebbi A, Askari FS, Hosseini SD, Tabarraei A. Hepatitis B virus reverse transcriptase polymorphisms between treated and treatment-naïve chronically infected patients. Virusdisease 2019; 30:219-226. [PMID: 31179360 PMCID: PMC6531556 DOI: 10.1007/s13337-018-00510-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/29/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of this study was investigation of variation(s) in the Hepatitis B virus (HBV) reverse transcriptase domain. 120 patients with chronic HBV infection recruited. 104 patients were received nucleos(t)ide analogs treatments. DNA extractions were done from plasma samples. Direct sequencing and alignment of Polymerase Chain Reaction products were applied for further analysis. HBV genotypes determined by NCBI's Genotyping Tool. Polymorphism(s) were detected by using DnaSP software. Of 120 samples, 98 were sequenced. All of products were HBV genotype D. 13/98 (13.27%) of patients had M539I/V substitutions corresponding to YMDD motif. FLLAQ to FLMAQ was observed among 22/98 (22.98) patients. Two substitutions N459Y and L515M were significantly correlated (R2 = 0.486 and R2 = 0.941 respectively) with FLLAQ motif variation. Mutation ratio among treatment-received patients to treatment-naïve patients was 0.2-0.6. Drug resistance conferring substitutions (DRCSs) were rtL180M (22/98), rtA194V (11/98), rtM204V (1/98), and rtM204I (11/98). Furthermore, six variants were observed among all patients. Appearance of DRCSs in HBV polymerase is a major obstacle to the virus treatments. In the present study, it was shown that DRCSs are more prevalent among treated patients. Therefore, replacement of current anti-viral regimen with novel anti-HBV drugs is warranted in the future.
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Affiliation(s)
- Masoumeh Rezanezhadi
- Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alireza Mohebbi
- Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Diseases Research Centre, Golestan University of Medical Sciences, Gorgan, Iran
| | - Fatemeh Sana Askari
- Student Research Committee, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Alijan Tabarraei
- Infectious Diseases Research Centre, Golestan University of Medical Sciences, Gorgan, Iran
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HIV-1 genetic diversity and demographic characteristics in Bulgaria. PLoS One 2019; 14:e0217063. [PMID: 31136611 PMCID: PMC6538145 DOI: 10.1371/journal.pone.0217063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
HIV-1 strain diversity in Bulgaria is extensive and includes contributions from nearly all major subtypes and the Circulating Recombinant Forms (CRF): 01_AE, 02_AG, and 05_DF. Prior to this study, HIV-1 sequence information from Bulgaria has been based solely on the pro-RT gene, which represent less than 15% of the viral genome. To further characterize HIV-1 in Bulgaria, assess participant risk behaviors, and strengthen knowledge of circulating strains in the region, the study “Genetic Subtypes of HIV-1 in Bulgaria (RV240)” was conducted. This study employed the real time-PCR based Multi-region Hybridization Assay (MHA) B/non-B and HIV-1 sequencing to survey 215 of the approximately 1100 known HIV-1 infected Bulgarian adults (2008–2009) and determine if they were infected with subtype B HIV-1. The results indicated a subtype B prevalence of 40% and demonstrate the application of the MHA B/non-B in an area containing broad HIV-1 strain diversity. Within the assessed risk behaviors, the proportion of subtype B infection was greatest in men who have sex with men and lowest among those with drug use risk factors. During this study, 15 near full-length genomes and 22 envelope sequences were isolated from study participants. Phylogenetic analysis shows the presence of subtypes A1, B, C, F1, and G, CRF01_AE, CRF02_AG, CRF05_DF, and one unique recombinant form (URF). These sequences also show the presence of two strain groups containing participants with similar risk factors. Previous studies in African and Asian cohorts have shown that co-circulation of multiple subtypes can lead to viral recombination within super-infected individuals and the emergence of new URFs. The low prevalence of URFs in the presence of high subtype diversity in this study, may be the result of successful infection prevention and control programs. Continued epidemiological monitoring and support of infection prevention programs will help maintain control of the HIV-1 epidemic in Bulgaria.
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Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual. Immunity 2019; 50:677-691.e13. [PMID: 30876875 DOI: 10.1016/j.immuni.2019.02.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/13/2018] [Accepted: 02/13/2019] [Indexed: 12/21/2022]
Abstract
Lineage-based vaccine design is an attractive approach for eliciting broadly neutralizing antibodies (bNAbs) against HIV-1. However, most bNAb lineages studied to date have features indicative of unusual recombination and/or development. From an individual in the prospective RV217 cohort, we identified three lineages of bNAbs targeting the membrane-proximal external region (MPER) of the HIV-1 envelope. Antibodies RV217-VRC42.01, -VRC43.01, and -VRC46.01 used distinct modes of recognition and neutralized 96%, 62%, and 30%, respectively, of a 208-strain virus panel. All three lineages had modest levels of somatic hypermutation and normal antibody-loop lengths and were initiated by the founder virus MPER. The broadest lineage, VRC42, was similar to the known bNAb 4E10. A multimeric immunogen based on the founder MPER activated B cells bearing the unmutated common ancestor of VRC42, with modest maturation of early VRC42 intermediates imparting neutralization breadth. These features suggest that VRC42 may be a promising template for lineage-based vaccine design.
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Fedonin GG, Fantin YS, Favorov AV, Shipulin GA, Neverov AD. VirGenA: a reference-based assembler for variable viral genomes. Brief Bioinform 2019; 20:15-25. [PMID: 28968771 PMCID: PMC6488938 DOI: 10.1093/bib/bbx079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Characterization of the within-host genetic diversity of viral pathogens is required for selection of effective treatment of some important viral infections, e.g. HIV, HBV and HCV. Despite the technical ability of detection, there are conflicting data regarding the clinical significance of low-frequency variants, partially because of the difficulty of their distinguishing from experimental artifacts. The issue of cross-contamination is relevant for all highly sensitive techniques, including deep sequencing: even trace contamination leads to a significant increase of false positives in identified SNVs. Determination of infections by multiple genotypes of some viruses, the incidence of which can be considerable, especially in risk groups, is also clinically significant in some cases. We developed a new viral reference-guided assembler, VirGenA, that can separate mixtures of strains of different intraspecies genetic groups (genotypes, subtypes, clades, etc.) and assemble a separate consensus sequence for each group in a mixture. It produced long assemblies for mixture components of extremely low frequencies (<1%) allowing detection of cross-contamination of samples by divergent genotypes. We tested VirGenA on both clinical and simulated data. On both types of data, VirGenA shows better or similar results than the existing de novo assemblers. Cross-platform implementation (including source code) is freely available at https://github.com/gFedonin/VirGenA/releases.
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Affiliation(s)
- Gennady G Fedonin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Yury S Fantin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Alexnader V Favorov
- Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University
| | - German A Shipulin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
| | - Alexey D Neverov
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology
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Bioinformatics Applications in Advancing Animal Virus Research. RECENT ADVANCES IN ANIMAL VIROLOGY 2019. [PMCID: PMC7121192 DOI: 10.1007/978-981-13-9073-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Viruses serve as infectious agents for all living entities. There have been various research groups that focus on understanding the viruses in terms of their host-viral relationships, pathogenesis and immune evasion. However, with the current advances in the field of science, now the research field has widened up at the ‘omics’ level. Apparently, generation of viral sequence data has been increasing. There are numerous bioinformatics tools available that not only aid in analysing such sequence data but also aid in deducing useful information that can be exploited in developing preventive and therapeutic measures. This chapter elaborates on bioinformatics tools that are specifically designed for animal viruses as well as other generic tools that can be exploited to study animal viruses. The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. Various databases that organize information on animal and human viruses have also been described. The chapter will converse on overview of the current advances, online and downloadable tools and databases in the field of bioinformatics that will enable the researchers to study animal viruses at gene level.
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Biswas A, Firdaus R, Saha K, Chowdhury P, Bhattacharya D, Bhattacharyya M, Sadhukhan PC. Post-transfusion hepatitis C virus infection among β-thalassaemic individuals with associated clinical parameters. Indian J Med Res 2018; 147:581-587. [PMID: 30168490 PMCID: PMC6118143 DOI: 10.4103/ijmr.ijmr_127_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background & objectives Multiple transfusions in β-thalassaemia patients undergoing regular transfusion regimen are at a risk of developing transfusion transmitted infections, including hepatitis C virus (HCV). The present study was conducted to investigate the association of HCV viraemia and genotype with clinical parameters in HCV seroreactive β-thalassaemic individuals. Methods A total of 172 HCV seroreactive β-thalassaemic individuals aged between 2-35 yr with at least 25 units of blood transfusion were catagorized into four groups (2-12 yr, group 1; 13-19 yr, group 2; 20-29 yr, group 3; 30-35 yr, group 4). Aged matched control samples (n=87; β-thalassaemics without HCV infection) were also included. HCV RNA was detected by nested reverse transcriptase polymerase chain reaction (RT-PCR) based on 5' UTR of HCV genome, viral load was determined by real-time RT-PCR. Nested RT-PCR amplified partial core region was used for DNA sequencing. Liver function parameters [serum total bilirubin, alanine aminotransferase (ALT) and aspartate aminotransferase (AST)] were also determined. Results Of the 172 HCV seroreactive individuals, 59.30 per cent (n=102) were HCV RNA positive. HCV viral load ranged from 173 to 32.04×10[5] IU/ml; 87.65 per cent were infected with HCV genotype 3. Liver enzymes, such as ALT, AST and serum total bilirubin were significantly elevated in all age groups compared to control groups. Serum ferritin levels were found to be high in all individuals, but 16.27 per cent of HCV-infected individuals with >10,000 IU/ml viral load also showed high ferritin levels (>1500 μg/l) where the majority of them were infected with HCV genotype 3. Interpretation & conclusions HCV genotype 3 was the major circulating genotype among β-thalassaemia patients in this region. Our findings indicated an association between HCV replication and hepatic iron load and also highlighted the need for sensitive quantitative RT-PCR-based detection of HCV RNA in the high risk population.
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Affiliation(s)
- Aritra Biswas
- ICMR Virus Unit, Peerless Hospital & B. K. Roy Research Centre, Kolkata, India
| | - Rushna Firdaus
- ICMR Virus Unit, Peerless Hospital & B. K. Roy Research Centre, Kolkata, India
| | - Kallol Saha
- ICMR Virus Unit, Peerless Hospital & B. K. Roy Research Centre, Kolkata, India
| | - Prosanto Chowdhury
- Department of Hematology, Peerless Hospital & B. K. Roy Research Centre, Kolkata, India
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An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes. PLoS One 2018; 13:e0206409. [PMID: 30427878 PMCID: PMC6235296 DOI: 10.1371/journal.pone.0206409] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/14/2018] [Indexed: 01/11/2023] Open
Abstract
For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers. This potentially exposes sensitive patient data to unauthorized access, and makes it impossible to determine how classifications are made and to maintain the data provenance of clinical bioinformatic workflows. We propose an open-source supervised and alignment-free subtyping method (Kameris) that operates on k-mer frequencies in HIV-1 sequences. We performed a detailed study of the accuracy and performance of subtype classification in comparison to four state-of-the-art programs. Based on our testing data set of manually curated real-world HIV-1 sequences (n = 2, 784), Kameris obtained an overall accuracy of 97%, which matches or exceeds all other tested software, with a processing rate of over 1,500 sequences per second. Furthermore, our fully standalone general-purpose software provides key advantages in terms of data security and privacy, transparency and reproducibility. Finally, we show that our method is readily adaptable to subtype classification of other viruses including dengue, influenza A, and hepatitis B and C virus.
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HCV Infection among Injecting Drug Users in Prishtina, Kosovo. HEPATITIS MONTHLY 2018. [DOI: 10.5812/hepatmon.80189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Fung J, Cheung KS, Wong DKH, Mak LY, To WP, Seto WK, Lai CL, Yuen MF. Long-term outcomes and predictive scores for hepatocellular carcinoma and hepatitis B surface antigen seroclearance after hepatitis B e-antigen seroclearance. Hepatology 2018. [PMID: 29534307 DOI: 10.1002/hep.29874] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
UNLABELLED The significance of hepatitis B e-antigen (HBeAg) seroclearance (ESC) in the long term is not well defined. The current study aimed to determine the clinical outcomes, the factors and predictive scores for hepatocellular carcinoma (HCC), and hepatitis B surface antigen (HBsAg) seroclearance of a large cohort of patients undergoing ESC. Patients with documented ESC were followed up 3- to 6-monthly. Baseline characteristics and longitudinal laboratory results were recorded. Predictive scores for HCC (HCC-ESC) and HBsAg seroclearance (HBsAg-ESC) were derived from multivariate Cox regression models. A total of 723 patients underwent ESC with a median ESC age and follow-up of 36.0 and 18.3 years, respectively. Only 3.5% and 3.0% had persistently normal alanine aminotransferase (ALT) and HBV DNA <2logs IU/mL, respectively, after ESC. For patients with 100%, 100%-90%, 90%-50%, 50%-10%, 10%-0%, and 0% normal ALT after HBeAg seroclearance, the rate of HCC was 4.3%, 2.2%, 3.6%, 3.9%, 17.3%, and 37.2% at 20 years after ESC, respectively (P < 0.001). At 20 years after ESC, the cumulative incidence of HCC and HBsAg seroclearance was 7.9% and 13.5%, respectively, with an overall survival of 91.5%. ESC age, male sex, cirrhosis, hypoalbuminemia, viral load, and ALT were significant factors for HCC, whereas ESC age, male sex, viral load, and antiviral therapy were significant factors for HBsAg seroclearance. The area under receiver operating characteristics for HCC-ESC and HBsAg-ESC scores to predict HCC and HBsAg seroclearance at 20 years after ESC was 0.92 and 0.74, respectively. CONCLUSION Male sex, older age at ESC, ALT, and higher level of HBV DNA were associated with higher rates of HCC after ESC. HCC-ESC and HBsAg-ESC predictive scores can determine the likelihood of developing HCC and achieving HBsAg seroclearance. (Hepatology 2018).
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Affiliation(s)
- James Fung
- Department of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR
| | - Ka-Shing Cheung
- Department of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Danny Ka-Ho Wong
- Department of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR
| | - Lung-Yi Mak
- Department of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Wai-Pan To
- Department of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Wai-Kay Seto
- Department of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR
| | - Ching-Lung Lai
- Department of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR
| | - Man-Fung Yuen
- Department of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong SAR
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Rhee SY, Shafer RW. Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences. Sci Data 2018; 5:180148. [PMID: 30063225 PMCID: PMC6067049 DOI: 10.1038/sdata.2018.148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/21/2018] [Indexed: 12/11/2022] Open
Abstract
Accurate classification of HIV-1 group M lineages, henceforth referred to as subtyping, is essential for understanding global HIV-1 molecular epidemiology. Because most HIV-1 sequencing is done for genotypic resistance testing pol gene, we sought to develop a set of geographically-stratified pol sequences that represent HIV-1 group M sequence diversity. Representative pol sequences differ from representative complete genome sequences because not all CRFs have pol recombination points and because complete genome sequences may not faithfully reflect HIV-1 pol diversity. We developed a software pipeline that compiled 6,034 one-per-person complete HIV-1 pol sequences annotated by country and year belonging to 11 pure subtypes and 70 CRFs and selected a set of sequences whose average distance to the remaining sequences is minimized for each subtype/CRF and country to generate a Geographically-Stratified set of 716 Pol Subtype/CRF (GSPS) reference sequences. We provide extensive data on pol diversity within each subtype/CRF and country combination. The GSPS reference set will also be useful for HIV-1 pol subtyping.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94301, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94301, USA
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Virtanen E, Mannonen L, Lappalainen M, Auvinen E. Genotyping of hepatitis C virus by nucleotide sequencing: A robust method for a diagnostic laboratory. MethodsX 2018; 5:414-418. [PMID: 30050759 PMCID: PMC6060086 DOI: 10.1016/j.mex.2018.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 04/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hepatitis C virus (HCV) is a globally significant blood-borne agent causing liver diseases, and it has infected over 170 million people worldwide. HCV is a diverse group of RNA viruses currently divided into genotypes 1-7 as well as subtypes. HCV infection can be treated with antiviral drugs, but the HCV genotype has to be determined for optimal selection of treatment strategy. The aim of this study was to set up a sequencing-based HCV genotyping method suitable for the workflow of a diagnostic laboratory. The established method is robust and stable, and it utilizes a one-step reverse transcription and PCR amplification of the 5' untranslated region (5'UTR) and partial Core region of the HCV genome. Amplification products are sequenced using the standard Sanger method, and the genotype is determined by using a freely accessible web-based genotyping tool. The method was validated at the Helsinki University Hospital Laboratory using 238 previously genotyped serum samples. •A new one-step RT-PCR method for the amplification of the 5' untranslated region and partial Core region of hepatitis C virus was established.•HCV genotype is determined using Sanger sequencing and a freely accessible, easy-to-use web-based genotyping tool.•The method is robust, reproducible and suitable for diagnostic laboratory workflow, and it requires no costly instrumentation or specialized sequence analysis skills.
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Evolutionary dynamics of Hepatitis C virus in a chronic HIV co-infected patient and its correlation with the immune status. INFECTION GENETICS AND EVOLUTION 2018; 63:30-38. [PMID: 29733983 DOI: 10.1016/j.meegid.2018.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/23/2018] [Accepted: 05/03/2018] [Indexed: 01/06/2023]
Abstract
The HCV evolutionary dynamics play a key role in the infection onset, maintenance of chronicity, pathogenicity, and drug resistance variants fixation, and are thought to be one of the main caveats in the development of an effective vaccine. Previous studies in HCV/HIV co-infected patients suggest that a decline in the immune status is related with increases in the HCV intra-host genetic diversity. However, these findings are based on single point sequence diversity measures or coalescence analyses in several virus-host interactions. In this work, we describe the molecular evolution of HCV-E2 region in a single HIV-co-infected patient with two clearly defined immune conditions. The phylogenetic analysis of the HCV-1a sequences from the studied patient showed that he was co-infected with three different viral lineages. These lineages were not evenly detected throughout time. The sequence diversity and coalescence analyses of these lineages suggested the action of different evolutionary patterns in different immune conditions: a slow rate, drift-like process in an immunocompromised condition (low levels of CD4+ T lymphocytes); and a fast rate, variant-switch process in an immunocompetent condition (high levels of CD4+ T lymphocytes).
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Complete Genome Sequence of a Circulating Hepatitis B Virus Genotype C Strain Isolated from a Chronically Infected Patient Identified at an Outdoor Hospital in Bangladesh. GENOME ANNOUNCEMENTS 2018; 6:6/9/e01601-17. [PMID: 29496845 PMCID: PMC5834336 DOI: 10.1128/genomea.01601-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Hepatitis B virus (HBV) causes significant global health problems despite the presence of a potential vaccine. HBV chronic cases are increasing rapidly in developing countries like Bangladesh. Here, we report the complete genome sequence of an HBV genotype C strain isolated from a chronic patient identified at an outdoor hospital section.
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Ambachew H, Zheng M, Pappoe F, Shen J, Xu Y. Genotyping and sero-virological characterization of hepatitis B virus (HBV) in blood donors, Southern Ethiopia. PLoS One 2018; 13:e0193177. [PMID: 29462187 PMCID: PMC5819820 DOI: 10.1371/journal.pone.0193177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/06/2018] [Indexed: 12/18/2022] Open
Abstract
Hepatitis B virus (HBV) prevalence is highest in Sub-Saharan Africa including Ethiopia. HBV genotypes have distinct geographic distributions and play a role in course of infection and treatment management. However, in Ethiopia there is paucity of information about distribution of HBV genotypes. This study was done to determine genotype, mutation and sero-virological profiles of HBV isolates in Southern Ethiopia. Cross-sectional, laboratory based study was conducted on 103HBsAg sero-positive samples from a total of 2,237 screened blood donors. HBV serological markers and biochemical assays were done. Serum viral load was measured using quantitative real-time PCR. Partial HBV S-gene was amplified with nested PCR and sequenced. Bioinformatics tools were utilized to determine genotypes, serotypes and mutations. Of 103 HBsAg reactive serum samples, 14.6% and 70.9% were sero-positive for HBeAg and HBeAb, respectively. Ninety-eight samples gave detectable viral load with a median of 3.46(2.62-4.82) log IU/ml. HBeAg sero-positive donors carried elevated levels of viral load. Eighty five isolates were successfully amplified, sequenced and genotyped into 58 (68.2%) genotype A (HBV/A) and 27 (31.8%) genotype D (HBV/D). HBV serotypes found were adw2 (74.1%), ayw2 (24.7%), and ayw3 (1.2%). In twenty-four (28.2%) samples mutations in the major hydrophilic region (MHR) were observed. Donors infected with HBV/A had higher viral load and more frequent MHR mutation than HBV/D infected donors. This study illustrated distribution of HBV genotype A and D among blood donors in southern Ethiopia. It also demonstrated occurrence HBV variants that may influence clinical aspects of HBV infection. The study contributes in narrowing the existing gap of HBV molecular study in Ethiopia.
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Affiliation(s)
- Henock Ambachew
- Department of Clinical Laboratory, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Clinical Laboratory Diagnostics, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Meijuan Zheng
- Department of Clinical Laboratory, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Clinical Laboratory Diagnostics, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Faustina Pappoe
- Department of Immunology and Parasitology, Provincial Laboratory of Microbiology and Parasitology and the Key Laboratory of Zoonoses Anhui, Anhui Medical University, Hefei, Anhui, China
- Department of Microbiology and Immunology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Jilong Shen
- Department of Clinical Laboratory Diagnostics, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Immunology and Parasitology, Provincial Laboratory of Microbiology and Parasitology and the Key Laboratory of Zoonoses Anhui, Anhui Medical University, Hefei, Anhui, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Clinical Laboratory Diagnostics, First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Immunology and Parasitology, Provincial Laboratory of Microbiology and Parasitology and the Key Laboratory of Zoonoses Anhui, Anhui Medical University, Hefei, Anhui, China
- * E-mail:
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Kafando A, Fournier E, Serhir B, Martineau C, Doualla-Bell F, Sangaré MN, Sylla M, Chamberland A, El-Far M, Charest H, Tremblay CL. HIV-1 envelope sequence-based diversity measures for identifying recent infections. PLoS One 2017; 12:e0189999. [PMID: 29284009 PMCID: PMC5746209 DOI: 10.1371/journal.pone.0189999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/06/2017] [Indexed: 12/17/2022] Open
Abstract
Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC) of the receiver operating characteristic (ROC). Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001). Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806), gp120 C2_3 (AUC = 0.805) and gp120 V3 (AUC = 0.812). Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.
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Affiliation(s)
- Alexis Kafando
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Eric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Bouchra Serhir
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Florence Doualla-Bell
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of medicine, division of experimental medicine, McGill University, Montreal, Québec, Canada
| | - Mohamed Ndongo Sangaré
- Département de médecine sociale et préventive, École de santé publique, université de Montréal, Montréal, Québec, Canada
| | - Mohamed Sylla
- Centre de recherche du centre hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Annie Chamberland
- Centre de recherche du centre hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Mohamed El-Far
- Centre de recherche du centre hospitalier de l’Université de Montréal, Montréal, Québec, Canada
| | - Hugues Charest
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Cécile L. Tremblay
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
- Centre de recherche du centre hospitalier de l’Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Novel Genetic Variants of Hepatitis B Virus in Fulminant Hepatitis. J Pathog 2017; 2017:1231204. [PMID: 29410920 PMCID: PMC5749291 DOI: 10.1155/2017/1231204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023] Open
Abstract
Fulminant hepatitis (FH) is a life-threatening liver disease characterised by intense immune attack and massive liver cell death. The common precore stop codon mutation of hepatitis B virus (HBV), A1896, is frequently associated with FH, but lacks specificity. This study attempts to uncover all possible viral nucleotides that are specifically associated with FH through a compiled sequence analysis of FH and non-FH cases from acute infection. We retrieved 67 FH and 280 acute non-FH cases of hepatitis B from GenBank and applied support vector machine (SVM) model to seek candidate nucleotides highly predictive of FH. Six best candidates with top predictive accuracy, 92.5%, were used to build a SVM model; they are C2129 (85.3%), T720 (83.0%), Y2131 (82.4%), T2013 (82.1%), K2048 (82.1%), and A2512 (82.1%). This model gave a high specificity (99.3%), positive predictive value (95.6%), and negative predictive value (92.1%), but only moderate sensitivity (64.2%). We successfully built a SVM model comprising six variants that are highly predictive and specific for FH: four in the core region and one each in the polymerase and the surface regions. These variants indicate that intracellular virion/core retention could play an important role in the progression to FH.
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Liu Z, Liu F, Wang L, Liu Y, Zhang M, Li T. Clinical characteristics and outcomes of patients with recurrent chronic hepatitis B after nucleos(t)ide analog withdrawal with stringent cessation criteria: A prospective cohort study. Hepatol Res 2017; 47:1000-1007. [PMID: 27917568 DOI: 10.1111/hepr.12836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/02/2016] [Accepted: 10/30/2016] [Indexed: 12/28/2022]
Abstract
AIM The aim of this study was to explore the clinical characteristics and outcomes of patients with recurrent chronic hepatitis B meeting the cessation criteria outlined by the 2008 Asian Pacific Association for the Study of the Liver guidelines. METHODS In total, 223 chronic hepatitis B patients who met the cessation criteria and discontinued nucleos(t)ide analog therapy were prospectively included. They were monitored monthly during the first 4 months and every 3-6 months thereafter. Early relapse was defined as viral relapse (serum hepatitis B virus [HBV] DNA >104 copies/mL) confirmed within 3 months after cessation. RESULTS Of the 38 hepatitis B e antigen (HBeAg)-positive relapse cases, 44.7%, 65.8%, 76.3% and 89.5% occurred within 3 months, 6 months, 12 months, and 48 months, respectively; in the 49 HBeAg-negative relapse cases, 44.9%, 51.0%, 77.6% and 91.8% occurred within 3, 6, 12 and 36 months, respectively. Time to undetectable HBV DNA was a predictive factor of early relapse. Viral relapses were accompanied by elevated alanine aminotransferase in 70 (80.5%) patients. A peak alanine aminotransferase 10 times over the upper limit of normal after relapse was observed in 15.8% of the HBeAg-positive and 22.4% of the HBeAg-negative patients. Hepatic decompensation and liver failure were not observed. CONCLUSIONS For HBeAg-positive and HBeAg-negative patients meeting stringent cessation criteria, at least 4 years and 3 years of close follow-up are necessary. For those with a longer time to undetectable HBV DNA, more attention should be paid to the early stages after cessation. Nucleos(t)ide analog withdrawal in selected non-cirrhotic patients is generally safe, although close monitoring and timely intervention are needed.
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Affiliation(s)
- Zhirong Liu
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China.,Jinan Infectious Disease Hospital, Shandong University School of Medicine, Jinan, China
| | - Feng Liu
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China
| | - Lei Wang
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China
| | - Youde Liu
- Yantai Infectious Disease Hospital, Yantai, China
| | - Meng Zhang
- Jinan Infectious Disease Hospital, Shandong University School of Medicine, Jinan, China
| | - Tao Li
- Department of Infectious Diseases and Hepatology, The Second Hospital of Shandong University, Jinan, China
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Ndow G, Gore ML, Shimakawa Y, Suso P, Jatta A, Tamba S, Sow A, Touré-Kane C, Sadiq F, Sabally S, Njie R, Thursz MR, Lemoine M. Hepatitis B testing and treatment in HIV patients in The Gambia-Compliance with international guidelines and clinical outcomes. PLoS One 2017; 12:e0179025. [PMID: 28614401 PMCID: PMC5470698 DOI: 10.1371/journal.pone.0179025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Compliance with WHO guidelines on HBV screening and treatment in HIV-coinfected patients is often challenging in resource limited countries and has been poorly assessed in sub-Saharan Africa. METHODS Between 2015 and 2016, we assessed physician's compliance with WHO guidelines on HIV-HBV coinfection in the largest HIV clinic in The Gambia, and the hepatic outcomes in HIV-HBV coinfected patients as compared to randomly selected HIV-monoinfected controls. RESULTS 870 HIV-infected patients regularly seen in this clinic agreed to participate in our study. Only 187 (21.5%, 95% CI 18.8-24.3) had previously been screened for HBsAg, 23 (12.3%, 95% CI 8.0-17.9) were positive of whom none had liver assessment and only 6 (26.1%) had received Tenofovir. Our HBV testing intervention was accepted by all participants and found 94/870 (10.8%, 95% CI 8.8-13.1) positive, 78 of whom underwent full liver assessment along with 40 HBsAg-negative controls. At the time of liver assessment, 61/78 (78.2%) HIV-HBV coinfected patients received ART with 7 (11.5%) on Tenofovir and 54 (88.5%) on Lamivudine alone. HIV-HBV coinfected patients had higher APRI score compared to controls (0.58 vs 0.42, p = 0.002). HBV DNA was detectable in 52/53 (98.1%) coinfected patients with 14/53 (26.4%) having HBV DNA >20,000 IU/L. 10/12 (83.3%) had at least one detectable 3TC-associated HBV resistance, which tended to be associated with increase in liver fibrosis after adjusting for age and sex (p = 0.05). CONCLUSIONS Compliance with HBV testing and treatment guidelines is poor in this Gambian HIV programme putting coinfected patients at risk of liver complications. However, the excellent uptake of HBV screening and linkage to care in our study suggests feasible improvements.
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Affiliation(s)
- Gibril Ndow
- Division of Digestive Diseases, Department of Surgery & Cancer, St. Mary’s Hospital Campus, Imperial College London, United Kingdom
- Hepatitis Unit, Disease Control & Elimination, MRC Unit The Gambia, Fajara, The Gambia
| | - Mindy L. Gore
- Section of Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Yusuke Shimakawa
- Unité d’Épidémiologie des Maladies Émergentes, Institut Pasteur, Paris, France
| | - Penda Suso
- Hepatitis Unit, Disease Control & Elimination, MRC Unit The Gambia, Fajara, The Gambia
| | - Abdoulie Jatta
- Hepatitis Unit, Disease Control & Elimination, MRC Unit The Gambia, Fajara, The Gambia
| | - Saydiba Tamba
- Hepatitis Unit, Disease Control & Elimination, MRC Unit The Gambia, Fajara, The Gambia
| | - Amina Sow
- Laboratoire Bactériologie-Virologie, CHU Aristide Le Dantec, Université Cheikh Anta DIOP, Dakar, Senegal
| | - Coumba Touré-Kane
- Laboratoire Bactériologie-Virologie, CHU Aristide Le Dantec, Université Cheikh Anta DIOP, Dakar, Senegal
| | - Fouzia Sadiq
- Division of Digestive Diseases, Department of Surgery & Cancer, St. Mary’s Hospital Campus, Imperial College London, United Kingdom
| | - Saihou Sabally
- Hands on Care HIV Clinic, Brikama Health Centre, Brikama, The Gambia
| | - Ramou Njie
- Hepatitis Unit, Disease Control & Elimination, MRC Unit The Gambia, Fajara, The Gambia
- International Agency for Research on Cancer (IARC), WHO, Lyon, France
| | - Mark R. Thursz
- Division of Digestive Diseases, Department of Surgery & Cancer, St. Mary’s Hospital Campus, Imperial College London, United Kingdom
| | - Maud Lemoine
- Division of Digestive Diseases, Department of Surgery & Cancer, St. Mary’s Hospital Campus, Imperial College London, United Kingdom
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Smoleń-Dzirba J, Rosińska M, Kruszyński P, Bratosiewicz-Wąsik J, Wojtyczka R, Janiec J, Szetela B, Beniowski M, Bociąga-Jasik M, Jabłonowska E, Wąsik TJ, The Cascade Collaboration In EuroCoord A. Prevalence of Transmitted Drug-Resistance Mutations and Polymorphisms in HIV-1 Reverse Transcriptase, Protease, and gp41 Sequences Among Recent Seroconverters in Southern Poland. Med Sci Monit 2017; 23:682-694. [PMID: 28167814 PMCID: PMC5310230 DOI: 10.12659/msm.898656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Monitoring of drug resistance-related mutations among patients with recent HIV-1 infection offers an opportunity to describe current patterns of transmitted drug resistance (TDR) mutations. Material/Methods Of 298 individuals newly diagnosed from March 2008 to February 2014 in southern Poland, 47 were deemed to have recent HIV-1 infection by the limiting antigen avidity immunoassay. Proviral DNA was amplified and sequenced in the reverse transcriptase, protease, and gp41 coding regions. Mutations were interpreted according to the Stanford Database algorithm and/or the International Antiviral Society USA guidelines. TDR mutations were defined according to the WHO surveillance list. Results Among 47 patients with recent HIV-1 infection only 1 (2%) had evidence of TDR mutation. No major resistance mutations were found, but the frequency of strains with ≥1 accessory resistance-associated mutations was high, at 98%. Accessory mutations were present in 11% of reverse transcriptase, 96% of protease, and 27% of gp41 sequences. Mean number of accessory resistance mutations in the reverse transcriptase and protease sequences was higher in viruses with no compensatory mutations in the gp41 HR2 domain than in strains with such mutations (p=0.031). Conclusions Despite the low prevalence of strains with TDR mutations, the frequency of accessory mutations was considerable, which may reflect the history of drug pressure among transmitters or natural viral genetic diversity, and may be relevant for future clinical outcomes. The accumulation of the accessory resistance mutations within the pol gene may restrict the occurrence of compensatory mutations related to enfuvirtide resistance or vice versa.
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Affiliation(s)
- Joanna Smoleń-Dzirba
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Magdalena Rosińska
- Department of Epidemiology, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
| | - Piotr Kruszyński
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Jolanta Bratosiewicz-Wąsik
- Department of Biopharmacy, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Robert Wojtyczka
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
| | - Janusz Janiec
- Department of Epidemiology, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Hepatology, and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Marek Beniowski
- Outpatient Clinic for AIDS Diagnostics and Therapy, Specialistic Hospital in Chorzów, Chorzów, Poland
| | - Monika Bociąga-Jasik
- Department of Infectious Diseases, Jagiellonian University Medical College, Cracow, Poland
| | - Elżbieta Jabłonowska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | - Tomasz J Wąsik
- Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Katowice, Poland
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Tsimpidis M, Bachoumis G, Mimouli K, Kyriakopoulou Z, Robertson DL, Markoulatos P, Amoutzias GD. T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics 2017; 18:13. [PMID: 28056784 PMCID: PMC5216575 DOI: 10.1186/s12859-016-1420-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/10/2016] [Indexed: 12/22/2022] Open
Abstract
Background Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods. Results T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. Conclusions T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
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Affiliation(s)
- Michail Tsimpidis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Georgios Bachoumis
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Kalliopi Mimouli
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece
| | - Zaharoula Kyriakopoulou
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | | | - Panayotis Markoulatos
- Department of Biochemistry and Biotechnology, Molecular Virology Laboratory, University of Thessaly, Larisa, Greece
| | - Grigoris D Amoutzias
- Department of Biochemistry and Biotechnology, Bioinformatics Laboratory, University of Thessaly, Larisa, Greece.
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Mossoro-Kpinde CD, Mboumba Bouassa RS, Jenabian MA, Wolyec ST, Robin L, Matta M, Longo JDD, Grésenguet G, Andreoletti L, Bélec L. Analytical Performances of Human Immunodeficiency Virus Type 1 RNA-Based Amplix® Real-Time PCR Platform for HIV-1 RNA Quantification. AIDS Res Treat 2016; 2016:7954810. [PMID: 28050283 PMCID: PMC5165142 DOI: 10.1155/2016/7954810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/03/2016] [Indexed: 11/22/2022] Open
Abstract
Objectives. We evaluated the performances of Amplix real-time PCR platform developed by Biosynex (Strasbourg, France), combining automated station extraction (Amplix station 16 Dx) and real-time PCR (Amplix NG), for quantifying plasma HIV-1 RNA by lyophilized HIV-1 RNA-based Amplix reagents targeting gag and LTR, using samples from HIV-1-infected adults from Central African Republic. Results. Amplix real-time PCR assay showed low limit of detection (28 copies/mL), across wide dynamic range (1.4-10 log copies/mL), 100% sensitivity and 99% specificity, high reproducibility, and accuracy with mean bias < 5%. The assay showed excellent correlations and concordance of 95.3% with the reference HIV-1 RNA load assay (Roche), with mean absolute bias of +0.097 log copies/mL by Bland-Altman analysis. The assay was able to detect and quantify the most prevalent HIV-1 subtype strains and the majority of non-B subtypes, CRFs of HIV-1 group M, and HIV-1 groups N and O circulating in Central Africa. The Amplix assay showed 100% sensitivity and 99.6% specificity to diagnose virological failure in clinical samples from antiretroviral drug-experienced patients. Conclusions. The HIV-1 RNA-based Amplix real-time PCR platform constitutes sensitive and reliable system for clinical monitoring of HIV-1 RNA load in HIV-1-infected children and adults, particularly adapted to intermediate laboratory facilities in sub-Saharan Africa.
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Affiliation(s)
- Christian Diamant Mossoro-Kpinde
- Laboratoire National de Biologie Clinique et de Santé Publique, Bangui, Central African Republic
- Faculté des Sciences de la Santé, Université de Bangui, Bangui, Central African Republic
| | - Ralph-Sydney Mboumba Bouassa
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
- Université Paris Descartes, Paris Sorbonne Cité, Paris, France
| | - Mohammad-Ali Jenabian
- Département des Sciences Biologiques et Centre de Recherche BioMed, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Serge Tonen Wolyec
- Faculté de Médecine, Université de Bunia, Bunia, Democratic Republic of the Congo
| | - Leman Robin
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Mathieu Matta
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Jean de Dieu Longo
- Faculté des Sciences de la Santé, Université de Bangui, Bangui, Central African Republic
- Centre National de Référence des Maladies Sexuellement Transmissibles et de la Thérapie Antirétrovirale, Bangui, Central African Republic
- Unité de Recherches et d'Intervention sur les Maladies Sexuellement Transmissibles et le SIDA, Département de Santé Publique, Faculté des Sciences de la Santé de Bangui, Bangui, Central African Republic
| | - Gérard Grésenguet
- Faculté des Sciences de la Santé, Université de Bangui, Bangui, Central African Republic
- Unité de Recherches et d'Intervention sur les Maladies Sexuellement Transmissibles et le SIDA, Département de Santé Publique, Faculté des Sciences de la Santé de Bangui, Bangui, Central African Republic
| | - Laurent Andreoletti
- Laboratoire de Virologie Médicale et Moléculaire, EA-4684/SFR CAP-SANTE, Reims, France
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
- Université Paris Descartes, Paris Sorbonne Cité, Paris, France
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