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Laiho JE, Oikarinen S, Morfopoulou S, Oikarinen M, Renner A, Depledge D, Ross MC, Gerling IC, Breuer J, Petrosino JF, Plagnol V, Pugliese A, Toniolo A, Lloyd RE, Hyöty H. Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.11.24313112. [PMID: 39314969 PMCID: PMC11419248 DOI: 10.1101/2024.09.11.24313112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Aims/hypothesis The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas and other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of pancreas samples collected to date. Methods We analysed pancreas, spleen, pancreatic lymph nodes, and duodenum samples from the following donor groups: a) donors with type 1 diabetes (n=71), with (n=35) or without (n=36) insulin-containing islets, (b) donors with single or double islet autoantibody positivity without diabetes (n=22) and c) autoantibody-negative donors without diabetes (control donors) (n=74). Five research laboratories participated in this collaborative effort using approaches for unbiased discovery of RNA viruses (two RNA-Seq platforms), targeted detection of Enterovirus A-D species using RT-PCR, and tests for virus growth in cell-culture. Results Direct RNA-Seq did not detect virus signal in pancreas samples, whereas RT-PCR detected enterovirus RNA confirmed by sequencing in low amounts in pancreas samples in three of the five donor groups, namely donors with type 1 diabetes with insulin-containing islets, 16% (5/32) donors being positive, donors with single islet autoantibody positivity with 53% (8/15) donors being positive, and non-diabetic donors with 8% (4/49) being enterovirus RNA positive. Detection of enterovirus RNA was significantly more frequent in single islet autoantibody-positive donors compared to donors with type 1 diabetes with insulin-deficient islets (p-value <0.001) and control donors (p-value 0.004). In some donors, pancreatic lymph nodes were also positive. RT-PCR detected enterovirus RNA also in spleen of a small number of donors and virus enrichment in susceptible cell lines before RT-PCR resulted in much higher rate in spleen positivity, particularly in donors with type 1 diabetes. Interestingly, the enterovirus strains detected did not cause a typical lytic infection, possibly reflecting their persistence-prone nature. Conclusions/interpretation This was the largest coordinated effort to examine the presence of enterovirus RNA in pancreas of organ donors with type 1 diabetes, using a multitude of assays. These findings are consistent with the notion that both the subjects with type 1 diabetes and those with islet autoantibodies may carry a low-grade enterovirus infection in the pancreas and lymphoid tissues.
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Affiliation(s)
- Jutta E Laiho
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Sofia Morfopoulou
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Maarit Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Ashlie Renner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Depledge
- NYU, Grossman School of Medicine, New York, New York, United States
| | - Matthew C Ross
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan C Gerling
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Alberto Pugliese
- Department of Diabetes Immunology, Arthur Riggs Diabetes & Metabolism Research Institute, Beckmann Research Institute, City of Hope, Duarte, United States
| | | | - Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Finland
- Fimlab Laboratories, Tampere, Finland
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland
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Ortigas-Vasquez A, Szpara M. Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity. Annu Rev Virol 2024; 11:67-87. [PMID: 38848592 DOI: 10.1146/annurev-virology-100422-010336] [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] [Indexed: 06/09/2024]
Abstract
The arrival of novel sequencing technologies throughout the past two decades has led to a paradigm shift in our understanding of herpesvirus genomic diversity. Previously, herpesviruses were seen as a family of DNA viruses with low genomic diversity. However, a growing body of evidence now suggests that herpesviruses exist as dynamic populations that possess standing variation and evolve at much faster rates than previously assumed. In this review, we explore how strategies such as deep sequencing, long-read sequencing, and haplotype reconstruction are allowing scientists to dissect the genomic composition of herpesvirus populations. We also discuss the challenges that need to be addressed before a detailed picture of herpesvirus diversity can emerge.
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Affiliation(s)
- Alejandro Ortigas-Vasquez
- Departments of Biology and of Biochemistry and Molecular Biology; Center for Infectious Disease Dynamics; and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Moriah Szpara
- Departments of Biology and of Biochemistry and Molecular Biology; Center for Infectious Disease Dynamics; and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA;
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Venturini C, Colston JM, Charles O, Lankina A, Best T, Atkinson C, Forrest C, Williams CA, Rao K, Worth A, Thorburn D, Harber M, Griffiths P, Breuer J. Persistent Low-Level Variants in a Subset of Viral Genes Are Highly Predictive of Poor Outcome in Immunocompromised Patients With Cytomegalovirus Infection. J Infect Dis 2024; 230:e427-e436. [PMID: 38181168 PMCID: PMC11326829 DOI: 10.1093/infdis/jiae001] [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: 01/09/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Human cytomegalovirus (HCMV) is the most common and serious opportunistic infection after solid organ and hematopoietic stem cell transplantation. In this study, we used whole-genome HCMV data to investigate viral factors associated with the clinical outcome. METHODS We sequenced HCMV samples from 16 immunocompromised pediatric patients with persistent viremia. Eight of the 16 patients died of complications due to HCMV infection. We also sequenced samples from 35 infected solid organ adult recipients, of whom 1 died with HCMV infection. RESULTS We showed that samples from both groups have fixed variants at resistance sites and mixed infections. Next-generation sequencing also revealed nonfixed variants at resistance sites in most of the patients who died (6/9). A machine learning approach identified 10 genes with nonfixed variants in these patients. These genes formed a viral signature that discriminated patients with HCMV infection who died from those who survived with high accuracy (area under the curve = 0.96). Lymphocyte numbers for a subset of patients showed no recovery posttransplant in the patients who died. CONCLUSIONS We hypothesize that the viral signature identified in this study may be a useful biomarker for poor response to antiviral drug treatment and indirectly for poor T-cell function, potentially identifying early those patients requiring nonpharmacological interventions.
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Affiliation(s)
- Cristina Venturini
- Infection, Immunity and Inflammation, Institute of Child Health, University College London (UCL)
| | - Julia M Colston
- North Bristol National Health Service (NHS) Trust, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol
| | - Oscar Charles
- Infection, Immunity and Inflammation, Institute of Child Health, University College London (UCL)
| | - Anastasia Lankina
- Infection, Immunity and Inflammation, Institute of Child Health, University College London (UCL)
| | - Timothy Best
- Virology Department, Great Ormond Street Hospital for Children NHS Foundation Trust
| | - Claire Atkinson
- Applied Science, London South Bank University
- Division of Infection and Immunity, Institute for Immunity and Transplantation, UCL
| | - Calum Forrest
- Division of Infection and Immunity, Institute for Immunity and Transplantation, UCL
| | - Charlotte A Williams
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, UCL
| | | | - Austen Worth
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, London
| | - Doug Thorburn
- Department of Nephrology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Mark Harber
- Department of Nephrology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Paul Griffiths
- Division of Infection and Immunity, Institute for Immunity and Transplantation, UCL
| | - Judith Breuer
- Infection, Immunity and Inflammation, Institute of Child Health, University College London (UCL)
- Virology Department, Great Ormond Street Hospital for Children NHS Foundation Trust
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Medina JE, Castañeda S, Camargo M, Garcia-Corredor DJ, Muñoz M, Ramírez JD. Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle. Vet Res Commun 2024; 48:2029-2049. [PMID: 38865041 DOI: 10.1007/s11259-024-10403-2] [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: 10/10/2023] [Accepted: 05/01/2024] [Indexed: 06/13/2024]
Abstract
Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Mosquera, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Farrall T, Brawner J, Dinsdale A, Kehoe M. A Review of Probe-Based Enrichment Methods to Inform Plant Virus Diagnostics. Int J Mol Sci 2024; 25:8348. [PMID: 39125919 PMCID: PMC11312432 DOI: 10.3390/ijms25158348] [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: 06/06/2024] [Revised: 07/20/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Modern diagnostic techniques based on DNA sequence similarity are currently the gold standard for the detection of existing and emerging pathogens. Whilst individual assays are inexpensive to use, assay development is costly and carries risks of not being sensitive or specific enough to capture an increasingly diverse range of targets. Sequencing can provide the entire nucleic acid content of a sample and may be used to identify all pathogens present in the sample when the depth of coverage is sufficient. Targeted enrichment techniques have been used to increase sequence coverage and improve the sensitivity of detection within virus samples, specifically, to capture sequences for a range of different viruses or increase the number of reads from low-titre virus infections. Vertebrate viruses have been well characterised using in-solution hybridisation capture to target diverse virus families. The use of probes for genotyping and strain identification has been limited in plants, and uncertainty around sensitivity is an impediment to the development of a large-scale virus panel to use within regulatory settings and diagnostic pipelines. This review aims to compare significant studies that have used targeted enrichment of viruses to identify approaches to probe design and potential for use in plant virus detection and characterisation.
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Affiliation(s)
- Thomas Farrall
- Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra, ACT 2601, Australia; (T.F.); (A.D.)
- Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Jeremy Brawner
- Forest Research Institute, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | - Adrian Dinsdale
- Plant Innovation Centre, Australian Government, Department of Agriculture, Fisheries and Forestry (DAFF), Canberra, ACT 2601, Australia; (T.F.); (A.D.)
| | - Monica Kehoe
- Diagnostic Laboratory Services, Biosecurity and Sustainability, Department of Primary Industries and Regional Development (DPIRD), Perth, WA 6151, Australia
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Meng Z, Wang S, Yu L, Zhao K, Wu T, Zhu X, Yang N, Qiao Q, Ma J, Wu B, Ge Y, Cui L. A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition. mSystems 2024; 9:e0122223. [PMID: 38564711 PMCID: PMC11097644 DOI: 10.1128/msystems.01222-23] [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: 12/05/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Rapid and accurate sequencing of the entire viral genome, coupled with continuous monitoring of genetic changes, is crucial for understanding the epidemiology of coronaviruses. We designed a novel method called micro target hybrid capture system (MT-Capture) to enable whole-genome sequencing in a timely manner. The novel design of probes used in target binding exhibits a unique and synergistic "hand-in-hand" conjugation effect. The entire hybrid capture process is within 2.5 hours, overcoming the time-consuming and complex operation characteristics of the traditional liquid-phase hybrid capture (T-Capture) system. By designing specific probes for these coronaviruses, MT-Capture effectively enriched isolated strains and 112 clinical samples of coronaviruses with cycle threshold values below 37. Compared to multiplex PCR sequencing, it does not require frequent primer updates and has higher compatibility. MT-Capture is highly sensitive and capable of tracking variants.IMPORTANCEMT-Capture is meticulously designed to enable the efficient acquisition of the target genome of the common human coronavirus. Coronavirus is a kind of virus that people are generally susceptible to and is epidemic and infectious, and it is the virus with the longest genome among known RNA viruses. Therefore, common human coronavirus samples are selected to evaluate the accuracy and sensitivity of MT-Capture. This method utilizes innovative probe designs optimized through probe conjugation techniques, greatly shortening the time and simplifying the handwork compared with traditional hybridization capture processes. Our results demonstrate that MT-Capture surpasses multiplex PCR in terms of sensitivity, exhibiting a thousandfold increase. Moreover, MT-Capture excels in the identification of mutation sites. This method not only is used to target the coronaviruses but also may be used to diagnose other diseases, including various infectious diseases, genetic diseases, or tumors.
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Affiliation(s)
- Zixinrong Meng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuo Wang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Liping Yu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Kangchen Zhao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Tao Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaojuan Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ning Yang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiao Qiao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Junyan Ma
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bin Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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Davies EA, Dutton L, Guiver M. Evaluation of a custom designed hybridisation assay for whole genome sequencing of human adenoviruses direct from clinical samples. J Clin Virol 2024; 171:105640. [PMID: 38219683 DOI: 10.1016/j.jcv.2024.105640] [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: 09/27/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
BACKGROUND Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelectXT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples. METHODS Modifications were made to the SureSelectXT low input protocol to enhance performance for viral targets. Consensus sequences were generated using an in-house designed three stage bioinformatics pipeline. We assessed, percentage of on target reads, average depth of coverage and percentage genome coverage to determine assay performance across a range of sample matrices. RESULTS Whole genome sequences were successfully generated for 91.6 % of samples assessed. Adenovirus DNA concentration was a good indicator of enrichment success. Highly specific enrichment was observed with only 6 % of samples showing < 50 % on target reads. Respiratory and faecal samples performed well where bloods showed higher levels of non-specific enrichment likely confounded by low adenovirus DNA concentrations. Protocol performance did not appear impacted by Adenovirus type or species. CONCLUSION Overall performance of this modified SureSelectXT protocol appears in line with previously published works although there are some confounding factors requiring further investigation. The use of a small RNA bait set has the potential to reduce associated costs which can be prohibitive.
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Affiliation(s)
- Emma Ann Davies
- UKHSA Manchester Virology Laboratory, Manchester Medical Microbiology Partnership, Manchester Foundation Trust, Manchester, UK.
| | - Laura Dutton
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester Foundation Trust, Manchester, UK
| | - Malcolm Guiver
- UKHSA Manchester Virology Laboratory, Manchester Medical Microbiology Partnership, Manchester Foundation Trust, Manchester, UK
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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Ceballos-Garzon A, Comtet-Marre S, Peyret P. Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2. Virus Res 2024; 340:199293. [PMID: 38101578 PMCID: PMC10767490 DOI: 10.1016/j.virusres.2023.199293] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.
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Affiliation(s)
| | | | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France.
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King S. Whole Genome Sequencing of Epizootic Hemorrhagic Disease Virus. Methods Mol Biol 2024; 2838:211-219. [PMID: 39126635 DOI: 10.1007/978-1-0716-4035-7_15] [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] [Indexed: 08/12/2024]
Abstract
Next-generation sequencing (NGS) technologies are continuously being developed and are becoming a more cost-effective tool for the characterization of viral genomes. Whole genome sequencing of segmented viruses, such as epizootic hemorrhagic disease virus (EHDV), provides insights into the molecular epidemiology as well as such viral evolutionary mechanisms as genetic reassortment. Here, we present a detailed method for obtaining full genome sequence data for EHDV using Illumina technology. The protocol includes details from RNA extraction and purification, the synthesis of cDNA, sequencing library preparation, to genome assembly.
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Affiliation(s)
- Simon King
- The Pirbright Institute, Pirbright, Woking, UK.
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Ladner JT, Sahl JW. Towards a post-pandemic future for global pathogen genome sequencing. PLoS Biol 2023; 21:e3002225. [PMID: 37527248 PMCID: PMC10393143 DOI: 10.1371/journal.pbio.3002225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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Peñafiel-Ricaurte A, Price SJ, Leung WTM, Alvarado-Rybak M, Espinoza-Zambrano A, Valdivia C, Cunningham AA, Azat C. Is Xenopus laevis introduction linked with Ranavirus incursion, persistence and spread in Chile? PeerJ 2023; 11:e14497. [PMID: 36874973 PMCID: PMC9979829 DOI: 10.7717/peerj.14497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/10/2022] [Indexed: 03/03/2023] Open
Abstract
Ranaviruses have been associated with amphibian, fish and reptile mortality events worldwide and with amphibian population declines in parts of Europe. Xenopus laevis is a widespread invasive amphibian species in Chile. Recently, Frog virus 3 (FV3), the type species of the Ranavirus genus, was detected in two wild populations of this frog near Santiago in Chile, however, the extent of ranavirus infection in this country remains unknown. To obtain more information about the origin of ranavirus in Chile, its distribution, species affected, and the role of invasive amphibians and freshwater fish in the epidemiology of ranavirus, a surveillance study comprising wild and farmed amphibians and wild fish over a large latitudinal gradient (2,500 km) was carried out in 2015-2017. In total, 1,752 amphibians and 496 fish were tested using a ranavirus-specific qPCR assay, and positive samples were analyzed for virus characterization through whole genome sequencing of viral DNA obtained from infected tissue. Ranavirus was detected at low viral loads in nine of 1,011 X. laevis from four populations in central Chile. No other amphibian or fish species tested were positive for ranavirus, suggesting ranavirus is not threatening native Chilean species yet. Phylogenetic analysis of partial ranavirus sequences showed 100% similarity with FV3. Our results show a restricted range of ranavirus infection in central Chile, coinciding with X. laevis presence, and suggest that FV3 may have entered the country through infected X. laevis, which appears to act as a competent reservoir host, and may contribute to the spread the virus locally as it invades new areas, and globally through the pet trade.
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Affiliation(s)
- Alexandra Peñafiel-Ricaurte
- Sustainability Research Centre & PhD in Conservation Medicine Program, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile.,Institute of Zoology, Zoological Society of London, London, United Kingdom
| | | | - William T M Leung
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Mario Alvarado-Rybak
- Sustainability Research Centre & PhD in Conservation Medicine Program, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile.,Institute of Zoology, Zoological Society of London, London, United Kingdom.,Núcleo de Ciencias Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago, Chile
| | - Andrés Espinoza-Zambrano
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Catalina Valdivia
- Sustainability Research Centre & PhD in Conservation Medicine Program, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile
| | | | - Claudio Azat
- Sustainability Research Centre & PhD in Conservation Medicine Program, Life Sciences Faculty, Universidad Andres Bello, Santiago, Chile
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13
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Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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14
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Agwati EO, Oduor CI, Ayieko C, Ong’echa JM, Moormann AM, Bailey JA. Profiling genome-wide recombination in Epstein Barr virus reveals type-specific patterns and associations with endemic-Burkitt lymphoma. Virol J 2022; 19:208. [PMID: 36482473 PMCID: PMC9733152 DOI: 10.1186/s12985-022-01942-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Endemic Burkitt lymphoma (eBL) is potentiated through the interplay of Epstein Barr virus (EBV) and holoendemic Plasmodium falciparum malaria. To better understand EBV's biology and role in eBL, we characterized genome-wide recombination sites and patterns as a source of genetic diversity in EBV genomes in our well-defined population of eBL cases and controls from Western Kenya. METHODS EBV genomes representing 54 eBL cases and 32 healthy children from the same geographic region in Western Kenya that we previously sequenced were analyzed. Whole-genome multiple sequence alignment, recombination analyses, and phylogenetic inference were made using multiple alignment with fast Fourier transform, recombination detection program 4, and molecular evolutionary genetics analysis. RESULTS We identified 28 different recombination events and 71 (82.6%) of the 86 EBV genomes analyzed contained evidence of one or more recombinant segments. Associated recombination breakpoints were found to occur in a total of 42 different genes, with only 7 (16.67%) being latent genes. Recombination events were major drivers of clustering within genome-wide phylogenetic trees. The occurrence of recombination segments was comparable between genomes from male and female participants and across age groups. More recombinant segments were found in EBV type 1 genomes (p = 6.4e - 06) and the genomes from the eBLs (p = 0.037). Two recombination events were enriched in the eBLs; event 47 (OR = 4.07, p = 0.038) and event 50 (OR = 14.24, p = 0.012). CONCLUSIONS EBV genomes have extensive evidence of recombination likely acquired progressively and cumulatively over time. Recombination patterns display a heterogeneous occurrence rate across the genome with enrichment in lytic genes. Overall, recombination appears to be a major evolutionary force impacting EBV diversity and genome structure with evidence of the association of specific recombinants with eBL.
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Affiliation(s)
- Eddy O. Agwati
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya ,grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Cliff I. Oduor
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
| | - Cyrus Ayieko
- grid.442486.80000 0001 0744 8172Department of Zoology, Maseno University, Maseno, Kenya
| | - John Michael Ong’echa
- grid.33058.3d0000 0001 0155 5938Center for Global Health Research (CGHR), Kenya Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine and the Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Jeffrey A. Bailey
- grid.40263.330000 0004 1936 9094Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02903 USA
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15
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Kuchinski KS, Duan J, Himsworth C, Hsiao W, Prystajecky NA. ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa. BMC Genomics 2022; 23:579. [PMID: 35953803 PMCID: PMC9371634 DOI: 10.1186/s12864-022-08790-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enrichment in many fields, but their application to viral sequencing faces a major obstacle: it is difficult to design panels of probe oligo sequences that broadly target many viral taxa due to their rapid evolution, extensive diversity, and genetic hypervariability. To address this challenge, we created ProbeTools, a package of bioinformatic tools for generating effective viral capture panels, and for assessing coverage of target sequences by probe panel designs in silico. In this study, we validated ProbeTools by designing a panel of 3600 probes for subtyping the hypervariable haemagglutinin (HA) and neuraminidase (NA) genome segments of avian-origin influenza A viruses (AIVs). Using in silico assessment of AIV reference sequences and in vitro capture on egg-cultured viral isolates, we demonstrated effective performance by our custom AIV panel and ProbeTools' suitability for challenging viral probe design applications. RESULTS Based on ProbeTool's in silico analysis, our panel provided broadly inclusive coverage of 14,772 HA and 11,967 NA reference sequences. For each reference sequence, we calculated the percentage of nucleotide positions covered by our panel in silico; 90% of HA and NA references sequences had at least 90.8 and 95.1% of their nucleotide positions covered respectively. We also observed effective in vitro capture on a representative collection of 23 egg-cultured AIVs that included isolates from wild birds, poultry, and humans and representatives from all HA and NA subtypes. Forty-two of forty-six HA and NA segments had over 98.3% of their nucleotide positions significantly enriched by our custom panel. These in vitro results were further used to validate ProbeTools' in silico coverage assessment algorithm; 89.2% of in silico predictions were concordant with in vitro results. CONCLUSIONS ProbeTools generated an effective panel for subtyping AIVs that can be deployed for genomic surveillance, outbreak prevention, and pandemic preparedness. Effective probe design against hypervariable AIV targets also validated ProbeTools' design and coverage assessment algorithms, demonstrating their suitability for other challenging viral capture applications.
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Affiliation(s)
- Kevin S Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
- , Vancouver, Canada.
| | - Jun Duan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea Himsworth
- Animal Health Centre, British Columbia Ministry of Agriculture, Food, and Fisheries, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - William Hsiao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Natalie A Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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16
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Götting J, Baier C, Panagiota V, Maecker-Kolhoff B, Dhingra A, Heim A. High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years. Virus Evol 2022; 8:veac067. [PMID: 36533152 PMCID: PMC9748976 DOI: 10.1093/ve/veac067] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/29/2022] [Accepted: 08/03/2022] [Indexed: 06/22/2024] Open
Abstract
Type 31 of human adenovirus species A (HAdV-A31) is a significant pathogen primarily associated with diarrhoea in children but also with life-threatening disseminated disease in allogeneic haematopoietic stem cell transplant (HSCT) recipients. Nosocomial outbreaks of HAdV-A31 have been frequently described. However, the evolution of HAdV-A31 has not been studied in detail. The evolution of other HAdV types is driven either by intertypic recombination, where different types exchange genome regions, or by immune escape selection of neutralisation determinants. Complete genomic HAdV-A31 sequences from sixty diagnostic specimens of the past 18 years (2003-21) were generated, including fourteen specimens of a presumed outbreak on two HSCT wards. Additionally, twenty-three complete genomes from GenBank were added to our phylogenetic analysis as well as in silico generated and previously published restriction fragment polymorphism (RFLP) data. Phylogenetic analysis of eighty-three genomes indicated that HAdV-A31 evolved slowly with six lineages co-circulating. The two major lineages were lineage 1, which included the prototype from 1962 and nine recent isolates, and lineage 2, which split into four sublineages and included most isolates from 2003 to 2021. The average nucleotide identity within lineages was high (99.8 per cent) and identity between lineages was 98.7 and 99.2 per cent. RFLP data allowed the construction of a lower-resolution phylogeny with two additional putative lineages. Surprisingly, regions of higher diversity separating lineages were found in gene regions coding for non-structural and minor capsid proteins. Intertypic recombinations were not observed, but the phylogeny of lineage 3 was compatible with an interlineage recombination event in the fibre gene. Applying the phylogenetic analysis to the presumed nosocomial outbreak excluded two suspected transmission events and separated it into two different, simultaneous outbreaks caused by different sublineages of lineage 2. However, due to the high nucleotide identity within HAdV-A31 lineages, the proof of infection chains remains debatable. This in-depth study on the molecular phylogeny of HAdV-A31 highlights the high genetic stability of co-circulating HAdV-A31 lineages over almost six decades. It also supports the epidemiological hypothesis that HAdV-A31 circulates as an etiological agent of a childhood disease infecting immunologically naive patients without strong positive selection of immune escape variants and recombinants.
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Affiliation(s)
- Jasper Götting
- Institute of Virology, Hannover Medical
School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Claas Baier
- Institute for Medical Microbiology and Hospital
Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover
30625, Germany
| | - Victoria Panagiota
- Department of Hematology, Hemostaseology,
Oncology and Stem Cell Transplantation, Hannover Medical School,
Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Britta Maecker-Kolhoff
- Department of Paediatric Haematology and
Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625,
Germany
| | - Akshay Dhingra
- Institute of Virology, Hannover Medical
School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Albert Heim
- Institute of Virology, Hannover Medical
School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
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17
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Kondo S, Okuno Y, Murata T, Dochi H, Wakisaka N, Mizokami H, Moriyama-Kita M, Kobayashi E, Kano M, Komori T, Hirai N, Ueno T, Nakanishi Y, Endo K, Sugimoto H, Kimura H, Yoshizaki T. EBV genome variations enhance clinicopathological features of nasopharyngeal carcinoma in a non-endemic region. Cancer Sci 2022; 113:2446-2456. [PMID: 35485636 PMCID: PMC9277247 DOI: 10.1111/cas.15381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/17/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is caused by infection with Epstein–Barr virus (EBV) and endemic in certain geographic regions. EBV lytic gene, BALF2, closely associates with viral reactivation and BALF2 gene variation, the H‐H‐H strain, causes NPC in endemic region, southern China. Here, we investigate whether such EBV variations also affect NPC in a non‐endemic region, Japan. Viral genome sequencing with 47 EBV isolates of Japanese NPC were performed and compared with those of other EBV‐associated diseases from Japan or NPC in Southern China. EBV genomes of Japanese NPC are different from those of other diseases in Japan or endemic NPC; Japanese NPC was not affected by the endemic strain (the BALF2 H‐H‐H) but frequently carried the type 2 EBV or the strain with intermediate risk of endemic NPC (the BALF2 H‐H‐L). Seven single nucleotide variations were specifically associated with Japanese NPC, of which six were present in both type 1 and 2 EBV genomes, suggesting the contribution of the type 2 EBV‐derived haplotype. This observation was supported by a higher viral titer and stronger viral reactivation in NPC with either type 2 or H‐H‐L strains. Our results highlight the importance of viral strains and viral reactivation in the pathogenesis of non‐endemic NPC.
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Affiliation(s)
- Satoru Kondo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan.,These authors contributed equally to this work
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan.,Pediatric Cancer Treatment Center, Nagoya University Hospital, Nagoya, Aichi, Japan.,These authors contributed equally to this work
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Hirotomo Dochi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Naohiro Wakisaka
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Harue Mizokami
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Makiko Moriyama-Kita
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Eiji Kobayashi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Makoto Kano
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Takeshi Komori
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Nobuyuki Hirai
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Takayoshi Ueno
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Yosuke Nakanishi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Kazuhira Endo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Hisashi Sugimoto
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University, Graduate school of Medicine, Nagoya, Aichi, Japan
| | - Tomokazu Yoshizaki
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
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18
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Clement Dobbins G, Kimberlin D, Ross S. Cytomegalovirus variation among newborns treated with valganciclovir. Antiviral Res 2022; 203:105326. [DOI: 10.1016/j.antiviral.2022.105326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022]
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19
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Do Epstein–Barr Virus Mutations and Natural Genome Sequence Variations Contribute to Disease? Biomolecules 2021; 12:biom12010017. [PMID: 35053165 PMCID: PMC8774192 DOI: 10.3390/biom12010017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Most of the world’s population is infected by the Epstein–Barr virus (EBV), but the incidence of the diseases associated with EBV infection differs greatly in different parts of the world. Many factors may determine those differences, but variation in the virus genome is likely to be a contributing factor for some of the diseases. Here, we describe the main forms of EBV genome sequence variation, and the mechanisms by which variations in the virus genome are likely to contribute to disease. EBV genome deletions or polymorphisms can also provide useful markers for monitoring disease. If some EBV strains prove to be more pathogenic than others, this suggests the possible value of immunising people against infection by those pathogenic strains.
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20
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El Bouzidi K, Datir RP, Kwaghe V, Roy S, Frampton D, Breuer J, Ogbanufe O, Murtala-Ibrahim F, Charurat M, Dakum P, Sabin CA, Ndembi N, Gupta RK. Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria. J Antimicrob Chemother 2021; 77:474-482. [PMID: 34741609 PMCID: PMC8809188 DOI: 10.1093/jac/dkab385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/28/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Deep sequencing could improve understanding of HIV treatment failure and viral population dynamics. However, this tool is often inaccessible in low- and middle-income countries. OBJECTIVES To determine the genetic patterns of resistance emerging in West African HIV-1 subtypes during first-line virological failure, and the implications for future antiretroviral options. PATIENTS AND METHODS Participants were selected from a Nigerian cohort of people living with HIV who had failed first-line ART and subsequently switched to second-line therapy. Whole HIV-1 genome sequences were generated from first-line virological failure samples with Illumina MiSeq. Mutations detected at ≥2% frequency were analysed and compared by subtype. RESULTS HIV-1 sequences were obtained from 101 participants (65% female, median age 30 years, median 32.9 months of nevirapine- or efavirenz-based ART). Thymidine analogue mutations (TAMs) were detected in 61%, other core NRTI mutations in 92% and NNRTI mutations in 99%. Minority variants (<20% frequency) comprised 18% of all mutations. K65R was more prevalent in CRF02_AG than G subtypes (33% versus 7%; P = 0.002), and ≥3 TAMs were more common in G than CRF02_AG (52% versus 24%; P = 0.004). Subtype G viruses also contained more RT cleavage site mutations. Cross-resistance to at least one of the newer NNRTIs, doravirine, etravirine or rilpivirine, was predicted in 81% of participants. CONCLUSIONS Extensive drug resistance had accumulated in people with West African HIV-1 subtypes, prior to second-line ART. Deep sequencing significantly increased the detection of resistance-associated mutations. Caution should be used if considering newer-generation NNRTI agents in this setting.
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Affiliation(s)
- Kate El Bouzidi
- Division of Infection & Immunity, University College London, London, UK.,Institute for Global Health, University College London, London, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Vivian Kwaghe
- University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Sunando Roy
- Division of Infection & Immunity, University College London, London, UK
| | - Dan Frampton
- Division of Infection & Immunity, University College London, London, UK.,Farr Institute of Health Informatics Research, University College London, London, UK
| | - Judith Breuer
- Division of Infection & Immunity, University College London, London, UK
| | - Obinna Ogbanufe
- U.S. Centers for Disease Control and Prevention, U.S. Embassy, Abuja, Nigeria
| | | | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | | | - Caroline A Sabin
- Institute for Global Health, University College London, London, UK
| | - Nicaise Ndembi
- Institute of Human Virology Nigeria, Abuja, Nigeria.,Africa Centres for Disease Control and Prevention, African Union Commission, Addis Ababa, Ethiopia
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
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21
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Santos PD, Ziegler U, Szillat KP, Szentiks CA, Strobel B, Skuballa J, Merbach S, Grothmann P, Tews BA, Beer M, Höper D. In action-an early warning system for the detection of unexpected or novel pathogens. Virus Evol 2021; 7:veab085. [PMID: 34703624 PMCID: PMC8542707 DOI: 10.1093/ve/veab085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/06/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Proactive approaches in preventing future epidemics include pathogen discovery prior to their emergence in human and/or animal populations. Playing an important role in pathogen discovery, high-throughput sequencing (HTS) enables the characterization of microbial and viral genetic diversity within a given sample. In particular, metagenomic HTS allows the unbiased taxonomic profiling of sequences; hence, it can identify novel and highly divergent pathogens such as viruses. Newly discovered viral sequences must be further investigated using genomic characterization, molecular and serological screening, and/or invitro and invivo characterization. Several outbreak and surveillance studies apply unbiased generic HTS to characterize the whole genome sequences of suspected pathogens. In contrast, this study aimed to screen for novel and unexpected pathogens in previously generated HTS datasets and use this information as a starting point for the establishment of an early warning system (EWS). As a proof of concept, the EWS was applied to HTS datasets and archived samples from the 2018–9 West Nile virus (WNV) epidemic in Germany. A metagenomics read classifier detected sequences related to genome sequences of various members of Riboviria. We focused the further EWS investigation on viruses belonging to the families Peribunyaviridae and Reoviridae, under suspicion of causing co-infections in WNV-infected birds. Phylogenetic analyses revealed that the reovirus genome sequences clustered with sequences assigned to the species Umatilla virus (UMAV), whereas a new peribunyavirid, tentatively named ‘Hedwig virus’ (HEDV), belonged to a putative novel genus of the family Peribunyaviridae. In follow-up studies, newly developed molecular diagnostic assays detected fourteen UMAV-positive wild birds from different German cities and eight HEDV-positive captive birds from two zoological gardens. UMAV was successfully cultivated in mosquito C6/36 cells inoculated with a blackbird liver. In conclusion, this study demonstrates the power of the applied EWS for the discovery and characterization of unexpected viruses in repurposed sequence datasets, followed by virus screening and cultivation using archived sample material. The EWS enhances the strategies for pathogen recognition before causing sporadic cases and massive outbreaks and proves to be a reliable tool for modern outbreak preparedness.
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Affiliation(s)
- Pauline Dianne Santos
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Ute Ziegler
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Kevin P Szillat
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Claudia A Szentiks
- 4Department of Wildlife Diseases, Leibniz-Institute for Zoo- and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin 10315, Germany
| | - Birte Strobel
- Chemical and Veterinary Investigations Office Karlsruhe (CVUA Karlsruhe), Weissenburgerstrasse 3, Karlsruhe 76187, Germany
| | - Jasmin Skuballa
- Chemical and Veterinary Investigations Office Karlsruhe (CVUA Karlsruhe), Weissenburgerstrasse 3, Karlsruhe 76187, Germany
| | - Sabine Merbach
- State Institute for Chemical and Veterinary Analysis (CVUA) Westfalen, Zur Taubeneiche 10-12, Arnsberg 59821, Germany
| | - Pierre Grothmann
- Practice for Zoo, Game and Wild Animals, Lintiger Str. 74, Geestland 27624, Germany
| | - Birke Andrea Tews
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Infectology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
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22
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Guerra-Assunção JA, van Kampen JJ, Roy S, Remeijer L, Breuer J, Verjans GMM. Cluster of Symptomatic Graft-to-Host Transmission of Herpes Simplex Virus Type 1 in an Endothelial Keratoplasty Setting. OPHTHALMOLOGY SCIENCE 2021; 1:100051. [PMID: 36247820 PMCID: PMC9562293 DOI: 10.1016/j.xops.2021.100051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 11/26/2022]
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23
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Wang H, Fu BB, Gale RP, Liang Y. NK-/T-cell lymphomas. Leukemia 2021; 35:2460-2468. [PMID: 34117356 PMCID: PMC8410593 DOI: 10.1038/s41375-021-01313-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 01/31/2023]
Abstract
Natural killer/T-cell lymphoma (NKTL) is a sub-type of Epstein-Barr virus (EBV)-related non-Hodgkin lymphomas common in Asia and Latin America but rare elsewhere. Its pathogenesis is complex and incompletely understood. Lymphoma cells are transformed from NK- or T-cells, sometimes both. EBV-infection and subsequent genetic alterations in infected cells are central to NKTL development. Hemophagocytic syndrome is a common complication. Accurate staging is important to predict outcomes but there is controversy which system is best. More than two-thirds of NKTL lympohmas are localized at diagnosis, are frequently treated with radiation therapy only and have 5-year survival of about 70 percent. Persons with advanced NKTLs receive radiation therapy synchronously or metachronously with diverse multi-drug chemotherapy typically including L-asparginase with 5-year survival of about 40 percent. Some persons with widespread NKTL receive chemotherapy only. There are few data on safety and efficacy of high-dose therapy and a haematopoietic cell autotransplant. Immune therapies, histone deacetylase (HDAC)-inhibitors and other drugs are in early clinical trials. There are few randomized controlled clinical trials in NKTLs and no therapy strategy is clearly best; more effective therapy(ies) are needed. Some consensus recommendations are not convincingly evidence-based. Mechanisms of multi-drug resistance are considered. We discuss these issues including recent advances in our understanding of and therapy of NKTLs.
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Affiliation(s)
- Hua Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Bi-Bo Fu
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Robert Peter Gale
- Haematology Research Centre, Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Yang Liang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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24
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Depledge DP, Breuer J. Varicella-Zoster Virus-Genetics, Molecular Evolution and Recombination. Curr Top Microbiol Immunol 2021; 438:1-23. [PMID: 34374828 DOI: 10.1007/82_2021_238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter first details the structure, organization and coding content of the VZV genome to provide a foundation on which the molecular evolution of the virus can be projected. We subsequently describe the evolution of molecular profiling approaches from restriction fragment length polymorphisms to single nucleotide polymorphism profiling to modern day high-throughput sequencing approaches. We describe how the application of these methodologies led to our current model of VZV phylogeograpy including the number and structure of geographic clades and the role of recombination in reshaping these.
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Affiliation(s)
- Daniel P Depledge
- Institute of Virology, Hannover Medical School (MHH), Hannover, Germany. .,Department of Microbiology, NYU School of Medicine, New York, USA.
| | - Judith Breuer
- Department of Infection & Immunology, University College London, London, UK
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25
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Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures. Viruses 2021; 13:v13071323. [PMID: 34372528 PMCID: PMC8310033 DOI: 10.3390/v13071323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
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26
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Myers CE, Houldcroft CJ, Roy S, Margetts BK, Best T, Venturini C, Guerra-Assunção JA, Williams CA, Williams R, Dunn H, Hartley JC, Rao K, Rolfe KJ, Breuer J. Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit. Front Microbiol 2021; 12:667790. [PMID: 34276599 PMCID: PMC8284422 DOI: 10.3389/fmicb.2021.667790] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
A recent surge in human mastadenovirus (HAdV) cases, including five deaths, amongst a haematopoietic stem cell transplant population led us to use whole genome sequencing (WGS) to investigate. We compared sequences from 37 patients collected over a 20-month period with sequences from GenBank and our own database of HAdVs. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships, paired with the epidemiological data from routine infection prevention and control (IPC) records and hospital activity data. During this time period, two formal outbreaks had been declared by IPC, while WGS detected nine monophyletic clusters, seven were corroborated by epidemiological evidence and by comparison of single-nucleotide polymorphisms. One of the formal outbreaks was confirmed, and the other was not. Of the five HAdV-associated deaths, three were unlinked and the remaining two considered the source of transmission. Mixed infection was frequent (10%), providing a sentinel source of recombination and superinfection. Immunosuppressed patients harboring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of these findings, HAdV WGS is being incorporated routinely into clinical practice to influence IPC policy contemporaneously.
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Affiliation(s)
- Chloe E Myers
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | | | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ben K Margetts
- Division of Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Timothy Best
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, United Kingdom
| | | | - Charlotte A Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Helen Dunn
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - John C Hartley
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - Kanchan Rao
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - Kathryn J Rolfe
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom.,Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
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27
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C. Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados. Parasit Vectors 2021; 14:343. [PMID: 34187544 PMCID: PMC8244189 DOI: 10.1186/s13071-021-04840-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito populations in Brazil for almost 2 years before it was identified by the World Health Organization in 2015. Metagenomic detection assays have the potential to detect emerging pathogens without prior knowledge of their genomic nucleic acid sequence. Yet their applicability as vector surveillance tools has been widely limited by the complexity of DNA populations from field-collected mosquito preparations. The aim of this study was to investigate local vector biology and characterize metagenomic arbovirus diversity in Aedes mosquitoes during the ongoing 2015/2016 ZIKV epidemic. Methods We performed a short-term vector screening study on the island of Barbados during the ongoing 2015/2016 ZIKV epidemic, where we sampled local Aedes mosquitoes. We reanalyzed mosquito viral microbiome data derived from standard Illumina MiSeq sequencing to detect arbovirus sequences. Additionally, we employed deep sequencing techniques (Illumina HiSeq) and designed a novel bait capture enrichment assay to increase sequencing efficiency for arbovirus sequences from complex DNA samples. Results We found that Aedes aegypti seemed to be the most likely vector of ZIKV, although it prevailed at a low density during the observed time period. The number of detected viruses increased with sequencing depth. Arbovirus sequence enrichment of metagenomic DNA preparations allowed the detection of arbovirus sequences of two different ZIKV genotypes, including a novel one. To our knowledge, this is the first report of the S3116W mutation in the NS5 gene region of ZIKV polyprotein. Conclusions The metagenomic arbovirus detection approach presented here may serve as a useful tool for the identification of epidemic-causing arboviruses with the additional benefit of enabling the collection of phylogenetic information on the source. Apart from detecting more than 88 viruses using this approach, we also found evidence of novel ZIKV variants circulating in the local mosquito population during the observed time period. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04840-0.
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Affiliation(s)
- J Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - N Rascovan
- Department of Genomes & Genetics, Institut Pasteur, Paris, France
| | - A Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - I Klymiuk
- Department of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - C Zittra
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - H P Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - T Scantlebury-Manning
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | | | - S Austin
- Department of Biological and Chemical Sciences, University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
| | - R C Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown, Barbados
| | - C Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
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28
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Comprehensive Evolutionary Analysis of Complete Epstein-Barr Virus Genomes from Argentina and Other Geographies. Viruses 2021; 13:v13061172. [PMID: 34207433 PMCID: PMC8235469 DOI: 10.3390/v13061172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
The sequence variability of the Epstein–Barr virus has been extensively studied throughout previous years in isolates from various geographic regions and consequent variations at both genetic and genomic levels have been described. However, isolates from South America were underrepresented in these studies. Here, we sequenced 15 complete EBV genomes that we analyzed together with publicly available raw NGS data for 199 EBV isolates from other parts of the globe by means of a custom-built bioinformatic pipeline. The phylogenetic relations of the genomes, the geographic structure and variability of the data set, and the evolution rates for the whole genome and each gene were assessed. The present work contributes to overcoming the scarcity of complete EBV genomes from South America and is the most comprehensive geography-related variability study, which involved determining the actual contribution of each EBV gene to the geographic segregation of the entire genome. Moreover, to the best of our knowledge, we established for the first time the evolution rate for the entire EBV genome based on a host–virus codivergence-independent assumption and assessed their evolution rates on a gene-by-gene basis, which were related to the encoded protein function. Considering the evolution of dsDNA viruses with a codivergence-independent approach may lay the basis for future research on EBV evolution. The exhaustive bioinformatic analysis performed on this new dataset allowed us to draw a novel set of conclusions regarding the genome evolution of EBV.
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29
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Aswad A, Aimola G, Wight D, Roychoudhury P, Zimmermann C, Hill J, Lassner D, Xie H, Huang ML, Parrish NF, Schultheiss HP, Venturini C, Lager S, Smith GCS, Charnock-Jones DS, Breuer J, Greninger AL, Kaufer BB. Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa. Mol Biol Evol 2021; 38:96-107. [PMID: 32722766 PMCID: PMC7782865 DOI: 10.1093/molbev/msaa190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human herpesvirus 6A and 6B (HHV-6) can integrate into the germline, and as a result, ∼70 million people harbor the genome of one of these viruses in every cell of their body. Until now, it has been largely unknown if 1) these integrations are ancient, 2) if they still occur, and 3) whether circulating virus strains differ from integrated ones. Here, we used next-generation sequencing and mining of public human genome data sets to generate the largest and most diverse collection of circulating and integrated HHV-6 genomes studied to date. In genomes of geographically dispersed, only distantly related people, we identified clades of integrated viruses that originated from a single ancestral event, confirming this with fluorescent in situ hybridization to directly observe the integration locus. In contrast to HHV-6B, circulating and integrated HHV-6A sequences form distinct clades, arguing against ongoing integration of circulating HHV-6A or “reactivation” of integrated HHV-6A. Taken together, our study provides the first comprehensive picture of the evolution of HHV-6, and reveals that integration of heritable HHV-6 has occurred since the time of, if not before, human migrations out of Africa.
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Affiliation(s)
- Amr Aswad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Giulia Aimola
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Darren Wight
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | | | - Joshua Hill
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Dirk Lassner
- HighTech Center, Vinmec Hospital, Hanoi, Vietnam.,Institut Kardiale Diagnostik und Therapie, Berlin, Germany
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Cristina Venturini
- Division of Infection and Immunity, UCL Research Department of Infection, UCL, London, United Kingdom
| | - Susanne Lager
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Department of Obstetrics and Gynaecology, Cambridge University, United Kingdom
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, Cambridge University, United Kingdom
| | | | - Judith Breuer
- Division of Infection and Immunity, UCL Research Department of Infection, UCL, London, United Kingdom
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
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30
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Götting J, Lazar K, Suárez NM, Steinbrück L, Rabe T, Goelz R, Schulz TF, Davison AJ, Hamprecht K, Ganzenmueller T. Human Cytomegalovirus Genome Diversity in Longitudinally Collected Breast Milk Samples. Front Cell Infect Microbiol 2021; 11:664247. [PMID: 33937103 PMCID: PMC8085339 DOI: 10.3389/fcimb.2021.664247] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Reactivation and shedding of human cytomegalovirus (HCMV) in breast milk during lactation is highly frequent in HCMV-seropositive mothers. This represents a key transmission route for postnatal HCMV infection and can lead to severe disease in preterm neonates. Little is known about HCMV strain composition or longitudinal intrahost viral population dynamics in breast milk from immunocompetent women. We performed HCMV-specific target enrichment and high-throughput sequencing of 38 breast milk samples obtained in Germany between days 10 and 60 postpartum from 15 mothers with HCMV DNA lactia, and assembled HCMV consensus sequences de novo. The genotype distribution and number of HCMV strains present in each sample were determined by quantifying genotype-specific sequence motifs in 12 hypervariable viral genes, revealing a wide range of genotypes (82/109) for these genes in the cohort and a unique, longitudinally stable strain composition in each mother. Reactivation of up to three distinct HCMV strains was detected in 8/15 of mothers, indicating that a representative subset of the woman’s HCMV reservoir might be locally reactivated early during lactation. As described previously, nucleotide diversity of samples with multiple strains was much higher than that of samples with single strains. Breast milk as a main source of postnatal mother-to-infant transmission may serve as a repository for viral diversity and thus play an essential role in the natural epidemiology of HCMV.
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Affiliation(s)
- Jasper Götting
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Katrin Lazar
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tabea Rabe
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Rangmar Goelz
- Department of Neonatology, University Children's Hospital, Tuebingen, Germany
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Klaus Hamprecht
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Tina Ganzenmueller
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
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31
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Haidar Ahmad S, Al Moussawi F, El Baba R, Nehme Z, Pasquereau S, Kumar A, Molimard C, Monnien F, Algros MP, Karaky R, Stamminger T, Diab Assaf M, Herbein G. Identification of UL69 Gene and Protein in Cytomegalovirus-Transformed Human Mammary Epithelial Cells. Front Oncol 2021; 11:627866. [PMID: 33937031 PMCID: PMC8085531 DOI: 10.3389/fonc.2021.627866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/26/2021] [Indexed: 12/15/2022] Open
Abstract
A growing body of evidence addressing the involvement of human cytomegalovirus (HCMV) in malignancies had directed attention to the oncomodulation paradigm. HCMV-DB infected human mammary epithelial cells (HMECs) in culture showed the emergence of clusters of rapidly proliferating, spheroid-shaped transformed cells named CTH (CMV-Transformed HMECs) cells. CTH cells assessment suggests a direct contribution of HCMV to oncogenesis, from key latent and lytic genes activating oncogenic pathways to fueling tumor evolution. We hypothesized that the presence of HCMV genome in CTH cells is of pivotal importance for determining its oncogenic potential. We previously reported the detection of a long non-coding (lnc) RNA4.9 gene in CTH cells. Therefore, we assessed here the presence of UL69 gene, located nearby and downstream of the lncRNA4.9 gene, in CTH cells. The HCMV UL69 gene in CTH cells was detected using polymerase chain reaction (PCR) and sequencing of UL69 gene was performed using Sanger method. The corresponding amino acid sequence was then blasted against the UL69 sequence derived from HCMV-DB genome using NCBI Protein BLAST tool. A 99% identity was present between the nucleotide sequence present in CTH cells and HCMV-DB genome. UL69 transcript was detected in RNA extracts of CTH cells, using a reverse transcription polymerase chain reaction (RT-PCR) assay, and pUL69 protein was identified in CTH lysates using western blotting. Ganciclovir-treated CTH cells showed a decrease in UL69 gene detection and cellular proliferation. In CTH cells, the knockdown of UL69 with siRNA was assessed by RT-qPCR and western blot to reveal the impact of pUL69 on HCMV replication and CTH cell proliferation. Finally, UL69 gene was detected in breast cancer biopsies. Our results indicate a close link between the UL69 gene detected in the HCMV-DB isolate used to infect HMECs, and the UL69 gene present in transformed CTH cells and tumor biopsies, further highlighting a direct role for HCMV in breast tumor development.
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Affiliation(s)
- Sandy Haidar Ahmad
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France.,Molecular Cancer and Pharmaceutical Biology Laboratory, Lebanese University, Beyrouth, Lebanon
| | - Fatima Al Moussawi
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France.,Molecular Cancer and Pharmaceutical Biology Laboratory, Lebanese University, Beyrouth, Lebanon
| | - Ranim El Baba
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France.,Molecular Cancer and Pharmaceutical Biology Laboratory, Lebanese University, Beyrouth, Lebanon
| | - Zeina Nehme
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France.,Molecular Cancer and Pharmaceutical Biology Laboratory, Lebanese University, Beyrouth, Lebanon
| | - Sébastien Pasquereau
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France
| | - Amit Kumar
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France
| | - Chloé Molimard
- Department of Pathology, CHRU Besançon, Besançon, France
| | - Franck Monnien
- Department of Pathology, CHRU Besançon, Besançon, France
| | | | - Racha Karaky
- Molecular Cancer and Pharmaceutical Biology Laboratory, Lebanese University, Beyrouth, Lebanon
| | | | - Mona Diab Assaf
- Molecular Cancer and Pharmaceutical Biology Laboratory, Lebanese University, Beyrouth, Lebanon
| | - Georges Herbein
- Department Pathogens & Inflammation-EPILAB EA4266, University of Bourgogne France-Comté, Besançon, France.,Department of Virology, CHRU Besancon, Besancon, France
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32
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Rüeger S, Hammer C, Loetscher A, McLaren PJ, Lawless D, Naret O, Khanna N, Bernasconi E, Cavassini M, Günthard HF, Kahlert CR, Rauch A, Depledge DP, Morfopoulou S, Breuer J, Zdobnov E, Fellay J. The influence of human genetic variation on Epstein-Barr virus sequence diversity. Sci Rep 2021; 11:4586. [PMID: 33633271 PMCID: PMC7907281 DOI: 10.1038/s41598-021-84070-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imprint of host genomic variation on the EBV sequence, we jointly analyzed paired viral and human genomic data from 268 HIV-coinfected individuals with CD4 + T cell count < 200/mm3 and elevated EBV viremia. We hypothesized that the reactivated virus circulating in these patients could carry sequence variants acquired during primary EBV infection, thereby providing a snapshot of early adaptation to the pressure exerted on EBV by the individual immune response. We searched for associations between host and pathogen genetic variants, taking into account human and EBV population structure. Our analyses revealed significant associations between human and EBV sequence variation. Three polymorphic regions in the human genome were found to be associated with EBV variation: one at the amino acid level (BRLF1:p.Lys316Glu); and two at the gene level (burden testing of rare variants in BALF5 and BBRF1). Our findings confirm that jointly analyzing host and pathogen genomes can identify sites of genomic interactions, which could help dissect pathogenic mechanisms and suggest new therapeutic avenues.
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Affiliation(s)
- Sina Rüeger
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Alexis Loetscher
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Dylan Lawless
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Naret
- School of Life Sciences, EPFL, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nina Khanna
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Childrens Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Evgeny Zdobnov
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jacques Fellay
- School of Life Sciences, EPFL, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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Wylezich C, Calvelage S, Schlottau K, Ziegler U, Pohlmann A, Höper D, Beer M. Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. MICROBIOME 2021; 9:51. [PMID: 33610182 DOI: 10.1186/s40168-020-00973-z/figures/4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/07/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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34
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Wylezich C, Calvelage S, Schlottau K, Ziegler U, Pohlmann A, Höper D, Beer M. Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. MICROBIOME 2021; 9:51. [PMID: 33610182 PMCID: PMC7896545 DOI: 10.1186/s40168-020-00973-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/07/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma. PLoS Pathog 2021; 17:e1008594. [PMID: 33465147 PMCID: PMC7845968 DOI: 10.1371/journal.ppat.1008594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 01/29/2021] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Intra-host tumor virus variants may influence the pathogenesis and treatment responses of some virally-associated cancers. However, the intra-host variability of Kaposi sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi sarcoma (KS), has to date been explored with sequencing technologies that possibly introduce more errors than that which occurs in the viral population, and these studies have only studied variable regions. Here, full-length KSHV genomes in tumors and/or oral swabs from 9 Ugandan adults with HIV-associated KS were characterized. Furthermore, we used deep, short-read sequencing using duplex unique molecular identifiers (dUMI)–random double-stranded oligonucleotides that barcode individual DNA molecules before library amplification. This allowed suppression of PCR and sequencing errors to ~10−9/base as well as afforded accurate determination of KSHV genome numbers sequenced in each sample. KSHV genomes were assembled de novo, and rearrangements observed were confirmed by PCR and Sanger sequencing. 131-kb KSHV genome sequences, excluding major repeat regions, were successfully obtained from 23 clinical specimens, averaging 2.3x104 reads/base. Strikingly, KSHV genomes were virtually identical within individuals at the point mutational level. The intra-host heterogeneity that was observed was confined to tumor-associated KSHV mutations and genome rearrangements, all impacting protein-coding sequences. Although it is unclear whether these changes were important to tumorigenesis or occurred as a result of genomic instability in tumors, similar changes were observed across individuals. These included inactivation of the K8.1 gene in tumors of 3 individuals and retention of a region around the first major internal repeat (IR1) in all instances of genomic deletions and rearrangements. Notably, the same breakpoint junctions were found in distinct tumors within single individuals, suggesting metastatic spread of rearranged KSHV genomes. These findings define KSHV intra-host heterogeneity in vivo with greater precision than has been possible in the past and suggest the possibility that aberrant KSHV genomes may contribute to aspects of KS tumorigenesis. Furthermore, study of KSHV with use of dUMI provides a proof of concept for utilizing this technique for detailed study of other virus populations in vivo. Kaposi sarcoma (KS) is a leading cancer in sub-Saharan Africa and in persons with HIV co-infection. Kaposi sarcoma-associated herpesvirus (KSHV, also referred to as human herpesvirus-8, or HHV-8) is the etiologic agent of KS, but the factors that contribute to the development of KS, which occurs in only a small subset of infected individuals, remain largely unknown. While strain differences or mutations in other tumor viruses are known to affect the risk and progression of their associated cancers, whether genetic variation in KSHV is important to the natural history of KS is unclear. Most studies of KSHV diversity have only characterized ~4% of its 165-kb genome, and the observed variation in some studies is likely to have been impacted by PCR or cloning artifacts. To precisely define genomic diversity of KSHV in vivo, we evaluated full-length viral genomes (except the internal repeat regions) using a technique that greatly lowers sequencing error rates and thus measures genomic diversity much more accurately than previous studies. In addition, we extended our analyses to look for potential tumor-specific changes in the KSHV genomes by examining viruses in both tumor and non-tumor tissues. To these ends, we performed highly sensitive, single-molecule sequencing of whole KSHV genomes in paired KS tumors and oral swabs from 9 individuals with KS. We found that KSHV genomes were virtually identical within the 9 individuals, with no evidence of quasispecies formation or multi-strain infection. However, KSHV genome aberrations and gene-inactivating mutations were found to be common in KS tumors, often impacting the same genes and genomic regions across individuals. Whether theses mutations influence KS tumorigenesis or result from genomic instability commonly found in tumors warrants further study. Lastly, aberrant KSHV genomes were found to be shared by distinct tumors within individuals, suggesting the capacity of KS tumor cells to metastasize and seed new lesions.
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36
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Yajima M, Kakuta R, Saito Y, Kitaya S, Toyoda A, Ikuta K, Yasuda J, Ohta N, Kanda T. A global phylogenetic analysis of Japanese tonsil-derived Epstein-Barr virus strains using viral whole-genome cloning and long-read sequencing. J Gen Virol 2021; 102. [PMID: 33433312 DOI: 10.1099/jgv.0.001549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epstein-Barr virus (EBV) establishes lifelong latent infection in the majority of healthy individuals, while it is a causative agent for various diseases, including some malignancies. Recent high-throughput sequencing results indicate that there are substantial levels of viral genome heterogeneity among different EBV strains. However, the extent of EBV strain variation among asymptomatically infected individuals remains elusive. Here, we present a streamlined experimental strategy to clone and sequence EBV genomes derived from human tonsillar tissues, which are the reservoirs of asymptomatic EBV infection. Complete EBV genome sequences, including those of repetitive regions, were determined for seven tonsil-derived EBV strains. Phylogenetic analyses based on the whole viral genome sequences of worldwide non-tumour-derived EBV strains revealed that Asian EBV strains could be divided into several distinct subgroups. EBV strains derived from nasopharyngeal carcinoma-endemic areas constitute different subgroups from a subgroup of EBV strains from non-endemic areas, including Japan. The results could be consistent with biased regional distribution of EBV-associated diseases depending on the different EBV strains colonizing different regions in Asian countries.
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Affiliation(s)
- Misako Yajima
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Risako Kakuta
- Present address: Department of Otolaryngology, Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Yutaro Saito
- Present address: Department of Otolaryngology, Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Shiori Kitaya
- Present address: Department of Otolaryngology, Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazufumi Ikuta
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Jun Yasuda
- Present address: Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Miyagi, Japan.,Division of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Nobuo Ohta
- Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Teru Kanda
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
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37
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Brown AC. Whole-Genome Sequencing of Mycobacterium tuberculosis Directly from Sputum Samples. Methods Mol Biol 2021; 2314:459-480. [PMID: 34235666 DOI: 10.1007/978-1-0716-1460-0_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing pathogens, such as Mycobacterium tuberculosis. However, clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variations found within M. tuberculosis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of M. tuberculosis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
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Affiliation(s)
- Amanda Claire Brown
- Oxford Gene Technology, Oxford, UK. .,Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL), College Station, TX, USA. .,Department of Animal Science, Texas A&M University, Kleberg Center, College Station, TX, USA.
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38
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Dhingra A, Götting J, Varanasi PR, Steinbrueck L, Camiolo S, Zischke J, Heim A, Schulz TF, Weissinger EM, Kay-Fedorov PC, Davison AJ, Suárez NM, Ganzenmueller T. Human cytomegalovirus multiple-strain infections and viral population diversity in haematopoietic stem cell transplant recipients analysed by high-throughput sequencing. Med Microbiol Immunol 2021; 210:291-304. [PMID: 34611744 PMCID: PMC8541999 DOI: 10.1007/s00430-021-00722-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/21/2021] [Indexed: 01/22/2023]
Abstract
Human cytomegalovirus (HCMV) is an important opportunistic pathogen in allogeneic haematopoietic stem cell transplant (HSCT) recipients. High-throughput sequencing of target-enriched libraries was performed to characterise the diversity of HCMV strains present in this high-risk group. Forty-four HCMV-DNA-positive plasma specimens (median viral input load 321 IU per library) collected at defined time points from 23 HSCT recipients within 80 days of transplantation were sequenced. The genotype distribution for 12 hypervariable HCMV genes and the number of HCMV strains present (i.e. single- vs. multiple-strain infection) were determined for 29 samples from 16 recipients. Multiple-strain infection was observed in seven of these 16 recipients, and five of these seven recipients had the donor (D)/recipient (R) HCMV-serostatus combination D + R + . A very broad range of genotypes was detected, with an intrahost composition that was generally stable over time. Multiple-strain infection was not associated with particular virological or clinical features, such as altered levels or duration of antigenaemia, development of acute graft-versus-host disease or increased mortality. In conclusion, despite relatively low viral plasma loads, a high frequency of multiple-strain HCMV infection and a high strain complexity were demonstrated in systematically collected clinical samples from this cohort early after HSCT. However, robust evaluation of the pathogenic role of intrahost viral diversity and multiple-strain infection will require studies enrolling larger numbers of recipients.
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Affiliation(s)
- A. Dhingra
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - J. Götting
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - P. R. Varanasi
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany ,Department of Haematology, Haemostasis and Oncology, Hannover Medical School, Hannover, Germany ,Present Address: National Centre for Biological Sciences, Bangalore, India
| | - L. Steinbrueck
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - S. Camiolo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - J. Zischke
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - A. Heim
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - T. F. Schulz
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - E. M. Weissinger
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany ,Department of Haematology, Haemostasis and Oncology, Hannover Medical School, Hannover, Germany
| | - P. C. Kay-Fedorov
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - A. J. Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - N. M. Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - T. Ganzenmueller
- Hannover Medical School, Institute of Virology, Hannover, Germany ,German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany ,Institute for Medical Virology and Epidemiology, University Hospital Tuebingen, Elfriede-Aulhorn-Str. 6, 72076 Tuebingen, Germany
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39
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Maboko BB, Featherston J, Sibeko-Matjila KP, Mans BJ. Whole genome sequencing of Theileria parva using target capture. Genomics 2020; 113:429-438. [PMID: 33370583 DOI: 10.1016/j.ygeno.2020.12.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 12/02/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Protozoan parasite isolation and purification are laborious and time-consuming processes required for high quality genomic DNA used in whole genome sequencing. The objective of this study was to capture whole Theileria parva genomes directly from cell cultures and blood samples using RNA baits. Cell culture material was bait captured or sequenced directly, while blood samples were all captured. Baits had variable success in capturing T. parva genomes from blood samples but were successful in cell cultures. Genome mapping uncovered extensive host contamination in blood samples compared to cell cultures. Captured cell cultures had over 81 fold coverage for the reference genome compared to 0-33 fold for blood samples. Results indicate that baits are specific to T. parva, are a good alternative to conventional methods and thus ideal for genomic studies. This study also reports the first whole genome sequencing of South African T. parva.
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Affiliation(s)
- Boitumelo B Maboko
- Agricultural Research Council, Onderstepoort Veterinary Research, Private Bag X05, Onderstepoort, 0110 Pretoria, South Africa; Department of Veterinary Tropical Diseases, Vector and Vector-borne Disease Research Programme, University of Pretoria, Private Bag X04, Onderstepoort, 0110 Pretoria, South Africa
| | - Jonathan Featherston
- Agricultural Research Council, Biotechnology Platform, Private Bag X05, Onderstepoort, 0110 Pretoria, South Africa
| | - Kgomotso P Sibeko-Matjila
- Department of Veterinary Tropical Diseases, Vector and Vector-borne Disease Research Programme, University of Pretoria, Private Bag X04, Onderstepoort, 0110 Pretoria, South Africa
| | - Ben J Mans
- Agricultural Research Council, Onderstepoort Veterinary Research, Private Bag X05, Onderstepoort, 0110 Pretoria, South Africa; Department of Veterinary Tropical Diseases, Vector and Vector-borne Disease Research Programme, University of Pretoria, Private Bag X04, Onderstepoort, 0110 Pretoria, South Africa; School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; Department of Life and Consumer Sciences, University of South Africa, Florida 1709, South Africa.
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40
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Anis E, Ilha MRS, Engiles JB, Wilkes RP. Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples. J Vet Diagn Invest 2020; 33:227-234. [PMID: 33305693 DOI: 10.1177/1040638720978381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Equine infectious disease outbreaks may have profound economic impact, resulting in losses of millions of dollars of revenue as a result of horse loss, quarantine, and cancelled events. Early and accurate diagnosis is essential to limit the spread of infectious diseases. However, laboratory detection of infectious agents, especially the simultaneous detection of multiple agents, can be challenging to the clinician and diagnostic laboratory. Next-generation sequencing (NGS), which allows millions of DNA templates to be sequenced simultaneously in a single reaction, is an ideal technology for comprehensive testing. We conducted a proof-of-concept study of targeted NGS to detect 62 common equine bacterial, viral, and parasitic pathogens in clinical samples. We designed 264 primers and constructed a bioinformatics tool for the detection of targeted pathogens. The designed primers were able to specifically detect the intended pathogens. Results of testing 27 clinical samples with our targeted NGS assay compared with results of routine tests (assessed as a group) yielded positive percent agreement of 81% and negative percent agreement of 83%, overall agreement of 81%, and kappa of 0.56 (moderate agreement). This moderate agreement was likely the result of low sensitivity of some primers. However, our NGS assay successfully detected multiple pathogens in the clinical samples, including some pathogens missed by routine techniques.
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Affiliation(s)
- Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA.,Department of Virology, Faculty of Veterinary Medicine, University of Sadat, El Beheira Governorate, Sadat City, Egypt
| | - Marcia R S Ilha
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA
| | - Julie B Engiles
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA
| | - Rebecca P Wilkes
- Tifton Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN
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Abstract
Alphaherpesviruses, as large double-stranded DNA viruses, were long considered to be genetically stable and to exist in a homogeneous state. Recently, the proliferation of high-throughput sequencing (HTS) and bioinformatics analysis has expanded our understanding of herpesvirus genomes and the variations found therein. Recent data indicate that herpesviruses exist as diverse populations, both in culture and in vivo, in a manner reminiscent of RNA viruses. In this review, we discuss the past, present, and potential future of alphaherpesvirus genomics, including the technical challenges that face the field. We also review how recent data has enabled genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures, including those introduced by cell culture. While we focus on the human alphaherpesviruses, we draw key insights from related veterinary species and from the beta- and gamma-subfamilies of herpesviruses. Promising technologies and potential future directions for herpesvirus genomics are highlighted as well, including the potential to link viral genetic differences to phenotypic and disease outcomes.
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Affiliation(s)
- Chad V. Kuny
- Departments of Biology, and Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Moriah L. Szpara
- Departments of Biology, and Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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42
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Roy S, Hartley J, Dunn H, Williams R, Williams CA, Breuer J. Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A. Clin Infect Dis 2020; 69:1649-1656. [PMID: 30993315 PMCID: PMC6821348 DOI: 10.1093/cid/ciz020] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Influenza A virus causes annual epidemics in humans and is associated with significant morbidity and mortality. Haemagglutinin (HA) and neuraminidase (NA) gene sequencing have traditionally been used to identify the virus genotype, although their utility in detecting outbreak clusters is still unclear. The objective of this study was to determine the utility, if any, of whole-genome sequencing over HA/NA sequencing for infection prevention and control (IPC) in hospitals. Methods We obtained all clinical samples from influenza (H1N1)-positive patients at the Great Ormond Street Hospital between January and March 2016. Samples were sequenced using targeted enrichment on an Illumina MiSeq sequencer. Maximum likelihood trees were computed for both whole genomes and concatenated HA/NA sequences. Epidemiological data was taken from routine IPC team activity during the period. Results Complete genomes were obtained for 65/80 samples from 38 patients. Conventional IPC analysis recognized 1 outbreak, involving 3 children, and identified another potential cluster in the haemato-oncology ward. Whole-genome and HA/NA phylogeny both accurately identified the previously known outbreak cluster. However, HA/NA sequencing additionally identified unrelated strains as part of this outbreak cluster. A whole-genome analysis identified a further cluster of 2 infections that had been previously missed and refuted suspicions of transmission in the haemato-oncology wards. Conclusions Whole-genome sequencing is better at identifying outbreak clusters in a hospital setting than HA/NA sequencing. Whole-genome sequencing could provide a faster and more reliable method for outbreak monitoring and supplement routine IPC team work to allow the prevention of transmission.
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Affiliation(s)
- Sunando Roy
- Division of Infection and Immunity, University College London, United Kingdom
| | - John Hartley
- Great Ormond Street Hospital for Children, United Kingdom
| | - Helen Dunn
- Great Ormond Street Hospital for Children, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, United Kingdom
| | | | - Judith Breuer
- Division of Infection and Immunity, University College London, United Kingdom.,Great Ormond Street Hospital for Children, United Kingdom.,Infection, Immunity, Inflammation and Physiological Medicine, Institute of Child Health, University College London, United Kingdom
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43
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Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma. J Virol 2020; 94:JVI.02007-19. [PMID: 32581102 DOI: 10.1128/jvi.02007-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Endemic Burkitt lymphoma (eBL), the most prevalent pediatric cancer in sub-Saharan Africa, is distinguished by its inclusion of Epstein-Barr virus (EBV). In order to better understand the impact of EBV variation in eBL tumorigenesis, we improved viral DNA enrichment methods and generated a total of 98 new EBV genomes from both eBL cases (n = 58) and healthy controls (n = 40) residing in the same geographic region in Kenya. Using our unbiased methods, we found that EBV type 1 was significantly more prevalent in eBL patients (74.5%) than in healthy children (47.5%) (odds ratio = 3.24, 95% confidence interval = 1.36 to 7.71, P = 0.007), as opposed to similar proportions in both groups. Controlling for EBV type, we also performed a genome-wide association study identifying six nonsynonymous variants in the genes EBNA1, EBNA2, BcLF1, and BARF1 that were enriched in eBL patients. In addition, viruses isolated from plasma of eBL patients were identical to their tumor counterparts consistent with circulating viral DNA originating from the tumor. We also detected three intertypic recombinants carrying type 1 EBNA2 and type 2 EBNA3 regions, as well as one novel genome with a 20-kb deletion, resulting in the loss of multiple lytic and virion genes. Comparing EBV types, viral genes displayed differential variation rates as type 1 appeared to be more divergent, while type 2 demonstrated novel substructures. Overall, our findings highlight the complexities of the EBV population structure and provide new insight into viral variation, potentially deepening our understanding of eBL oncogenesis.IMPORTANCE Improved viral enrichment methods conclusively demonstrate EBV type 1 to be more prevalent in eBL patients than in geographically matched healthy controls, which previously underrepresented the prevalence of EBV type 2. Genome-wide association analysis between cases and controls identifies six eBL-associated nonsynonymous variants in EBNA1, EBNA2, BcLF1, and BARF1 genes. Analysis of population structure reveals that EBV type 2 exists as two genomic subgroups and was more commonly found in female than in male eBL patients.
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44
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A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture. Viruses 2020; 12:v12080895. [PMID: 32824272 PMCID: PMC7472420 DOI: 10.3390/v12080895] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 02/08/2023] Open
Abstract
Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts.
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45
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Berg MG, Olivo A, Forberg K, Harris BJ, Yamaguchi J, Shirazi R, Gozlan Y, Sauleda S, Kaptue L, Rodgers MA, Mor O, Cloherty GA. Advanced molecular surveillance approaches for characterization of blood borne hepatitis viruses. PLoS One 2020; 15:e0236046. [PMID: 32678844 PMCID: PMC7367454 DOI: 10.1371/journal.pone.0236046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Defining genetic diversity of viral infections directly from patient specimens is the ultimate goal of surveillance. Simple tools that can provide full-length sequence information on blood borne viral hepatitis viruses: hepatitis C, hepatitis B and hepatitis D viruses (HCV, HBV and HDV) remain elusive. Here, an unbiased metagenomic next generation sequencing approach (mNGS) was used for molecular characterization of HCV infections (n = 99) from Israel which yielded full-length HCV sequences in 89% of samples, with 7 partial sequences sufficient for classification. HCV genotypes were primarily 1b (68%) and 1a (19%), with minor representation of genotypes 2c (1%) and 3a (8%). HBV/HDV coinfections were characterized by suppressed HBV viral loads, resulting in sparse mNGS coverage. A probe-based enrichment approach (xGen) aiming to increase HBV and HDV coverage was validated on a panel of diverse genotypes, geography and titers. The method extended HBV genome coverage a median 61% (range 8–84%) and provided orders of magnitude boosts in reads and sequence depth for both viruses. When HBV-xGen was applied to Israeli samples, coverage was improved by 28–73% in 4 samples and identified HBV genotype A1, A2, D1 specimens and a dual B/D infection. Abundant HDV reads in mNGS libraries yielded 18/26 (69%) full genomes and 8 partial sequences, with HDV-xGen only providing minimal extension (3–11%) of what were all genotype 1 genomes. Advanced molecular approaches coupled to virus-specific capture probes promise to enhance surveillance of viral infections and aid in monitoring the spread of local subtypes.
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Affiliation(s)
- Michael G. Berg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
- * E-mail:
| | - Ana Olivo
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Kenn Forberg
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Barbara J. Harris
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Julie Yamaguchi
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Rachel Shirazi
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
| | - Yael Gozlan
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
| | - Silvia Sauleda
- Transfusion Safety Laboratory, Banc de Sang i Teixits, Servei Català de la Salut, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Mary A. Rodgers
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
| | - Orna Mor
- Central Virology Laboratory, National HIV and Viral Hepatitis Reference Center, Public Health Services, Ministry of Health, Tel-Hashomer, Ramat-Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Israel
| | - Gavin A. Cloherty
- Infectious Diseases Research, Abbott Diagnostics, Abbott Park, Illinois, United States of America
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46
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Hiltbrunner M, Heckel G. Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples. Viruses 2020; 12:v12070749. [PMID: 32664593 PMCID: PMC7412162 DOI: 10.3390/v12070749] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.
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Affiliation(s)
- Melanie Hiltbrunner
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland;
- Swiss Institute of Bioinformatics, Quartier Sorge, 1011 Lausanne, Switzerland
- Correspondence:
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47
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Gaccioli F, Lager S, de Goffau MC, Sovio U, Dopierala J, Gong S, Cook E, Sharkey A, Moffett A, Lee WK, Delles C, Venturini C, Breuer J, Parkhill J, Peacock SJ, Charnock-Jones DS, Smith GCS. Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia. Nat Microbiol 2020; 5:901-908. [PMID: 32367053 PMCID: PMC7610361 DOI: 10.1038/s41564-020-0711-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 03/18/2020] [Indexed: 12/16/2022]
Abstract
Pre-eclampsia (typically characterized by new-onset hypertension and proteinuria in the second half of pregnancy) represents a major determinant of the global burden of disease1,2. Its pathophysiology involves placental dysfunction, but the mechanism is unclear. Viral infection can cause organ dysfunction, but its role in placentally related disorders of human pregnancy is unknown3. We addressed this using RNA sequencing metagenomics4-6 of placental samples from normal and complicated pregnancies. Here, we show that human herpesvirus 6 (HHV-6, A or B) RNA was detected in 6.1% of cases of pre-eclampsia and 2.2% of other pregnancies. Fetal genotyping demonstrated that 70% of samples with HHV-6 RNA in the placenta exhibited inherited, chromosomally integrated HHV-6 (iciHHV-6). We genotyped 467 pre-eclampsia cases and 3,854 controls and found an excess of iciHHV-6 in the cases (odds ratio of 2.8, 95% confidence intervals of 1.4-5.6, P = 0.008). We validated this finding by comparing iciHHV-6 in a further 740 cases with controls from large-scale population studies (odds ratio of 2.5, 95% confidence intervals of 1.4-4.4, P = 0.0013). We conclude that iciHHV-6 results in the transcription of viral RNA in the human placenta and predisposes the mother to pre-eclampsia.
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Affiliation(s)
- Francesca Gaccioli
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Susanne Lager
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Marcus C de Goffau
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Justyna Dopierala
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Functional Genomics, GlaxoSmithKline Limited, Stevenage, UK
| | - Sungsam Gong
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
| | - Andrew Sharkey
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ashley Moffett
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wai Kwong Lee
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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48
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Suárez NM, Wilkie GS, Hage E, Camiolo S, Holton M, Hughes J, Maabar M, Vattipally SB, Dhingra A, Gompels UA, Wilkinson GWG, Baldanti F, Furione M, Lilleri D, Arossa A, Ganzenmueller T, Gerna G, Hubáček P, Schulz TF, Wolf D, Zavattoni M, Davison AJ. Human Cytomegalovirus Genomes Sequenced Directly From Clinical Material: Variation, Multiple-Strain Infection, Recombination, and Gene Loss. J Infect Dis 2020; 220:781-791. [PMID: 31050742 PMCID: PMC6667795 DOI: 10.1093/infdis/jiz208] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/24/2019] [Indexed: 11/29/2022] Open
Abstract
The genomic characteristics of human cytomegalovirus (HCMV) strains sequenced directly from clinical pathology samples were investigated, focusing on variation, multiple-strain infection, recombination, and gene loss. A total of 207 datasets generated in this and previous studies using target enrichment and high-throughput sequencing were analyzed, in the process enabling the determination of genome sequences for 91 strains. Key findings were that (i) it is important to monitor the quality of sequencing libraries in investigating variation; (ii) many recombinant strains have been transmitted during HCMV evolution, and some have apparently survived for thousands of years without further recombination; (iii) mutants with nonfunctional genes (pseudogenes) have been circulating and recombining for long periods and can cause congenital infection and resulting clinical sequelae; and (iv) intrahost variation in single-strain infections is much less than that in multiple-strain infections. Future population-based studies are likely to continue illuminating the evolution, epidemiology, and pathogenesis of HCMV.
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Affiliation(s)
- Nicolás M Suárez
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Gavin S Wilkie
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Elias Hage
- Institute of Virology, Hannover Medical School, United Kingdom.,German Center for Infection Research, Hannover-Braunschweig site, United Kingdom
| | - Salvatore Camiolo
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Marylouisa Holton
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Maha Maabar
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sreenu B Vattipally
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Akshay Dhingra
- Institute of Virology, Hannover Medical School, United Kingdom
| | - Ursula A Gompels
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Gavin W G Wilkinson
- Division of Infection and Immunity, School of Medicine, Cardiff University, United Kingdom
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Italy
| | - Milena Furione
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Italy
| | - Daniele Lilleri
- Laboratory of Genetics-Transplantology and Cardiovascular Diseases, Italy
| | - Alessia Arossa
- Departments of Obstetrics and Gynecology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Tina Ganzenmueller
- Institute of Virology, Hannover Medical School, United Kingdom.,German Center for Infection Research, Hannover-Braunschweig site, United Kingdom.,Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Giuseppe Gerna
- Laboratory of Genetics-Transplantology and Cardiovascular Diseases, Italy
| | - Petr Hubáček
- Department of Medical Microbiology, Motol University Hospital, Prague, Czech Republic, Israel
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, United Kingdom.,German Center for Infection Research, Hannover-Braunschweig site, United Kingdom
| | - Dana Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
| | - Maurizio Zavattoni
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Italy
| | - Andrew J Davison
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
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49
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Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
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50
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Fong W, Rockett R, Timms V, Sintchenko V. Optimization of sample preparation for culture-independent sequencing of Bordetella pertussis. Microb Genom 2020; 6:e000332. [PMID: 32108565 PMCID: PMC7200065 DOI: 10.1099/mgen.0.000332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/09/2020] [Indexed: 12/14/2022] Open
Abstract
Bordetella pertussis, the aetiological agent of whooping cough, is re-emerging globally despite widespread vaccination. B. pertussis is highly infectious and, prior to vaccination programmes, was the leading cause of infant mortality. The WHO estimated that over 600 000 deaths are prevented annually by pertussis vaccination, but B. pertussis infection was still responsible for over 63 000 deaths globally in 2013. The re-emergence of B. pertussis has been linked to strains with inactive or absent major virulence factors included in vaccines such as pertactin, pertussis toxin and filamentous haemagglutinin. Thus, the molecular surveillance of currently circulating strains is critical in understanding and controlling B. pertussis. Such information provides data on strains to inform control measures and the identification of future vaccine antigens. Current surveillance and typing methods for B. pertussis rely on the availability of clinical isolates. However, since the 1990s, the majority of pertussis cases have been diagnosed by PCR, where an isolate is not needed. The rapid decline in the availability of B. pertussis isolates impacts our ability to monitor this infection. The growing uptake of next-generation sequencing (NGS) has offered the opportunity for culture-independent genome sequencing and typing of this fastidious pathogen. Therefore, the objective of the study was to optimize respiratory sample preparation, independent of culture, in order to type B. pertussis using NGS. The study compared commercial depletion kits and specimen-processing methods using selective lysis detergents. The goal was to deplete human DNA, the major obstacle for sequencing a pathogen directly from a clinical sample. Samples spiked with a clinically relevant amount of B. pertussis were used to provide comparison between the different methods. Commercial depletion kits including the MolYsis, Qiagen Microbiome and NEBNext Kits were tested. Previously published methods, for Saponin and TritonX-100, were also trialled as a depletion. The ratio of B. pertussis to human DNA was determined by real-time PCR for ERV3 and IS481 (as markers of human and B. pertussis DNA, respectively), then samples were sequenced using the Illumina NextSeq 500 platform. The number of human and B. pertussis sequenced reads were then compared between treatments. The results showed that commercial kits reduced the human DNA present, but also reduced the concentration of target B. pertussis. However, selective lysis with Saponin treatment resulted in almost undetectable levels of human DNA, with minimal loss of target B. pertussis DNA. Sequencing read depth improved five-fold in reads to B. pertussis. Our investigation delivered a potential protocol that will enable the public health laboratory surveillance of B. pertussis in the era of culture-independent testing.
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Affiliation(s)
- Winkie Fong
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, The University of Sydney, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia
| | - Rebecca Rockett
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, The University of Sydney, Westmead, NSW, Australia
| | - Verlaine Timms
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, The University of Sydney, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, NSW, Australia
- Westmead Clinical School, The University of Sydney, Westmead, NSW, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Camperdown, NSW, Australia
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