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Kampouri E, Little JS, Crocchiolo R, Hill JA. Human herpesvirus-6, HHV-8 and parvovirus B19 after allogeneic hematopoietic cell transplant: the lesser-known viral complications. Curr Opin Infect Dis 2024; 37:245-253. [PMID: 38726832 DOI: 10.1097/qco.0000000000001020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
PURPOSE OF REVIEW Viral infections continue to burden allogeneic hematopoietic cell transplant (HCT) recipients. We review the epidemiology, diagnosis, and management of human herpesvirus (HHV)-6, HHV-8 and parvovirus B19 following HCT. RECENT FINDINGS Advances in HCT practices significantly improved outcomes but impact viral epidemiology: post-transplant cyclophosphamide for graft-versus-host disease prevention increases HHV-6 reactivation risk while the impact of letermovir for CMV prophylaxis - and resulting decrease in broad-spectrum antivirals - is more complex. Beyond the well established HHV-6 encephalitis, recent evidence implicates HHV-6 in pneumonitis. Novel less toxic therapeutic approaches (brincidofovir, virus-specific T-cells) may enable preventive strategies in the future. HHV-8 is the causal agent of Kaposi's sarcoma, which is only sporadically reported after HCT, but other manifestations are possible and not well elucidated. Parvovirus B19 can cause severe disease post-HCT, frequently manifesting with anemia, but can also be easily overlooked due to lack of routine screening and ambiguity of manifestations. SUMMARY Studies should establish the contemporary epidemiology of HHV-6, and other more insidious viruses, such as HHV-8 and parvovirus B19 following HCT and should encompass novel cellular therapies. Standardized and readily available diagnostic methods are key to elucidate epidemiology and optimize preventive and therapeutic strategies to mitigate the burden of infection.
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Affiliation(s)
- Eleftheria Kampouri
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jessica S Little
- Dana-Farber Cancer Institute
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Roberto Crocchiolo
- Servizio di Immunoematologia e Medicina Trasfusionale, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Joshua A Hill
- Vaccine and Infectious Disease Division
- Clinical Research Division, Fred Hutchinson Cancer Center
- Department of Medicine, University of Washington, Seattle, Washington, USA
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Kampouri E, Handley G, Hill JA. Human Herpes Virus-6 (HHV-6) Reactivation after Hematopoietic Cell Transplant and Chimeric Antigen Receptor (CAR)- T Cell Therapy: A Shifting Landscape. Viruses 2024; 16:498. [PMID: 38675841 PMCID: PMC11054085 DOI: 10.3390/v16040498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/04/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
HHV-6B reactivation affects approximately half of all allogeneic hematopoietic cell transplant (HCT) recipients. HHV-6B is the most frequent infectious cause of encephalitis following HCT and is associated with pleiotropic manifestations in this setting, including graft-versus-host disease, myelosuppression, pneumonitis, and CMV reactivation, although the causal link is not always clear. When the virus inserts its genome in chromosomes of germ cells, the chromosomally integrated form (ciHHV6) is inherited by offspring. The condition of ciHHV6 is characterized by the persistent detection of HHV-6 DNA, often confounding diagnosis of reactivation and disease-this has also been associated with adverse outcomes. Recent changes in clinical practice in the field of cellular therapies, including a wider use of post-HCT cyclophosphamide, the advent of letermovir for CMV prophylaxis, and the rapid expansion of novel cellular therapies require contemporary epidemiological studies to determine the pathogenic role and spectrum of disease of HHV-6B in the current era. Research into the epidemiology and clinical significance of HHV-6B in chimeric antigen receptor T cell (CAR-T cell) therapy recipients is in its infancy. No controlled trials have determined the optimal treatment for HHV-6B. Treatment is reserved for end-organ disease, and the choice of antiviral agent is influenced by expected toxicities. Virus-specific T cells may provide a novel, less toxic therapeutic modality but is more logistically challenging. Preventive strategies are hindered by the high toxicity of current antivirals. Ongoing study is needed to keep up with the evolving epidemiology and impact of HHV-6 in diverse and expanding immunocompromised patient populations.
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Affiliation(s)
- Eleftheria Kampouri
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Guy Handley
- Department of Medicine, Division of Infectious Disease and International Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Joshua A. Hill
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA;
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
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Li N, Zhang R, Wang J, Zhu X, Meng F, Cao Y, Wang G, Yang Y. Case report: Acute HHV6B encephalitis/myelitis post CAR-T cell therapy in patients with relapsed/refractory aggressive B-cell lymphoma. Front Neurol 2024; 15:1334000. [PMID: 38487325 PMCID: PMC10937551 DOI: 10.3389/fneur.2024.1334000] [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: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024] Open
Abstract
Background The development of chimeric antigen receptor (CAR)-T cell therapy has revolutionized treatment outcomes in patients with lymphoid malignancies. However, several studies have reported a relatively high rate of infection in adult patients following CD19-targeting CAR T-cell therapy, particularly in the first 28 days. Notably, acute human herpesvirus 6 B (HHV6B) reactivation occurs in up to two-thirds of allogeneic hematopoietic stem cell transplantation patients. Case presentations Herein, we describe a report of HHV6B encephalitis/myelitis in three patients with relapsed/refractory diffuse large B-cell lymphoma post CAR T-cell therapy. All three patients received multiple lines of prior treatment (range: 2-9 lines). All patients presented with fever that persisted for at least 2 weeks after CAR-T cell infusion (CTI). Both the onset time and duration were similar to those of the cytokine release syndrome (CRS); nevertheless, the CRS grades of the patients were low (grade 1 or 2). Delirium and memory loss after CTI were the earliest notable mental presentations. Neurological manifestations progressed rapidly, with patients experiencing varying degrees of impaired consciousness, seizures, and coma. Back pain, lumbago, lower limb weakness and uroschesis were also observed in Patient 3, indicating myelitis. High HHV6B loads were detected in all Cerebral spinal fluid (CSF) samples using metagenomic next-generation sequencing (mNGS). Only one patient required high-activity antivirals and IgG intravenous pulse treatment finally recovered, whereas the other two patients died from HHV6B encephalitis. Conclusion Considering its fatal potential, HHV6B encephalitis/myelitis should be urgently diagnosed post CAR-T cell-based therapy. Furthermore, hematologists should differentially diagnose these conditions from CRS or other immunotherapy-related neurotoxicities as early as possible. The results of this study demonstrate the potential of mNGS in the early diagnosis of HHV6B infection, particularly when the organism is difficult to culture.
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Affiliation(s)
- Ningwen Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Ruoxuan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Jue Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Xiaojian Zhu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Fankai Meng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Yang Cao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Gaoxiang Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Yang Yang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
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Tan Z, Chia YMF, Mu X, Tan YJ. Inherited chromosomally-integrated human herpes virus 6 confounding test results in a patient with myelitis and optic neuritis - A case report. J Neuroimmunol 2024; 387:578283. [PMID: 38184892 DOI: 10.1016/j.jneuroim.2024.578283] [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: 12/17/2023] [Revised: 12/25/2023] [Accepted: 12/31/2023] [Indexed: 01/09/2024]
Abstract
A case of the 'perfect storm' of myelin oligodendrocyte glycoprotein (MOG) antibody-mediated myelitis, human herpesvirus 6 (HHV-6) reactivation, and COVID-19 infection was reported in 2021. This article reports a case of a similarly observed clinical triad, but with a different conclusion and explanation supported by laboratory test results and evidence from our literature review.
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Affiliation(s)
- Zhibin Tan
- Department of Neurology, National Neuroscience Institute, Singapore; Neuroscience Academic Clinical Programme, SingHealth Duke-NUS Academic Medical Centre, Singapore.
| | | | - Xiaomin Mu
- Department of Neurology, National Neuroscience Institute, Singapore
| | - You-Jiang Tan
- Department of Neurology, National Neuroscience Institute, Singapore; Neuroscience Academic Clinical Programme, SingHealth Duke-NUS Academic Medical Centre, Singapore
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Wormser VR, Agudelo Higuita NI, Ramaswami R, Melendez DP. Hematopoietic stem cell transplantation and the noncytomegalovirus herpesviruses. Transpl Infect Dis 2023; 25 Suppl 1:e14201. [PMID: 38041493 DOI: 10.1111/tid.14201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/12/2023] [Accepted: 11/12/2023] [Indexed: 12/03/2023]
Abstract
Although hematopoietic stem cell transplantation (HSCT) and other cellular therapies have significantly improved outcomes in the management of multiple hematological and nonhematological malignancies, the resulting impairment in humoral and cellular response increases the risk for opportunistic infection as an undesirable side effect. With their ability to establish latent infection and reactivate when the host immune system is at its weakest point, the Herpesviridae family constitutes a significant proportion of these opportunistic pathogens. Despite recent advancements in preventing and managing herpesvirus infections, they continue to be a common cause of significant morbidity and mortality in transplanted patients. Herein, we aim to provide and update on herpesvirus other than cytomegalovirus (CMV) affecting recipients of HSCT and other cellular therapies.
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Affiliation(s)
- Vanessa R Wormser
- Division of Infectious Diseases, Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
| | - Nelson Iván Agudelo Higuita
- Section of Infectious Diseases, Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Instituto de Enfermedades Infecciosas y Parasitología Antonio Vidal, Tegucigalpa, Honduras
| | - Ramya Ramaswami
- HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, Bethesda, Maryland, USA
| | - Dante P Melendez
- Division of Infectious Diseases, Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah, USA
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Wang H, Tomatis-Souverbielle C, Everhart K, Oyeniran SJ, Leber AL. Detection of human herpesvirus 6 in pediatric CSF samples: causing disease or incidental distraction? Diagn Microbiol Infect Dis 2023; 107:116029. [PMID: 37527599 DOI: 10.1016/j.diagmicrobio.2023.116029] [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: 01/31/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 08/03/2023]
Abstract
Interpretation of human herpesvirus type 6 (HHV6) detection in the cerebrospinal fluid (CSF) of children can be complex; the virus can cause acute infection, reactivation, or can be inherited chromosomally integrated (iciHHV6). Our objectives were to determine the prevalence of HHV6 including iciHHV6 in CSF and compare the clinical and laboratory characteristics with and without iciHHV6 in our patient population. Overall, the prevalence of HHV6 and iciHHV6 was 2.4% and 0.85%, respectively. Children with iciHHV6 were significantly younger and less likely to present with fever. Septic infants (≤60 days) accounted for 65.2% (15/23) of the iciHHV6 patients. Patients with iciHHV6 had higher viral loads in CSF and whole blood. Twenty-one (91.3%) patients with iciHHV6 and 12 (33.3%) without ici-HHV6 were determined to have an incidental detection of HHV6 not associated with presenting symptoms. Molecular detection of HHV6 in CSF is not always associated with HHV6 infection and may represent iciHHV6 particularly in infants evaluated for sepsis.
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Affiliation(s)
- Huanyu Wang
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Cristina Tomatis-Souverbielle
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Kathy Everhart
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sophonie J Oyeniran
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Amy L Leber
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA.
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7
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Shinde M, Lavania M, Rawal J, Chavan N, Shinde P. Evaluation of droplet digital qRT-PCR (dd qRT-PCR) for quantification of SARS CoV-2 RNA in stool and urine specimens of COVID-19 patients. Front Med (Lausanne) 2023; 10:1148688. [PMID: 37469662 PMCID: PMC10352106 DOI: 10.3389/fmed.2023.1148688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction There have been a few reports of viral load detection in stool and urine samples of patients with coronavirus disease 2019 (COVID-19), and the transmission of the virus through faecal oral route. For clinical diagnosis and treatment, the widely used reverse transcription-polymerase chain reaction (qRT-PCR) method has some limitations. Methods The aim of our study to assess the presence and concentration of SARS CoV-2 RNA in stool and urine samples from COVID-19 patients with mild, moderate, and severe disease, we compared a traditional qRT-PCR approach with a ddPCR. ddPCR and qRT-PCR-based target gene analysis were performed on 107 COVID-19-confirmed patients paired samples (N1 and N2). The MagMax magnetic beads base method was used to isolate RNA. Real-time qRT-PCR and dd PCR were performed on all patients. Results and Discussion The average cycle threshold (Ct) of qRT-PCR was highly correlated with the average copy number of 327.10 copies/l analyzed in ddPCR. In ddPCR, urine samples showed 27.1% positivity while for stool it was 100%. Conclusion This study's findings not only show that SARS CoV-2 is present in urine and faeces, but also suggest that low concentrations of the viral target ddPCR make it easier to identify positive samples and help resolve for cases of inconclusive diagnosis.
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8
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Wang J, Fan H, Li Y, Zhang TF, Liu YH. Trehalose-6-phosphate phosphatases are involved in trehalose synthesis and metamorphosis in Bactrocera minax. INSECT SCIENCE 2022; 29:1643-1658. [PMID: 35075784 DOI: 10.1111/1744-7917.13010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/24/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Trehalose is the principal sugar circulating in the hemolymph of insects, and trehalose synthesis is catalyzed by trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). Insect TPS is a fused enzyme containing both TPS domain and TPP domain. Thus, many insects do not possess TPP genes as TPSs have replaced the function of TPPs. However, TPPs are widely distributed across the dipteran insects, while the roles they play remain largely unknown. In this study, 3 TPP genes from notorious dipteran pest Bactrocera minax (BmiTPPB, BmiTPPC1, and BmiTPPC2) were identified and characterized. The different temporal-spatial expression patterns of 3 BmiTPPs implied that they exert different functions in B. minax. Recombinant BmiTPPs were heterologously expressed in yeast cells, and all purified proteins exhibited enzymatic activities, despite the remarkable disparity in performance between BmiTPPB and BmiTPPCs. RNA interference revealed that all BmiTPPs were successfully downregulated after double-stranded RNA injection, leading to decreased trehalose content and increased glucose content. Also, suppression of BmiTPPs significantly affected expression of downstream genes and increased the mortality and malformation rate. Collectively, these results indicated that all 3 BmiTPPs in B. minax are involved in trehalose synthesis and metamorphosis. Thus, these genes could be evaluated as insecticidal targets for managing B. minax, and even for other dipteran pests.
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Affiliation(s)
- Jia Wang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Huan Fan
- College of Plant Protection, Southwest University, Chongqing, China
| | - Ying Li
- College of Plant Protection, Southwest University, Chongqing, China
| | - Tong-Fang Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - Ying-Hong Liu
- College of Plant Protection, Southwest University, Chongqing, China
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9
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Sandhu A, Kim J, Bell LM, Jyonouchi S, Akhtar LN, Henrickson SE. Persistent HHV-6 DNAemia in a Patient Presenting With Meningoencephalitis. Pediatrics 2022; 150:189904. [PMID: 36330748 DOI: 10.1542/peds.2022-056759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
| | | | - Louis M Bell
- Division of Infectious Diseases.,Division of General Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Sarah E Henrickson
- Division of Allergy and Immunology.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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10
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Hogestyn JM, Salois G, Xie L, Apa C, Youngyunpipatkul J, Pröschel C, Mayer-Pröschel M. Expression of the human herpesvirus 6A latency-associated transcript U94A impairs cytoskeletal functions in human neural cells. Mol Cell Neurosci 2022; 123:103770. [PMID: 36055520 PMCID: PMC10124163 DOI: 10.1016/j.mcn.2022.103770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/12/2022] [Accepted: 08/20/2022] [Indexed: 12/30/2022] Open
Abstract
Many neurodegenerative diseases have a multifactorial etiology and variable course of progression that cannot be explained by current models. Neurotropic viruses have long been suggested to play a role in these diseases, although their exact contributions remain unclear. Human herpesvirus 6A (HHV-6A) is one of the most common viruses detected in the adult brain, and has been clinically associated with multiple sclerosis (MS), and, more recently, Alzheimer's disease (AD). HHV-6A is a ubiquitous viral pathogen capable of infecting glia and neurons. Primary infection in childhood is followed by the induction of latency, characterized by expression of the U94A viral transcript in the absence of viral replication. Here we examine the effects of U94A on cells of the central nervous system. We found that U94A expression inhibits the migration and impairs cytoplasmic maturation of human oligodendrocyte precursor cells (OPCs) without affecting their viability, a phenotype that may contribute to the failure of remyelination seen in many patients with MS. A subsequent proteomics analysis of U94A expression OPCs revealed altered expression of genes involved in tubulin associated cytoskeletal regulation. As HHV-6A seems to significantly be associated with early AD pathology, we extended our initially analysis of the impact of U94A on human derived neurons. We found that U94A expression inhibits neurite outgrowth of primary human cortical neurons and impairs synapse maturation. Based on these data we suggest that U94A expression by latent HHV-6A in glial cells and neurons renders them susceptible to dysfunction and degeneration. Therefore, latent viral infections of the brain represent a unique pathological risk factor that may contribute to disease processes.
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Affiliation(s)
- Jessica M Hogestyn
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Garrick Salois
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Li Xie
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Connor Apa
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Stem cell and Regenerative Medicine Institute, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Justin Youngyunpipatkul
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Stem cell and Regenerative Medicine Institute, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Margot Mayer-Pröschel
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA,.
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11
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Mills MG, Hajian P, Bakhash SM, Xie H, Mantzke D, Zhu H, Perchetti GA, Huang ML, Pepper G, Jerome KR, Roychoudhury P, Greninger AL. Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR). J Clin Virol 2022; 154:105218. [PMID: 35779343 PMCID: PMC9212762 DOI: 10.1016/j.jcv.2022.105218] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/05/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Some mutations in the receptor binding domain of the SARS-CoV-2 Spike protein are associated with increased transmission or substantial reductions in vaccine efficacy, including in recently described Omicron subvariants. The changing frequencies of these mutations combined with their differing susceptibility to available therapies have posed significant problems for clinicians and public health professionals. OBJECTIVE To develop an assay capable of rapidly and accurately identifying variants including Omicron in clinical specimens to enable case tracking and/or selection of appropriate clinical treatment. STUDY DESIGN Using three duplex RT-ddPCR reactions targeting four amino acids, we tested 419 positive clinical specimens from February to December 2021 during a period of rapidly shifting variant prevalences and compared genotyping results to genome sequences for each sample, determining the sensitivity and specificity of the assay for each variant. RESULTS Mutation determinations for 99.7% of detected samples agree with NGS data for those samples, and are accurate despite wide variation in RNA concentration and potential confounding factors like transport medium, presence of additional respiratory viruses, and additional mutations in primer and probe sequences. The assay accurately identified the first 15 Omicron variants in our laboratory including the first Omicron in Washington State and discriminated against S-gene dropout Delta specimen. CONCLUSION We describe an accurate, precise, and specific RT-ddPCR assay for variant detection that remains robust despite being designed prior the emergence of Delta and Omicron variants. The assay can quickly identify mutations in current and past SARS-CoV-2 variants, and can be adapted to future mutations.
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Affiliation(s)
- Margaret G Mills
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA.
| | - Pooneh Hajian
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Shah Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Derrek Mantzke
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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12
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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13
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Izquierdo L, Canivet CM, De Martin E, Antonini TM, Roque-Afonso AM, Coilly A, Deback C. Investigation of Inherited Chromosomally Integrated Human Herpesvirus-6A+ and -6B+ in a Patient with Ulipristal Acetate-Induced Fulminant Hepatic Failure. Viruses 2021; 14:v14010062. [PMID: 35062266 PMCID: PMC8778448 DOI: 10.3390/v14010062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 01/01/2023] Open
Abstract
Inherited chromosomally integrated (ici) human herpes virus 6 (HHV-6) is estimated to occur in 0.6–2.7% of people worldwide. HHV-6 comprises two distinct species: HHV-6A and HHV-6B. Both HHV-6A and HHV-6B integration have been reported. Several drugs are capable of activating iciHHV-6 in tissues, the consequences of which are poorly understood. We report herein a case of a woman with iciHHV-6A+ and iciHHV-6B+, who developed ulipristal acetate (a selective progesterone receptor modulator)-induced fulminant hepatic failure that required liver transplantation. We confirmed the presence of ~one copy per cell of both HHV-6A and HHV-6B DNA in her hair follicles using multiplex HHV-6A/B real-time PCR and demonstrated the Mendelian inheritance of both iciHHV-6A and iciHHV-6B in her family members over three generations. Because of the rarity of this presentation, we discuss herein the possible links between reactivated HHV-6 from iciHHV-6A and/or iciHHV-6B and adverse drug reactions, suggesting that iciHHV-6 could be screened before the introduction of any hepatotoxic drugs to exclude HHV-6 active disease or combined idiosyncratic drug-induced liver injury in these patients.
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Affiliation(s)
- Laure Izquierdo
- Laboratoire de Virologie, Institut National de la Santé et de la Recherche Médicale Unité 1193 AP-HP, Hôpitaux Universitaires Paris Saclay, Hôpital Paul-Brousse, 94800 Villejuif, France; (L.I.); (A.-M.R.-A.)
| | - Clémence M. Canivet
- Laboratoire HIFIH, UPRES EA3859, SFR 4208, Service d’Hépato-Gastroentérologie et Oncologie Digestive, Centre Hospitalier Universitaire d’Angers, Université d’Angers, 49000 Angers, France;
| | - Eleonora De Martin
- Centre Hépato-Biliaire, AP-HP, Institut National de la Santé et de la Recherche Médicale Unité 1193, Hôpitaux Universitaires Paris Saclay, Hôpital Paul-Brousse, 94800 Villejuif, France; (E.D.M.); (T.M.A.); (A.C.)
| | - Teresa M. Antonini
- Centre Hépato-Biliaire, AP-HP, Institut National de la Santé et de la Recherche Médicale Unité 1193, Hôpitaux Universitaires Paris Saclay, Hôpital Paul-Brousse, 94800 Villejuif, France; (E.D.M.); (T.M.A.); (A.C.)
| | - Anne-Marie Roque-Afonso
- Laboratoire de Virologie, Institut National de la Santé et de la Recherche Médicale Unité 1193 AP-HP, Hôpitaux Universitaires Paris Saclay, Hôpital Paul-Brousse, 94800 Villejuif, France; (L.I.); (A.-M.R.-A.)
| | - Audrey Coilly
- Centre Hépato-Biliaire, AP-HP, Institut National de la Santé et de la Recherche Médicale Unité 1193, Hôpitaux Universitaires Paris Saclay, Hôpital Paul-Brousse, 94800 Villejuif, France; (E.D.M.); (T.M.A.); (A.C.)
| | - Claire Deback
- Laboratoire de Virologie, AP-HP, Hôpitaux Universitaires Paris Saclay, Hôpital Paul-Brousse, 94800 Villejuif, France
- Inserm U996, Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, 92140 Clamart, France
- Correspondence: ; Tel.: +33-141-28-80-00
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14
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Zheng Y, Jin J, Shao Z, Liu J, Zhang R, Sun R, Hu B. Development and clinical validation of a droplet digital PCR assay for detecting Acinetobacter baumannii and Klebsiella pneumoniae in patients with suspected bloodstream infections. Microbiologyopen 2021; 10:e1247. [PMID: 34964298 PMCID: PMC8594765 DOI: 10.1002/mbo3.1247] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/20/2021] [Indexed: 12/11/2022] Open
Abstract
The relatively long turnaround time and low sensitivity of traditional blood culture-based diagnosis may delay effective antibiotic therapy for patients with bloodstream infections (BSIs). A rapid and sensitive pathogen detection method is urgently required to reduce the morbidity and mortality associated with BSIs. Acinetobacter baumannii and Klebsiella pneumoniae are two major microorganisms that cause BSIs. Here we report a novel droplet digital polymerase chain reaction (ddPCR) assay that can detect A. baumannii and K. pneumoniae in blood samples within 4 h, with a specificity of 100% for each strain and a limit of detection at 0.93 copies/μl for A. baumannii and 0.27 copies/μl for K. pneumoniae. Clinical validation of 170 patients with suspected BSIs showed that compared to blood cultures that detected four (2.4%) A. baumannii cases and seven (4.1%) K. pneumoniae cases, ddPCR detected 23 (13.5%) A. baumannii cases, 26 (15.3%) K. pneumoniae cases, and four (2.4%) co-infection cases, including the 11 cases detected via blood culture. In addition, patients who tested positive via ddPCR alone (n = 42) had significantly lower serum concentrations of procalcitonin and lactate, SOFA and APACHE II scores, and 28-day mortality than those reported positive via both blood culture and ddPCR (n = 11), suggesting that patients with less severe symptoms can potentially benefit from ddPCR-based diagnosis. In conclusion, our study suggests that ddPCR represents a sensitive and rapid method for identifying causal pathogens in blood samples and guiding treatment decisions in the early stages of BSIs.
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Affiliation(s)
- Yang Zheng
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Jun Jin
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Ziqiang Shao
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Jingquan Liu
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Run Zhang
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Renhua Sun
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Bangchuan Hu
- Intensive Care UnitZhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhouChina
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15
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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16
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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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17
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Wang X, Patel SA, Haddadin M, Cerny J. Post-allogeneic hematopoietic stem cell transplantation viral reactivations and viremias: a focused review on human herpesvirus-6, BK virus and adenovirus. Ther Adv Infect Dis 2021; 8:20499361211018027. [PMID: 34104434 PMCID: PMC8155777 DOI: 10.1177/20499361211018027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/27/2021] [Indexed: 12/30/2022] Open
Abstract
Human cytomegalovirus and Epstein-Barr virus have been recognized as potential drivers of morbidity and mortality of patients undergoing allogeneic stem cell transplantation for years. Specific protocols for monitoring, prophylaxis and pre-emptive therapy are in place in many transplant settings. In this review, we focus on the next three most frequent viruses, human herpesvirus-6, BK virus and adenovirus, causing reactivation and/or viremia after allogeneic transplant, which are increasingly detected in patients in the post-transplant period owing to emerging techniques of molecular biology, recipients' characteristics, treatment modalities used for conditioning and factors related donors or stem cell source. Given the less frequent detection of an illness related to these viruses, there are often no specific protocols in place for the management of affected patients. While some patients develop significant morbidity (generally older), others may not need therapy at all (generally younger or children). Furthermore, some of the antiviral therapies used are potentially toxic. With the addition of increased risk of secondary infections, risk of graft failure or increased risk of graft-versus-host disease as well as the relationship with other post-transplant complications, the outcomes of patients with these viremias remain unsatisfactory and even long-term survivors experience increased morbidity.
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Affiliation(s)
- Xin Wang
- Department of Medicine, UMass Memorial Medical Center, Worcester, MA, USA
| | - Shyam A Patel
- Division of Hematology-Oncology, Department of Medicine, UMass Memorial Medical Center, Worcester, MA, USA
| | - Michael Haddadin
- Division of Hematology-Oncology, Department of Medicine, UMass Memorial Medical Center, Worcester, MA, USA
| | - Jan Cerny
- Division of Hematology and Oncology, Department of Medicine, UMass Memorial Medical Center, 55 Lake Avenue North, Worcester, MA, 01655, USA
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18
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Vasudevan HN, Xu P, Servellita V, Miller S, Liu L, Gopez A, Chiu CY, Abate AR. Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification. Sci Rep 2021; 11:780. [PMID: 33436939 PMCID: PMC7804156 DOI: 10.1038/s41598-020-80715-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus motivates diverse diagnostic approaches due to the novel causative pathogen, incompletely understood clinical sequelae, and limited availability of testing resources. Given the variability in viral load across and within patients, absolute viral load quantification directly from crude lysate is important for diagnosis and surveillance. Here, we investigate the use of digital droplet PCR (ddPCR) for SARS-CoV-2 viral load measurement directly from crude lysate without nucleic acid purification. We demonstrate ddPCR accurately quantifies SARS-CoV-2 standards from purified RNA and multiple sample matrices, including commonly utilized universal transport medium (UTM). In addition, we find ddPCR functions robustly at low input viral copy numbers on nasopharyngeal swab specimens stored in UTM without upfront RNA extraction. We also show ddPCR, but not qPCR, from crude lysate shows high concordance with viral load measurements from purified RNA. Our data suggest ddPCR offers advantages to qPCR for SARS-CoV-2 detection with higher sensitivity and robustness when using crude lysate rather than purified RNA as input. More broadly, digital droplet assays provide a potential method for nucleic acid measurement and infectious disease diagnosis with limited sample processing, underscoring the utility of such techniques in laboratory medicine.
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Affiliation(s)
- Harish N Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th St, San Francisco, CA, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Peng Xu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th St, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th St, San Francisco, CA, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th St, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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19
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Vasudevan H, Xu P, Servellita V, Miller S, Liu L, Gopez A, Chiu CY, Abate AR. Digital droplet PCR accurately quantifies SARS-CoV-2 viral load from crude lysate without nucleic acid purification. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.02.20186023. [PMID: 32908995 PMCID: PMC7480047 DOI: 10.1101/2020.09.02.20186023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus motivates diverse diagnostic approaches due to the novel causative pathogen, incompletely understood clinical sequelae, and limited availability of testing resources. Given the variability in viral load across and within patients, absolute viral load quantification directly from crude lysate is important for diagnosis and surveillance. Here, we investigate the use of digital droplet PCR (ddPCR) for SARS-CoV-2 viral load measurement directly from crude lysate without nucleic acid purification. We demonstrate ddPCR accurately quantifies SARS-CoV-2 standards from purified RNA and multiple sample matrices, including commonly utilized universal transport medium (UTM). In addition, we find ddPCR functions robustly at low input viral copy numbers on nasopharyngeal swab specimens stored in UTM without upfront RNA extraction. We also show ddPCR, but not qPCR, from crude lysate shows high concordance with viral load measurements from purified RNA. Our data suggest ddPCR offers advantages to qPCR for SARS-CoV-2 detection with higher sensitivity and robustness when using crude lysate rather than purified RNA as input. More broadly, digital droplet assays provide a potential method for nucleic acid measurement and infectious disease diagnosis with limited sample processing, underscoring the utility of such techniques in laboratory medicine.
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20
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Liu X, Kosugi S, Koide R, Kawamura Y, Ito J, Miura H, Matoba N, Matsuzaki M, Fujita M, Kamada AJ, Nakagawa H, Tamiya G, Matsuda K, Murakami Y, Kubo M, Aswad A, Sato K, Momozawa Y, Ohashi J, Terao C, Yoshikawa T, Parrish NF, Kamatani Y. Endogenization and excision of human herpesvirus 6 in human genomes. PLoS Genet 2020; 16:e1008915. [PMID: 32776928 PMCID: PMC7444522 DOI: 10.1371/journal.pgen.1008915] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/20/2020] [Accepted: 06/07/2020] [Indexed: 12/12/2022] Open
Abstract
Sequences homologous to human herpesvirus 6 (HHV-6) are integrated within the nuclear genome of about 1% of humans, but it is not clear how this came about. It is also uncertain whether integrated HHV-6 can reactivate into an infectious virus. HHV-6 integrates into telomeres, and this has recently been associated with polymorphisms affecting MOV10L1. MOV10L1 is located on the subtelomere of chromosome 22q (chr22q) and is required to make PIWI-interacting RNAs (piRNAs). As piRNAs block germline integration of transposons, piRNA-mediated repression of HHV-6 integration has been proposed to explain this association. In vitro, recombination of the HHV-6 genome along its terminal direct repeats (DRs) leads to excision from the telomere and viral reactivation, but the expected "solo-DR scar" has not been described in vivo. Here we screened for integrated HHV-6 in 7,485 Japanese subjects using whole-genome sequencing (WGS). Integrated HHV-6 was associated with polymorphisms on chr22q. However, in contrast to prior work, we find that the reported MOV10L1 polymorphism is physically linked to an ancient endogenous HHV-6A variant integrated into the telomere of chr22q in East Asians. Unexpectedly, an HHV-6B variant has also endogenized in chr22q; two endogenous HHV-6 variants at this locus thus account for 72% of all integrated HHV-6 in Japan. We also report human genomes carrying only one portion of the HHV-6B genome, a solo-DR, supporting in vivo excision and possible viral reactivation. Together these results explain the recently-reported association between integrated HHV-6 and MOV10L1/piRNAs, suggest potential exaptation of HHV-6 in its coevolution with human chr22q, and clarify the evolution and risk of reactivation of the only intact (non-retro)viral genome known to be present in human germlines.
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Affiliation(s)
- Xiaoxi Liu
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shunichi Kosugi
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Rie Koide
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroki Miura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nana Matoba
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Motomichi Matsuzaki
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anselmo Jiro Kamada
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Gen Tamiya
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory for Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Amr Aswad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nicholas F. Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research and RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- * E-mail:
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Japan
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21
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Human herpesvirus 6 in transplant recipients: an update on diagnostic and treatment strategies. Curr Opin Infect Dis 2020; 32:584-590. [PMID: 31567413 DOI: 10.1097/qco.0000000000000592] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW The current review article focuses on recent advances in the approach to the diagnosis and treatment of human herpesvirus 6B (HHV-6B) in hematopoietic cell and solid organ transplant recipients. RECENT FINDINGS Over the past few years, key studies have broadened our understanding of best practices for the prevention and treatment of HHV-6B encephalitis after transplantation. Moreover, important data have been reported that support a potential role of HHV-6B reactivation in the development of acute graft-versus-host disease and lower respiratory tract disease in transplant recipients. Finally, increasing recognition of inherited chromosomally integrated HHV-6 (iciHHV-6) and an expanding array of diagnostic tools have increased our understanding of the potential for complications related to viral reactivation originating from iciHHV-6 in donors or recipients. SUMMARY Recent advances in diagnostic tools, disease associations, and potential treatments for HHV-6B present abundant opportunities for improving our understanding and management of this complex virus in transplant recipients.
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22
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Dantuluri KL, Konvinse KC, Crook J, Thomsen IP, Banerjee R. Human Herpesvirus 6 Detection during the Evaluation of Sepsis in Infants Using the FilmArray Meningitis/Encephalitis Panel. J Pediatr 2020; 223:204-206.e1. [PMID: 32417077 DOI: 10.1016/j.jpeds.2020.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/28/2020] [Accepted: 03/12/2020] [Indexed: 12/19/2022]
Abstract
We used the FilmArray meningitis/encephalitis panel for evaluation of sepsis in febrile neonates. We detected human herpesvirus 6, a virus we did not routinely test for previously, in the cerebrospinal fluid of 7 neonates. In all 7 cases, detection of the virus did not warrant antiviral treatment.
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Affiliation(s)
- Keerti L Dantuluri
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN.
| | | | - Jennifer Crook
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN
| | - Isaac P Thomsen
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Ritu Banerjee
- Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
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Pathogen or Bystander: Clinical Significance of Detecting Human Herpesvirus 6 in Pediatric Cerebrospinal Fluid. J Clin Microbiol 2020; 58:JCM.00313-20. [PMID: 32102858 DOI: 10.1128/jcm.00313-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/22/2020] [Indexed: 02/08/2023] Open
Abstract
Human herpesvirus 6 (HHV-6) is an important cause of meningitis and meningoencephalitis. As testing for HHV-6 in cerebrospinal fluid (CSF) is more readily available using the FilmArray Meningitis/Encephalitis panel (FA-ME; BioFire Diagnostics, Salt Lake City, UT), we aimed to determine the clinical significance of detecting HHV-6 in order to identify true infections and to ensure appropriate antiviral initiation. Chart review on 25 patients positive for HHV-6 by FA-ME was performed to determine clinical presentation, comorbidity, treatment, and outcome. The presence of chromosomally integrated HHV-6 (ciHHV-6) DNA was also investigated. Of 1,005 children tested by FA-ME, HHV-6 was detected in 25 (2.5%). Five patients were diagnosed with either HHV-6 meningitis or meningoencephalitis based on HHV-6 detection in CSF, clinical presentation, and radiographic findings. Detection of HHV-6 by FA-ME led to discontinuation of acyclovir within 12.0 h in all 12 patients empirically treated with acyclovir. Six of the 12 patients were started on ganciclovir therapy within 6.8 h; 4 of these were treated specifically for HHV-6 infection, whereas therapy was discontinued in the remaining 2 patients. CSF parameters were not generally predictive of HHV-6 positivity. The presence of ciHHV-6 was confirmed in 3 of 18 patients who could be tested. Five of the 25 patients included in the study were diagnosed with HHV-6 meningitis/meningoencephalitis. FA-ME results led to discontinuation of empirical antiviral treatment in 12 patients and appropriate initiation of ganciclovir in 4 patients. In our institution, detection of HHV-6 using FA-ME led to faster establishment of disease etiology and optimization of antimicrobial therapy.
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HHV-6-Associated Neurological Disease in Children: Epidemiologic, Clinical, Diagnostic, and Treatment Considerations. Pediatr Neurol 2020; 105:10-20. [PMID: 31932119 DOI: 10.1016/j.pediatrneurol.2019.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/12/2019] [Accepted: 10/17/2019] [Indexed: 02/04/2023]
Abstract
Human herpesviruses 6A and 6B, often referred to collectively as human herpesvirus 6, are a pair of beta-herpesviruses known to cause a variety of clinical syndromes in both immunocompetent and immunocompromised individuals. Most humans are infected with human herpesvirus 6B, and many with human herpesvirus 6A. Primary infection typically occurs in early childhood, although large-scale reviews on the topic are limited. Herein, the authors explore the clinical manifestations of human herpesvirus 6-associated disease in both immunocompetent and immunocompromised pediatric patients, the risk factors for development of human herpesvirus 6-associated neurological disease, the risk of autoimmunity associated with development of active or latent infection, the relevance of human herpesvirus 6-specific diagnostic tests, and the medications used to treat human herpesvirus 6. The goal of this review is to improve the current understanding of human herpesvirus 6 in pediatric populations and to examine the most effective diagnostic and therapeutic interventions in this disease state.
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25
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Current understanding of human herpesvirus 6 (HHV-6) chromosomal integration. Antiviral Res 2020; 176:104720. [PMID: 32044155 DOI: 10.1016/j.antiviral.2020.104720] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
Human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are members of the genus Roseolovirus in the Betaherpesvirinae subfamily. HHV-6B infects humans in the first years of life, has a seroprevalence of more than 90% and causes Roseola Infantum, but less is known about HHV-6A. While most other herpesviruses maintain their latent genome as a circular episome, HHV-6A and HHV-6B (HHV-6A/B) have been shown to integrate their genome into the telomeres of infected cells. HHV-6A/B can also integrate into the chromosomes of germ cells, resulting in individuals carrying a copy of the virus genome in every nucleated cell of their bodies. This review highlights our current understanding of HHV-6A/B integration and reactivation as well as aspects that should be addressed in the future of this relatively young research area. It forms part of an online symposium on the prevention and therapy of DNA virus infections, dedicated to the memory of Mark Prichard.
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26
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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27
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Inherited Chromosomally Integrated Human Herpesvirus 6 Demonstrates Tissue-Specific RNA Expression In Vivo That Correlates with an Increased Antibody Immune Response. J Virol 2019; 94:JVI.01418-19. [PMID: 31597766 PMCID: PMC6912112 DOI: 10.1128/jvi.01418-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
HHV-6A and -6B are human herpesviruses that have the unique property of being able to integrate into the telomeric regions of human chromosomes. Approximately 1% of the world’s population carries integrated HHV-6A/B genome in every cell of their body. Whether viral genes are transcriptionally active in these individuals is unclear. By taking advantage of a unique tissue-specific gene expression data set, we showed that the majority of tissues from iciHHV-6 individuals do not show HHV-6 gene expression. Brain and testes showed the highest tissue-specific expression of HHV-6 genes in two separate data sets. Two HHV-6 genes, U90 (immediate early 1 protein) and U100 (glycoproteins Q1 and Q2), were found to be selectively and consistently expressed across several human tissues. Expression of U90 translates into an increase in antigen-specific antibody response in iciHHV-6A/B+ subjects relative to controls. Future studies will be needed to determine the mechanism of gene expression, the effects of these genes on human gene transcription networks, and the pathophysiological impact of having increased viral protein expression in tissue in conjunction with increased antigen-specific antibody production. Human herpesviruses 6A and 6B (HHV-6A and HHV-6B) are human viruses capable of chromosomal integration. Approximately 1% of the human population carries one copy of HHV-6A/B integrated into every cell in their body, referred to as inherited chromosomally integrated human herpesvirus 6A/B (iciHHV-6A/B). Whether iciHHV-6A/B is transcriptionally active in vivo and how it shapes the immunological response are still unclear. In this study, we screened DNA sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) data for 650 individuals available through the Genotype-Tissue Expression (GTEx) project and identified 2 iciHHV-6A- and 4 iciHHV-6B-positive candidates. When corresponding tissue-specific gene expression signatures were analyzed, low levels HHV-6A/B gene expression was found across multiple tissues, with the highest levels of gene expression in the brain (specifically for HHV-6A), testis, esophagus, and adrenal gland. U90 and U100 were the most highly expressed HHV-6 genes in both iciHHV-6A- and iciHHV-6B-positive individuals. To assess whether tissue-specific gene expression from iciHHV-6A/B influences the immune response, a cohort of 15,498 subjects was screened and 85 iciHHV-6A/B+ subjects were identified. Plasma samples from iciHHV-6A/B+ and age- and sex-matched controls were analyzed for antibodies to control antigens (cytomegalovirus [CMV], Epstein-Barr virus [EBV], and influenza virus [FLU]) or HHV-6A/B antigens. Our results indicate that iciHHV-6A/B+ subjects have significantly more antibodies against the U90 gene product (IE1) than do non-iciHHV-6-positive individuals. Antibody responses against EBV and FLU antigens or HHV-6A/B gene products either not expressed or expressed at low levels, such as U47, U57, and U72, were identical between controls and iciHHV-6A/B+ subjects. CMV-seropositive individuals with iciHHV-6A/B+ have more antibodies against CMV pp150 than do CMV-seropositive controls. These results argue that spontaneous gene expression from integrated HHV-6A/B leads to an increase in antigenic burden that translates into a more robust HHV-6A/B-specific antibody response. IMPORTANCE HHV-6A and -6B are human herpesviruses that have the unique property of being able to integrate into the telomeric regions of human chromosomes. Approximately 1% of the world’s population carries integrated HHV-6A/B genome in every cell of their body. Whether viral genes are transcriptionally active in these individuals is unclear. By taking advantage of a unique tissue-specific gene expression data set, we showed that the majority of tissues from iciHHV-6 individuals do not show HHV-6 gene expression. Brain and testes showed the highest tissue-specific expression of HHV-6 genes in two separate data sets. Two HHV-6 genes, U90 (immediate early 1 protein) and U100 (glycoproteins Q1 and Q2), were found to be selectively and consistently expressed across several human tissues. Expression of U90 translates into an increase in antigen-specific antibody response in iciHHV-6A/B+ subjects relative to controls. Future studies will be needed to determine the mechanism of gene expression, the effects of these genes on human gene transcription networks, and the pathophysiological impact of having increased viral protein expression in tissue in conjunction with increased antigen-specific antibody production.
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28
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Weschke DP, Leisenring WM, Lawler RL, Stevens-Ayers T, Huang ML, Jerome KR, Zerr DM, Hansen JA, Boeckh M, Hill JA. Inflammatory Cytokine Profile in Individuals with Inherited Chromosomally Integrated Human Herpesvirus 6. Biol Blood Marrow Transplant 2019; 26:254-261. [PMID: 31678540 DOI: 10.1016/j.bbmt.2019.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/16/2022]
Abstract
Acute graft-versus-host-disease (aGVHD) is a major complication following hematopoietic cell transplantations (HCTs). We have shown that HCT recipients in whom either the donor or patient had inherited chromosomally integrated human herpesvirus 6 (iciHHV-6) have a higher incidence of developing more severe aGVHD. Previous studies established that increased proinflammatory cytokines are associated with increased risk for aGVHD and nonrelapse mortality post-HCT. We hypothesized that HCT recipients with donor or recipient iciHHV-6 (iciHHV-6pos HCT cases) will have higher cytokine levels compared with HCT recipients without iciHHV-6 (iciHHV-6neg HCT controls). We identified 64 iciHHV-6pos HCT cases with plasma from days 7, 14, and/or 21 post-HCT and before aGVHD onset in patients who developed aGVHD. We identified 64 iciHHV-6neg HCT controls matched for aGVHD risk factors. We also identified 28 donors with iciHHV-6 and 56 matched donors without iciHHV-6. We measured plasma cytokine concentrations for IL-6, suppression of tumorigenicity 2, T cell immunoglobulin and mucin-domain containing 3, TNFα, soluble TNF receptor 1 (TNFRp55), and C-reactive protein (CRP). We used Mann-Whitney tests and repeated-measures models to compare cytokine levels. iciHHV-6pos HCT cases had higher CRP levels on day 7 and day 21 and higher TNFRp55 levels on day 14 and day 21 compared with iciHHV-6neg HCT controls. These findings were recapitulated in a repeated-measures model. The differences were most evident among patients who subsequently developed aGVHD grades 2 to 4. Additionally, iciHHV-6pos HCT cases had earlier-onset aGVHD (median, 20 versus 27 days post-HCT; P = .02). There were no differences in cytokine levels among healthy donors with or without iciHHV-6. This study demonstrates that HCT recipients with iciHHV-6 have higher proinflammatory cytokines that may be associated with increased risk for aGVHD.
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Affiliation(s)
- Daniel P Weschke
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wendy M Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Richard L Lawler
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Terry Stevens-Ayers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - John A Hansen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington
| | - Joshua A Hill
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, Washington.
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The Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing. J Clin Microbiol 2019; 57:57/10/e02016-18. [PMID: 31551347 DOI: 10.1128/jcm.02016-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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30
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Ward KN, Hill JA, Hubacek P, de la Camara R, Crocchiolo R, Einsele H, Navarro D, Robin C, Cordonnier C, Ljungman P. Guidelines from the 2017 European Conference on Infections in Leukaemia for management of HHV-6 infection in patients with hematologic malignancies and after hematopoietic stem cell transplantation. Haematologica 2019; 104:2155-2163. [PMID: 31467131 PMCID: PMC6821622 DOI: 10.3324/haematol.2019.223073] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/27/2019] [Indexed: 01/15/2023] Open
Abstract
Of the two human herpesvirus 6 (HHV-6) species, human herpesvirus 6B (HHV-6B) encephalitis is an important cause of morbidity and mortality after allogeneic hematopoietic stem cell transplant. Guidelines for the management of HHV-6 infections in patients with hematologic malignancies or post-transplant were prepared a decade ago but there have been no other guidelines since then despite significant advances in the understanding of HHV-6 encephalitis, its therapy, and other aspects of HHV-6 disease in this patient population. Revised guidelines prepared at the 2017 European Conference on Infections in Leukaemia covering diagnosis, preventative strategies and management of HHV-6 disease are now presented.
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Affiliation(s)
- Katherine N Ward
- Division of Infection and Immunity, University College London, London, UK
| | - Joshua A Hill
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Petr Hubacek
- Department of Medical Microbiology and Department of Paediatric Haematology and Oncology 2 Medical Faculty of Charles University and Motol University Hospital, Prague, Czech Republic
| | | | | | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Julius Maximilians Universität, Würzburg, Germany
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA and Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Christine Robin
- Department of Haematology, Henri Mondor Hospital, Assistance Publique-Hopitaux de Paris, Université Paris-Est Créteil, Créteil, France
| | - Catherine Cordonnier
- Department of Haematology, Henri Mondor Hospital, Assistance Publique-Hopitaux de Paris, Université Paris-Est Créteil, Créteil, France
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31
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Possible reactivation of chromosomally integrated human herpesvirus 6 after treatment with histone deacetylase inhibitor. Blood Adv 2019; 2:1367-1370. [PMID: 29898877 DOI: 10.1182/bloodadvances.2018015982] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/11/2018] [Indexed: 01/21/2023] Open
Abstract
Key Points
HDAC inhibitors might induce ciHHV-6 reactivation. In ciHHV-6 HSCT recipients posttransplant viral load can estimate persistent host chimerism when the donor is ciHHV-6 negative.
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32
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Pellett Madan R, Hand J. Human herpesvirus 6, 7, and 8 in solid organ transplantation: Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice. Clin Transplant 2019; 33:e13518. [PMID: 30844089 DOI: 10.1111/ctr.13518] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
These updated guidelines from the Infectious Diseases Community of Practice of the American Society of Transplantation review the diagnosis, prevention, and management of HHV-6A, HHV-6B, HHV-7, and HHV-8 in the pre- and post-transplant period. The majority of HHV-6 (A and B) and HHV-7 infections in transplant recipients are asymptomatic; symptomatic disease is reported infrequently across organs. Routine screening for HHV-6 and 7 DNAemia is not recommended in asymptomatic patients, nor is prophylaxis or preemptive therapy. Detection of viral nucleic acid by quantitative PCR in blood or CSF is the preferred method for diagnosis of HHV-6 and HHV-7 infection. The possibility of chromosomally integrated HHV-6 DNA should be considered in individuals with persistently high viral loads. Antiviral therapy should be initiated for HHV-6 encephalitis and should be considered for other manifestations of disease. HHV-8 causes Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman disease and is also associated with hemophagocytic syndrome and bone marrow failure. HHV-8 screening and monitoring may be indicated to prevent disease. Treatment of HHV-8 related disease centers on reduction of immunosuppression and conversion to sirolimus, while chemotherapy may be needed for unresponsive disease. The role of antiviral therapy for HHV-8 infection has not yet been defined.
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Affiliation(s)
- Rebecca Pellett Madan
- Department of Pediatrics, New York University Langone School of Medicine, New York City, New York
| | - Jonathan Hand
- Department of Infectious Diseases, Ochsner Clinical School, Ochsner Medical Center, The University of Queensland School of Medicine, New Orleans, Louisiana
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Li HT, Lin BC, Huang ZF, Yang CZ, Huang WM. [Clinical value of droplet digital PCR in rapid diagnosis of invasive fungal infection in neonates]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21:45-51. [PMID: 30675863 PMCID: PMC7390180 DOI: 10.7499/j.issn.1008-8830.2019.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To evaluate the clinical value of droplet digital PCR (ddPCR) in rapid and accurate diagnosis of invasive fungal infection (IFI) in neonates. METHODS The highly conserved sequence of fungi 18S RNA was selected as the target sequence, and primers were designed to establish a ddPCR fungal detection system. Blood samples were collected from 83 neonates with high-risk factors for IFI and/or related clinical symptoms in the neonatal intensive care unit (NICU) of a hospital in Shenzhen, China. Blood culture and ddPCR were used for fungal detection. RESULTS The ddPCR fungal detection system had a specificity of 100% and a sensitivity of 3.2 copies/μL, and had a good reproducibility. Among the 22 blood samples from neonates with a confirmed or clinical diagnosis of IFI, 19 were detected positive by ddPCR. Among the 61 blood samples from neonates who were suspected of IFI or had no IFI, 2 were detected positive by ddPCR. CONCLUSIONS The ddPCR technique can be used for the detection of neonatal IFI and is a promising tool for the screening and even diagnosis of neonatal IFI.
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Affiliation(s)
- Hui-Tao Li
- Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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34
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Zerr DM. Human Herpesvirus 6B in the Transplant Recipient: When to Worry, When to Act. J Pediatric Infect Dis Soc 2018; 7:S75-S78. [PMID: 30590622 DOI: 10.1093/jpids/piy111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Human herpesvirus 6B (HHV-6B) is a ubiquitous pathogen that infects most individuals before the age of three years. HHV-6B reactivates in approximately 40% of transplant recipients where it has been associated with a number of important outcomes, especially in allogeneic transplant recipients. This article will review the epidemiology, clinical manifestations, diagnosis, and treatment of HHV-6B infection.
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Affiliation(s)
- Danielle M Zerr
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington, Seattle
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35
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Flamand L. Chromosomal Integration by Human Herpesviruses 6A and 6B. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1045:209-226. [PMID: 29896669 DOI: 10.1007/978-981-10-7230-7_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Upon infection and depending on the infected cell type, human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) can replicate or enter a state of latency. HHV-6A and HHV-6B can integrate their genomes into host chromosomes as one way to establish latency. Viral integration takes place near the subtelomeric/telomeric junction of chromosomes. When HHV-6 infection and integration occur in gametes, the virus can be genetically transmitted. Inherited chromosomally integrated HHV-6 (iciHHV-6)-positive individuals carry one integrated HHV-6 copy per somatic cell. The prevalence of iciHHV-6+ individuals varies between 0.6% and 2%, depending on the geographical region sampled. In this chapter, the mechanisms leading to viral integration and reactivation from latency, as well as some of the biological and medical consequences associated with iciHHV-6, were discussed.
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Affiliation(s)
- Louis Flamand
- Division of Infectious and Immune Diseases, CHU de Québec Research Center, QC, Quebec, Canada. .,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, QC, Quebec, Canada.
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36
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Bosman KJ, Wensing AMJ, Pijning AE, van Snippenberg WJ, van Ham PM, de Jong DMC, Hoepelman AIM, Nijhuis M. Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms. J Int AIDS Soc 2018; 21:e25185. [PMID: 30375818 PMCID: PMC6138437 DOI: 10.1002/jia2.25185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The latent reservoir is the main barrier on the road to HIV cure, and clinical approaches towards eradication are often evaluated by their effect on proviral DNA. To ensure inclusiveness and representativeness in HIV cure studies, proviral DNA quantification assays that are able to detect all common circulating HIV clades are urgently needed. Here, three HIV DNA assays targeting three different genomic regions were evaluated for their sensitivity and subtype-tolerance using digital PCR. METHODS A subtype-B-specific assay targeting gag (GAG) and two assays targeting conserved sequences in ltr and pol (LTR and JO) were assessed for their sensitivity and subtype-tolerance in digital PCR (Bio-Rad QX200), using a panel of serially diluted subtype reference plasmids as well as a panel of clinical isolates. Both panels represent subtypes A, B, C, D, F, G and circulating recombinant forms (CRFs) AE and AG, which together are responsible for 94% of HIV infections worldwide. RESULTS HIV subtype was observed to greatly affect HIV DNA quantification results. Robust regression analysis of the serially diluted plasmid panel showed that the GAG assay was only able to linearly quantify subtype B, D and G isolates (4/13 reference plasmids, average R2 = 0.99), whereas LTR and JO were able to quantify all tested isolates (13/13 reference plasmids, respective average R2 = 0.99 and 0.98). In the clinical isolates panel, isolates were considered detectable if all replicates produced a positive result. The GAG assay could detect HIV DNA in four out of five subtype B and one out of two subtype D isolates, whereas the LTR and JO assays detected HIV DNA in all twenty-nine tested isolates. LTR and JO results were found to be equally precise but more precise than GAG. CONCLUSIONS The results demonstrate the need for a careful validation of proviral reservoir quantification assays prior to investigations into non-B subtype reservoirs. The LTR and JO assays can sensitively and reliably quantify HIV DNA in a panel that represents the worldwide most prevalent subtypes and CRFs (A, B, C, D, AE, F, G and AG), justifying their application in future trials aimed at global HIV cure.
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Affiliation(s)
- Kobus J Bosman
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Annemarie MJ Wensing
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Aster E Pijning
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | - Petra M van Ham
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Dorien MC de Jong
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Andy IM Hoepelman
- Department of Internal Medicine and Infectious DiseasesUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Monique Nijhuis
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
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37
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Yeung CC, Hockenbery DM, Westerhoff M, Coutre SE, Sedlak RH, Dubowy RL, Munugalavadla V, Taylor K, Bosch F. Pathological assessment of gastrointestinal biopsies from patients with idelalisib-associated diarrhea and colitis. Future Oncol 2018; 14:2265-2277. [PMID: 29569483 DOI: 10.2217/fon-2017-0528] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
AIM Idelalisib (IDELA) treatment is associated with diarrhea/colitis (incidence of ∼15% grade ≥3). We performed a retrospective analysis of gastrointestinal biopsies from 29 patients treated with IDELA across nine clinical trials. METHODS A central core laboratory performed histopathologic review, immunohistochemistry, and droplet digital PCR viral studies. These results were correlated with tissue immune profiling data and morphologic features per modified Geboes score. RESULTS Out of 29 eligible patients with abdominal pain or diarrhea, 24 (82.8%) had reported adverse event terms of diarrhea and/or colitis. Infectious pathogens were detected in 9/29 samples. Most biopsies presented with mixed/inflammatory infiltrates and contained increased numbers of FOXP3+ cells versus normal controls. CONCLUSION This study revealed evidence of T-cell dysregulation and a substantial infectious component in association with IDELA-related diarrhea/colitis.
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Affiliation(s)
- Cecilia Cs Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 980403, USA.,Department of Pathology, University of Washington, Seattle, WA 943055, USA
| | - David M Hockenbery
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 980403, USA
| | - Maria Westerhoff
- Department of Pathology, University of Washington, Seattle, WA 943055, USA
| | - Steven E Coutre
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305-58215, USA
| | - Ruth H Sedlak
- Department of Laboratory Medicine, University of Washington, Seattle, WA 94404, USA
| | | | | | - Kerry Taylor
- Icon Cancer Care, South Brisbane, QLD, Australia
| | - Francesc Bosch
- Department of Hematology, University Hospital Vall d'Hebron, Barcelona, Spain
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Greninger AL, Knudsen GM, Roychoudhury P, Hanson DJ, Sedlak RH, Xie H, Guan J, Nguyen T, Peddu V, Boeckh M, Huang ML, Cook L, Depledge DP, Zerr DM, Koelle DM, Gantt S, Yoshikawa T, Caserta M, Hill JA, Jerome KR. Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6. BMC Genomics 2018; 19:204. [PMID: 29554870 PMCID: PMC5859498 DOI: 10.1186/s12864-018-4604-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/13/2018] [Indexed: 12/19/2022] Open
Abstract
Background Human herpesvirus-6A and -6B (HHV-6) are betaherpesviruses that reach > 90% seroprevalence in the adult population. Unique among human herpesviruses, HHV-6 can integrate into the subtelomeric regions of human chromosomes; when this occurs in germ line cells it causes a condition called inherited chromosomally integrated HHV-6 (iciHHV-6). Only two complete genomes are available for replicating HHV-6B, leading to numerous conflicting annotations and little known about the global genomic diversity of this ubiquitous virus. Results Using a custom capture panel for HHV-6B, we report complete genomes from 61 isolates of HHV-6B from active infections (20 from Japan, 35 from New York state, and 6 from Uganda), and 64 strains of iciHHV-6B (mostly from North America). HHV-6B sequence clustered by geography and illustrated extensive recombination. Multiple iciHHV-6B sequences from unrelated individuals across the United States were found to be completely identical, consistent with a founder effect. Several iciHHV-6B strains clustered with strains from recent active pediatric infection. Combining our genomic analysis with the first RNA-Seq and shotgun proteomics studies of HHV-6B, we completely reannotated the HHV-6B genome, altering annotations for more than 10% of existing genes, with multiple instances of novel splicing and genes that hitherto had gone unannotated. Conclusion Our results are consistent with a model of intermittent de novo integration of HHV-6B into host germline cells during active infection with a large contribution of founder effect in iciHHV-6B. Our data provide a significant advance in the genomic annotation of HHV-6B, which will contribute to the detection, diversity, and control of this virus. Electronic supplementary material The online version of this article (10.1186/s12864-018-4604-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA. .,, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Derek J Hanson
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Ruth Hall Sedlak
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Jon Guan
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Thuy Nguyen
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Vikas Peddu
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Michael Boeckh
- , Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Linda Cook
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Soren Gantt
- University of British Columbia, BC Children's Hospital Research Institute, Vancouver, Canada
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University, Fujita, Toyoake, Japan
| | - Mary Caserta
- University of Rochester Medical Center School of Medicine, Rochester, New York, USA
| | - Joshua A Hill
- , Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.,, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Telford M, Navarro A, Santpere G. Whole genome diversity of inherited chromosomally integrated HHV-6 derived from healthy individuals of diverse geographic origin. Sci Rep 2018; 8:3472. [PMID: 29472617 PMCID: PMC5823862 DOI: 10.1038/s41598-018-21645-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Human herpesviruses 6-A and -B (HHV-6A, HHV-6B) are ubiquitous in human populations worldwide. These viruses have been associated with several diseases such as multiple sclerosis, Hodgkin's lymphoma or encephalitis. Despite of the need to understand the genetic diversity and geographic stratification of these viruses, the availability of complete viral sequences from different populations is still limited. Here, we present nine new inherited chromosomally integrated HHV-6 sequences from diverse geographical origin which were generated through target DNA enrichment on lymphoblastoid cell lines derived from healthy individuals. Integration with available HHV-6 sequences allowed the assessment of HHV-6A and -6B phylogeny, patterns of recombination and signatures of natural selection. Analysis of the intra-species variability showed differences between A and B diversity levels and revealed that the HHV-6B reference (Z29) is an uncommon sequence, suggesting the need for an alternative reference sequence. Signs of geographical variation are present and more defined in HHV-6A, while they appear partly masked by recombination in HHV-6B. Finally, we conducted a scan for signatures of selection in protein coding genes that yielded at least 6 genes (4 and 2 respectively for the A and B species) showing significant evidence for accelerated evolution, and 1 gene showing evidence of positive selection in HHV-6A.
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Affiliation(s)
- Marco Telford
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.
- National Institute for Bioinformatics (INB), PRBB, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Barcelona, Catalonia, Spain.
- Center for Genomic Regulation (CRG), PRBB, Barcelona, Catalonia, Spain.
| | - Gabriel Santpere
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
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40
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Powell EA, Babady NE. Digital PCR in the Clinical Microbiology Laboratory: Another Tool on the Molecular Horizon. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.clinmicnews.2018.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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41
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Abstract
Human herpesvirus 6 (HHV-6A and HHV-6B) can cause primary infection or reactivate from latency in liver transplant recipients, which can result in a variety of clinical syndromes, including fever, hepatitis, encephalitis and higher rates of graft dysfunction as well as indirect effects including increased risks of mortality, CMV disease, hepatitis C progression and greater fibrosis scores. Although HHV-6 infection is currently diagnosed by quantifying viral DNA in plasma or blood, biopsy to demonstrate histopathological effects of HHV-6 remains the gold standard for diagnosis of end-organ disease. HHV-6 reactivation may be restricted to the infected organ with no evidence of active infection in the blood. HHV-6 infections in liver transplant patients are mostly asymptomatic, but clinically significant tissue-invasive infections have been treated successfully with ganciclovir, foscarnet or cidofovir. Inherited chromosomally integrated HHV-6 (ciHHV-6), in either the recipient or the donor organ, may create confusion about systemic HHV-6 infection. Recipients with inherited ciHHV-6 may have an increased risk of opportunistic infection and graft rejection. This article reviews the current scientific data on the clinical effects, risk factors, pathogenesis, diagnosis and treatment of HHV-6 infections in liver transplant recipients.
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Affiliation(s)
| | - Irmeli Lautenschlager
- Department of Virology, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Raymund R Razonable
- Division of Infectious Diseases, Department of Medicine and the William J von Liebig Center for Transplantation and Clinical Regeneration, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Flor M Munoz
- Department of Pediatrics, Transplant Infectious Diseases, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
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42
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Vellucci A, Leibovitch EC, Jacobson S. Using Droplet Digital PCR to Detect Coinfection of Human Herpesviruses 6A and 6B (HHV-6A and HHV-6B) in Clinical Samples. Methods Mol Biol 2018; 1768:99-109. [PMID: 29717439 DOI: 10.1007/978-1-4939-7778-9_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Droplet digital™ polymerase chain reaction (ddPCR™) is a unique digital PCR technique that allows for absolute quantification of nucleic acid samples. This technique operates on the basis of amplification within water-oil emulsion droplets and can detect very small quantities of target molecules, yielding extremely precise data. Here, we describe in detail a ddPCR procedure for multiplexed detection of two clinically relevant herpesviruses, HHV-6A and HHV-6B.
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Affiliation(s)
- Ashley Vellucci
- Neuroimmunology Branch, Viral Immunology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, USA
| | - Emily C Leibovitch
- Neuroimmunology Branch, Viral Immunology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, USA
- Institute for Biomedical Sciences, School of Medicine and Health Sciences, Washington, DC, USA
| | - Steven Jacobson
- Neuroimmunology Branch, Viral Immunology Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health, Bethesda, MD, USA.
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43
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Droplet-based digital PCR system for detection of single-cell level of foodborne pathogens. BIOCHIP JOURNAL 2017. [DOI: 10.1007/s13206-017-1410-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Rashidi A, Obeid K, Hill J, Warlick ED, Weisdorf DJ. Multiple transmissions of chromosomally integrated human herpesvirus-6 in one family. Transpl Infect Dis 2017; 20. [PMID: 29156094 DOI: 10.1111/tid.12816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 07/18/2017] [Accepted: 08/13/2017] [Indexed: 12/01/2022]
Abstract
Chromosomally integrated human herpesvirus-6 (ciHHV-6) can be transmitted from parent to child or via allogeneic hematopoietic cell transplantation (HCT). We report a case of ciHHV-6 transmitted via syngeneic HCT, and vertically across 3 generations. ciHHV-6 was transmitted from a parent to the patient and her identical twin, and from the patient to her son. The patient underwent syngeneic HCT as rescue from chemotherapy-induced aplasia during which ciHHV-6 was re-transmitted to her, this time from her identical twin. This is the first report, to our knowledge, of a patient acquiring ciHHV-6 once via germline from a parent and again via syngeneic HCT from an identical twin.
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Affiliation(s)
- Armin Rashidi
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Karam Obeid
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Joshua Hill
- Department of Medicine, University of Washington and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Erica D Warlick
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Weisdorf
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
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45
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Wood ML, Royle NJ. Chromosomally Integrated Human Herpesvirus 6: Models of Viral Genome Release from the Telomere and Impacts on Human Health. Viruses 2017; 9:E184. [PMID: 28704957 PMCID: PMC5537676 DOI: 10.3390/v9070184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/30/2017] [Accepted: 07/05/2017] [Indexed: 12/11/2022] Open
Abstract
Human herpesvirus 6A and 6B, alongside some other herpesviruses, have the striking capacity to integrate into telomeres, the terminal repeated regions of chromosomes. The chromosomally integrated forms, ciHHV-6A and ciHHV-6B, are proposed to be a state of latency and it has been shown that they can both be inherited if integration occurs in the germ line. The first step in full viral reactivation must be the release of the integrated viral genome from the telomere and here we propose various models of this release involving transcription of the viral genome, replication fork collapse, and t-circle mediated release. In this review, we also discuss the relationship between ciHHV-6 and the telomere carrying the insertion, particularly how the presence and subsequent partial or complete release of the ciHHV-6 genome may affect telomere dynamics and the risk of disease.
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Affiliation(s)
- Michael L Wood
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.
| | - Nicola J Royle
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.
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46
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Abstract
Human roseoloviruses include three different species, human herpesviruses 6A, 6B, and 7 (HHV-6A, HHV-6B, HHV-7), genetically related to human cytomegalovirus. They exhibit a wide cell tropism in vivo and, like other herpesviruses, induce a lifelong latent infection in humans. In about 1% of the general population, HHV-6 DNA is covalently integrated into the subtelomeric region of cell chromosomes (ciHHV-6). Many active infections, corresponding to primary infections, reactivations, or exogenous reinfections, are asymptomatic. They also may cause serious diseases, particularly in immunocompromised individuals, including hematopoietic stem-cell transplant (HSCT) and solid-organ transplant recipients, and acquired immunodeficiency syndrome (AIDS) patients. This opportunistic pathogenic role is formally established for HHV-6 infection and less clear for HHV-7. It mainly concerns the central-nervous system, bone marrow, lungs, gastrointestinal tract, skin, and liver. As the best example, HHV-6 causes both exanthema subitum, a benign disease associated with primary infection, and severe encephalitis associated with virus reactivations in HSCT recipients. Diagnosis using serologic and direct antigen-detection methods currently exhibits limitations. The most prominent technique is the quantification of viral DNA in blood, other body fluids, and organs by means of real-time polymerase-chain reaction (PCR). The antiviral compounds ganciclovir, foscarnet, and cidofovir are effective against active infections, but there is currently no consensus regarding the indications of treatment or specifics of drug administration. Numerous questions about HHV-6A, HHV-6B, HHV-7 are still pending, concerning in particular clinical impact and therapeutic options in immunocompromised patients.
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47
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Stabilization of Telomere G-Quadruplexes Interferes with Human Herpesvirus 6A Chromosomal Integration. J Virol 2017; 91:JVI.00402-17. [PMID: 28468887 DOI: 10.1128/jvi.00402-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/29/2017] [Indexed: 11/20/2022] Open
Abstract
Human herpesviruses 6A and 6B (HHV-6A/B) can integrate their genomes into the telomeres of human chromosomes using a mechanism that remains poorly understood. To achieve a better understanding of the HHV-6A/B integration mechanism, we made use of BRACO-19, a compound that stabilizes G-quadruplex secondary structures and prevents telomere elongation by the telomerase complex. First, we analyzed the folding of telomeric sequences into G-quadruplex structures and their binding to BRACO-19 using G-quadruplex-specific antibodies and surface plasmon resonance. Circular dichroism studies indicate that BRACO-19 modifies the conformation and greatly stabilizes the G-quadruplexes formed in G-rich telomeric DNA. Subsequently we assessed the effects of BRACO-19 on the HHV-6A initial phase of infection. Our results indicate that BRACO-19 does not affect entry of HHV-6A DNA into cells. We next investigated if stabilization of G-quadruplexes by BRACO-19 affected HHV-6A's ability to integrate its genome into host chromosomes. Incubation of telomerase-expressing cells with BRACO-19, such as HeLa and MCF-7, caused a significant reduction in the HHV-6A integration frequency (P < 0.002); in contrast, BRACO-19 had no effect on HHV-6 integration frequency in U2OS cells that lack telomerase activity and elongate their telomeres through alternative lengthening mechanisms. Our data suggest that the fluidity of telomeres is important for efficient chromosomal integration of HHV-6A and that interference with telomerase activity negatively affects the generation of cellular clones containing integrated HHV-6A.IMPORTANCE HHV-6A/B can integrate their genomes into the telomeres of infected cells. Telomeres consist of repeated hexanucleotides (TTAGGG) of various lengths (up to several kilobases) and end with a single-stranded 3' extension. To avoid recognition and induce a DNA damage response, the single-stranded overhang folds back on itself and forms a telomeric loop (T-loop) or adopts a tertiary structure, referred to as a G-quadruplex. In the current study, we have examined the effects of a G-quadruplex binding and stabilizing agent, BRACO-19, on HHV-6A chromosomal integration. By stabilizing G-quadruplex structures, BRACO-19 affects the ability of the telomerase complex to elongate telomeres. Our results indicate that BRACO-19 reduces the number of clones harboring integrated HHV-6A. This study is the first of its kind and suggests that telomerase activity is essential to restore a functional telomere of adequate length following HHV-6A integration.
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48
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Collin V, Flamand L. HHV-6A/B Integration and the Pathogenesis Associated with the Reactivation of Chromosomally Integrated HHV-6A/B. Viruses 2017; 9:E160. [PMID: 28672870 PMCID: PMC5537652 DOI: 10.3390/v9070160] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 01/03/2023] Open
Abstract
Unlike other human herpesviruses, human herpesvirus 6A and 6B (HHV-6A/B) infection can lead to integration of the viral genome in human chromosomes. When integration occurs in germinal cells, the integrated HHV-6A/B genome can be transmitted to 50% of descendants. Such individuals, carrying one copy of the HHV-6A/B genome in every cell, are referred to as having inherited chromosomally-integrated HHV-6A/B (iciHHV-6) and represent approximately 1% of the world's population. Interestingly, HHV-6A/B integrate their genomes in a specific region of the chromosomes known as telomeres. Telomeres are located at chromosomes' ends and play essential roles in chromosomal stability and the long-term proliferative potential of cells. Considering that the integrated HHV-6A/B genome is mostly intact without any gross rearrangements or deletions, integration is likely used for viral maintenance into host cells. Knowing the roles played by telomeres in cellular homeostasis, viral integration in such structure is not likely to be without consequences. At present, the mechanisms and factors involved in HHV-6A/B integration remain poorly defined. In this review, we detail the potential biological and medical impacts of HHV-6A/B integration as well as the possible chromosomal integration and viral excision processes.
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Affiliation(s)
- Vanessa Collin
- Division of Infectious and Immune Diseases, CHU de Quebec Research Center-Laval University, Québec, QC G1V 4G2, Canada.
| | - Louis Flamand
- Division of Infectious and Immune Diseases, CHU de Quebec Research Center-Laval University, Québec, QC G1V 4G2, Canada.
- Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Laval University, Québec, QC G1V 0A6, Canada.
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Cell Culture Systems To Study Human Herpesvirus 6A/B Chromosomal Integration. J Virol 2017; 91:JVI.00437-17. [PMID: 28468878 DOI: 10.1128/jvi.00437-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/22/2017] [Indexed: 01/01/2023] Open
Abstract
Human herpesviruses 6A/B (HHV-6A/B) can integrate their viral genomes in the telomeres of human chromosomes. The viral and cellular factors contributing to HHV-6A/B integration remain largely unknown, mostly due to the lack of efficient and reproducible cell culture models to study HHV-6A/B integration. In this study, we characterized the HHV-6A/B integration efficiencies in several human cell lines using two different approaches. First, after a short-term infection (5 h), cells were processed for single-cell cloning and analyzed for chromosomally integrated HHV-6A/B (ciHHV-6A/B). Second, cells were infected with HHV-6A/B and allowed to grow in bulk for 4 weeks or longer and then analyzed for the presence of ciHHV-6. Using quantitative PCR (qPCR), droplet digital PCR, and fluorescent in situ hybridization, we could demonstrate that HHV-6A/B integrated in most human cell lines tested, including telomerase-positive (HeLa, MCF-7, HCT-116, and HEK293T) and telomerase-negative cell lines (U2OS and GM847). Our results also indicate that inhibition of DNA replication, using phosphonoacetic acid, did not affect HHV-6A/B integration. Certain clones harboring ciHHV-6A/B spontaneously express viral genes and proteins. Treatment of cells with phorbol ester or histone deacetylase inhibitors triggered the expression of many viral genes, including U39, U90, and U100, without the production of infectious virus, suggesting that the tested stimuli were not sufficient to trigger full reactivation. In summary, both integration models yielded comparable results and should enable the identification of viral and cellular factors contributing to HHV-6A/B integration and the screening of drugs influencing viral gene expression, as well as the release of infectious HHV-6A/B from the integrated state.IMPORTANCE The analysis and understanding of HHV-6A/B genome integration into host DNA is currently limited due to the lack of reproducible and efficient viral integration systems. In the present study, we describe two quantitative cell culture viral integration systems. These systems can be used to define cellular and viral factors that play a role in HHV-6A/B integration. Furthermore, these systems will allow us to decipher the conditions resulting in virus gene expression and excision of the integrated viral genome resulting in reactivation.
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50
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Ihira M, Urashima A, Miura H, Hattori F, Kawamura Y, Sugata K, Yoshikawa T. Development of real-time RT-PCR assays for detection of three classes of HHV-6A gene transcripts. J Med Virol 2017; 89:1830-1836. [DOI: 10.1002/jmv.24862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/17/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Masaru Ihira
- Faculty of Clinical Engineering; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Akiko Urashima
- Faculty of Medical Technology; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Hiroki Miura
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Fumihiko Hattori
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Yoshiki Kawamura
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Ken Sugata
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
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