Detection and Quantification of Classic and Emerging Viruses by Skimmed
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Identification of an Overprinting Gene in Merkel Cell Polyomavirus Provides Evolutionary Insight Into the Birth of Viral Genes
Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes Joseph J. Cartera,b,1,2, Matthew D. Daughertyc,1, Xiaojie Qia, Anjali Bheda-Malgea,3, Gregory C. Wipfa, Kristin Robinsona, Ann Romana, Harmit S. Malikc,d, and Denise A. Gallowaya,b,2 Divisions of aHuman Biology, bPublic Health Sciences, and cBasic Sciences and dHoward Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 Edited by Peter M. Howley, Harvard Medical School, Boston, MA, and approved June 17, 2013 (received for review February 24, 2013) Many viruses use overprinting (alternate reading frame utiliza- mammals and birds (7, 8). Polyomaviruses leverage alternative tion) as a means to increase protein diversity in genomes severely splicing of the early region (ER) of the genome to generate pro- constrained by size. However, the evolutionary steps that facili- tein diversity, including the large and small T antigens (LT and ST, tate the de novo generation of a novel protein within an ancestral respectively) and the middle T antigen (MT) of murine poly- ORF have remained poorly characterized. Here, we describe the omavirus (MPyV), which is generated by a novel splicing event and identification of an overprinting gene, expressed from an Alter- overprinting of the second exon of LT. Some polyomaviruses can nate frame of the Large T Open reading frame (ALTO) in the early drive tumorigenicity, and gene products from the ER, especially region of Merkel cell polyomavirus (MCPyV), the causative agent SV40 LT and MPyV MT, have been extraordinarily useful models of most Merkel cell carcinomas. -
Marine Surface Microlayer As a Source of Enteric Viruses
MARINE SURFACE MICROLAYER AS A SOURCE OF ENTERIC VIRUSES Ana Catarina Bispo Prata Tese de Doutoramento em Ciências do Mar e do Ambiente 2014 Ana Catarina Bispo Prata MARINE SURFACE MICROLAYER AS A SOURCE OF ENTERIC VIRUSES Tese de Candidatura ao grau de Doutor em Ciências do Mar e do Ambiente Especialidade em Oceanografia e Ecossistemas Marinhos submetida ao Instituto de Ciências Biomédicas de Abel Salazar da Universidade do Porto. Programa Doutoral da Universidade do Porto (Instituto de Ciências Biomédicas de Abel Salazar e Faculdade de Ciências) e da Universidade de Aveiro. Orientador – Doutor Adelaide Almeida Categoria – Professora Auxiliar Afiliação – Departamento de Biologia da Universidade de Aveiro Co-orientador – Doutor Newton Carlos Marcial Gomes Categoria – Investigador Principal do CESAM Afiliação – Departamento de Biologia da Universidade de Aveiro LEGAL DETAILS In compliance with what is stated in the legislation in vigor, it is hereby declared that the author of this thesis participated in the creation and execution of the experimental work leading to the results here stated, as well as in their interpretation and writing of the respective manuscripts. This thesis includes one scientific paper published in an international journal and three articles in preparation originated from part of the results obtained in the experimental work referenced as: • Prata C, Ribeiro A, Cunha A , Gomes NCM, Almeida A, 2012, Ultracentrifugation as a direct method to concentrate viruses in environmental waters: virus-like particles enumeration as a new approach to determine the efficiency of recovery, Journal of Environmental Monitoring, 14 (1), 64-70. • Prata C, Cunha A, Gomes N, Almeida A, Surface Microlayer as a source of health relevant enteric viruses in Ria de Aveiro. -
Merkel Cell Polyomavirus DNA in Immunocompetent and Immunocompromised Patients with Respiratory Disease
Journal of Medical Virology 83:2220–2224 (2011) Merkel Cell Polyomavirus DNA in Immunocompetent and Immunocompromised Patients With Respiratory Disease Bahman Abedi Kiasari,1,3* Pamela J. Vallely,1 and Paul E. Klapper1,2 1Department of Virology, Genomic Epidemiology Research Group, School of Translational Medicine, University of Manchester, Manchester, United Kingdom 2Clinical Virology, Manchester Medical Microbiology Partnership, Manchester Royal Infirmary, Oxford Road, Manchester, United Kingdom 3Human Viral Vaccine Department, Razi Vaccine & Serum Research Institute, Hesarak, Karaj, Iran Merkel cell polyomavirus (MCPyV) was identi- INTRODUCTION fied originally in association with a rare but aggressive skin cancer, Merkel cell carcinoma. In the past few years, a number of new human poly- The virus has since been found in the respirato- omaviruses, KI, WU, human polyomavirus 6 (HPyV6), ry tract of some patients with respiratory human polyomavirus 7 (HPyV7), trichodysplasia spi- disease. However, the role of MCPyV in the nulosa virus (TSV), human polyomavirus 9 (HPyV9), causation of respiratory disease has not been and Merkel cell polyomavirus (MCPyV) have been established. To determine the prevalence of discovered [Allander et al., 2007; Gaynor et al., 2007; MCPyV in 305 respiratory samples from Feng et al., 2008; Schowalter et al., 2010; van der immunocompetent and immunocompromised Meijden et al., 2010; Scuda et al., 2011]. MCPyV was patients and evaluate their contribution to re- discovered by digital transcriptome subtraction from a spiratory diseases, specimens were screened human skin cancer, Merkel cell carcinoma [Feng for MCPyV using single, multiplex, or real-time et al., 2008]. The finding of MCPyV in human Merkel PCR; co-infection with other viruses was exam- cell carcinoma suggests a role for this virus in the ined. -
Zika and Ebola Assays for Droplet Digital PCR Systems
Fast, Accurate, and High-Sensitivity Virus Detection: Zika and Ebola Assays for Droplet Digital PCR Systems Dianna Maar, Nick Heredia, Madhuri Ganta, Carolyn Reifsnyder Digital Biology Center, Bio-Rad Laboratories, Pleasanton, CA. Droplet Digital PCR Bulletin 7111 Abstract Virus quantification and detection are critical for effectively identifying, monitoring, and mitigating viruses. Viral infections can ebb and flow seasonally in the population or spread rapidly in a seemingly sudden and intense outbreak, such as the recent outbreaks of Zika and Ebola viruses. During such outbreaks, testing becomes important for understanding and managing the spread and treatment of that virus. Sensitivity and specificity are important for responding effectively. However, RNA viruses, such as Ebola and Zika, have high variability and need to be detected in high backgrounds of DNA/RNA. Droplet Digital PCR (ddPCR) is a useful tool for viral detection, offering several key advantages over qPCR alone; for example, ddPCR enables accurate quantification of standards for qPCR. Additionally, ddPCR can verify the accuracy of a qPCR assay for cases where the virus contains sequence variants, which is common in RNA viruses. Ultimately, for low-level quantification, digital PCR provides easy, accurate results with high confidence. Droplet Digital PCR results with the new Zika and Ebola ddPCR assays are shown and discussed. Introduction Quantifying and Detecting Zika and Ebola with ddPCR When a viral outbreak occurs it is important to be able to In 2007 the first recorded outbreak of Zika occurred. In 2015 rapidly detect and monitor the virus accurately. Droplet Digital large outbreaks occurred in Brazil. Zika virus is spread mostly PCR (ddPCR) technology is ideal for detecting and quantifying by mosquitos (Aedes aegypti and Aedes albopictus). -
An Overview on Human Polyomaviruses Developing Cancer
The Journal of Medical Research 2020; 6(4): 125-127 Review Article An overview on human polyomaviruses developing cancer in JMR 2020; 6(4): 125-127 humans July- August ISSN: 2395-7565 Mohammad Salim1, Mohammad Shahid Masroor2, Shagufta parween3, I.P. Prajapati1 © 2020, All rights reserved 1 Sanjay Gandhi Smriti Govt. Autonomous P.G. College, Sidhi, (affiliated to APS University, Rewa), Madhya Pradesh- www.medicinearticle.com 486661, India Received: 22-06-2020 2 People’s College of Dental Sciences & Research Center, People's University, Bhopal, Madhya Pradesh- 462037, Accepted: 14-07-2020 India 3 All India Institute of Medical sciences (AIIMS), Bhopal, Madhya Pradesh-462020, India Abstract The family Polyomaviridae included about a dozen of human polyomaviruses (HPyVs), of which MCPyV, SV-40, JCV and BKV viruses have been reported to cause cancer in human. Merkel cell carcinoma is a very aggressive type of skin cancer caused by the MCPyV5. Similarly, while SV-40 and JCV viruses developed brain tumor cancer, the BK virus has been linked to renal transplantations and nephropathy producing urinary bladder tumor and prostate cancer in human. In this paper we have tried to summarize the recent information gained in the field of human polyomaviruses causing cancer in human. Keywords: Human polyomaviruses, Cancer, Virus. INTRODUCTION Viruses are among the few causes of cancer contributing to a variety of malignancies. In 1966, when Peyton Rous was awarded a Nobel prize in physiology and medicine for his discovery of Rous chicken sarcoma virus as a cause of cancer, a renewed interest came in the field of microbial origin of cancer. -
Viruses in Transplantation - Not Always Enemies
Viruses in transplantation - not always enemies Virome and transplantation ECCMID 2018 - Madrid Prof. Laurent Kaiser Head Division of Infectious Diseases Laboratory of Virology Geneva Center for Emerging Viral Diseases University Hospital of Geneva ESCMID eLibrary © by author Conflict of interest None ESCMID eLibrary © by author The human virome: definition? Repertoire of viruses found on the surface of/inside any body fluid/tissue • Eukaryotic DNA and RNA viruses • Prokaryotic DNA and RNA viruses (phages) 25 • The “main” viral community (up to 10 bacteriophages in humans) Haynes M. 2011, Metagenomic of the human body • Endogenous viral elements integrated into host chromosomes (8% of the human genome) • NGS is shaping the definition Rascovan N et al. Annu Rev Microbiol 2016;70:125-41 Popgeorgiev N et al. Intervirology 2013;56:395-412 Norman JM et al. Cell 2015;160:447-60 ESCMID eLibraryFoxman EF et al. Nat Rev Microbiol 2011;9:254-64 © by author Viruses routinely known to cause diseases (non exhaustive) Upper resp./oropharyngeal HSV 1 Influenza CNS Mumps virus Rhinovirus JC virus RSV Eye Herpes viruses Parainfluenza HSV Measles Coronavirus Adenovirus LCM virus Cytomegalovirus Flaviviruses Rabies HHV6 Poliovirus Heart Lower respiratory HTLV-1 Coxsackie B virus Rhinoviruses Parainfluenza virus HIV Coronaviruses Respiratory syncytial virus Parainfluenza virus Adenovirus Respiratory syncytial virus Coronaviruses Gastro-intestinal Influenza virus type A and B Human Bocavirus 1 Adenovirus Hepatitis virus type A, B, C, D, E Those that cause -
Quantitative Real-Time PCR
Current PCR http://www.horizonpress.com/pcrbooks Quantitative Real-Time PCR N. A. Saunders Abstract Unlike classical end-point analysis PCR, real-time PCR provides the data required for quantification of the target nucleic acid. The results can be expressed in absolute terms by reference to external quantified standards or in relative terms compared to another target sequence present within the sample. Absolute quantification requires that the efficiency of the amplification reaction is the same in all samples and in the external quantified standards. Consequently, it is important that the efficiency of the PCR does not vary greatly due to minor differences between samples. Careful optimisation of the PCR conditions is therefore required. The use of probes in quantitative real- time PCR improves its performance and a range of suitable systems is now available. Generally quantitative real-time assays have excellent performance characteristics including a wide dynamic range, high sensitivity and accuracy. This has led to their use in a wide range of applications and two examples are presented. Viral quantification is now an important factor in the control of infection. The problems associated with virus quantification in cytomegalovirus (HCMV) infection are similar to those presented by other viruses. Quantitative PCR is finding an increasing role in the diagnosis of cancer. The assessment of c-erbB2/Her2/neu gene duplication is useful in predicting the disease http://www.horizonpress.com Current PCR http://www.horizonpress.com/pcrbooks prognosis in breast cancer. Several different real-time quantitative PCR protocols are available for these applications and have been applied successfully to their respective diseases. -
Cancer Patients Have a Higher Risk Regarding COVID-19–And Vice Versa?
pharmaceuticals Opinion Cancer Patients Have a Higher Risk Regarding COVID-19–and Vice Versa? Franz Geisslinger, Angelika M. Vollmar and Karin Bartel * Pharmaceutical Biology, Department Pharmacy, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany; [email protected] (F.G.); [email protected] (A.M.V.) * Correspondence: [email protected] Received: 29 May 2020; Accepted: 3 July 2020; Published: 6 July 2020 Abstract: The world is currently suffering from a pandemic which has claimed the lives of over 230,000 people to date. The responsible virus is called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and causes the coronavirus disease 2019 (COVID-19), which is mainly characterized by fever, cough and shortness of breath. In severe cases, the disease can lead to respiratory distress syndrome and septic shock, which are mostly fatal for the patient. The severity of disease progression was hypothesized to be related to an overshooting immune response and was correlated with age and comorbidities, including cancer. A lot of research has lately been focused on the pathogenesis and acute consequences of COVID-19. However, the possibility of long-term consequences caused by viral infections which has been shown for other viruses are not to be neglected. In this regard, this opinion discusses the interplay of SARS-CoV-2 infection and cancer with special focus on the inflammatory immune response and tissue damage caused by infection. We summarize the available literature on COVID-19 suggesting an increased risk for severe disease progression in cancer patients, and we discuss the possibility that SARS-CoV-2 could contribute to cancer development. -
Application of One-Step Reverse Transcription Droplet Digital PCR for Dengue Virus Detection and Quantification in Clinical Specimens
diagnostics Article Application of One-Step Reverse Transcription Droplet Digital PCR for Dengue Virus Detection and Quantification in Clinical Specimens Dumrong Mairiang 1,2,†, Adisak Songjaeng 2,3,†, Prachya Hansuealueang 4, Yuwares Malila 5 , Paphavee Lertsethtakarn 6, Sasikorn Silapong 6, Yongyuth Poolpanichupatam 7, Chonticha Klungthong 7, Kwanrutai Chin-Inmanu 8 , Somchai Thiemmeca 3,9, Nattaya Tangthawornchaikul 1,2, Kanokwan Sriraksa 10, Wannee Limpitikul 11, Sirijitt Vasanawathana 10, Damon W. Ellison 7, Prida Malasit 1,2,3, Prapat Suriyaphol 8,* and Panisadee Avirutnan 1,2,3,* 1 Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand; [email protected] (D.M.); [email protected] (N.T.); [email protected] (P.M.) 2 Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; [email protected] 3 Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; [email protected] 4 Graduate Program in Medical Biochemistry and Molecular Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; [email protected] Citation: Mairiang, D.; Songjaeng, 5 Food Biotechnology Research Team, National -
The Mirna World of Polyomaviruses Ole Lagatie1*, Luc Tritsmans2 and Lieven J Stuyver1
Lagatie et al. Virology Journal 2013, 10:268 http://www.virologyj.com/content/10/1/268 REVIEW Open Access The miRNA world of polyomaviruses Ole Lagatie1*, Luc Tritsmans2 and Lieven J Stuyver1 Abstract Polyomaviruses are a family of non-enveloped DNA viruses infecting several species, including humans, primates, birds, rodents, bats, horse, cattle, raccoon and sea lion. They typically cause asymptomatic infection and establish latency but can be reactivated under certain conditions causing severe diseases. MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in several cellular processes by binding to and inhibiting the translation of specific mRNA transcripts. In this review, we summarize the current knowledge of microRNAs involved in polyomavirus infection. We review in detail the different viral miRNAs that have been discovered and the role they play in controlling both host and viral protein expression. We also give an overview of the current understanding on how host miRNAs may function in controlling polyomavirus replication, immune evasion and pathogenesis. Keywords: Polyomaviruses, microRNAs, Virus-host interaction, Immune evasion Review for BKPyV, Merkel cell carcinoma (MCC) for Merkel General overview of polyomaviruses Cell Virus (MCPyV) and trichodysplasia spinulosa for Polyomaviruses comprise a family of DNA tumor vi- Trichodysplasia spinulosa-associated Polyomavirus (TSPyV) ruses. They are non-enveloped and have a circular, [4,10,11,14-20]. One of the most striking observations is the double stranded DNA genome of around 5,100 bp [1]. fact that asymptomatic infection occurs during childhood The virion consists of 72 pentamers of the capsid pro- which is followed ordinarily by life-long asymptomatic tein VP1 with a single copy of VP2 and VP3 associated persistence [21]. -
Human Merkel Cell Polyomavirus Small T Antigen Is an Oncoprotein
Research article Human Merkel cell polyomavirus small T antigen is an oncoprotein targeting the 4E-BP1 translation regulator Masahiro Shuda, Hyun Jin Kwun, Huichen Feng, Yuan Chang, and Patrick S. Moore Cancer Virology Program, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. Merkel cell polyomavirus (MCV) is the recently discovered cause of most Merkel cell carcinomas (MCCs), an aggressive form of nonmelanoma skin cancer. Although MCV is known to integrate into the tumor cell genome and to undergo mutation, the molecular mechanisms used by this virus to cause cancer are unknown. Here, we show that MCV small T (sT) antigen is expressed in most MCC tumors, where it is required for tumor cell growth. Unlike the closely related SV40 sT, MCV sT transformed rodent fibroblasts to anchorage- and contact-independent growth and promoted serum-free proliferation of human cells. These effects did not involve protein phosphatase 2A (PP2A) inhibition. MCV sT was found to act downstream in the mam- malian target of rapamycin (mTOR) signaling pathway to preserve eukaryotic translation initiation factor 4E–binding protein 1 (4E-BP1) hyperphosphorylation, resulting in dysregulated cap-dependent translation. MCV sT–associated 4E-BP1 serine 65 hyperphosphorylation was resistant to mTOR complex (mTORC1) and mTORC2 inhibitors. Steady-state phosphorylation of other downstream Akt-mTOR targets, including S6K and 4E-BP2, was also increased by MCV sT. Expression of a constitutively active 4E-BP1 that could not be phosphorylated antagonized the cell transformation activity of MCV sT. Taken together, these experiments showed that 4E-BP1 inhibition is required for MCV transformation. Thus, MCV sT is an oncoprotein, and its effects on dysregulated cap-dependent translation have clinical implications for the prevention, diagnosis, and treatment of MCV-related cancers. -
Real-Time PCR: an Essential Guide
Real-Time PCR: An Essential Guide Publisher: Horizon Bioscience Editor: Kirstin Edwards, Julie Logan and Nick Saunders Genomics Proteomics and Bioinformatics Unit, Health Protection Agency, London Publication date: May 2004 ISBN: 0-9545232-7-X Price: GB £95 or US $180 (hardback). Pages: vi + 346 Chapter abstracts How to Order Real-time PCR (RT-PCR) is a powerful and rapid technique for nucleic acid amplification. The accumulation of specific products in a reaction is monitored continuously during cycling. This is usually achieved by monitoring changes in fluorescence within the PCR tube. This essential manual presents a comprehensive guide to the most appropriate and up-to-date technologies and applications as well as providing an overview of the theory of this important technique. Written by recognized experts in the field this timely and authoritative volume is an essential requirement for all laboratories using PCR. Topics covered include: Real- time PCR instruments and probe chemistries, set-up, controls and validation, quantitative real-time PCR, analysis of mRNA expression, mutation detection, NASBA, application in clinical microbiology and diagnosis of infection. Key Features: • Completely up-to-date • Internationally renown authors • Fully illustrated throughout • Comprehensive coverage of the latest RT PCR technology • Explains key principles and concepts • Includes a broad range of applications • Useful index Chapter List: Chapter 1 An Introduction to Real-Time PCR N.A. Saunders Chapter 2 An Overview of Real-Time PCR Platforms J.M.J. Logan and K.J. Edwards Chapter 3 Homogeneous Fluorescent Chemistries for Real-Time PCR M.A. Lee, D.J. Squirrell, D.L. Leslie, and T.