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Banks JM, Capistrano KJ, Brandini DA, Zaidi F, Thakkar P, Rahat R, Schwartz J, Naqvi AR. Herpesviruses and SARS-CoV-2: Viral Association with Oral Inflammatory Diseases. Pathogens 2024; 13:58. [PMID: 38251365 PMCID: PMC10819702 DOI: 10.3390/pathogens13010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/27/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The oral cavity is a niche for diverse microbes, including viruses. Members of the Herpesviridae family, comprised of dsDNA viruses, as well as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an ssRNA virus, are among the most prevalent viruses infecting the oral cavity, and they exhibit clinical manifestations unique to oral tissues. Viral infection of oral mucosal epithelia triggers an immune response that results in prolonged inflammation. The clinical and systemic disease manifestations of HHV have been researched extensively, and several recent studies have illuminated the relationship between HHV and oral inflammatory diseases. Burgeoning evidence suggests the oral manifestation of SARS-CoV-2 infection includes xerostomia, dysgeusia, periodontal disease, mucositis, and opportunistic viral and bacterial infections, collectively described as oral post-acute sequelae of COVID-19 (PASC). These diverse sequelae could be a result of intensified immune responses initially due to the copious production of proinflammatory cytokines: the so-called "cytokine storm syndrome", facilitating widespread oral and non-oral tissue damage. This review explores the interplay between HHV, SARS-CoV-2, and oral inflammatory diseases such as periodontitis, endodontic disease, and peri-implantitis. Additionally, the review discusses proper diagnostic techniques for identifying viral infection and how viral diagnostics can lead to improved overall patient health.
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Affiliation(s)
- Jonathan M. Banks
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Kristelle J. Capistrano
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Daniela A. Brandini
- Department of Diagnosis and Surgery, School of Dentistry, São Paulo State University (UNESP), Araçatuba 16015-050, SP, Brazil;
| | - Filza Zaidi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Pari Thakkar
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Rani Rahat
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
| | - Joel Schwartz
- Department of Oral Medicine and Diagnostics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Afsar R. Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL 60612, USA; (J.M.B.); (K.J.C.); (F.Z.); (P.T.); (R.R.)
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
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Ramalingam M, Jaisankar A, Cheng L, Krishnan S, Lan L, Hassan A, Sasmazel HT, Kaji H, Deigner HP, Pedraz JL, Kim HW, Shi Z, Marrazza G. Impact of nanotechnology on conventional and artificial intelligence-based biosensing strategies for the detection of viruses. Discov Nano 2023; 18:58. [PMID: 37032711 PMCID: PMC10066940 DOI: 10.1186/s11671-023-03842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Recent years have witnessed the emergence of several viruses and other pathogens. Some of these infectious diseases have spread globally, resulting in pandemics. Although biosensors of various types have been utilized for virus detection, their limited sensitivity remains an issue. Therefore, the development of better diagnostic tools that facilitate the more efficient detection of viruses and other pathogens has become important. Nanotechnology has been recognized as a powerful tool for the detection of viruses, and it is expected to change the landscape of virus detection and analysis. Recently, nanomaterials have gained enormous attention for their value in improving biosensor performance owing to their high surface-to-volume ratio and quantum size effects. This article reviews the impact of nanotechnology on the design, development, and performance of sensors for the detection of viruses. Special attention has been paid to nanoscale materials, various types of nanobiosensors, the internet of medical things, and artificial intelligence-based viral diagnostic techniques.
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Affiliation(s)
- Murugan Ramalingam
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
- grid.411982.70000 0001 0705 4288Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Department of Nanobiomedical Science, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan, 31116 South Korea
- grid.440424.20000 0004 0595 4604Department of Metallurgical and Materials Engineering, Faculty of Engineering, Atilim University, 06836 Ankara, Turkey
| | - Abinaya Jaisankar
- grid.412813.d0000 0001 0687 4946Centre for Biomaterials, Cellular and Molecular Theranostics, School of Mechanical Engineering, Vellore Institute of Technology, Vellore, 632014 India
| | - Lijia Cheng
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
| | - Sasirekha Krishnan
- grid.412813.d0000 0001 0687 4946Centre for Biomaterials, Cellular and Molecular Theranostics, School of Mechanical Engineering, Vellore Institute of Technology, Vellore, 632014 India
| | - Liang Lan
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
| | - Anwarul Hassan
- grid.412603.20000 0004 0634 1084Department of Mechanical and Industrial Engineering, Biomedical Research Center, Qatar University, 2713, Doha, Qatar
| | - Hilal Turkoglu Sasmazel
- grid.440424.20000 0004 0595 4604Department of Metallurgical and Materials Engineering, Faculty of Engineering, Atilim University, 06836 Ankara, Turkey
| | - Hirokazu Kaji
- grid.265073.50000 0001 1014 9130Department of Biomechanics, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, 101-0062 Japan
| | - Hans-Peter Deigner
- grid.21051.370000 0001 0601 6589Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, 78054 Villingen-Schwenningen, Germany
| | - Jose Luis Pedraz
- grid.11480.3c0000000121671098NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country, 01006 Vitoria-Gasteiz, Spain
- Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine, 28029 Madrid, Spain
| | - Hae-Won Kim
- grid.411982.70000 0001 0705 4288Institute of Tissue Regeneration Engineering, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Department of Nanobiomedical Science, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288BK21 NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288Mechanobiology Dental Medicine Research Center, Dankook University, Cheonan, 31116 Republic of Korea
- grid.411982.70000 0001 0705 4288UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan, 31116 South Korea
| | - Zheng Shi
- grid.411292.d0000 0004 1798 8975School of Basic Medical Sciences, Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610106 China
| | - Giovanna Marrazza
- grid.8404.80000 0004 1757 2304Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Florence, Italy
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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Shiaelis N, Tometzki A, Peto L, McMahon A, Hepp C, Bickerton E, Favard C, Muriaux D, Andersson M, Oakley S, Vaughan A, Matthews PC, Stoesser N, Crook DW, Kapanidis AN, Robb NC. Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning. ACS Nano 2023; 17:697-710. [PMID: 36541630 PMCID: PMC9836350 DOI: 10.1021/acsnano.2c10159] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The increasing frequency and magnitude of viral outbreaks in recent decades, epitomized by the COVID-19 pandemic, has resulted in an urgent need for rapid and sensitive diagnostic methods. Here, we present a methodology for virus detection and identification that uses a convolutional neural network to distinguish between microscopy images of fluorescently labeled intact particles of different viruses. Our assay achieves labeling, imaging, and virus identification in less than 5 min and does not require any lysis, purification, or amplification steps. The trained neural network was able to differentiate SARS-CoV-2 from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses. We were also able to differentiate closely related strains of influenza, as well as SARS-CoV-2 variants. Additional and novel pathogens can easily be incorporated into the test through software updates, offering the potential to rapidly utilize the technology in future infectious disease outbreaks or pandemics. Single-particle imaging combined with deep learning therefore offers a promising alternative to traditional viral diagnostic and genomic sequencing methods and has the potential for significant impact.
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Affiliation(s)
- Nicolas Shiaelis
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Alexander Tometzki
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Leon Peto
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Andrew McMahon
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Christof Hepp
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
| | - Erica Bickerton
- The
Pirbright Institute, Ash Road, Pirbright, Woking, SurreyGU24 0NF, United
Kingdom
| | - Cyril Favard
- Membrane
Domains and Viral Assembly, IRIM, UMR 9004 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
| | - Delphine Muriaux
- Membrane
Domains and Viral Assembly, IRIM, UMR 9004 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
- CEMIPAI, UMS 3725 CNRS and University of Montpellier, 1919, route de Mende, 34293Montpellier, France
| | - Monique Andersson
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Sarah Oakley
- Department
of Microbiology, Oxford University Hospitals
NHS Foundation Trust, OxfordOX3 9DU, United
Kingdom
| | - Ali Vaughan
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Oxford Biomedical Research Centre, University
of Oxford, OxfordOX3 9DU, United
Kingdom
| | - Philippa C. Matthews
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Nicole Stoesser
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Health Protection Research Unit in Healthcare Associated Infections
and Antimicrobial Resistance, in partnership with Public Health England, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Derrick W. Crook
- Nuffield
Department of Medicine, University of Oxford, OxfordOX3 9DU, United Kingdom
- NIHR
Oxford Biomedical Research Centre, University
of Oxford, OxfordOX3 9DU, United
Kingdom
- NIHR
Health Protection Research Unit in Healthcare Associated Infections
and Antimicrobial Resistance, in partnership with Public Health England, University of Oxford, OxfordOX3 9DU, United Kingdom
| | - Achillefs N. Kapanidis
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, OxfordOX1 3QU, United Kingdom
| | - Nicole C. Robb
- Biological
Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, OxfordOX1 3PU, United Kingdom
- Warwick
Medical School, University of Warwick, CoventryCV4 7AL, United Kingdom
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5
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Shvets D, Vinogradova S. Occurrence and Genetic Characterization of Grapevine Pinot Gris Virus in Russia. Plants (Basel) 2022; 11:1061. [PMID: 35448789 PMCID: PMC9028157 DOI: 10.3390/plants11081061] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Grapevine Pinot gris virus (GPGV) is a widespread grapevine pathogen associated with symptoms of leaf mottling and deformation. In order to study the distribution and genetic diversity of GPGV in Russia, we tested 1347 grapevine samples from 3 regions of Russia-the Krasnodar Krai, Stavropol Krai, and Republic of Crimea-using duplex real-time RT-PCR. GPGV was detected in 993 grapevines, both symptomatic and asymptomatic. In 119 isolates, we sequenced complete movement protein (MP) and coat protein (CP) genes of the GPGV genome. The percentage of identity of the obtained nucleotide MP/CP sequences with the closest isolates from the GenBank was 97.75-99.56%. A phylogenetic analysis showed that these Russian GPGV isolates are mainly grouped with previously described representative asymptomatic isolates. New post-translational modifications of the MP and CP at the positions of polymorphisms in the genomes of Russian isolates were predicted. The present work is the first study on the distribution and genetic diversity of GPGV in Russia.
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Marais G, Naidoo M, McMullen K, Stanley A, Bryer A, van der Westhuizen D, Bateman K, Hardie DR. Varicella-zoster virus reactivation is frequently detected in HIV-infected individuals presenting with stroke. J Med Virol 2022; 94:2675-2683. [PMID: 35133008 DOI: 10.1002/jmv.27651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/07/2022]
Abstract
Infections are an underappreciated cause of stroke, particularly in young and immunocompromised individuals. Varicella-zoster virus (VZV) reactivation, particularly ophthalmic zoster, has been linked to increased risk of stroke but diagnosing VZV-associated cerebral vasculopathy is challenging as neither a recent Zoster rash, nor detectable levels of VZV DNA are universally present at stroke presentation. Detection of VZV IgG in cerebrospinal fluid (CSF-VZVG) presents a promising alternative, but requires evaluation of individual blood-CSF dynamics, particularly in the setting of chronic inflammatory states such as HIV infection. Consequently, its use has not been broadly adopted as simple diagnostic algorithms are not available. In this study looking at young adults presenting with acute stroke, we used an algorithm that includes testing for both VZV nucleic acids and CSF-VZVG which was corrected for blood-CSF barrier dynamics and poly-specific immune activation. We found that 13 of 35 (37%), including 7 with a positive CSF VZV PCR, young HIV-infected adults presenting with stroke, 3 of 34 (9%) young HIV-uninfected adults presenting with stroke and 1 of 18 (6%) HIV-infected non-stroke controls demonstrated evidence of central nervous system reactivation of VZV. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gert Marais
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Michelle Naidoo
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Kate McMullen
- Department of Medicine, Division of Neurology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Alan Stanley
- Department of Neurology, Hawke's Bay Fallen Soldiers Memorial Hospital, Hastings, New Zealand
| | - Alan Bryer
- Department of Medicine, Division of Neurology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Diederick van der Westhuizen
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
- Division of Chemical Pathology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kathleen Bateman
- Department of Medicine, Division of Neurology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Diana Ruth Hardie
- Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
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7
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Silva FSR, Erdogmus E, Shokr A, Kandula H, Thirumalaraju P, Kanakasabapathy MK, Hardie JM, Pacheco LGC, Li JZ, Kuritzkes DR, Shafiee H. SARS-CoV-2 RNA Detection by a Cellphone-Based Amplification-Free System with CRISPR/CAS-Dependent Enzymatic (CASCADE) Assay. Adv Mater Technol 2021; 6:2100602. [PMID: 34514084 PMCID: PMC8420437 DOI: 10.1002/admt.202100602] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/17/2021] [Indexed: 05/16/2023]
Abstract
CRISPR (Clustered regularly interspaced short palindromic repeats)-based diagnostic technologies have emerged as a promising alternative to accelerate delivery of SARS-CoV-2 molecular detection at the point of need. However, efficient translation of CRISPR-diagnostic technologies to field application is still hampered by dependence on target amplification and by reliance on fluorescence-based results readout. Herein, an amplification-free CRISPR/Cas12a-based diagnostic technology for SARS-CoV-2 RNA detection is presented using a smartphone camera for results readout. This method, termed Cellphone-based amplification-free system with CRISPR/CAS-dependent enzymatic (CASCADE) assay, relies on mobile phone imaging of a catalase-generated gas bubble signal within a microfluidic channel and does not require any external hardware optical attachments. Upon specific detection of a SARS-CoV-2 reverse-transcribed DNA/RNA heteroduplex target (orf1ab) by the ribonucleoprotein complex, the transcleavage collateral activity of the Cas12a protein on a Catalase:ssDNA probe triggers the bubble signal on the system. High analytical sensitivity in signal detection without previous target amplification (down to 50 copies µL-1) is observed in spiked samples, in ≈71 min from sample input to results readout. With the aid of a smartphone vision tool, high accuracy (AUC = 1.0; CI: 0.715 - 1.00) is achieved when the CASCADE system is tested with nasopharyngeal swab samples of PCR-positive COVID-19 patients.
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Affiliation(s)
- Filipe S. R. Silva
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
- Department of BiotechnologyInstitute of Health SciencesFederal University of BahiaSalvadorBA40110‐100Brazil
| | - Eda Erdogmus
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Ahmed Shokr
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Hemanth Kandula
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Prudhvi Thirumalaraju
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Manoj K. Kanakasabapathy
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Joseph M. Hardie
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Luis G. C. Pacheco
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
- Department of BiotechnologyInstitute of Health SciencesFederal University of BahiaSalvadorBA40110‐100Brazil
| | - Jonathan Z. Li
- Harvard Medical SchoolBostonMA02115USA
- Division of Infectious DiseasesBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Daniel R. Kuritzkes
- Harvard Medical SchoolBostonMA02115USA
- Division of Infectious DiseasesBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
| | - Hadi Shafiee
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMA02139USA
- Harvard Medical SchoolBostonMA02115USA
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8
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Kobayashi GS, Brito LA, Moreira DDP, Suzuki AM, Hsia GSP, Pimentel LF, de Paiva APB, Dias CR, Lourenço NCV, Oliveira BA, Manuli ER, Corral MA, Cavaçana N, Mitne-Neto M, Sales MM, Dell’ Aquila LP, Filho AR, Parrillo EF, Mendes-Corrêa MC, Sabino EC, Costa SF, Leal FE, Sgro GG, Farah CS, Zatz M, Passos-Bueno MR. A Novel Saliva RT-LAMP Workflow for Rapid Identification of COVID-19 Cases and Restraining Viral Spread. Diagnostics (Basel) 2021; 11:1400. [PMID: 34441334 PMCID: PMC8391450 DOI: 10.3390/diagnostics11081400] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/25/2021] [Accepted: 07/16/2021] [Indexed: 12/19/2022] Open
Abstract
Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP (reverse transcription loop-mediated isothermal amplification) workflow for viral detection in saliva, and to provide more information regarding its potential in curbing COVID-19 transmission. Clinical and contrived specimens were used to optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate the clinical performance of the test and to characterize saliva based on age, gender and time from onset of symptoms. Our workflow achieved an overall sensitivity of 77.2% (n = 90), with 93.2% sensitivity, 97% specificity, and 0.895 Kappa for specimens containing >102 copies/μL (n = 77). Further analyses in saliva showed that viral load peaks in the first days of symptoms and decreases afterwards, and that viral load is ~10 times lower in females compared to males, and declines following symptom onset. NOP RT-PCR data did not yield relevant associations. This work suggests that saliva reflects the transmission dynamics better than NOP specimens, and reveals gender differences that may reflect higher transmission by males. This saliva RT-LAMP workflow can be applied to track viral spread and, to maximize detection, testing should be performed immediately after symptoms are presented, especially in females.
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Affiliation(s)
- Gerson Shigeru Kobayashi
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Luciano Abreu Brito
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Danielle de Paula Moreira
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Angela May Suzuki
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Gabriella Shih Ping Hsia
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Lylyan Fragoso Pimentel
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Ana Paula Barreto de Paiva
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Carolina Regoli Dias
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Naila Cristina Vilaça Lourenço
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Beatriz Araujo Oliveira
- Instituto de Medicina Tropical, Universidade de São Paulo (USP), São Paulo 05403-000, Brazil; (B.A.O.); (E.R.M.); (M.C.M.-C.); (E.C.S.); (S.F.C.)
| | - Erika Regina Manuli
- Instituto de Medicina Tropical, Universidade de São Paulo (USP), São Paulo 05403-000, Brazil; (B.A.O.); (E.R.M.); (M.C.M.-C.); (E.C.S.); (S.F.C.)
| | - Marcelo Andreetta Corral
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Natale Cavaçana
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Miguel Mitne-Neto
- Grupo Fleury, Research and Development, São Paulo 04344-070, Brazil;
| | - Maria Mirtes Sales
- Instituto de Ensino e Pesquisa Prevent Senior, São Paulo 04547-100, Brazil; (M.M.S.); (L.P.D.A.); (A.R.F.); (E.F.P.)
| | - Luiz Phellipe Dell’ Aquila
- Instituto de Ensino e Pesquisa Prevent Senior, São Paulo 04547-100, Brazil; (M.M.S.); (L.P.D.A.); (A.R.F.); (E.F.P.)
| | - Alvaro Razuk Filho
- Instituto de Ensino e Pesquisa Prevent Senior, São Paulo 04547-100, Brazil; (M.M.S.); (L.P.D.A.); (A.R.F.); (E.F.P.)
| | - Eduardo Fagundes Parrillo
- Instituto de Ensino e Pesquisa Prevent Senior, São Paulo 04547-100, Brazil; (M.M.S.); (L.P.D.A.); (A.R.F.); (E.F.P.)
| | - Maria Cássia Mendes-Corrêa
- Instituto de Medicina Tropical, Universidade de São Paulo (USP), São Paulo 05403-000, Brazil; (B.A.O.); (E.R.M.); (M.C.M.-C.); (E.C.S.); (S.F.C.)
| | - Ester Cerdeira Sabino
- Instituto de Medicina Tropical, Universidade de São Paulo (USP), São Paulo 05403-000, Brazil; (B.A.O.); (E.R.M.); (M.C.M.-C.); (E.C.S.); (S.F.C.)
| | - Silvia Figueiredo Costa
- Instituto de Medicina Tropical, Universidade de São Paulo (USP), São Paulo 05403-000, Brazil; (B.A.O.); (E.R.M.); (M.C.M.-C.); (E.C.S.); (S.F.C.)
| | - Fabio Eudes Leal
- Faculdade de Medicina, Universidade Municipal de São Caetano do Sul (USCS), São Paulo 09521-160, Brazil;
| | - Germán Gustavo Sgro
- Instituto de Química, Universidade de São Paulo (USP), São Paulo 05508-000, Brazil; (G.G.S.); (C.S.F.)
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil
| | - Chuck Shaker Farah
- Instituto de Química, Universidade de São Paulo (USP), São Paulo 05508-000, Brazil; (G.G.S.); (C.S.F.)
| | - Mayana Zatz
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
| | - Maria Rita Passos-Bueno
- Centro de Pesquisa Sobre o Genoma Humano e Células-Tronco (HUG-CELL), Instituto de Biociências, Universidade de São Paulo (USP), São Paulo 05508-090, Brazil; (L.A.B.); (D.d.P.M.); (A.M.S.); (G.S.P.H.); (L.F.P.); (A.P.B.d.P.); (C.R.D.); (N.C.V.L.); (M.A.C.); (N.C.); (M.Z.)
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9
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Jeong S, González-Grandío E, Navarro N, Pinals RL, Ledesma F, Yang D, Landry MP. Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV-2 Quantitative Reverse Transcription Polymerase Chain Reaction Detection Sensitivity. ACS Nano 2021; 15:10309-10317. [PMID: 34105936 PMCID: PMC8204751 DOI: 10.1021/acsnano.1c02494] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/04/2021] [Indexed: 05/25/2023]
Abstract
The global SARS-CoV-2 coronavirus pandemic has led to a surging demand for rapid and efficient viral infection diagnostic tests, generating a supply shortage in diagnostic test consumables including nucleic acid extraction kits. Here, we develop a modular method for high-yield extraction of viral single-stranded nucleic acids by using "capture" ssDNA sequences attached to carbon nanotubes. Target SARS-CoV-2 viral RNA can be captured by ssDNA-nanotube constructs via hybridization and separated from the liquid phase in a single-tube system with minimal chemical reagents, for downstream quantitative reverse transcription polymerase chain reaction (RT-qPCR) detection. This nanotube-based extraction method enables 100% extraction yield of target SARS-CoV-2 RNA from phosphate-buffered saline in comparison to ∼20% extraction yield when using a commercial silica-column kit. Notably, carbon nanotubes enable extraction of nucleic acids directly from 50% human saliva with a similar efficiency as achieved with commercial DNA/RNA extraction kits, thereby bypassing the need for further biofluid purification and avoiding the use of commercial extraction kits. Carbon nanotube-based extraction of viral nucleic acids facilitates high-yield and high-sensitivity identification of viral nucleic acids such as the SARS-CoV-2 viral genome with a reduced reliance on reagents affected by supply chain obstacles.
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Affiliation(s)
- Sanghwa Jeong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Nicole Navarro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Francis Ledesma
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute (IGI), Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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10
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Santiago-Frangos A, Hall LN, Nemudraia A, Nemudryi A, Krishna P, Wiegand T, Wilkinson RA, Snyder DT, Hedges JF, Cicha C, Lee HH, Graham A, Jutila MA, Taylor MP, Wiedenheft B. Intrinsic signal amplification by type III CRISPR-Cas systems provides a sequence-specific SARS-CoV-2 diagnostic. Cell Rep Med 2021; 2:100319. [PMID: 34075364 PMCID: PMC8157118 DOI: 10.1016/j.xcrm.2021.100319] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/04/2021] [Accepted: 05/20/2021] [Indexed: 12/23/2022]
Abstract
There is an urgent need for inexpensive new technologies that enable fast, reliable, and scalable detection of viruses. Here, we repurpose the type III CRISPR-Cas system for sensitive and sequence-specific detection of SARS-CoV-2. RNA recognition by the type III CRISPR complex triggers Cas10-mediated polymerase activity, which simultaneously generates pyrophosphates, protons, and cyclic oligonucleotides. We show that all three Cas10-polymerase products are detectable using colorimetric or fluorometric readouts. We design ten guide RNAs that target conserved regions of SARS-CoV-2 genomes. Multiplexing improves the sensitivity of amplification-free RNA detection from 107 copies/μL for a single guide RNA to 106 copies/μL for ten guides. To decrease the limit of detection to levels that are clinically relevant, we developed a two-pot reaction consisting of RT-LAMP followed by T7-transcription and type III CRISPR-based detection. The two-pot reaction has a sensitivity of 200 copies/μL and is completed using patient samples in less than 30 min.
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Affiliation(s)
| | - Laina N. Hall
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Anna Nemudraia
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Artem Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Pushya Krishna
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Royce A. Wilkinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Deann T. Snyder
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Jodi F. Hedges
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Calvin Cicha
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Helen H. Lee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Ava Graham
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Mark A. Jutila
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Matthew P. Taylor
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
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11
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Porotikova E, Terehova U, Volodin V, Yurchenko E, Vinogradova S. Distribution and Genetic Diversity of Grapevine Viruses in Russia. Plants (Basel) 2021; 10:plants10061080. [PMID: 34072229 PMCID: PMC8229536 DOI: 10.3390/plants10061080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/02/2022]
Abstract
Viral diseases can seriously damage the vineyard productivity and the quality of grape and wine products. Therefore, the study of the species composition and range of grapevine viruses is important for the development and implementation of strategies and tactics to limit their spread and increase the economic benefits of viticulture. In 2014–2019, we carried out a large-scale phytosanitary monitoring of Russian commercial vineyards in the Krasnodar region, Stavropol region and Republic of Crimea. A total of 1857 samples were collected and tested for the presence of Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine virus A (GVA), Grapevine leafroll-associated virus-1 (GLRaV-1), Grapevine leafroll-associated virus-2 (GLRaV-2), Grapevine leafroll-associated virus-3 (GLRaV-3), Grapevine fanleaf virus (GFLV), and Grapevine fleck virus (GFkV) using RT-PCR. Out of all samples tested, 54.5% were positive for at least one of the viruses (GRSPaV, GVA, GLRaV-1, GLRaV-2, GLRaV-3, GFLV, GFkV) in the Stavropol region, 49.8% in the Krasnodar region and 49.5% in the Republic of Crimea. Some plants were found to be infected with several viruses simultaneously. In the Republic of Crimea, for instance, a number of plants were infected with five viruses. In the Krasnodar region and the Republic of Crimea, 4.7% and 3.3% of the samples were predominantly infected with both GFkV and GRSPaV, whereas in the Stavropol region, 6% of the selected samples had both GLRaV-1 and GVA infections. We carried out a phylogenetic analysis of the coat protein genes of the detected viruses and identified the presence of GVA of groups I and IV, GRSPaV of groups BS and SG1, GLRaV-1 of group III, GLRaV-2 of groups PN and H4, GLRaV-3 of groups I and III. The results obtained make it possible to assess the viral load and the distribution of the main grapevine viruses on plantations in the viticultural zones of Russia, emphasizing the urgent need to develop and implement long-term strategies for the control of viral diseases of grapes.
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Affiliation(s)
- Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.P.); (U.T.)
| | - Uliana Terehova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.P.); (U.T.)
| | - Vitalii Volodin
- All-Russian National Scientific Research Institute of Vine and Wine Growing “Magarach” Ras, Str. Kirova 31, 298600 Yalta, Crimea;
| | - Eugeniya Yurchenko
- North Caucasian Regional Research Institute of Horticulture and Viticulture, 40 Years of Victory Street 39, 350072 Krasnodar, Russia;
| | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.P.); (U.T.)
- Correspondence:
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12
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Abstract
Despite numerous viral outbreaks in the last decade, including a devastating global pandemic, diagnostic and therapeutic technologies remain severely lacking. CRISPR-Cas systems have the potential to address these critical needs in the response against infectious disease. Initially discovered as the bacterial adaptive immune system, these systems provide a unique opportunity to create programmable, sequence-specific technologies for detection of viral nucleic acids and inhibition of viral replication. This review summarizes how CRISPR-Cas systems-in particular the recently discovered DNA-targeting Cas12 and RNA-targeting Cas13, both possessing a unique trans-cleavage activity-are being harnessed for viral diagnostics and therapies. We further highlight the numerous technologies whose development has accelerated in response to the COVID-19 pandemic.
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Affiliation(s)
- Catherine A. Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA,Ph.D. Program in Virology, Harvard Medical School, Boston, MA 02115, USA,Corresponding author
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA,Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA,Corresponding author
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13
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Evans SE, Jennerich AL, Azar MM, Cao B, Crothers K, Dickson RP, Herold S, Jain S, Madhavan A, Metersky ML, Myers LC, Oren E, Restrepo MI, Semret M, Sheshadri A, Wunderink RG, Dela Cruz CS. Nucleic Acid-based Testing for Noninfluenza Viral Pathogens in Adults with Suspected Community-acquired Pneumonia. An Official American Thoracic Society Clinical Practice Guideline. Am J Respir Crit Care Med 2021; 203:1070-1087. [PMID: 33929301 PMCID: PMC8314899 DOI: 10.1164/rccm.202102-0498st] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background: This document provides evidence-based clinical practice guidelines on the diagnostic utility of nucleic acid–based testing of respiratory samples for viral pathogens other than influenza in adults with suspected community-acquired pneumonia (CAP). Methods: A multidisciplinary panel developed a Population–Intervention–Comparison–Outcome question, conducted a pragmatic systematic review, and applied Grading of Recommendations, Assessment, Development, and Evaluation methodology for clinical recommendations. Results: The panel evaluated the literature to develop recommendations regarding whether routine diagnostics should include nucleic acid–based testing of respiratory samples for viral pathogens other than influenza in suspected CAP. The evidence addressing this topic was generally adjudicated to be of very low quality because of risk of bias and imprecision. Furthermore, there was little direct evidence supporting a role for routine nucleic acid–based testing of respiratory samples in improving critical outcomes such as overall survival or antibiotic use patterns. However, on the basis of direct and indirect evidence, recommendations were made for both outpatient and hospitalized patients with suspected CAP. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was not addressed in the literature at the time of the evidence review. Conclusions: The panel formulated and provided their rationale for recommendations on nucleic acid–based diagnostics for viral pathogens other than influenza for patients with suspected CAP.
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14
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Courtney SJ, Stromberg ZR, Kubicek-Sutherland JZ. Nucleic Acid-Based Sensing Techniques for Diagnostics and Surveillance of Influenza. Biosensors (Basel) 2021; 11:bios11020047. [PMID: 33673035 PMCID: PMC7918464 DOI: 10.3390/bios11020047] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Influenza virus poses a threat to global health by causing seasonal outbreaks as well as three pandemics in the 20th century. In humans, disease is primarily caused by influenza A and B viruses, while influenza C virus causes mild disease mostly in children. Influenza D is an emerging virus found in cattle and pigs. To mitigate the morbidity and mortality associated with influenza, rapid and accurate diagnostic tests need to be deployed. However, the high genetic diversity displayed by influenza viruses presents a challenge to the development of a robust diagnostic test. Nucleic acid-based tests are more accurate than rapid antigen tests for influenza and are therefore better candidates to be used in both diagnostic and surveillance applications. Here, we review various nucleic acid-based techniques that have been applied towards the detection of influenza viruses in order to evaluate their utility as both diagnostic and surveillance tools. We discuss both traditional as well as novel methods to detect influenza viruses by covering techniques that require nucleic acid amplification or direct detection of viral RNA as well as comparing advantages and limitations for each method. There has been substantial progress in the development of nucleic acid-based sensing techniques for the detection of influenza virus. However, there is still an urgent need for a rapid and reliable influenza diagnostic test that can be used at point-of-care in order to enhance responsiveness to both seasonal and pandemic influenza outbreaks.
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15
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Soria ME, García-Crespo C, Martínez-González B, Vázquez-Sirvent L, Lobo-Vega R, de Ávila AI, Gallego I, Chen Q, García-Cehic D, Llorens-Revull M, Briones C, Gómez J, Ferrer-Orta C, Verdaguer N, Gregori J, Rodríguez-Frías F, Buti M, Esteban JI, Domingo E, Quer J, Perales C. Amino Acid Substitutions Associated with Treatment Failure for Hepatitis C Virus Infection. J Clin Microbiol 2020; 58:JCM.01985-20. [PMID: 32999010 PMCID: PMC7685896 DOI: 10.1128/jcm.01985-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Despite the high virological response rates achieved with current directly acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. The identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultradeep sequencing (UDS) methods, for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV, which are not bona fide resistance-associated substitutions (RAS), from 220 patients who failed therapy. They were present frequently in basal and posttreatment virus of patients who failed different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. They also have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value for treatment response, are discussed.
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Affiliation(s)
- María Eugenia Soria
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Brenda Martínez-González
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Qian Chen
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Damir García-Cehic
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Meritxell Llorens-Revull
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Briones
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Centro de Astrobiología (CAB, CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Josep Gregori
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L., Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Departments, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- Liver Unit, Internal Medicine Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
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16
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Waghmare A, Krantz EM, Baral S, Vasquez E, Loeffelholz T, Chung EL, Pandey U, Kuypers J, Duke ER, Jerome KR, Greninger AL, Reeves DB, Hladik F, Cardozo-Ojeda EF, Boeckh M, Schiffer JT. Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics. J Infect Dis 2020; 226:278-286. [PMID: 32710762 PMCID: PMC7454707 DOI: 10.1093/infdis/jiaa451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/20/2020] [Indexed: 12/16/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrates the need for accurate and convenient approaches to diagnose and therapeutically monitor respiratory viral infections. We demonstrated that self-sampling with mid-nasal foam swabs is well-tolerated and provides quantitative viral output concordant with flocked swabs. Using longitudinal home-based self-sampling, we demonstrate that nasal cytokine levels correlate and cluster according to immune cell of origin. Periods of stable viral loads are followed by rapid elimination, which could be coupled with cytokine expansion and contraction. Nasal foam swab self-sampling at home provides a precise, mechanistic readout of respiratory virus shedding and local immune responses.
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Affiliation(s)
- Alpana Waghmare
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Pediatrics, University of Washington.,Center for Clinical and Translational Research, Seattle Children's Research Institute
| | - Elizabeth M Krantz
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Subhasish Baral
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Emma Vasquez
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Tillie Loeffelholz
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - E Lisa Chung
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Urvashi Pandey
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Obstetrics and Gynecology, University of Washington
| | - Jane Kuypers
- Department of Laboratory Medicine, University of Washington
| | - Elizabeth R Duke
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Medicine, University of Washington
| | - Keith R Jerome
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Laboratory Medicine, University of Washington
| | | | - Daniel B Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center
| | - Florian Hladik
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Obstetrics and Gynecology, University of Washington.,Department of Medicine, University of Washington
| | | | - Michael Boeckh
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Medicine, University of Washington.,Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Joshua T Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center.,Department of Medicine, University of Washington.,Clinical Research Division, Fred Hutchinson Cancer Research Center
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17
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Sreepadmanabh M, Sahu AK, Chande A. COVID-19: Advances in diagnostic tools, treatment strategies, and vaccine development. J Biosci 2020; 45:148. [PMID: 33410425 PMCID: PMC7683586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/15/2020] [Indexed: 09/18/2023]
Abstract
An unprecedented worldwide spread of the SARS-CoV-2 has imposed severe challenges on healthcare facilities and medical infrastructure. The global research community faces urgent calls for the development of rapid diagnostic tools, effective treatment protocols, and most importantly, vaccines against the pathogen. Pooling together expertise across broad domains to innovate effective solutions is the need of the hour. With these requirements in mind, in this review, we provide detailed critical accounts on the leading efforts at developing diagnostics tools, therapeutic agents, and vaccine candidates. Importantly, we furnish the reader with a multidisciplinary perspective on how conventional methods like serology and RT-PCR, as well as cutting-edge technologies like CRISPR/Cas and artificial intelligence/machine learning, are being employed to inform and guide such investigations. We expect this narrative to serve a broad audience of both active and aspiring researchers in the field of biomedical sciences and engineering and help inspire radical new approaches towards effective detection, treatment, and prevention of this global pandemic.
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Affiliation(s)
- M Sreepadmanabh
- Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
| | - Amit Kumar Sahu
- Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research, Bhopal, India
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18
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Karaba AH, Blair PW, Martin K, Saheed MO, Carroll KC, Borowitz MJ. The Effects of a Systemwide Diagnostic Stewardship Change on West Nile Virus Disease Ordering Practices. Open Forum Infect Dis 2019; 6:ofz488. [PMID: 32128331 PMCID: PMC7047944 DOI: 10.1093/ofid/ofz488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/13/2019] [Indexed: 11/23/2022] Open
Abstract
We report that removing the clinically insensitive West Nile virus CSF nucleic acid amplification test (NAAT) from the electronic health record (EHR) test. This diagnostic stewardship intervention decreased costs and may have improved diagnostic yield.
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Affiliation(s)
- Andrew H Karaba
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paul W Blair
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Austere Environments Consortium for Enhanced Sepsis Outcomes, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland
| | - Kevin Martin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mustapha O Saheed
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael J Borowitz
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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19
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Ek P, Böttiger B, Dahlman D, Hansen KB, Nyman M, Nilsson AC. A combination of naso- and oropharyngeal swabs improves the diagnostic yield of respiratory viruses in adult emergency department patients. Infect Dis (Lond) 2019; 51:241-248. [PMID: 30760088 DOI: 10.1080/23744235.2018.1546055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND Along with the current development of molecular diagnostic methods of respiratory viruses, the bedside patient sampling techniques need to be evaluated. We here asked the question whether the addition of an oropharynx swab to the traditional nasopharynx swab might improve the diagnostic yield of multiplex PCR analysis. Ct values from the two sampling sites were compared as well as patient tolerability. METHODS In an emergency department in Malmö, Sweden, 98 adult patients with respiratory disease were sampled both from the nasopharynx and oropharynx for virus diagnostics by PCR. RESULTS Influenza (AH1, AH3, B), human metapneumovirus (hMPV) or respiratory syncytial virus (RSV) were detected by PCR in 58 subjects. The diagnostic yield was improved by combining nasopharyngeal and oropharyngeal sampling - a virus was detected in another 6 patients compared to traditional nasopharyngeal sampling (p = .031, McNemar's test). In 38/55 subjects viral load was higher in the nasopharynx than in the oropharynx. Self-reported discomfort was significantly lower from oropharyngeal sampling than from nasopharyngeal sampling. CONCLUSIONS Adding an oropharynx sample to a nasopharynx sample increased the diagnostic yield of respiratory viruses. Oropharyngeal sampling was well tolerated.
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Affiliation(s)
- Peter Ek
- a Infectious Disease Research Unit, Department of Translational Medicine , Lund University , Malmö , Sweden
| | - Blenda Böttiger
- b Department of Clinical Microbiology, Division of Laboratory Medicine , Lund University , Lund , Sweden
| | - Disa Dahlman
- c Division of Psychiatry, Department of Clinical Sciences Lund , Lund University , Lund , Sweden.,d Malmö Addiction Centre , Skåne University Hospital , Malmö , Sweden.,e Center for Primary Health Care Research, Department of Clinical Sciences , Lund University/Region Skåne , Malmö , Sweden
| | - Karin B Hansen
- a Infectious Disease Research Unit, Department of Translational Medicine , Lund University , Malmö , Sweden
| | - Mattias Nyman
- b Department of Clinical Microbiology, Division of Laboratory Medicine , Lund University , Lund , Sweden
| | - Anna C Nilsson
- a Infectious Disease Research Unit, Department of Translational Medicine , Lund University , Malmö , Sweden
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20
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Cook L, Starr K, Boonyaratanakornkit J, Hayden R, Sam SS, Caliendo AM. Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods. J Clin Microbiol 2018; 56:e01061-18. [PMID: 30282788 DOI: 10.1128/JCM.01061-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022] Open
Abstract
An element essential for PCR detection of microbial agents in many sample types is the extraction step, designed to purify nucleic acids. Despite the importance of this step, yields have not been extensively compared across methods to determine whether the method used contributes to quantitative differences and the lack of commutability seen with existing clinical methods. This may in part explain why plasma and blood viral load assays have proven difficult to standardize. Also, studies have identified small DNA fragments of <200 bp in plasma (cell-free DNA [cfDNA]), which may include significant quantities of viral DNA. Our study evaluated extraction yields for 11 commercially available extraction methods, including 4 new methods designed to isolate cfDNA. Solutions of DNA fragments with sizes ranging from 50 to 1,500 bp were extracted, and then the eluates were tested by droplet digital PCR to determine the DNA fragment yield for each method. The results demonstrated a wide range of extraction yields across the variety of methods/instruments used, with the 50- and 100-bp fragment sizes showing especially inconsistent quantitative results and poor yields of less than 20%. Slightly higher, more consistent yields were seen with 2 of the 4 circulating cell-free extraction kits. These results demonstrate a significant need for further evaluation of nucleic acid yields across the variety of extraction platforms and highlight the poor extraction yields of small DNA fragments by existing methods. Further work is necessary to determine the impact of this inconsistency across instruments and the relevance of the low yields for smaller DNA fragments in clinical virology testing.
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21
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Vijayakumar P, Macdonald J. A DNA Logic Gate Automaton for Detection of Rabies and Other Lyssaviruses. Chemphyschem 2017; 18:1735-1741. [PMID: 28342196 DOI: 10.1002/cphc.201700072] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/21/2017] [Indexed: 11/08/2022]
Abstract
Immediate activation of biosensors is not always desirable, particularly if activation is due to non-specific interactions. Here we demonstrate the use of deoxyribozyme-based logic gate networks arranged into visual displays to precisely control activation of biosensors, and demonstrate a prototype molecular automaton able to discriminate between seven different genotypes of Lyssaviruses, including Rabies virus. The device uses novel mixed-base logic gates to enable detection of the large diversity of Lyssavirus sequence populations, while an ANDNOT logic gate prevents non-specific activation across genotypes. The resultant device provides a user-friendly digital-like, but molecule-powered, dot-matrix text output for unequivocal results read-out that is highly relevant for point of care applications.
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Affiliation(s)
- Pavithra Vijayakumar
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630 W 168thSt, New York, NY, 10032, USA
| | - Joanne Macdonald
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, 630 W 168thSt, New York, NY, 10032, USA.,Genecology Research Centre; Inflammation and Healing Research Cluster, School of Science and Engineering, University of the Sunshine Coast, Queensland, Australia
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22
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Boisen ML, Hartnett JN, Goba A, Vandi MA, Grant DS, Schieffelin JS, Garry RF, Branco LM. Epidemiology and Management of the 2013-16 West African Ebola Outbreak. Annu Rev Virol 2016; 3:147-171. [PMID: 27578439 DOI: 10.1146/annurev-virology-110615-040056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 2013-16 West African Ebola outbreak is the largest, most geographically dispersed, and deadliest on record, with 28,616 suspected cases and 11,310 deaths recorded to date in Guinea, Liberia, and Sierra Leone. We provide a review of the epidemiology and management of the 2013-16 Ebola outbreak in West Africa aimed at stimulating reflection on lessons learned that may improve the response to the next international health crisis caused by a pathogen that emerges in a region of the world with a severely limited health care infrastructure. Surveillance efforts employing rapid and effective point-of-care diagnostics designed for environments that lack advanced laboratory infrastructure will greatly aid in early detection and containment efforts during future outbreaks. Introduction of effective therapeutics and vaccines against Ebola into the public health system and the biodefense armamentarium is of the highest priority if future outbreaks are to be adequately managed and contained in a timely manner.
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Affiliation(s)
- M L Boisen
- Corgenix Inc., Broomfield, Colorado 80020.,Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112; .,Zalgen Labs, LLC, Germantown, Maryland 20876;
| | - J N Hartnett
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112;
| | - A Goba
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - M A Vandi
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - D S Grant
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - J S Schieffelin
- Section of Infectious Diseases, Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana 70112
| | - R F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112; .,Zalgen Labs, LLC, Germantown, Maryland 20876;
| | - L M Branco
- Zalgen Labs, LLC, Germantown, Maryland 20876;
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23
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Sue PK, Pisanic N, Heaney CD, Mixson-Hayden T, Kamili S, Nelson K, Schwarz KB, Forman M, Valsamakis A, Ticehurst J, Karnsakul W. Variability of hepatitis E serologic assays in a pediatric liver transplant recipient: challenges to diagnosing hepatitis E virus infection in the United States. Transpl Infect Dis 2015; 17:284-8. [PMID: 25648626 PMCID: PMC4428568 DOI: 10.1111/tid.12366] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/27/2014] [Accepted: 01/28/2015] [Indexed: 12/11/2022]
Abstract
Hepatitis E virus (HEV) is an emerging cause of viral hepatitis among immunocompromised individuals in developed countries. Yet the diagnosis of HEV infection in the United States remains challenging, because of the variable sensitivity and specificity of currently available tests, and the lack of a US Food and Drug Administration-approved test. We report a case of multiple discordant HEV serology results in a pediatric liver transplant recipient with idiopathic hepatitis, and review the challenges to diagnosis of HEV infection in the United States.
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Affiliation(s)
- P K Sue
- Division of Pediatric Infectious Disease, Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Albuquerque MCM, Rocha LN, Benati FJ, Soares CC, Maranhão AG, Ramírez ML, Erdman D, Santos N. Human bocavirus infection in children with gastroenteritis, Brazil. Emerg Infect Dis 2007; 13. [PMID: 18217564 PMCID: PMC2878208 DOI: 10.3201/eid1311.060671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human bocavirus (HBoV) was detected in 14 (2%) of 705 fecal specimens from Brazilian children with gastroenteritis. Coinfection with rotavirus, adenovirus, or norovirus was found in 3 (21.4%) HBoV-positive specimens. None of the HBoV-positive patients had respiratory symptoms.
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Affiliation(s)
| | | | | | | | | | | | - Dean Erdman
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Norma Santos
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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