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Oruganti S, Lakshmi Gundimeda S, Buddolla V, Anantha Lakshmi B, Kim YJ. Paper-based diagnostic chips for viral detection. Clin Chim Acta 2023:117413. [PMID: 37263536 DOI: 10.1016/j.cca.2023.117413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Viruses cause various diseases in humans, and pose serious health risks to individuals and populations worldwide. As a result, various diagnostic procedures and methods have been developed to prevent, manage, and reduce the burden of viral diseases, each with its own benefits and drawbacks. Among these, paper-based diagnostic chips are becoming increasingly common because of their speed, accuracy, convenience, and economical and environmental friendliness. These paper-based diagnostic tests have ideal point-of-care (POC) diagnostic applications, particularly in personalized healthcare. Paper-based diagnostics have emerged as innovative and low-cost solutions for diagnosing viral diseases in remote and underdeveloped regions where traditional diagnostic methods are not readily available. These tests are easy to use, require minimal equipment, and can be performed by nonspecialized personnel, making them accessible even in resource-constrained settings. In this review, we discuss recent developments in paper-based diagnostic chips, the importance of improved methods for identifying viral pathogens, drawbacks of traditional detection techniques, and challenges and prospects of paper-based diagnostic chips for the detection of viruses.
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Affiliation(s)
- Srividya Oruganti
- Dr. Buddolla's Institute of Life Sciences, Tirupati-517506, Andhra Pradesh, India
| | | | - Viswanath Buddolla
- Dr. Buddolla's Institute of Life Sciences, Tirupati-517506, Andhra Pradesh, India
| | - Buddolla Anantha Lakshmi
- Department of Electronic Engineering, Gachon University, 1342 Seongnam-Daero, Seongnam, Gyeonggi-Do 13120, Republic of Korea.
| | - Young-Joon Kim
- Department of Electronic Engineering, Gachon University, 1342 Seongnam-Daero, Seongnam, Gyeonggi-Do 13120, Republic of Korea.
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2
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Altindiş M, Kahraman Kilbaş EP. Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics. Diagnostics (Basel) 2023; 13:diagnostics13081421. [PMID: 37189522 DOI: 10.3390/diagnostics13081421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.
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Affiliation(s)
- Mustafa Altindiş
- Medical Microbiology Department, Faculty of Medicine, Sakarya University, Sakarya 54050, Türkiye
| | - Elmas Pınar Kahraman Kilbaş
- Medical Laboratory Techniques, Vocational School of Health Services, Fenerbahce University, Istanbul 34758, Türkiye
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3
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Abstract
Several tropical or geographically confined infectious diseases may lead to organ failure requiring management in an intensive care unit (ICU), both in endemic low- and middle-income countries where ICU facilities are increasingly being developed and in (nonendemic) high-income countries through an increase in international travel and migration. The ICU physician must know which of these diseases may be encountered and how to recognize, differentiate, and treat them. The four historically most prevalent "tropical" diseases (malaria, enteric fever, dengue, and rickettsiosis) can present with single or multiple organ failure in a very similar manner, which makes differentiation based solely on clinical signs very difficult. Specific but frequently subtle symptoms should be considered and related to the travel history of the patient, the geographic distribution of these diseases, and the incubation period. In the future, ICU physicians may also be more frequently confronted with rare but frequently lethal diseases, such as Ebola and other viral hemorrhagic fevers, leptospirosis, and yellow fever. No one could have foreseen the worldwide 2019-up to now coronavirus disease 2019 (COVID-19) crisis caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was initially spread by travel too. In addition, the actual pandemic due to SARS-CoV-2 reminds us of the actual and potential threat of (re)-emerging pathogens. If left untreated or when treated with a delay, many travel-related diseases remain an important cause of morbidity and even mortality, even when high-quality critical care is provided. Awareness and a high index of suspicion of these diseases is a key skill for the ICU physicians of today and tomorrow to develop.
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Recent Advances in Early Diagnosis of Viruses Associated with Gastroenteritis by Biosensors. BIOSENSORS 2022; 12:bios12070499. [PMID: 35884302 PMCID: PMC9313180 DOI: 10.3390/bios12070499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022]
Abstract
Gastroenteritis, as one of the main worldwide health challenges, especially in children, leads to 3–6 million deaths annually and causes nearly 20% of the total deaths of children aged ˂5 years, of which ~1.5 million gastroenteritis deaths occur in developing nations. Viruses are the main causative agent (~70%) of gastroenteritis episodes and their specific and early diagnosis via laboratory assays is very helpful for having successful antiviral therapy and reduction in infection burden. Regarding this importance, the present literature is the first review of updated improvements in the employing of different types of biosensors such as electrochemical, optical, and piezoelectric for sensitive, simple, cheap, rapid, and specific diagnosis of human gastroenteritis viruses. The Introduction section is a general discussion about the importance of viral gastroenteritis, types of viruses that cause gastroenteritis, and reasons for the combination of conventional diagnostic tests with biosensors for fast detection of viruses associated with gastroenteritis. Following the current laboratory detection tests for human gastroenteritis viruses and their limitations (with subsections: Electron Microscope (EM), Cell Culture, Immunoassay, and Molecular Techniques), structural features and significant aspects of various biosensing methods are discussed in the Biosensor section. In the next sections, basic information on viruses causing gastroenteritis and recent developments for fabrication and testing of different biosensors for each virus detection are covered, and the prospect of future developments in designing different biosensing platforms for gastroenteritis virus detection is discussed in the Conclusion and Future Directions section as well.
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Babaei A, Pouremamali A, Rafiee N, Sohrabi H, Mokhtarzadeh A, de la Guardia M. Genosensors as an alternative diagnostic sensing approaches for specific detection of various certain viruses: a review of common techniques and outcomes. Trends Analyt Chem 2022; 155:116686. [PMID: 35611316 PMCID: PMC9119280 DOI: 10.1016/j.trac.2022.116686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/08/2022] [Accepted: 05/15/2022] [Indexed: 12/19/2022]
Abstract
Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.
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Affiliation(s)
- Abouzar Babaei
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Pouremamali
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nastaran Rafiee
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
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Saeed OS, El-Deeb AH, Hussein Ahmed HA. No evidence of SARS-CoV-2 infection in Rousettus aegyptiacus bat in Egypt. Int J Vet Sci Med 2021; 9:59-61. [PMID: 34796231 PMCID: PMC8567868 DOI: 10.1080/23144599.2021.1991135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 01/20/2023] Open
Abstract
Bats are considered ideal reservoirs for zoonotic viruses with emerging capabilities over the past two decades and spotted evidence points out that they may play a role as a reservoir host for SARS-CoV-2. To investigate the possible role of bats as part of SARS-CoV-2 anthropozoonotic spill-over infections in Egypt, a total of 800 samples obtained from 200 Egyptian fruit bats (Rousettus aegyptiacus) were tested for SARS-CoV-2 using quantitative RT-PCR assay (RT-qPCR). RT-qPCR analysis of RNA extracted from bat tissues showed no positive results for SARS-CoV-2 nucleic acid. These findings suggest that during the study period, the Rousettus aegyptiacus bat was not a reservoir or amplifying host for SARS-CoV-2 infection in Egypt. The lack of SARS-CoV-2 nucleic acid in Egyptian fruit bats is thought to make a significant contribution to SARS-CoV-2 epidemiology.
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Affiliation(s)
- Omar Sayed Saeed
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Ayman Hany El-Deeb
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
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Bustin S, Kirvell S, Huggett JF, Nolan T. RT-qPCR Diagnostics: The "Drosten" SARS-CoV-2 Assay Paradigm. Int J Mol Sci 2021; 22:ijms22168702. [PMID: 34445406 PMCID: PMC8395416 DOI: 10.3390/ijms22168702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is an established tool for the diagnosis of RNA pathogens. Its potential for automation has caused it to be used as a presence/absence diagnostic tool even when RNA quantification is not required. This technology has been pushed to the forefront of public awareness by the COVID-19 pandemic, as its global application has enabled rapid and analytically sensitive mass testing, with the first assays targeting three viral genes published within days of the publication of the SARS-CoV-2 genomic sequence. One of those, targeting the RNA-dependent RNA polymerase gene, has been heavily criticised for supposed scientific flaws at the molecular and methodological level, and this criticism has been extrapolated to doubts about the validity of RT-qPCR for COVID-19 testing in general. We have analysed this assay in detail, and our findings reveal some limitations but also highlight the robustness of the RT-qPCR methodology for SARS-CoV-2 detection. Nevertheless, whilst our data show that some errors can be tolerated, it is always prudent to confirm that the primer and probe sequences complement their intended target, since, when errors do occur, they may result in a reduction in the analytical sensitivity. However, in this case, it is unlikely that a mismatch will result in poor specificity or a significant number of false-positive SARS-CoV-2 diagnoses, especially as this is routinely checked by diagnostic laboratories as part of their quality assurance.
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Affiliation(s)
- Stephen Bustin
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
- Correspondence:
| | - Sara Kirvell
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
| | - Jim F. Huggett
- National Measurement Laboratory, LGC, Queens Rd, Teddington, London TW11 0LY, UK;
| | - Tania Nolan
- Medical Technology Research Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University Chelmsford, Chelmsford CM1 1SQ, UK; (S.K.); (T.N.)
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Bidram E, Esmaeili Y, Amini A, Sartorius R, Tay FR, Shariati L, Makvandi P. Nanobased Platforms for Diagnosis and Treatment of COVID-19: From Benchtop to Bedside. ACS Biomater Sci Eng 2021; 7:2150-2176. [PMID: 33979143 PMCID: PMC8130531 DOI: 10.1021/acsbiomaterials.1c00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023]
Abstract
Human respiratory viral infections are the leading cause of morbidity and mortality around the world. Among the various respiratory viruses, coronaviruses (e.g., SARS-CoV-2) have created the greatest challenge and most frightening health threat worldwide. Human coronaviruses typically infect the upper respiratory tract, causing illnesses that range from common cold-like symptoms to severe acute respiratory infections. Several promising vaccine formulations have become available since the beginning of 2021. Nevertheless, achievement of herd immunity is still far from being realized. Social distancing remains the only effective measure against SARS-CoV-2 infection. Nanobiotechnology enables the design of nanobiosensors. These nanomedical diagnostic devices have opened new vistas for early detection of viral infections. The present review outlines recent research on the effectiveness of nanoplatforms as diagnostic and antiviral tools against coronaviruses. The biological properties of coronavirus and infected host organs are discussed. The challenges and limitations encountered in combating SARS-CoV-2 are highlighted. Potential nanodevices such as nanosensors, nanobased vaccines, and smart nanomedicines are subsequently presented for combating current and future mutated versions of coronaviruses.
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Affiliation(s)
- Elham Bidram
- Biosensor
Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Hezarjerib Avenue, Isfahan 8174673461, Iran
| | - Yasaman Esmaeili
- Biosensor
Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Hezarjerib Avenue, Isfahan 8174673461, Iran
| | - Abbas Amini
- Centre
for Infrastructure Engineering, Western
Sydney University, Locked
Bag 1797, Penrith 2751, New South Wales, Australia
- Department
of Mechanical Engineering, Australian College
of Kuwait, Al Aqsa Mosque
Street, Mishref, Safat 13015, Kuwait
| | - Rossella Sartorius
- Institute
of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), Via Pietro Castellino 111, Naples 80131, Italy
| | - Franklin R. Tay
- The
Graduate
School, Augusta University, 1120 15th Street, Augusta, Georgia 30912, United States
| | - Laleh Shariati
- Applied
Physiology Research Center, Isfahan Cardiovascular Research Institute, Isfahan University of Medical Sciences, Hezarjerib Avenue, Isfahan 8174673461, Iran
- Department
of Biomaterials, Nanotechnology and Tissue Engineering, School of
Advanced Technologies in Medicine, Isfahan
University of Medical Sciences, Hezarjerib Avenue, Isfahan 8174673461, Iran
| | - Pooyan Makvandi
- Centre
for Materials Interfaces, Istituto Italiano
di Tecnologia, viale
Rinaldo Piaggio 34, Pontedera 56025, Pisa, Italy
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9
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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10
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Mohammed AS, Balapure A, Khaja MN, Ganesan R, Dutta JR. Naked-eye colorimetric detection of HCV RNA mediated by a 5' UTR-targeted antisense oligonucleotide and plasmonic gold nanoparticles. Analyst 2021; 146:1569-1578. [PMID: 33586713 DOI: 10.1039/d0an02481c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The increasing incidence of hepatitis C viral (HCV) infection worldwide is a major concern for causing liver cirrhosis and hepatocellular carcinoma, leading to increased morbidity and mortality. Currently, the prevalence of HCV infection is estimated to be in the range of ∼3%. According to the World Health Organization, antiviral drugs can cure more than 95% of the HCV infected cases, if timely diagnosis and treatment are provided. The gold standard RT-qPCR assay is expensive and requires a minimum turnaround time of 4 h. Hence, a rapid and cost-effective detection assay that can be used even in resource-limited settings would be highly beneficial for mass level screening. Herein, we present an Au NP based facile strategy for rapid, early-stage, and sensitive detection of HCV RNA in clinical samples which avoids thiol tagging to the antisense oligonucleotide and expensive infrastructure. This technique utilizes the hybridization of a short-chain antisense oligonucleotide from the 5' untranslated region (UTR) of the viral genome with the isolated HCV RNA samples. Using a specific sequence universal to all HCV genotypes-obtained through the NCBI BLASTn tool-the HCV positive samples have stabilized the citrate capped Au NPs against salt-induced aggregation, retaining their red color. On the other hand, negative controls, including HBV and HIV positive samples, do not stabilize the Au NPs, which results in purple coloration. Besides, the assay is successfully tested with a RNase A enzyme-treated HCV positive sample, which does not stabilize the Au NPs, thus confirming the role of the viral HCV RNA in this strategy. This Au NP based assay takes about 30 min using the viral RNA isolate and has high specificity with a detection limit of 100 IU mL-1, which is ∼10 fold lower than the state-of-the-art Au NP based strategy.
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Affiliation(s)
- Almas Shamaila Mohammed
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India. and Bioviz Technologies Pvt Ltd, Plot No. 46, UBI Colony, Road No. 3, Banjara Hills, Hyderabad-500034, India
| | - Aniket Balapure
- Department of Chemistry, BITS Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India.
| | - Mahammad Nanne Khaja
- Bioviz Technologies Pvt Ltd, Plot No. 46, UBI Colony, Road No. 3, Banjara Hills, Hyderabad-500034, India
| | - Ramakrishnan Ganesan
- Department of Chemistry, BITS Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India.
| | - Jayati Ray Dutta
- Department of Biological Sciences, BITS Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India.
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11
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Kailasa SK, Mehta VN, Koduru JR, Basu H, Singhal RK, Murthy ZVP, Park TJ. An overview of molecular biology and nanotechnology based analytical methods for the detection of SARS-CoV-2: promising biotools for the rapid diagnosis of COVID-19. Analyst 2021; 146:1489-1513. [PMID: 33543178 DOI: 10.1039/d0an01528h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Currently, the 2019 novel coronavirus (2019-nCoV) is drastically affecting 214 countries, causing severe pneumonia in patients, which has resulted in lockdown being implemented in several countries to stop its local transmission. Considering this, the rapid screening and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; 2019-nCoV) play an essential role in the diagnosis of COVID-19, which can minimize local transmission and prevent an epidemic. Due to this public health emergency, the development of ultra-fast reliable diagnostic kits is essential for the diagnosis of COVID-19. Recently, molecular biology and nanotechnology based analytical methods have proven to be promising diagnostic tools for the rapid screening of 2019-nCoV with high accuracy and precision. The main aim of this review is to provide a retrospective overview on the molecular biology tools (reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP)) and nanotechnology based analytical tools (enzyme-linked immunosorbent assay (ELISA), RT-PCR, and lateral flow assay) for the rapid diagnosis of COVID-19. This review also presents recent reports on other analytical techniques including paper spray mass spectrometry for the diagnosis of COVID-19 in clinical samples. Finally, we provide a quick reference on molecular biology and nanotechnology based analytical tools for COVID-19 diagnosis in clinical samples.
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Affiliation(s)
- Suresh Kumar Kailasa
- Department of Chemistry, S. V. National Institute of Technology, Surat - 395007, Gujarat, India.
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12
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Young KT, Lahmers KK, Sellers HS, Stallknecht DE, Poulson RL, Saliki JT, Tompkins SM, Padykula I, Siepker C, Howerth EW, Todd M, Stanton JB. Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses. J Vet Diagn Invest 2020; 33:202-215. [PMID: 33357075 DOI: 10.1177/1040638720981019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.
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Affiliation(s)
- Kelsey T Young
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Kevin K Lahmers
- Department of Biomedical Sciences & Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech University, Blacksburg, VA
| | - Holly S Sellers
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Jerry T Saliki
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Stephen Mark Tompkins
- Center for Vaccines and Immunology, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Ian Padykula
- Center for Vaccines and Immunology, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Chris Siepker
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Elizabeth W Howerth
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
| | - Michelle Todd
- Department of Biomedical Sciences & Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech University, Blacksburg, VA
| | - James B Stanton
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA
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Corpuz MVA, Buonerba A, Vigliotta G, Zarra T, Ballesteros F, Campiglia P, Belgiorno V, Korshin G, Naddeo V. Viruses in wastewater: occurrence, abundance and detection methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140910. [PMID: 32758747 PMCID: PMC7368910 DOI: 10.1016/j.scitotenv.2020.140910] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/14/2023]
Abstract
This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.
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Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Giovanni Vigliotta
- Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy.
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines; Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States.
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
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Molecular and Immunological Diagnostic Techniques of Medical Viruses. Int J Microbiol 2020; 2020:8832728. [PMID: 32908530 PMCID: PMC7474384 DOI: 10.1155/2020/8832728] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/24/2020] [Accepted: 08/15/2020] [Indexed: 01/12/2023] Open
Abstract
Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries.
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Echocardiographic Follow-up of Perinatally HIV-infected Children and Adolescents: Results From a Single-center Retrospective Cohort Study in Brazil. Pediatr Infect Dis J 2020; 39:526-532. [PMID: 32412728 DOI: 10.1097/inf.0000000000002628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The effects of HIV and antiretroviral therapy on cardiovascular system of perinatally infected children throughout their development are not fully understood. OBJECTIVES To determine the prevalence of cardiac abnormalities in a retrospective cohort of perinatally HIV-infected patients and to investigate associations between echocardiographic and clinical data during their follow-up. METHODS Review of medical records and echocardiogram reports of 148 perinatally HIV-infected patients between January 1991 and December 2015. RESULTS Four hundred and eighty echocardiograms were analyzed and 46 (31%) patients showed cardiac abnormalities, frequently subclinical and transient. Nadir CD4 count was higher in patients with consistently normal echocardiogram: 263 (4-1480) versus 202 (5-1746) cells/μL, P = 0.021. Right ventricular (RV) dilation was detected in 18.9%, left ventricular (LV) dilation in 21.6%, septal hypertrophy in 12.2%, LV posterior wall hypertrophy in 6%, LV systolic dysfunction in 8% and pulmonary hypertension in 8.7% of patients. Opportunistic infections were associated with RV dilation [odds ratio (OR = 4.34; 1.78-10.53; P < 0.01)], pulmonary hypertension (OR = 8.78; 2.80-27.51; P < 0.01) and LV systolic dysfunction (OR = 5.38; 1.55-18.71; P < 0.01). Longer duration of highly active antiretroviral therapy was associated with reduced risk of LV dilation (OR = 0.91; 0.85-0.97; P < 0.01) and systolic dysfunction (OR = 0.71; 0.59-0.85; P < 0.01). Protease inhibitors use was associated with reduced risk of RV dilation (OR = 0.54; 0.30-0.97; P < 0.05), LV dilation (OR = 0.35; 0.21-0.60; P < 0.01) and LV systolic dysfunction (OR = 0.07; 0.02-0.31; P < 0.01). Higher CD4 count was associated with lower risk of LV systolic dysfunction (OR = 0.82; 0.69-0.98; P < 0.05). CONCLUSIONS Echocardiograms identified cardiac abnormalities among children with perinatally acquired HIV infection, and data suggest that immunologic status and therapeutic strategies throughout development can influence cardiac disease burden in this population.
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Dunbar S, Das S. Amplification chemistries in clinical virology. J Clin Virol 2019; 115:18-31. [PMID: 30953805 PMCID: PMC7106405 DOI: 10.1016/j.jcv.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 01/04/2023]
Abstract
Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.
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17
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Chen BC, Chang JT, Huang TS, Chen JJ, Chen YS, Jan MW, Chang TH. Parechovirus A Detection by a Comprehensive Approach in a Clinical Laboratory. Viruses 2018; 10:v10120711. [PMID: 30545147 PMCID: PMC6316871 DOI: 10.3390/v10120711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 12/15/2022] Open
Abstract
Parechovirus A (Human parechovirus, HPeV) causes symptoms ranging from severe neonatal infection to mild gastrointestinal and respiratory disease. Use of molecular approaches with RT-PCR and genotyping has improved the detection rate of HPeV. Conventional methods, such as viral culture and immunofluorescence assay, together with molecular methods facilitate comprehensive viral diagnosis. To establish the HPeV immunofluorescence assay, an antibody against HPeV capsid protein VP0 was generated by using antigenic epitope prediction data. The specificity of the anti-HPeV VP0 antibody was demonstrated on immunofluorescence assay, showing that this antibody was specific for HPeV but not enteroviruses. A total of 74 HPeV isolates, 7 non–polio-enteroviruses and 12 HPeV negative cell culture supernatant were used for evaluating the efficiency of the anti-HPeV VP0 antibody. The sensitivity of HPeV detection by the anti-HPeV VP0 antibody was consistent with 5′untranslated region (UTR) RT-PCR analysis. This study established comprehensive methods for HPeV detection that include viral culture and observation of cytopathic effect, immunofluorescence assay, RT-PCR and genotyping. The methods were incorporated into our routine clinical practice for viral diagnosis. In conclusion, this study established a protocol for enterovirus and HPeV virus identification that combines conventional and molecular methods and would be beneficial for HPeV diagnosis.
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Affiliation(s)
- Bao-Chen Chen
- Department of Microbiology, Kaohsiung Veterans General Hospital, Kaohsiung81362, Taiwan.
| | - Jenn-Tzong Chang
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan.
| | - Tsi-Shu Huang
- Department of Microbiology, Kaohsiung Veterans General Hospital, Kaohsiung81362, Taiwan.
| | - Jih-Jung Chen
- Faculty of Pharmacy, School of Pharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan.
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 404, Taiwan.
| | - Yao-Shen Chen
- Department of Infectious Diseases, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan.
| | - Ming-Wei Jan
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan.
| | - Tsung-Hsien Chang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan.
- Department of Medical Laboratory Science and Biotechnology, Chung Hwa University of Medical Technology, Tainan 717, Taiwan.
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Hassanpour S, Baradaran B, de la Guardia M, Baghbanzadeh A, Mosafer J, Hejazi M, Mokhtarzadeh A, Hasanzadeh M. Diagnosis of hepatitis via nanomaterial-based electrochemical, optical or piezoelectrical biosensors: a review on recent advancements. Mikrochim Acta 2018; 185:568. [DOI: 10.1007/s00604-018-3088-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/09/2018] [Indexed: 12/21/2022]
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19
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Otašević S, Momčilović S, Stojanović NM, Skvarč M, Rajković K, Arsić-Arsenijević V. Non-culture based assays for the detection of fungal pathogens. J Mycol Med 2018; 28:236-248. [PMID: 29605542 PMCID: PMC7110445 DOI: 10.1016/j.mycmed.2018.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 01/05/2023]
Abstract
Traditional, culture based methods for the diagnosis of fungal infections are still considered as gold standard, but they are time consuming and low sensitive. Therefore, in order to overcome the limitations, many researchers have focused on the development of new immunological and molecular based rapid assays that could enable early diagnosis of infection and accurate identification of fungal pathogens causing superficial and invasive infection. In this brief review, we highlighted the advantages and disadvantages of conventional diagnostic methods and possibility of non-culture based assays in diagnosis of superficial fungal infections and presented the overview on currently available immunochromatographic assays as well as availability of biomarkers detection by immunodiagnostic procedures in prompt and accurate diagnosis of invasive fungal infections. In addition, we presented diagnostic efficiency of currently available molecular panels and researches in this area.
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Affiliation(s)
- S Otašević
- Center of Microbiology and Parasitology, Public Health Institute Niš, Serbia, boulevard Zorana Djindjica 50, 18000 Niš, Serbia; Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia.
| | - S Momčilović
- Department of Microbiology and Immunology, Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - N M Stojanović
- Faculty of Medicine, University of Niš, Serbia, boulevard Zorana Djindjica 81, 18000 Niš, Serbia
| | - M Skvarč
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Zaloska 4, Ljubljana, Slovenia
| | - K Rajković
- High Chemical and Technological School for Professional Studies, Kosančićeva 36, 37000 Kruševac, Serbia
| | - V Arsić-Arsenijević
- Department for Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia, Dr Subotića 1, 11000 Belgrade, Serbia
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20
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Magouz A, Medhat S, Abou Asa S, Desouky A. Detection of infectious laryngotracheitis virus (Gallid herpesvirus-1) from clinically infected chickens in Egypt by different diagnostic methods. IRANIAN JOURNAL OF VETERINARY RESEARCH 2018; 19:194-201. [PMID: 30349566 PMCID: PMC6184029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/01/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Infectious laryngotracheitis (ILT) disease is an acute highly contagious viral disease leading to massive economic losses to the national poultry industry. This study aimed to identify the most accurate and rapid diagnostic methods to rescue layer poultry farms from intense outbreaks in Egypt. Fifty pathological specimens were collected and subjected to virus isolation (VI), histopathology, direct fluorescent antibody technique (FAT) and polymerase chain reaction (PCR). Egg inoculation revealed stunted growth and white pock lesions on chorioallantoic membranes (CAM) in 23 samples. Isolation and propagation of infectious laryngotracheitis virus (ILTV) in cell culture showed syncytia formation 5 days post infection in 20 inoculated samples. PCR resulted in successful amplification of a 647 bp fragment of the thymidine kinase (TK) gene in 25 field samples. Histopathological examination of inoculated CAM showed intranuclear inclusion bodies with infiltration of inflammatory cells. Direct FAT showed intra-cytoplasmic apple green reactions in 18 examined tracheal tissues. PCR has been shown to be more sensitive, accurate and rapid than VI, FAT and histopathological examination.
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Affiliation(s)
- A. Magouz
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - Sh. Medhat
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - S. Abou Asa
- Department of Pathology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - A. Desouky
- Department of Parasitology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
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21
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Nkili-Meyong AA, Bigarré L, Labouba I, Vallaeys T, Avarre JC, Berthet N. Contribution of Next-Generation Sequencing to Aquatic and Fish Virology. Intervirology 2017; 59:285-300. [PMID: 28668959 DOI: 10.1159/000477808] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/27/2017] [Indexed: 12/13/2022] Open
Abstract
The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.
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Affiliation(s)
- Andriniaina Andy Nkili-Meyong
- Département Zoonoses et Maladies Emergentes, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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A Four-Biomarker Blood Signature Discriminates Systemic Inflammation Due to Viral Infection Versus Other Etiologies. Sci Rep 2017; 7:2914. [PMID: 28588308 PMCID: PMC5460227 DOI: 10.1038/s41598-017-02325-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023] Open
Abstract
The innate immune system of humans and other mammals responds to pathogen-associated molecular patterns (PAMPs) that are conserved across broad classes of infectious agents such as bacteria and viruses. We hypothesized that a blood-based transcriptional signature could be discovered indicating a host systemic response to viral infection. Previous work identified host transcriptional signatures to individual viruses including influenza, respiratory syncytial virus and dengue, but the generality of these signatures across all viral infection types has not been established. Based on 44 publicly available datasets and two clinical studies of our own design, we discovered and validated a four-gene expression signature in whole blood, indicative of a general host systemic response to many types of viral infection. The signature’s genes are: Interferon Stimulated Gene 15 (ISG15), Interleukin 16 (IL16), 2′,5′-Oligoadenylate Synthetase Like (OASL), and Adhesion G Protein Coupled Receptor E5 (ADGRE5). In each of 13 validation datasets encompassing human, macaque, chimpanzee, pig, mouse, rat and all seven Baltimore virus classification groups, the signature provides statistically significant (p < 0.05) discrimination between viral and non-viral conditions. The signature may have clinical utility for differentiating host systemic inflammation (SI) due to viral versus bacterial or non-infectious causes.
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23
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Clouthier SC, McClure C, Schroeder T, Desai M, Hawley L, Khatkar S, Lindsay M, Lowe G, Richard J, Anderson ED. Diagnostic validation of three test methods for detection of cyprinid herpesvirus 3 (CyHV-3). DISEASES OF AQUATIC ORGANISMS 2017; 123:101-122. [PMID: 28262633 DOI: 10.3354/dao03093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of koi herpesvirus disease in koi and common carp. The disease is notifiable to the World Organisation for Animal Health. Three tests-quantitative polymerase chain reaction (qPCR), conventional PCR (cPCR) and virus isolation by cell culture (VI)-were validated to assess their fitness as diagnostic tools for detection of CyHV-3. Test performance metrics of diagnostic accuracy were sensitivity (DSe) and specificity (DSp). Repeatability and reproducibility were measured to assess diagnostic precision. Estimates of test accuracy, in the absence of a gold standard reference test, were generated using latent class models. Test samples originated from wild common carp naturally exposed to CyHV-3 or domesticated koi either virus free or experimentally infected with the virus. Three laboratories in Canada participated in the precision study. Moderate to high repeatability (81 to 99%) and reproducibility (72 to 97%) were observed for the qPCR and cPCR tests. The lack of agreement observed between some of the PCR test pair results was attributed to cross-contamination of samples with CyHV-3 nucleic acid. Accuracy estimates for the PCR tests were 99% for DSe and 93% for DSp. Poor precision was observed for the VI test (4 to 95%). Accuracy estimates for VI/qPCR were 90% for DSe and 88% for DSp. Collectively, the results show that the CyHV-3 qPCR test is a suitable tool for surveillance, presumptive diagnosis and certification of individuals or populations as CyHV-3 free.
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Affiliation(s)
- Sharon C Clouthier
- Fisheries and Oceans Canada, Freshwater Institute, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada
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Salman NA, Davies G, Majidy F, Shakir F, Akinrinade H, Perumal D, Ashrafi GH. Association of High Risk Human Papillomavirus and Breast cancer: A UK based Study. Sci Rep 2017; 7:43591. [PMID: 28240743 PMCID: PMC5378907 DOI: 10.1038/srep43591] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/25/2017] [Indexed: 02/07/2023] Open
Abstract
Infection by human papillomaviruses (HPVs) has been implicated in the aetiology of a variety of cancers. Studies evaluating the presence of HPVs in breast cancer (BC) have generated considerable controversy. To date, most studies have focused on the presence of viral DNA in BC; however there are important gaps in evidencing the role of HPV persistence in the invasiveness of BC. While these studies have been conducted in several countries, none, on the presence and biological activity of high risk (HR) HPV in BC has been done in the UK. Hence, we aimed to investigate these gaps by screening a total of 110 fresh breast tissue specimens from UK patients for the presence of twelve HR-HPV types DNA using PCR and Sanger sequencing. Samples positive for HPV-DNA were screened for viral oncoprotein expression using western blot and dot blot. Data obtained showed the presence of HR-HPVs in 42% of breast tissues of which the viral activity was only confirmed in a number of invasive carcinomas (5/26). This finding, the first to report in the UK, suggests that the selective expression of viral oncoprotein in invasive cases may propose a role for HR-HPVs in the development of some types of BC.
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Affiliation(s)
- Nadia Aziz Salman
- Kingston University London, Cancer theme, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston upon Thames, KT12EE, London, UK
| | - Giles Davies
- Kingston Hospital- Breast Surgery Department, Kingston upon Thames, KT2 7QB, London, UK
- The new Victoria hospital- Breast Surgery Department, Kingston upon Thames, KT2 7EG, London, UK
| | - Farida Majidy
- Kingston University London, Cancer theme, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston upon Thames, KT12EE, London, UK
| | - Fatima Shakir
- Kingston University London, Cancer theme, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston upon Thames, KT12EE, London, UK
| | - Hilda Akinrinade
- Kingston University London, Cancer theme, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston upon Thames, KT12EE, London, UK
| | - Dhayaneethie Perumal
- Kingston University London, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston upon Thames, KT12EE, London, UK
- Fatima College of Health Sciences, Institute of Applied Technology, Department of Pharmacy, UAE
| | - G. Hossein Ashrafi
- Kingston University London, Cancer theme, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston upon Thames, KT12EE, London, UK
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25
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Ding J, Lawrence RM, Jones PV, Hogue BG, Hayes MA. Concentration of Sindbis virus with optimized gradient insulator-based dielectrophoresis. Analyst 2017; 141:1997-2008. [PMID: 26878279 DOI: 10.1039/c5an02430g] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Biotechnology, separation science, and clinical research are impacted by microfluidic devices. Separation and manipulation of bioparticles such as DNA, protein and viruses are performed on these platforms. Microfluidic systems provide many attractive features, including small sample size, rapid detection, high sensitivity and short processing time. Dielectrophoresis (DEP) and electrophoresis are especially well suited to microscale bioparticle control and have been demonstrated in many formats. In this work, an optimized gradient insulator-based DEP device was utilized for concentration of Sindbis virus, an animal virus with a diameter of 68 nm. Within only a few seconds, the concentration of Sindbis virus can be increased by two to six times in the channel under easily accessible voltages as low as about 70 V. Compared with traditional diagnostic methods used in virology, DEP-based microfluidics can enable faster isolation, detection and concentration of viruses in a single step within a short time.
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Affiliation(s)
- Jie Ding
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
| | - Robert M Lawrence
- The Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA and Center for Applied Structural Design, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Paul V Jones
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
| | - Brenda G Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA and The Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA and Center for Applied Structural Design, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mark A Hayes
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA.
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Khajedaluee M, Babaei A, Vakili R, Valizade N, Homaei Shandiz F, Alavian SM, Seyed Nozadi M, Jazayeri SM, Hassannia T. Sero-Prevalence of Bloodborne Tumor Viruses (HCV, HBV, HTLV-I and KSHV Infections) and Related Risk Factors among Prisoners in Razavi Khorasan Province, Iran, in 2008. HEPATITIS MONTHLY 2016; 16:e31541. [PMID: 28123439 PMCID: PMC5237471 DOI: 10.5812/hepatmon.31541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/28/2015] [Accepted: 11/26/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Prisoners are at high risk of blood borne and sexually transmitted infections due to their high involvement in risky behaviors. In this descriptive/cross-sectional study, the prevalence, sero-prevalence, and risk factors for bloodborne tumor viruses including HTLV-I, HBV, HCV, and KSHV were evaluated among inmates of two central prisons in the northeast of Iran. METHODS Blood samples of 1114 inmates were analyzed for the presence of anti HTLV-I, KSHV, and HCV antibodies and HBsAg by ELISA. PCR tests were performed to confirm the presence of these viruses in plasma and identify the current infections. RESULTS The sero-prevalence of HCV, HBV, HTLV-I, and KSHV was 24.5%, 4.2%, 3.4%, and 3.2% and the prevalence of HCV, HBV, HTLV-I, and KSHV was 19.1%, 2.1%, 2%, and 3%, respectively. HCV infection was significantly associated with history of imprisonment, tobacco consumption, alcohol consumption, intravenous drug use, length of imprisonment, and type of crime committed. Thirty one (2.8%) prisoners had HCV-KSHV co-infection, 16 (1.5%) had HCV-HTLV-I co-infection, and 14 (1.3%) had HBV-HCV co-infection. Triple co-infection was observed in seven cases and one case had four infections concomitantly. CONCLUSIONS This epidemiological study indicated different rates and transmission risks for these viruses. HCV was the most contagious viral infection and HTLV-I was the weakest in the prisoners. Apart from KSHV infection which its prevalence was as twice as in the general population, the prevalence of HBV and HTLV-I in prisoners was nearly in ranges of the general population.
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Affiliation(s)
- Mohammad Khajedaluee
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, IR Iran
| | - Ali Babaei
- University of Applied Science and Technology, Mashhad Branch Region 6, (Prison Organization), Mashhad, IR Iran
| | - Rosita Vakili
- Center of Pathological and Medical Diagnostic Services, Iranian Academic Center for Education, Culture and Research (ACECR), Mashhad Branch, Mashhad, IR Iran
| | - Narges Valizade
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, IR Iran
| | - Fateme Homaei Shandiz
- Cancer Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, IR Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Diseases (MELD) Center, Tehran, IR Iran
| | - Mohsen Seyed Nozadi
- Inflammation and Inflammatory Diseases Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, IR Iran
| | - Seyed Mohammad Jazayeri
- Hepatitis B Molecular Laboratory, Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Tahereh Hassannia
- Internal Medicine Department, Arash Hospital, Tehran University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Tahereh Hassannia, Internal Medicine Department, Arash Hospital, Tehran University of Medical Sciences, Tehran, IR Iran. Tel: +98-5138012768, Fax: +98-5138436626, E-mail:
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De Paschale M, Clerici P. Microbiology laboratory and the management of mother-child varicella-zoster virus infection. World J Virol 2016; 5:97-124. [PMID: 27563537 PMCID: PMC4981827 DOI: 10.5501/wjv.v5.i3.97] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/08/2016] [Accepted: 07/22/2016] [Indexed: 02/05/2023] Open
Abstract
Varicella-zoster virus, which is responsible for varicella (chickenpox) and herpes zoster (shingles), is ubiquitous and causes an acute infection among children, especially those aged less than six years. As 90% of adults have had varicella in childhood, it is unusual to encounter an infected pregnant woman but, if the disease does appear, it can lead to complications for both the mother and fetus or newborn. The major maternal complications include pneumonia, which can lead to death if not treated. If the virus passes to the fetus, congenital varicella syndrome, neonatal varicella (particularly serious if maternal rash appears in the days immediately before or after childbirth) or herpes zoster in the early years of life may occur depending on the time of infection. A Microbiology laboratory can help in the diagnosis and management of mother-child infection at four main times: (1) when a pregnant woman has been exposed to varicella or herpes zoster, a prompt search for specific antibodies can determine whether she is susceptible to, or protected against infection; (2) when a pregnant woman develops clinical symptoms consistent with varicella, the diagnosis is usually clinical, but a laboratory can be crucial if the symptoms are doubtful or otherwise unclear (atypical patterns in immunocompromised subjects, patients with post-vaccination varicella, or subjects who have received immunoglobulins), or if there is a need for a differential diagnosis between varicella and other types of dermatoses with vesicle formation; (3) when a prenatal diagnosis of uterine infection is required in order to detect cases of congenital varicella syndrome after the onset of varicella in the mother; and (4) when the baby is born and it is necessary to confirm a diagnosis of varicella (and its complications), make a differential diagnosis between varicella and other diseases with similar symptoms, or confirm a causal relationship between maternal varicella and malformations in a newborn.
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Canberk S, Longatto-Filho A, Schmitt F. Molecular diagnosis of infectious diseases using cytological specimens. Diagn Cytopathol 2015; 44:156-64. [PMID: 26620694 DOI: 10.1002/dc.23394] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 11/13/2015] [Indexed: 01/02/2023]
Abstract
Pathologists have an important role in the diagnosis of infectious disease (ID). In many cases, a definitive diagnosis can be made using cytopathology alone. However, several ancillary techniques can be used on cytological material to reach a specific diagnosis by identifying the causative agent and consequently defining the management of the patient. This review aims to present the effectiveness of the application of molecular studies on cytological material to diagnose IDs and discuss the advantages and disadvantages of the various molecular techniques according to the type of cytological specimen and the infectious agents.
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Affiliation(s)
- Sule Canberk
- Department of Pathology-Cytopathology, Haydarpasa Numune Education and Research Hospital, Istanbul, Turkey
| | - Adhemar Longatto-Filho
- Laboratory of Medical Investigation (LIM) 14, Faculty of Medicine, São Paulo University, FMUSP, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga, Portugal.,Molecular Oncology Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Fernando Schmitt
- Department of Pathology and Medicine, Laboratoire National De Sante, Dudelange, Luxembourg.,Instituto De Patologia E Imunologia Molecular Da Universidade Do Porto (IPATIMUP) E Faculdade De Medicina Do Porto, Porto, Portugal
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Kocjan BJ, Hošnjak L, Poljak M. Detection of alpha human papillomaviruses in archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens. J Clin Virol 2015; 76 Suppl 1:S88-S97. [PMID: 26514313 DOI: 10.1016/j.jcv.2015.10.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/05/2015] [Accepted: 10/10/2015] [Indexed: 01/14/2023]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissue specimens stored in pathology departments worldwide are an invaluable source for diagnostic purposes when fresh clinical material is unavailable as well as for retrospective molecular and epidemiological studies, especially when dealing with rare clinical conditions for which prospective collection is not feasible. Accurate detection of HPV infection in these specimens is particularly challenging because nucleic acids are often degraded and therefore, not suitable for amplification of larger fragments of the viral genome or viral gene transcripts. This review provides a brief summary of molecular methods for detecting alpha-HPV DNA/RNA in FFPE tissue specimens. We specifically address the key procedural and environmental factors that have the greatest impact on the quality of nucleic acids extracted from FFPE tissue specimens, and describe some solutions that can be used to increase their integrity and/or amplifiability. Moreover, commonly used methods for HPV DNA/RNA detection in FFPE tissue specimens are presented and discussed, focusing on studies using polymerase chain reaction as an HPV detection method and published after 1999. Finally, we briefly summarize our 22 years of experience with HPV detection in FFPE tissue specimens.
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Affiliation(s)
- Boštjan J Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia; European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Forensic and Postmortem Microbiology (ESGFOR), Basel, Switzerland.
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Litster A, Wu CC, Leutenegger CM. Detection of feline upper respiratory tract disease pathogens using a commercially available real-time PCR test. Vet J 2015; 206:149-53. [PMID: 26324635 DOI: 10.1016/j.tvjl.2015.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/26/2015] [Accepted: 08/02/2015] [Indexed: 10/23/2022]
Abstract
Feline herpesvirus (FHV-1), feline calicivirus (FCV), Bordetella bronchiseptica (Bb), Chlamydia felis (Cf) and Mycoplasma felis (Mf) are common infectious agents identified in cats with upper respiratory tract disease (URTD). Each of these agents can either act as primary pathogens or cause subclinical infections, and pathogen identification can be used to prevent disease transmission in shelters, or to manage individual cats with recurrent URTD. The aim of this study was to compare pathogen detection rates using real-time PCR testing and virus isolation (VI) or bacterial culture in conjunctival, nasal and oropharyngeal swabs from 18 shelter-housed cats with clinical URTD. Co-infections were common; FHV-1 was most prevalent and Cf and FCV were least prevalent. Agents detected by PCR were FCV 2/18 (11%), FHV-1 17/18 (94%), Bb 8/18 (44%) and Mf 15/18 (83%). Agents detected by VI and bacterial culture were FCV 1/18 (6%), FHV-1 12/18 (67%), Bb 8/18 (44%) and Mf 12/18 (67%). Agreement between PCR results and the other two methods was: FHV-1, 57.4%; FCV, 98.1%; Bb, 75.0%; Mf, 60.0%. Discordancies included PCR-positive, VI-negative (FCV, n = 1/54, 1.9%; FHV-1, n = 23/54, 42.6%), PCR-positive, culture-negative (Bb, n = 6/36, 16.7%; Mf, n = 13/36, 36.1%) or PCR-negative, culture-positive (Bb, n = 3/36, 8.3%; Mf, n = 2/36, 5.6%) results. A combination of an oropharyngeal swab and either a conjunctival or a nasal swab submitted for PCR testing was able to detect all infectious agents tested for in each cat. PCR testing was a sensitive and convenient method of detection of infectious agents in cats with clinical signs of URTD.
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Affiliation(s)
- A Litster
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Purdue University, 625 Harrison St., West Lafayette, IN 47907, USA.
| | - C C Wu
- Department of Comparative Pathobiology, School of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
| | - C M Leutenegger
- IDEXX Laboratories, Inc., 2825 KOVR Drive, West Sacramento, CA 95605, USA
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Han SH, Choi HY, Kim JM, Park KR, Youn YC, Shin HW. Etiology of aseptic meningitis and clinical characteristics in immune-competent adults. J Med Virol 2015; 88:175-9. [DOI: 10.1002/jmv.24316] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Su-Hyun Han
- Department of Neurology, Asan Medical Center; Ulsan University College of Medicine; Seoul South Korea
| | - Hye-Yeon Choi
- Department of Neurology, Gangdong Kyung Hee University Hospital; Kyung Hee University College of Medicine; Seoul South Korea
| | - Jeong-Min Kim
- Department of Neurology; Chung-Ang University College of Medicine; Seoul South Korea
| | - Kwang-Ryul Park
- Department of Neurology; Chung-Ang University College of Medicine; Seoul South Korea
| | - Young Chul Youn
- Department of Neurology; Chung-Ang University College of Medicine; Seoul South Korea
| | - Hae-Won Shin
- Department of Neurology; Chung-Ang University College of Medicine; Seoul South Korea
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Behzadi P, Ranjbar R, Alavian SM. Nucleic Acid-based approaches for detection of viral hepatitis. Jundishapur J Microbiol 2014; 8:e17449. [PMID: 25789132 PMCID: PMC4350052 DOI: 10.5812/jjm.17449] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/14/2014] [Accepted: 06/14/2014] [Indexed: 12/12/2022] Open
Abstract
CONTEXT To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. RESULTS Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent. CONCLUSIONS Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages.
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Affiliation(s)
- Payam Behzadi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Reza Ranjbar, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran. Tel: +98-21-88039883, E-mail:
| | - Seyed Moayed Alavian
- Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
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Fan F, Day S, Lu X, Tang YW. Laboratory diagnosis of HSV and varicella zoster virus infections. Future Virol 2014. [DOI: 10.2217/fvl.14.61] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Heiat M, Ranjbar R, Alavian SM. Classical and modern approaches used for viral hepatitis diagnosis. HEPATITIS MONTHLY 2014; 14:e17632. [PMID: 24829586 PMCID: PMC4006100 DOI: 10.5812/hepatmon.17632] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 01/28/2014] [Indexed: 12/11/2022]
Abstract
CONTEXT Viral hepatitis diagnosis is an important issue in the treatment procedure of this infection. Late diagnosis and delayed treatment of viral hepatitis infections can lead to irreversible liver damages and occurrence of liver cirrhosis and hepatocellular carcinoma. A variety of laboratory methods including old and new technologies are being applied to detect hepatitis viruses. Here we have tried to review, categorize, compare and illustrate the classical and modern approaches used for diagnosis of viral hepatitis. EVIDENCE ACQUISITION In order to achieve a comprehensive aspect in viral hepatitis detection methods, an extensive search using related keywords was done in major medical library and data were collected, categorized and summarized in different sections. RESULTS Analyzing of collected data resulted in the wrapping up the hepatitis virus detection methods in separate sections including 1) immunological methods such as enzyme immunoassay (EIA), radio-immunoassay (RIA) immuno-chromatographic assay (ICA), and immuno-chemiluminescence 2) molecular approaches including non-amplification and amplification based methods, and finally 3) advanced biosensors such as mass-sensitive, electrical, electrochemical and optical based biosensors and also new generation of detection methods. CONCLUSIONS Detection procedures in the clinical laboratories possess a large diversity; each has their individual advantages and facilities' differences.
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Affiliation(s)
- Mohammad Heiat
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding Author: Reza Ranjbar, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran, Tel: +98-2182482556, Fax: +98-2188039883, E-mail:
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Sand L, Jalouli J. Viruses and oral cancer. Is there a link? Microbes Infect 2014; 16:371-8. [PMID: 24613199 DOI: 10.1016/j.micinf.2014.02.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 12/28/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignant tumour of the oral cavity. The aetiology of epithelial cancer of the head and neck is considered to be a multifactorial, sequential process. DNA viruses are found in many different cancers and are also capable of transforming cells to a malignant phenotype. Human Papilloma Virus (HPV) has been proposed as risk factors in OSCC development and HPV type 16 is the most important subtype. Other oncogenic virus species i.e., Epstein-Barr Virus and Herpes Simplex Virus Type 1 have been proposed to be involved in oral carcinogenesis. However, no convincing evidence exist that they are an established risk factor in OSCC. Therefore more studies are needed in order to clarify the different aspects of virus involvement. Here, we review the existing literature on viral involvement in oral cancer.
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Affiliation(s)
- Lars Sand
- Department of Surgical Sciences, Oral and Maxillofacial Surgery, Medical Faculty, Uppsala University, Akademiska sjukhuset, 751 85 Uppsala, Sweden.
| | - Jamshid Jalouli
- Department of Surgical Sciences, Oral and Maxillofacial Surgery, Medical Faculty, Uppsala University, Akademiska sjukhuset, 751 85 Uppsala, Sweden
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