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Shahbazi E, Moradi A, Mollasalehi H, Mohebbi SR. Unravelling the diagnostic methodologies for SARS-CoV-2; the Indispensable need for developing point-of-care testing. Talanta 2024; 275:126139. [PMID: 38696900 DOI: 10.1016/j.talanta.2024.126139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/13/2024] [Accepted: 04/20/2024] [Indexed: 05/04/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic that continues to be a global menace and since its emergence in the late 2019, SARS-CoV-2 has been vigorously spreading throughout the globe putting the whole world into a multidimensional calamity. The suitable diagnosis strategies are on the front line of the battle against preventing the spread of infections. Since the clinical manifestation of COVID-19 is shared between various diseases, detection of the unique impacts of the pathogen on the host along with the diagnosis of the virus itself should be addressed. Employing the most suitable approaches to specifically, sensitively and effectively recognize the infected cases may be a real game changer in controlling the outbreak and the crisis management. In that matter, point-of-care assays (POC) appears to be the potential option, due to sensitivity, specificity, affordable, and availability. Here we brief the most recent findings about the virus, its variants, and the conventional methods that have been used for its detection, along with the POC strategies that have been applied to the virus diagnosis and the developing technologies which can accelerate the diagnosis procedure yet maintain its efficiency.
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Affiliation(s)
- Erfan Shahbazi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Asma Moradi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Hamidreza Mollasalehi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Song R, Chen Z, Xiao H, Wang H. The CRISPR-Cas system in molecular diagnostics. Clin Chim Acta 2024; 561:119820. [PMID: 38901631 DOI: 10.1016/j.cca.2024.119820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Robust, sensitive, and rapid molecular detection tools are essential prerequisites for disease diagnosis and epidemiological control. However, the current mainstream tests necessitate expensive equipment and specialized operators, impeding the advancement of molecular diagnostics. The CRISPR-Cas system is an integral component of the bacterial adaptive immune system, wherein Cas proteins recognize PAM sequences by binding to CRISPR RNA, subsequently triggering DNA or RNA cleavage. The discovery of the CRISPR-Cas system has invigorated molecular diagnostics. With further in-depth research on this system, its application in molecular diagnosis is flourishing. In this review, we provide a comprehensive overview of recent research progress on the CRISPR-Cas system, specifically focusing on its application in molecular diagnosis.
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Affiliation(s)
- Rao Song
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Zhongyi Chen
- Department of Pathology, Suining Central Hospital, Suining 629000, China
| | - Hongtao Xiao
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Haojun Wang
- Department of Pathology, Suining Central Hospital, Suining 629000, China.
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Muzembo BA, Kitahara K, Ohno A, Khatiwada J, Dutta S, Miyoshi SI. Rapid diagnostic tests and loop-mediated isothermal amplification method for the detection of Shigella species: A systematic review and meta-analysis. J Infect Public Health 2024; 17:1065-1078. [PMID: 38705059 DOI: 10.1016/j.jiph.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
We meta-analyzed the diagnostic accuracy of rapid diagnostic tests (dipsticks) and loop-mediated isothermal amplification (LAMP) method to detect Shigella species. We searched MEDLINE, Embase, Web of Science and Google Scholar from inception to 2023 for studies reporting on the performance of Shigella dipstick and LAMP tests compared with culture or polymerase chain reaction (PCR). Our search identified 2618 studies, of which fourteen met the inclusion criteria for the systematic review. Ten studies covering 4056 tests (from twelve countries) were included in the meta-analysis. The overall pooled sensitivity and specificity were 98% (95% CI: 94-100) and 97% (95% CI: 92-99), respectively. Pooled sensitivity and specificity of dipsticks were 95% and 98%, respectively. In contrast, LAMP showed higher pooled sensitivity (100%) and diagnostic odds ratio (431752), but similar specificity (97%). LAMP and dipstick tests exhibited promising performance, suggesting that they could be useful for assisting in the diagnosis of shigellosis.
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Affiliation(s)
- Basilua Andre Muzembo
- Research Institute of Nursing Care for People and Community, University of Hyogo, Akashi, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Kei Kitahara
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Collaborative Research Centre of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, India
| | - Ayumu Ohno
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Collaborative Research Centre of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, India
| | | | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Lee SS, Kim AL, Park JH, Lee DH, Bae YK. Optimization of duplex digital PCR for the measurement of SARS-CoV-2 RNA. J Virol Methods 2024; 326:114911. [PMID: 38447644 DOI: 10.1016/j.jviromet.2024.114911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Quantitative PCR (qPCR) is the gold standard for detecting nucleic acid sequences specific to the target pathogen. For COVID-19 diagnosis, several molecular assays have been developed. In this study, we present an optimization strategy for the measurement of SARS-CoV-2 RNA via multiplex qPCR and digital PCR (dPCR). Compared to qPCR, both droplet and chip-based dPCR, which are known to be more sensitive and accurate, showed a better resilience to suboptimal assay compositions and cycling conditions following the proposed optimizations. In particular, the formation of heterodimers among assays greatly interfered with qPCR results, but only minimally with dPCR results. In dPCR, existing heterodimers lowered the PCR efficiency, producing a dampened fluorescent signal in positive partitions. This can be corrected by adjusting the PCR cycling conditions, after which dPCR shows the capability of measuring the expected copy number. In addition, we present a process to improve the existing RdRp assay by correcting the primer sequences and matching the melting temperature, ultimately producing highly sensitive and robust assays. The results of this study can reduce the cost and time of SARS-CoV-2 diagnosis while increasing accuracy. Furthermore, our results suggest that dPCR is a reliable method for the accurate measurement of nucleic acid targets.
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Affiliation(s)
- Sang-Soo Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Ah Leum Kim
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Jae-Hyung Park
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Da-Hye Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea.
| | - Young-Kyung Bae
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
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Vavougios GD, Tseriotis VS, Liampas A, Mavridis T, de Erausquin GA, Hadjigeorgiou G. Type I interferon signaling, cognition and neurodegeneration following COVID-19: update on a mechanistic pathogenetic model with implications for Alzheimer's disease. Front Hum Neurosci 2024; 18:1352118. [PMID: 38562226 PMCID: PMC10982434 DOI: 10.3389/fnhum.2024.1352118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
COVID-19's effects on the human brain reveal a multifactorial impact on cognition and the potential to inflict lasting neuronal damage. Type I interferon signaling, a pathway that represents our defense against pathogens, is primarily affected by COVID-19. Type I interferon signaling, however, is known to mediate cognitive dysfunction upon its dysregulation following synaptopathy, microgliosis and neuronal damage. In previous studies, we proposed a model of outside-in dysregulation of tonic IFN-I signaling in the brain following a COVID-19. This disruption would be mediated by the crosstalk between central and peripheral immunity, and could potentially establish feed-forward IFN-I dysregulation leading to neuroinflammation and potentially, neurodegeneration. We proposed that for the CNS, the second-order mediators would be intrinsic disease-associated molecular patterns (DAMPs) such as proteopathic seeds, without the requirement of neuroinvasion to sustain inflammation. Selective vulnerability of neurogenesis sites to IFN-I dysregulation would then lead to clinical manifestations such as anosmia and cognitive impairment. Since the inception of our model at the beginning of the pandemic, a growing body of studies has provided further evidence for the effects of SARS-CoV-2 infection on the human CNS and cognition. Several preclinical and clinical studies have displayed IFN-I dysregulation and tauopathy in gene expression and neuropathological data in new cases, correspondingly. Furthermore, neurodegeneration identified with a predilection for the extended olfactory network furthermore supports the neuroanatomical concept of our model, and its independence from fulminant neuroinvasion and encephalitis as a cause of CNS damage. In this perspective, we summarize the data on IFN-I as a plausible mechanism of cognitive impairment in this setting, and its potential contribution to Alzheimer's disease and its interplay with COVID-19.
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Affiliation(s)
- George D. Vavougios
- Department of Neurology, Medical School, University of Cyprus, Lefkosia, Cyprus
| | | | - Andreas Liampas
- Department of Neurology, Medical School, University of Cyprus, Lefkosia, Cyprus
| | - Theodore Mavridis
- Tallaght University Hospital (TUH)/The Adelaide and Meath Hospital Dublin, Incorporating the National Children's Hospital (AMNCH), Dublin, Ireland
| | - Gabriel A. de Erausquin
- Laboratory of Brain Development, Modulation and Repair, The Glenn Biggs Institute of Alzheimer's and Neurodegenerative Disorders, Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Lee NE, Kim KH, Cho Y, Kim J, Kwak S, Lee D, Yoon DS, Lee JH. Enhancing Loop-Mediated Isothermal Amplification through Nonpowered Nanoelectric Preconcentration. Anal Chem 2024; 96:3844-3852. [PMID: 38393745 DOI: 10.1021/acs.analchem.3c05236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The global threat posed by the COVID-19 pandemic has catalyzed the development of point-of-care (POC) molecular diagnostics. While loop-mediated isothermal amplification (LAMP) stands out as a promising technique among FDA-approved methods, it is occasionally susceptible to a high risk of false positives due to nonspecific amplification of a primer dimer. In this work, we report an enhancing LAMP technique in terms of assay sensitivity and reliability through streamlined integration with a nonpowered nanoelectric preconcentration (NPP). The NPP, serving as a sample preparation tool, enriched the virus concentration in samples prior to the subsequent LAMP assay. This enrichment enabled not only to achieve more sensitive assay but also to shorten the assay time for all tested clinical samples by ∼10 min compared to the conventional LAMP. The shortened assay time suppresses the occurrence of nonspecific amplification by not providing the necessary incubation time, effectively suppressing misidentification by false positives. Utilizing this technique, we also developed a prototype of the POC NPP-LAMP kit. This kit offers a streamlined diagnostic process for nontrained individuals, from the sample enrichment, transfer of the enriched sample to LAMP assays, which facilitates on-site/on-demand diagnosis of SARS-CoV-2. This development holds the potential to contribute toward preventing not only the current outbreak but also future occurrences of pandemic viruses.
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Affiliation(s)
- Na Eun Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Kang Hyeon Kim
- Department of Electrical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Youngkyu Cho
- Samsung Research, Samsung Electronics Co., Ltd., Seoul 06756, Republic of Korea
| | - Jinhwan Kim
- Department of Electrical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Seungmin Kwak
- Micro-Nano Fabrication Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk, Seoul 02792, South Korea
| | - Dohwan Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
- School of Electrical and Computer Engineering, Georgia Institute of Technology, 791 Atlantic Dr NW, Atlanta, Georgia 30332, United States
| | - Dae Sung Yoon
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
- Astrion Inc, Seoul 02841, Republic of Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
- CALTH Inc., Changeop-ro 54, Seongnam, Gyeonggi 13449, Republic of Korea
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Tao L, Chan A, Maris A, Schmitz JE. Internationally standardized respiratory viral load testing with limited resources: A derivative-of-care calibration strategy for SARS-CoV-2. Influenza Other Respir Viruses 2024; 18:e13207. [PMID: 38268611 PMCID: PMC10805620 DOI: 10.1111/irv.13207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 01/26/2024] Open
Abstract
Introduction SARS-CoV-2 has demonstrated that, in targeted circumstances, viral quantification within respiratory specimens can valuably inform patient management, as well as research. Nevertheless, the pandemic has illustrated concomitant challenges for obtaining high-quality (and broadly comparable) respiratory viral loads. This includes a critical need for standardization and calibration, even though the necessary resources may not always be available for emergent pathogens and non-bloodstream specimens. Methods To these ends, we describe a novel strategy for implementing quantitative SARS-CoV-2 testing with International Unit-based calibration. Earlier in the course of the pandemic-when analytic resources were far more limited-select residual SARS-CoV-2 positive specimens from routine care in our diagnostic laboratory were pooled to formulate a clinically realistic secondary standard of high volume and analyte concentration, which was cross-calibrated to the primary SARS-CoV-2 standard of the World Health Organization. Results The resultant calibrators were integrated into the original CDC RT-qPCR assay for SARS-CoV-2, whose (now broadened) performance characteristics were defined to generate a test appropriate for both clinical and research use. This test allowed for the quantification of virus in respiratory specimens down to a validated lower limit of quantification of 103.4 IU/ml. Conclusions By self-formulating calibrators from this derivative-of-care secondary standard, we successfully validated respiratory viral loads without the commercial availability (at that time) of quantitative assays or calibrators. As the SARS-CoV-2 pandemic continues to decline-and even beyond this pathogen-this strategy may be applicable for laboratories seeking to implement viral load testing for nontraditional specimen types despite limited resources.
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Affiliation(s)
- Lili Tao
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Allison Chan
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Alex Maris
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Jonathan E. Schmitz
- Department of Pathology, Microbiology, and ImmunologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of UrologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Institute for Infection, Immunology, and InflammationVanderbilt University Medical CenterNashvilleTennesseeUSA
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Clemente L, La Rocca M, Quaranta N, Iannuzzi L, Vecchio E, Brunetti A, Gentile E, Dibattista M, Lobasso S, Bevilacqua V, Stramaglia S, de Tommaso M. Prefrontal dysfunction in post-COVID-19 hyposmia: an EEG/fNIRS study. Front Hum Neurosci 2023; 17:1240831. [PMID: 37829821 PMCID: PMC10564993 DOI: 10.3389/fnhum.2023.1240831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/29/2023] [Indexed: 10/14/2023] Open
Abstract
Introduction Subtle cognitive dysfunction and mental fatigue are frequent after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, characterizing the so-called long COVID-19 syndrome. This study aimed to correlate cognitive, neurophysiological, and olfactory function in a group of subjects who experienced acute SARS-CoV-2 infection with persistent hyposmia at least 12 weeks before the observation. Methods For each participant (32 post-COVID-19 patients and 16 controls), electroencephalography (EEG) and functional near-infrared spectroscopy (fNIRS) data were acquired using an integrated EEG-fNIRS system during the execution of a P300 odd-ball task and a Stroop test. The Sniffin' Sticks test was conducted to assess subjects' olfactory performance. The Montreal Cognitive Assessment (MoCA) and the Frontal Assessment Battery (FAB) were also administered. Results The post-COVID-19 group consisted of 32 individuals (20 women and 12 men) with an average education level of 12.9 ± 3.12 years, while the control group consisted of 16 individuals (10 women and 6 men) with an average education level of 14.9 ± 3.2 years. There were no significant differences in gender (X2 = 0, p = 1) or age between the two groups (age 44.81 ± 13.9 vs. 36.62 ± 11.4, p = 0.058). We identified a lower concentration of oxyhemoglobin (p < 0.05) at the prefrontal cortical level in post-COVID-19 subjects during the execution of the Stroop task, as well as a reduction in the amplitude of the P3a response. Moreover, we found that post-COVID-19 subjects performed worst at the MoCA screening test (p = 0.001), Sniffin's Sticks test (p < 0.001), and Stroop task response latency test (p < 0.001). Conclusions This study showed that post-COVID-19 patients with persistent hyposmia present mild deficits in prefrontal function, even 4 months after the end of the infection. These deficits, although subtle, could have long-term implications for quality of life and cognitive wellbeing. It is essential to continue monitoring and evaluating these patients to better understand the extent and duration of cognitive impairments associated with long COVID-19.
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Affiliation(s)
- Livio Clemente
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Marianna La Rocca
- M. Merlin Inter-university Physics Department, University of Bari, Bari, Italy
- Laboratory of Neuroimaging, Keck School of Medicine of USC, USC Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, United States
| | - Nicola Quaranta
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Lucia Iannuzzi
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Eleonora Vecchio
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Antonio Brunetti
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Bari, Italy
| | - Eleonora Gentile
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Michele Dibattista
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Simona Lobasso
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
| | - Vitoantonio Bevilacqua
- Department of Electrical and Information Engineering, Polytechnic University of Bari, Bari, Italy
| | | | - Marina de Tommaso
- Department of Translational Biomedicine and Neuroscience (DiBraiN), University of Bari Aldo Moro, Bari, Italy
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Habibzadeh F. GPTZero Performance in Identifying Artificial Intelligence-Generated Medical Texts: A Preliminary Study. J Korean Med Sci 2023; 38:e319. [PMID: 37750374 PMCID: PMC10519776 DOI: 10.3346/jkms.2023.38.e319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/19/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND With emergence of chatbots to help authors with scientific writings, editors should have tools to identify artificial intelligence-generated texts. GPTZero is among the first websites that has sought media attention claiming to differentiate machine-generated from human-written texts. METHODS Using 20 text pieces generated by ChatGPT in response to arbitrary questions on various topics in medicine and 30 pieces chosen from previously published medical articles, the performance of GPTZero was assessed. RESULTS GPTZero had a sensitivity of 0.65 (95% confidence interval, 0.41-0.85); specificity, 0.90 (0.73-0.98); accuracy, 0.80 (0.66-0.90); and positive and negative likelihood ratios, 6.5 (2.1-19.9) and 0.4 (0.2-0.7), respectively. CONCLUSION GPTZero has a low false-positive (classifying a human-written text as machine-generated) and a high false-negative rate (classifying a machine-generated text as human-written).
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Affiliation(s)
- Farrokh Habibzadeh
- Past President, World Association of Medical Editors (WAME), Editorial Consultant, The Lancet, Associate Editor, Frontiers in Epidemiology.
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Yadav SK, Verma D, Yadav U, Kalkal A, Priyadarshini N, Kumar A, Mahato K. Point-of-Care Devices for Viral Detection: COVID-19 Pandemic and Beyond. MICROMACHINES 2023; 14:1744. [PMID: 37763907 PMCID: PMC10535693 DOI: 10.3390/mi14091744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
The pandemic of COVID-19 and its widespread transmission have made us realize the importance of early, quick diagnostic tests for facilitating effective cure and management. The primary obstacles encountered were accurately distinguishing COVID-19 from other illnesses including the flu, common cold, etc. While the polymerase chain reaction technique is a robust technique for the determination of SARS-CoV-2 in patients of COVID-19, there arises a high demand for affordable, quick, user-friendly, and precise point-of-care (POC) diagnostic in therapeutic settings. The necessity for available tests with rapid outcomes spurred the advancement of POC tests that are characterized by speed, automation, and high precision and accuracy. Paper-based POC devices have gained increasing interest in recent years because of rapid, low-cost detection without requiring external instruments. At present, microfluidic paper-based analysis devices have garnered public attention and accelerated the development of such POCT for efficient multistep assays. In the current review, our focus will be on the fabrication of detection modules for SARS-CoV-2. Here, we have included a discussion on various strategies for the detection of viral moieties. The compilation of these strategies would offer comprehensive insight into the detection of the causative agent preparedness for future pandemics. We also provide a descriptive outline for paper-based diagnostic platforms, involving the determination mechanisms, as well as a commercial kit for COVID-19 as well as their outlook.
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Affiliation(s)
- Sumit K. Yadav
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh 825301, Jharkhand, India
| | - Damini Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ujala Yadav
- Department of Life Sciences, Central University of Jharkhand, Ranchi 835205, Jharkhand, India
| | - Ashish Kalkal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nivedita Priyadarshini
- Department of Zoology, DAV PG College Siwan, Jai Prakash University, Chhapra 841226, Bihar, India
| | - Ashutosh Kumar
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46637, USA
| | - Kuldeep Mahato
- Department of Nanoengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, San Diego, CA 92093, USA
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Zhang X, Zhao Y, Zeng Y, Zhang C. Evolution of the Probe-Based Loop-Mediated Isothermal Amplification (LAMP) Assays in Pathogen Detection. Diagnostics (Basel) 2023; 13:diagnostics13091530. [PMID: 37174922 PMCID: PMC10177487 DOI: 10.3390/diagnostics13091530] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP), as the rank one alternative to a polymerase chain reaction (PCR), has been widely applied in point-of-care testing (POCT) due to its rapid, simple, and cost-effective characteristics. However, it is difficult to achieve real-time monitoring and multiplex detection with the traditional LAMP method. In addition, these approaches that use turbidimetry, sequence-independent intercalating dyes, or pH-sensitive indicators to indirectly reflect amplification can result in false-positive results if non-specific amplification occurs. To fulfill the needs of specific target detection and one-pot multiplex detection, a variety of probe-based LAMP assays have been developed. This review focuses on the principles of these assays, summarizes their applications in pathogen detection, and discusses their features and advantages over the traditional LAMP methods.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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Evaluation of the MAScIR SARS-CoV-2 M Kit 2.0 on the SARS-CoV-2 Infection. Adv Virol 2023; 2023:9313666. [PMID: 36816885 PMCID: PMC9929027 DOI: 10.1155/2023/9313666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 12/16/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
SARS-CoV-2 is a major public health problem worldwide. Since its emergence, several diagnostic kits have been developed to ensure rapid patient management. The aim of our study is to check the performance of the new Moroccan SARS-CoV-2 detection kit: MAScIR SARS-CoV-2 M 2.0. The following parameters were studied: repeatability, reproducibility, analytical specificity, analytical sensitivity, and comparison with the GeneFinder™ COVID-19 Plus RealAmp Kit. In addition, an external quality evaluation comprising five specimens was carried out as part of an international program for the external quality evaluation of sublaboratories of the WHO and the Laboratory Office of the National Institute of Hygiene of Morocco. The results of all parameters studied showed an analytical performance that complied with the requirements of the method verification/validation protocol adopted by the Central Laboratory of Virology and met the recommendations of COFRAC (French Accreditation Committee). During the current study, the sequencing of some randomly selected positive samples was performed, among which the carriers of the Alpha variant, the Delta variant, and the Omicron variant were detected. These results allowed us to deduce that this kit was valid for detecting these three variants.
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COVID-19 diagnostic approaches with an extensive focus on computed tomography in accurate diagnosis, prognosis, staging, and follow-up. Pol J Radiol 2023; 88:e53-e64. [PMID: 36819223 PMCID: PMC9907165 DOI: 10.5114/pjr.2023.124597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/12/2022] [Indexed: 02/10/2023] Open
Abstract
Although a long time has passed since its outbreak, there is currently no specific treatment for COVID-19, and it seems that the most appropriate strategy to combat this pandemic is to identify and isolate infected individuals. Various clinical diagnosis methods such as molecular techniques, serologic assays, and imaging techniques have been developed to identify suspected patients. Although reverse transcription-quantitative PCR (RT-qPCR) has emerged as a reference standard method for diagnosis of SARS-CoV-2, the high rate of false-negative results and limited supplies to meet current demand are the main shortcoming of this technique. Based on a comprehensive literature review, imaging techniques, particularly computed tomography (CT), show an acceptable level of sensitivity in the diagnosis and follow-up of COVID-19. Indeed, because lung infection or pneumonia is a common complication of COVID-19, the chest CT scan can be an alternative testing method in the early diagnosis and treatment assessment of the disease. In this review, we summarize all the currently available frontline diagnostic tools for the detection of SARS-CoV-2-infected individuals and highlight the value of chest CT scan in the diagnosis, prognosis, staging, management, and follow-up of infected patients.
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Cristina Diaconu C, Madalina Pitica I, Chivu-Economescu M, Georgiana Necula L, Botezatu A, Virginia Iancu I, Iulia Neagu A, L. Radu E, Matei L, Maria Ruta S, Bleotu C. SARS-CoV-2 Variant Surveillance in Genomic Medicine Era. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In the genomic medicine era, the emergence of SARS-CoV-2 was immediately followed by viral genome sequencing and world-wide sequences sharing. Almost in real-time, based on these sequences, resources were developed and applied around the world, such as molecular diagnostic tests, informed public health decisions, and vaccines. Molecular SARS-CoV-2 variant surveillance was a normal approach in this context yet, considering that the viral genome modification occurs commonly in viral replication process, the challenge is to identify the modifications that significantly affect virulence, transmissibility, reduced effectiveness of vaccines and therapeutics or failure of diagnostic tests. However, assessing the importance of the emergence of new mutations and linking them to epidemiological trend, is still a laborious process and faster phenotypic evaluation approaches, in conjunction with genomic data, are required in order to release timely and efficient control measures.
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Sahoo P, Dey J, Mahapatra SR, Ghosh A, Jaiswal A, Padhi S, Prabhuswamimath SC, Misra N, Suar M. Nanotechnology and COVID-19 Convergence: Toward New Planetary Health Interventions Against the Pandemic. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:473-488. [PMID: 36040392 DOI: 10.1089/omi.2022.0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
COVID-19 is a systemic disease affecting multiple organ systems and caused by infection with the SARS-CoV-2 virus. Two years into the COVID-19 pandemic and after the introduction of several vaccines, the pandemic continues to evolve in part owing to global inequities in access to preventive and therapeutic measures. We are also witnessing the introduction of antivirals against COVID-19. Against this current background, we review the progress made with nanotechnology-based approaches such as nanoformulations to combat the multiorgan effects of SARS-CoV-2 infection from a systems medicine lens. While nanotechnology has previously been widely utilized in the antiviral research domain, it has not yet received the commensurate interest in the case of COVID-19 pandemic response strategies. Notably, SARS-CoV-2 and nanomaterials are similar in size ranging from 50 to 200 nm. Nanomaterials offer the promise to reduce the side effects of antiviral drugs, codeliver multiple drugs while maintaining stability in the biological milieu, and sustain the release of entrapped drug(s) for a predetermined time period, to name but a few conceivable scenarios, wherein nanotechnology can enable and empower preventive medicine and therapeutic innovations against SARS-CoV-2. We conclude the article by underlining that nanotechnology-based interventions warrant further consideration to enable precision planetary health responses against the COVID-19 pandemic.
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Affiliation(s)
- Panchanan Sahoo
- Kalinga Institute of Medical Sciences, Kalinga Institute of Industrial Technology (KIIT) Deemed to Be University, Bhubaneswar, India
| | - Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Arpan Ghosh
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Aryan Jaiswal
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Santwana Padhi
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Samudyata C Prabhuswamimath
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT) Deemed to be University, Bhubaneswar, India
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The SARS-CoV-2 Variants and their Impacts. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Since the first detection of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus remains a public health concern. Several public health measures have been implemented in an effort to curb the infections. However, the effectiveness of these strategies was threatened with the emergence of numerous SARS-CoV-2 variants in all parts of the globe, due to the persistent mutations as part of the viral evolution. Mutations that usually occur in its spike glycoprotein, allow SARS-CoV-2 to possess advantageous characteristics for its survivability and persistence. This has led to poor performance of diagnostic kits which have caused non-specific and insensitive detection of these variants, resulting in undetermined infection. The variants also have caused the increased severity of COVID-19, involving hospitalisation rates, ICU admissions, and deaths. Many have reported the vaccine-breakthrough infections and reduced effectiveness of vaccination, which is supposed to provide an effective degree of protection against COVID-19 infections. Due to these issues, this review summarises the impacts related to SARS-CoV-2 variants emergence towards the performance of diagnostic kits, transmissibility of the virus, severity of disease, and effectiveness of COVID-19 vaccines.
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Habibzadeh F, Habibzadeh P, Yadollahie M. On Measuring Vaccine Effectiveness with Observational Study Designs. Acta Med Acad 2022; 51:134-146. [PMID: 36318007 PMCID: PMC9982864 DOI: 10.5644/ama2006-124.383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Herein, we present a bird's eye view of common observational study designs utilized for measurement of vaccine effectiveness. Assessing vaccines effectiveness is an integral part of vaccine research, particularly for the newly developed vaccines. A cohort study is prospective, directing from an exposure to one or more outcomes. The design is the best method to ascertain the attack rate of an infectious disease. A traditional case-control study is retrospective, directing from a given outcome to one or more exposures. The design cannot provide the relative risk, but it can provide the odds ratio, which is a good estimation of the relative risk when the attack rate is low. Critically depending on laboratory test results and performance, the test-negative case-control study design is another type of observational study commonly used nowadays for the evaluation of the vaccine effectiveness. Comparing to cohort and traditional case-control designs, conducting a test-negative case-control study is relatively cheaper and faster. Herein, we describe each of the above-mentioned study designs through examples generated by a Monte-Carlo simulation program assuming real-world conditions. CONCLUSION: The simulation shows that regardless of the study design employed, the diagnostic test specificity is of utmost importance in providing a valid estimate of the vaccine effectiveness.
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Affiliation(s)
| | - Parham Habibzadeh
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
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Tekeli T, Dénes A, Röst G. Adaptive group testing in a compartmental model of COVID-19 . MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:11018-11033. [PMID: 36124578 DOI: 10.3934/mbe.2022513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Various measures have been implemented around the world to prevent the spread of SARS-CoV-2. A potential tool to reduce disease transmission is regular mass testing of a high percentage of the population, possibly with pooling (testing a compound of several samples with one single test). We develop a compartmental model to study the applicability of this method and compare different pooling strategies: regular and Dorfman pooling. The model includes isolated compartments as well, from where individuals rejoin the active population after some time delay. We develop a method to optimize Dorfman pooling depending on disease prevalence and establish an adaptive strategy to select variable pool sizes during the course of the epidemic. It is shown that optimizing the pool size can avert a significant number of infections. The adaptive strategy is much more efficient, and may prevent an epidemic outbreak even in situations when a fixed pool size strategy can not.
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Affiliation(s)
- Tamás Tekeli
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary
| | - Attila Dénes
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary
| | - Gergely Röst
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary
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Araújo DC, Veloso AA, Borges KBG, Carvalho MDG. Prognosing the risk of COVID-19 death through a machine learning-based routine blood panel: A retrospective study in Brazil. Int J Med Inform 2022; 165:104835. [PMID: 35908372 PMCID: PMC9327247 DOI: 10.1016/j.ijmedinf.2022.104835] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 01/08/2023]
Abstract
Background: Despite an extensive network of primary care availability, Brazil has suffered profoundly during the COVID-19 pandemic, experiencing the greatest sanitary collapse in its history. Thus, it is important to understand phenotype risk factors for SARS-CoV-2 infection severity in the Brazilian population in order to provide novel insights into the pathogenesis of the disease. Objective: This study proposes to predict the risk of COVID-19 death through machine learning, using blood biomarkers data from patients admitted to two large hospitals in Brazil. Methods: We retrospectively collected blood biomarkers data in a 24-h time window from 6,979 patients with COVID-19 confirmed by positive RT-PCR admitted to two large hospitals in Brazil, of whom 291 (4.2%) died and 6,688 (95.8%) were discharged. We then developed a large-scale exploration of risk models to predict the probability of COVID-19 severity, finally choosing the best performing model regarding the average AUROC. To improve generalizability, for each model five different testing scenarios were conducted, including two external validations. Results: We developed a machine learning-based panel composed of parameters extracted from the complete blood count (lymphocytes, MCV, platelets and RDW), in addition to C-Reactive Protein, which yielded an average AUROC of 0.91 ± 0.01 to predict death by COVID-19 confirmed by positive RT-PCR within a 24-h window. Conclusion: Our study suggests that routine laboratory variables could be useful to identify COVID-19 patients under higher risk of death using machine learning. Further studies are needed for validating the model in other populations and contexts, since the natural history of SARS-CoV-2 infection and its consequences on the hematopoietic system and other organs is still quite recent.
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Affiliation(s)
- Daniella Castro Araújo
- Huna, São Paulo, SP, Brazil; Departamento de Ciência da Computação, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Adriano Alonso Veloso
- Departamento de Ciência da Computação, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Supervised Learning Models for the Preliminary Detection of COVID-19 in Patients Using Demographic and Epidemiological Parameters. INFORMATION 2022. [DOI: 10.3390/info13070330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The World Health Organization labelled the new COVID-19 breakout a public health crisis of worldwide concern on 30 January 2020, and it was named the new global pandemic in March 2020. It has had catastrophic consequences on the world economy and well-being of people and has put a tremendous strain on already-scarce healthcare systems globally, particularly in underdeveloped countries. Over 11 billion vaccine doses have already been administered worldwide, and the benefits of these vaccinations will take some time to appear. Today, the only practical approach to diagnosing COVID-19 is through the RT-PCR and RAT tests, which have sometimes been known to give unreliable results. Timely diagnosis and implementation of precautionary measures will likely improve the survival outcome and decrease the fatality rates. In this study, we propose an innovative way to predict COVID-19 with the help of alternative non-clinical methods such as supervised machine learning models to identify the patients at risk based on their characteristic parameters and underlying comorbidities. Medical records of patients from Mexico admitted between 23 January 2020 and 26 March 2022, were chosen for this purpose. Among several supervised machine learning approaches tested, the XGBoost model achieved the best results with an accuracy of 92%. It is an easy, non-invasive, inexpensive, instant and accurate way of forecasting those at risk of contracting the virus. However, it is pretty early to deduce that this method can be used as an alternative in the clinical diagnosis of coronavirus cases.
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Habibzadeh F, Habibzadeh P, Yadollahie M, Sajadi MM. Determining the SARS-CoV-2 serological immunoassay test performance indices based on the test results frequency distribution. Biochem Med (Zagreb) 2022; 32:020705. [PMID: 35799990 PMCID: PMC9195604 DOI: 10.11613/bm.2022.020705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/10/2022] [Indexed: 11/03/2022] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) is known to induce robust antibody response in most of the affected individuals. The objective of the study was to determine if we can harvest the test sensitivity and specificity of a commercial serologic immunoassay merely based on the frequency distribution of the SARS-CoV-2 immunoglobulin (Ig) G concentrations measured in a population-based seroprevalence study. Materials and methods The current study was conducted on a subset of a previously published dataset from the canton of Geneva. Data were taken from two non-consecutive weeks (774 samples from May 4-9, and 658 from June 1-6, 2020). Assuming that the frequency distribution of the measured SARS-CoV-2 IgG is binormal (an educated guess), using a non-linear regression, we decomposed the distribution into its two Gaussian components. Based on the obtained regression coefficients, we calculated the prevalence of SARS-CoV-2 infection, the sensitivity and specificity, and the most appropriate cut-off value for the test. The obtained results were compared with those obtained from a validity study and a seroprevalence population-based study. Results The model could predict more than 90% of the variance observed in the SARS-CoV-2 IgG distribution. The results derived from our model were in good agreement with the results obtained from the seroprevalence and validity studies. Altogether 138 of 1432 people had SARS-CoV-2 IgG ≥ 0.90, the cut-off value which maximized the Youden's index. This translates into a true prevalence of 7.0% (95% confidence interval 5.4% to 8.6%), which is in keeping with the estimated prevalence of 7.7% derived from our model. Our model can provide the true prevalence. Conclusions Having an educated guess about the distribution of test results, the test performance indices can be derived with acceptable accuracy merely based on the test results frequency distribution without the need for conducting a validity study and comparing the test results against a gold-standard test.
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Affiliation(s)
| | - Parham Habibzadeh
- Research Center for Health Sciences, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mohammad M. Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
- Global Virus Network, Baltimore, USA
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22
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Comparative Performance Evaluation of FilmArray BioFire RP2.1 and MAScIR 2.0 Assays for SARS-CoV-2 Detection. Adv Virol 2022; 2022:4510900. [PMID: 35693128 PMCID: PMC9177333 DOI: 10.1155/2022/4510900] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/11/2022] [Indexed: 12/20/2022] Open
Abstract
Background RT-PCR is the gold standard for COVID-19 diagnosis, but the lack of standardization of assays, whose diagnostic performance may widely vary, complicates the interpretation of the discrepancies that may be encountered. Study design. We conducted a retrospective study over a ten-month period at the Central Laboratory of Virology of Ibn Sina University Hospital of Rabat. We included nasopharyngeal swabs, positive and negative for SARS-CoV-2 on FilmArray BioFire® Respiratory Panel 2.1 Plus, which were subjected to our laboratory's reference test, MAScIR SARS-CoV-2 M kit 2.0, initially or after a freeze-thaw cycle. The results were compared, and each discrepant sample with sufficient volume underwent the third test, using ARGENE® SARS-CoV-2 R-GENE kit. Results Of 80 SARS-CoV-2 negative samples on FilmArray, there were no discordant results, whereas of 80 SARS-CoV-2 positive samples on FilmArray, 21 had discordant results on MAScIR, and only 11 could be tested on ARGENE, revealing positive results in 6 cases. 12.7% and 76.5% correspond to the discordance rates for MAScIR (with one or both targets detected on FilmArray), while 14.3% and 100% correspond to those of ARGENE. As the estimated sensitivity and specificity of FilmArray, compared with MAScIR, were 100% and 79.2%, respectively, its lower limit of detection, and ARGENE assay results, made it difficult to distinguish between false positives on FilmArray and false negatives on MAScIR without further investigations. Conclusion The implementation of a new assay in our laboratory revealed discrepancies suggesting a lack of sensitivity of our laboratory's reference test, leading us consequently to retain the SARS-CoV-2 positive result of these discordant samples on FilmArray, regardless of the detection of one or both targets. Our study, which is, to our knowledge, the first comparing FilmArray RP2.1 and MAScIR 2.0 assays for SARS-CoV-2 detection, highlights the urgent need to standardize RT-PCR assays for COVID-19 diagnosis.
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Silva J, Patricio F, Patricio-Martínez A, Santos-López G, Cedillo L, Tizabi Y, Limón ID. Neuropathological Aspects of SARS-CoV-2 Infection: Significance for Both Alzheimer's and Parkinson's Disease. Front Neurosci 2022; 16:867825. [PMID: 35592266 PMCID: PMC9111171 DOI: 10.3389/fnins.2022.867825] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/14/2022] [Indexed: 01/08/2023] Open
Abstract
Evidence suggests that SARS-CoV-2 entry into the central nervous system can result in neurological and/or neurodegenerative diseases. In this review, routes of SARS-Cov-2 entry into the brain via neuroinvasive pathways such as transcribrial, ocular surface or hematogenous system are discussed. It is argued that SARS-Cov-2-induced cytokine storm, neuroinflammation and oxidative stress increase the risk of developing neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. Further studies on the effects of SARS-CoV-2 and its variants on protein aggregation, glia or microglia activation, and blood-brain barrier are warranted.
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Affiliation(s)
- Jaime Silva
- Laboratorio de Neurofarmacología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Felipe Patricio
- Laboratorio de Neurofarmacología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Aleidy Patricio-Martínez
- Laboratorio de Neurofarmacología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Gerardo Santos-López
- Laboratorio de Biología Molecular y Virología, Centro de Investigación Biomédica de Oriente, Instituto Mexicano del Seguro Social, Atlixco, Mexico
| | - Lilia Cedillo
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Yousef Tizabi
- Department of Pharmacology, Howard University College of Medicine, Washington, DC, United States
| | - Ilhuicamina Daniel Limón
- Laboratorio de Neurofarmacología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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Arshadi M, Fardsanei F, Deihim B, Farshadzadeh Z, Nikkhahi F, Khalili F, Sotgiu G, Shahidi Bonjar AH, Centis R, Migliori GB, Nasiri MJ, Mirsaeidi M. Diagnostic Accuracy of Rapid Antigen Tests for COVID-19 Detection: A Systematic Review With Meta-analysis. Front Med (Lausanne) 2022; 9:870738. [PMID: 35463027 PMCID: PMC9021531 DOI: 10.3389/fmed.2022.870738] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Reverse transcription-polymerase chain reaction (RT-PCR) to detect SARS-CoV-2 is time-consuming and sometimes not feasible in developing nations. Rapid antigen test (RAT) could decrease the load of diagnosis. However, the efficacy of RAT is yet to be investigated comprehensively. Thus, the current systematic review and meta-analysis were conducted to evaluate the diagnostic accuracy of RAT against RT-PCR methods as the reference standard. Methods We searched the MEDLINE/Pubmed and Embase databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures [i.e., sensitivity, specificity, diagnostic odds ratio (DOR), positive likelihood ratios (PLR), negative likelihood ratios (NLR), and the area under the curve (AUC)] were pooled with a random-effects model. All statistical analyses were performed with Meta-DiSc (Version 1.4, Cochrane Colloquium, Barcelona, Spain). Results After reviewing retrieved records, we identified 60 studies that met the inclusion criteria. The pooled sensitivity and specificity of the rapid antigen tests against the reference test (the real-time PCR) were 69% (95% CI: 68–70) and 99% (95% CI: 99–99). The PLR, NLR, DOR and the AUC estimates were found to be 72 (95% CI: 44–119), 0.30 (95% CI: 0.26–0.36), 316 (95% CI: 167–590) and 97%, respectively. Conclusion The present study indicated that using RAT kits is primarily recommended for the early detection of patients suspected of having COVID-19, particularly in countries with limited resources and laboratory equipment. However, the negative RAT samples may need to be confirmed using molecular tests, mainly when the symptoms of COVID-19 are present.
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Affiliation(s)
- Maniya Arshadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Fardsanei
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Behnaz Deihim
- Department of Bacteriology and Virology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Zahra Farshadzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farhad Nikkhahi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farima Khalili
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Amir Hashem Shahidi Bonjar
- Clinician Scientist of Dental Materials and Restorative Dentistry, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rosella Centis
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Battista Migliori
- Clinical Epidemiology and Medical Statistics Unit, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, College of Medicine-Jacksonville, University of Florida, Gainesville, FL, United States
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Angulo J, Martinez-Valdebenito C, Pardo-Roa C, Almonacid LI, Fuentes-Luppichini E, Contreras AM, Maldonado C, Le Corre N, Melo F, Medina RA, Ferrés M. Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021. Front Med (Lausanne) 2022; 9:841073. [PMID: 35280916 PMCID: PMC8914012 DOI: 10.3389/fmed.2022.841073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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Affiliation(s)
- Jenniffer Angulo
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Constanza Martinez-Valdebenito
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Catalina Pardo-Roa
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo I. Almonacid
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Ana Maria Contreras
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Constanza Maldonado
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Nicole Le Corre
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
| | - Francisco Melo
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael A. Medina
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Interdisciplinary Rehabilitation Register – COVID-19 Working Group, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marcela Ferrés
- Departamento de Enfermedades Infeciosas e Inmmunologia Pediatricas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Infectious Disease and Molecular Virology Laboratory, Red Salud UC-Christus, Santiago, Chile
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Lasserre P, Balansethupathy B, Vezza VJ, Butterworth A, Macdonald A, Blair EO, McAteer L, Hannah S, Ward AC, Hoskisson PA, Longmuir A, Setford S, Farmer ECW, Murphy ME, Flynn H, Corrigan DK. SARS-CoV-2 Aptasensors Based on Electrochemical Impedance Spectroscopy and Low-Cost Gold Electrode Substrates. Anal Chem 2022; 94:2126-2133. [PMID: 35043638 PMCID: PMC8790822 DOI: 10.1021/acs.analchem.1c04456] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/24/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 diagnostic practices broadly involve either quantitative polymerase chain reaction (qPCR)-based nucleic amplification of viral sequences or antigen-based tests such as lateral flow assays (LFAs). Reverse transcriptase-qPCR can detect viral RNA and is the gold standard for sensitivity. However, the technique is time-consuming and requires expensive laboratory infrastructure and trained staff. LFAs are lower in cost and near real time, and because they are antigen-based, they have the potential to provide a more accurate indication of a disease state. However, LFAs are reported to have low real-world sensitivity and in most cases are only qualitative. Here, an antigen-based electrochemical aptamer sensor is presented, which has the potential to address some of these shortfalls. An aptamer, raised to the SARS-CoV-2 spike protein, was immobilized on a low-cost gold-coated polyester substrate adapted from the blood glucose testing industry. Clinically relevant detection levels for SARS-CoV-2 are achieved in a simple, label-free measurement format using sample incubation times as short as 15 min on nasopharyngeal swab samples. This assay can readily be optimized for mass manufacture and is compatible with a low-cost meter.
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Affiliation(s)
- Perrine Lasserre
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | | | - Vincent J. Vezza
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Adrian Butterworth
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Alexander Macdonald
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Ewen O. Blair
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Liam McAteer
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Stuart Hannah
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
| | - Andrew C. Ward
- Department
of Civil and Environmental Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, U.K.
| | - Paul A. Hoskisson
- Strathclyde
Institute of Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, U.K.
| | - Alistair Longmuir
- LifeScan
Scotland Ltd, Beechwood Park North, Inverness IV2 3ED, U.K.
| | - Steven Setford
- LifeScan
Scotland Ltd, Beechwood Park North, Inverness IV2 3ED, U.K.
| | - Eoghan C. W. Farmer
- NHS GGC,
Department of Microbiology, Glasgow Royal
Infirmary, NEW Lister Building, Glasgow G31 2ER, United Kingdom
| | - Michael E. Murphy
- NHS GGC,
Department of Microbiology, Glasgow Royal
Infirmary, NEW Lister Building, Glasgow G31 2ER, United Kingdom
- School
of Medicine, Dentistry & Nursing, College of Medical Veterinary
& Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Harriet Flynn
- Aptamer
Group, Suite 2.78−2.91,
Bio Centre, Innovation Way, Heslington, York YO10 5NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, United Kingdom
| | - Damion K. Corrigan
- Department
of Biomedical Engineering, University of
Strathclyde, 106 Rottenrow East, Glasgow G4 0NW, U.K.
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27
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Ju Y, Kim J, Park Y, Lee CY, Kim K, Hong KH, Lee H, Yong D, Park HG. Rapid and accurate clinical testing for COVID-19 by nicking and extension chain reaction system-based amplification (NESBA). Biosens Bioelectron 2022; 196:113689. [PMID: 34688112 PMCID: PMC8526110 DOI: 10.1016/j.bios.2021.113689] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 12/26/2022]
Abstract
We herein describe rapid and accurate clinical testing for COVID-19 by nicking and extension chain reaction system-based amplification (NESBA), an ultrasensitive version of NASBA. The primers to identify SARS-CoV-2 viral RNA were designed to additionally contain the nicking recognition sequence at the 5′-end of conventional NASBA primers, which would enable nicking enzyme-aided exponential amplification of T7 RNA promoter-containing double-stranded DNA (T7DNA). As a consequence of this substantially enhanced amplification power, the NESBA technique was able to ultrasensitively detect SARS-CoV-2 genomic RNA (gRNA) down to 0.5 copies/μL (= 10 copies/reaction) for both envelope (E) and nucleocapsid (N) genes within 30 min under isothermal temperature (41 °C). When the NESBA was applied to test a large cohort of clinical samples (n = 98), the results fully agreed with those from qRT-PCR and showed the excellent accuracy by yielding 100% clinical sensitivity and specificity. By employing multiple molecular beacons with different fluorophore labels, the NESBA was further modulated to achieve multiplex molecular diagnostics, so that the E and N genes of SARS-CoV-2 gRNA were simultaneously assayed in one-pot. By offering the superior analytical performances over the current qRT-PCR, the isothermal NESBA technique could serve as very powerful platform technology to realize the point-of-care (POC) diagnosis for COVID-19.
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Affiliation(s)
- Yong Ju
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jaemin Kim
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yeonkyung Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kyungnam Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Chukwudi CU. Consolidating and Upscaling Molecular Research Capacity in Nigeria: On Who's Account? Front Res Metr Anal 2022; 6:788673. [PMID: 35071971 PMCID: PMC8766846 DOI: 10.3389/frma.2021.788673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022] Open
Abstract
Molecular research and researchers engage in studies that seek to understand the structures, functions, and interactions of biomolecules as the basis for cellular and systemic effects in living organisms. This research approach was made possible by considerable technological advancements that equip researchers with tools to view biomolecules. Although molecular research holds great promises for improving lives and living, the technological requirements and equipment to undertake molecular research are quite expensive, often requiring a heavy start-up capital or investment. In developing countries such as Nigeria, where the majority of the population lives below the poverty line and research funding is abysmally low, such heavy investments into research that do not provide immediate solutions to societal problems are difficult. This is mostly due to limited resources available to tackle many urgent and pressing needs, and limited perspective and understanding of policymakers, leading to infrastructural and skilled personnel deficit to support molecular research. Despite all these, the field of molecular research continues to grow exponentially globally, hence, funding and investments into this critical life science research area have become imperative. With the rich biodiversity of humans, animals, and plants in Nigeria, and the huge burden of infectious diseases in the country or region, global advances in genomics and proteomics studies will be incomplete without adequate contribution from Nigeria and sub-Saharan Africa region. This paper examines the progression and challenges of undertaking molecular research in Nigeria, and how Nigerian molecular research scientists are tackling these issues, with recommendations for improved molecular research capacity and output in the country or region.
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29
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Jia Y, Sun H, Tian J, Song Q, Zhang W. Paper-Based Point-of-Care Testing of SARS-CoV-2. Front Bioeng Biotechnol 2021; 9:773304. [PMID: 34912791 PMCID: PMC8667078 DOI: 10.3389/fbioe.2021.773304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic has resulted in significant global social and economic disruption. The highly transmissive nature of the disease makes rapid and reliable detection critically important. Point-of-care (POC) tests involve performing diagnostic tests outside of a laboratory that produce a rapid and reliable result. It therefore allows the diagnostics of diseases at or near the patient site. Paper-based POC tests have been gaining interest in recent years as they allow rapid, low-cost detection without the need for external instruments. In this review, we focus on the development of paper-based POC devices for the detection of SARS-CoV-2. The review first introduces the principles of detection methods that are available to paper-based devices. It then summarizes the state-of-the-art paper devices and their analytical performances. The advantages and drawbacks among methods are also discussed. Finally, limitations of the existing devices are discussed, and prospects are given with the hope to identify research opportunities and directions in the field. We hope this review will be helpful for researchers to develop a clinically useful and economically efficient paper-based platform that can be used for rapid, accurate on-site diagnosis to aid in identifying acute infections and eventually contain the COVID-19 pandemic.
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Affiliation(s)
- Yuan Jia
- College of New Materials and New Energies, Shenzhen Technology University, Shenzhen, China
| | - Hao Sun
- School of Mechanical Engineering and Automation, Fuzhou University, Fuzhou, China
| | - Jinpeng Tian
- College of New Materials and New Energies, Shenzhen Technology University, Shenzhen, China
| | - Qiuming Song
- College of New Materials and New Energies, Shenzhen Technology University, Shenzhen, China
| | - Wenwei Zhang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, China
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Habibzadeh P, Dastsooz H, Eshraghi M, Łos MJ, Klionsky DJ, Ghavami S. Autophagy: The Potential Link between SARS-CoV-2 and Cancer. Cancers (Basel) 2021; 13:cancers13225721. [PMID: 34830876 PMCID: PMC8616402 DOI: 10.3390/cancers13225721] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/11/2021] [Accepted: 11/14/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Coronavirus disease 2019 (COVID-19) has led to a global crisis. With the increasing number of individuals infected worldwide, the long-term consequences of this disease have become an active area of research. The constellation of symptoms COVID-19 survivors suffer from is commonly referred to as post-acute COVID-19 syndrome in the scientific literature. In this paper, we discuss the potential long-term complications of this infection resulting from the persistence of the viral particles in body tissues interacting with host cells’ autophagy machinery in the context of the development of cancer, cancer progression and metastasis, as well as response to treatment. We also propose a structured framework for future studies to investigate the potential impact of COVID-19 infection on cancer. Abstract COVID-19 infection survivors suffer from a constellation of symptoms referred to as post-acute COVID-19 syndrome. However, in the wake of recent evidence highlighting the long-term persistence of SARS-CoV-2 antigens in tissues and emerging information regarding the interaction between SARS-CoV-2 proteins and various components of the host cell macroautophagy/autophagy machinery, the unforeseen long-term consequences of this infection, such as increased risk of malignancies, should be explored. Although SARS-CoV-2 is not considered an oncogenic virus, the possibility of increased risk of cancer among COVID-19 survivors cannot be ruled out. Herein, we provide an overview of the possible mechanisms leading to cancer development, particularly obesity-related cancers (e.g., colorectal cancer), resulting from defects in autophagy and the blockade of the autophagic flux, and also immune escape in COVID-19 survivors. We also highlight the potential long-term implications of COVID-19 infection in the prognosis of patients with cancer and their response to different cancer treatments. Finally, we consider future directions for further investigations on this matter.
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Affiliation(s)
- Parham Habibzadeh
- Research Center for Health Sciences, Institute of Health, Shiraz University of Medical Sciences, Shiraz 71348-14336, Iran;
| | - Hassan Dastsooz
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia, Albertina, 13, 10123 Torino, Italy;
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, 10126 Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Torino, Italy
| | - Mehdi Eshraghi
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Marek J. Łos
- Biotechnology Center, Silesian University of Technology, 44-100 Gliwice, Poland
- Correspondence: (M.J.Ł.); (S.G.)
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Faculty of Medicine, Katowice School of Technology, ul. Rolna 43, 40-555 Katowice, Poland
- Correspondence: (M.J.Ł.); (S.G.)
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31
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Butt RT, Janjua OS, Qureshi SM, Shaikh MS, Guerrero-Gironés J, Rodríguez-Lozano FJ, Zafar MS. Dental Healthcare Amid the COVID-19 Pandemic. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11008. [PMID: 34769526 PMCID: PMC8583530 DOI: 10.3390/ijerph182111008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023]
Abstract
The hustle and bustle of the planet Earth have come to a halt thanks to the novel coronavirus. The virus has affected approximately 219 million people globally; taken the lives of 4.55 million patients as of September 2021; and created an ambiance of fear, social distancing, and economic instability. The purpose of this review article is to trace the historical origin and evolution of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). The virus is highly contagious with a unique feature of rapid mutations-the scientific research is paving the way for discoveries regarding novel coronavirus disease (COVID-19) diagnosis, features, prevention, and vaccination. The connections between the coronavirus pandemic and dental practices are essential because COVID-19 is transmitted by aerosols, fomites, and respiratory droplets, which are also produced during dental procedures, putting both the patient and the dentist at risk. The main emphasis of this paper is to highlight the psychological, economic, and social impact of this pandemic on dental practices throughout the world and under what circumstances and guidelines can dental health care be provided. In the current situation of the pandemic, an appropriate screening tool must be established either by using rapid molecular testing or saliva point-of-care technology, which will be effective in identifying as well as isolating the potential contacts and carriers in hopes to contain and mitigate infection. The blessing in disguise is that this virus has united the leaders, scientists, health care providers, and people of all professions from all around the world to fight against a common enemy.
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Affiliation(s)
- Rabia Tariq Butt
- General Dental Practitioner, Al-Noor Clinics, Okara 56000, Pakistan;
| | - Omer Sefvan Janjua
- Department of Maxillofacial Surgery, PMC Dental Institute, Faisalabad Medical University, Faisalabad 38000, Pakistan;
| | - Sana Mehmood Qureshi
- Department of Oral Pathology, PMC Dental Institute, Faisalabad Medical University, Faisalabad 38000, Pakistan;
| | - Muhammad Saad Shaikh
- Department of Oral Biology, Sindh Institute of Oral Health Sciences, Jinnah Sindh Medical University, Karachi 75510, Pakistan;
| | - Julia Guerrero-Gironés
- Gerodontology and Special Care Dentistry Unit, Hospital Morales Meseguer, Medicine School, University of Murcia, 30100 Murcia, Spain;
| | - Francisco J. Rodríguez-Lozano
- Gerodontology and Special Care Dentistry Unit, Hospital Morales Meseguer, Medicine School, University of Murcia, 30100 Murcia, Spain;
- Cellular Therapy and Hematopoietic Transplant Research Group, Biomedical Research Institute of Murcia, Clinical University Hospital Virgen de laArrixaca, University of Murcia, 30120 Murcia, Spain
| | - Muhammad Sohail Zafar
- Department of Restorative Dentistry, College of Dentistry, Taibah University, Al Madinah, Al Munawwarah 41311, Saudi Arabia; or
- Department of Dental Materials, Islamic International Dental College, Riphah International University, Islamabad 44000, Pakistan
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32
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Mushtaq MZ, Shakoor S, Kanji A, Shaheen N, Nasir A, Ansar Z, Ahmed I, Mahmood SF, Hasan R, Hasan Z. Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays. BMC Res Notes 2021; 14:316. [PMID: 34404471 PMCID: PMC8369441 DOI: 10.1186/s13104-021-05722-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays. RESULTS Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche® assay. Further investigation using the BIOFIRE® Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was conducted using the TaqPath™ COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, variation at primer binding sites. Strains with SGTF indicate the presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control.
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Affiliation(s)
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.,Department of Pediatrics and Child Health, Division of Women and Child Health, Aga Khan University, Karachi, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Najma Shaheen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Asghar Nasir
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Imran Ahmed
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | | | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan.
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33
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SARS-COV2 Statistical Analysis–Constanta Family Medicine Cabinet in the Period 2020–2022. ARS MEDICA TOMITANA 2021. [DOI: 10.2478/arsm-2021-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Abstract
SARS-COV2 translates as a highlycontagious viral strain, being part of thegenusBetacoronavirus, the Sarbecovirus subgroup, consisting of a single molecule of single-stranded RNA, withpositivepolarityandhavingdimensions of 27-32 kb.
The timefromthetransposition of infectiontotheonset of symptomatology in order of frequency:cough,dysphagia, fever,breathlessness, anosmia, ageusia, headacheandfatiguabilityisbetween2-12days, with an average of 6days.
The purpose of thisstudyisthestatisticalanalysis of thecases of SARS-COV2 infectionassociatedwith medical assistance in a family medicine office in Constanta in the period 2020-2022.
The author notes thediscrepancybetweenthephases of exponentialgrowth, plateauandlatency, thankstothedemanding monitoring of theprovisions of Law no. 55/15 May 2020, whichregulatestheactivity of preventingandcombatingtheeffects of the COVID-19 pandemic.
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34
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Gitman MR, Shaban MV, Paniz-Mondolfi AE, Sordillo EM. Laboratory Diagnosis of SARS-CoV-2 Pneumonia. Diagnostics (Basel) 2021; 11:diagnostics11071270. [PMID: 34359353 PMCID: PMC8306256 DOI: 10.3390/diagnostics11071270] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/13/2021] [Indexed: 02/08/2023] Open
Abstract
The emergence and rapid proliferation of Coronavirus Disease-2019, throughout the past year, has put an unprecedented strain on the global schema of health infrastructure and health economy. The time-sensitive agenda of identifying the virus in humans and delivering a vaccine to the public constituted an effort to flatten the statistical curve of viral spread as it grew exponentially. At the forefront of this effort was an exigency of developing rapid and accurate diagnostic strategies. These have emerged in various forms over the past year—each with strengths and weaknesses. To date, they fall into three categories: (1) those isolating and replicating viral RNA in patient samples from the respiratory tract (Nucleic Acid Amplification Tests; NAATs), (2) those detecting the presence of viral proteins (Rapid Antigen Tests; RATs) and serology-based exams identifying antibodies to the virus in whole blood and serum. The latter vary in their detection of immunoglobulins of known prevalence in early-stage and late-stage infection. With this review, we delineate the categories of testing measures developed to date, analyze the efficacy of collecting patient specimens from diverse regions of the respiratory tract, and present the up and coming technologies which have made pathogen identification easier and more accessible to the public.
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Affiliation(s)
- Melissa R. Gitman
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.E.P.-M.); (E.M.S.)
- Correspondence: ; Tel.: +1-212-659-8173
| | - Maryia V. Shaban
- Emerging Pathogens and Zoonoses Network, Incubadora Venezolana de la Ciencia, Cabudare 3023, Venezuela;
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.E.P.-M.); (E.M.S.)
| | - Emilia M. Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (A.E.P.-M.); (E.M.S.)
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Ameratunga R, Woon ST, Jordan A, Longhurst H, Leung E, Steele R, Lehnert K, Snell R, Brooks AES. Perspective: diagnostic laboratories should urgently develop T cell assays for SARS-CoV-2 infection. Expert Rev Clin Immunol 2021; 17:421-430. [PMID: 33745411 DOI: 10.1080/1744666x.2021.1905525] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Diagnostic tests play a critical role in the management of Sars-CoV-2, the virus responsible for COVID-19. There are two groups of tests, which are in widespread use to identify patients who have contracted the virus. The commonly used reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) test becomes negative once viral shedding ceases by approximately 2-3weeks. Antibody tests directed to viral antigens become positive after the second week of infection. IgG antibody responses to the virus are muted in children, pregnant females, and those with mild symptoms. IgA and IgM antibodies rapidly wane, although IgG antibodies directed to the receptor-binding domain (RBD) of the spike (S) glycoprotein are more durable. Current data show variability in the sensitivity of commercial and in-house antibody tests to SARS-CoV-2.Areas covered: The role of T cells in acute illness is uncertain, but long-term protection against the virus may rely on memory T cell responses. Measuring memory T cell responses is important for retrospective confirmation of cases, who may have been infected early in the pandemic before reliable RT-qPCR tests were available and whose SARS-CoV-2 antibodies may have become undetectable. Relevant peer-reviewed published references from PubMed are included up to 15 March 2021.Expert opinion: After surveying the literature, the authors present the case for urgent development of diagnostic T cell assays for SARS-CoV-2 by accredited laboratories.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical Immunology, Auckland Hospital, Grafton Auckland, New Zealand.,Department of Virology and Immunology, Auckland Hospital, Grafton, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Grafton, Auckland, New Zealand
| | - Anthony Jordan
- Department of Clinical Immunology, Auckland Hospital, Grafton Auckland, New Zealand
| | - Hilary Longhurst
- Department of Clinical Immunology, Auckland Hospital, Grafton Auckland, New Zealand.,Department of Medicine, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zeland
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, Auckland Hospital, Grafton, Auckland, New Zealand.,Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences and Center for Brain Research, University of Auckland, Symonds St, Auckland, New Zealand
| | - Russell Snell
- School of Biological Sciences and Center for Brain Research, University of Auckland, Symonds St, Auckland, New Zealand
| | - Anna E S Brooks
- School of Biological Sciences and Center for Brain Research, University of Auckland, Symonds St, Auckland, New Zealand.,Maurice Wilkins Centre, University of Auckland, New Zealand
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