1
|
Sugishita Y, Moriuchi R, Ishii Y. External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021. J Infect Chemother 2024; 30:633-641. [PMID: 38325625 DOI: 10.1016/j.jiac.2024.01.016] [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: 11/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
INTRODUCTION Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests. METHODS In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/μL, positive sample B with 5 copies/μL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/μL was prepared using a simulated saliva sample. RESULTS Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory. CONCLUSIONS The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results.
Collapse
Affiliation(s)
- Yoshiyuki Sugishita
- Quality Control Section, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan.
| | - Rie Moriuchi
- Quality Control Section, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan.
| |
Collapse
|
2
|
Aboagye FT, Annison L, Hackman HK, Acquah ME, Ashong Y, Owusu-Frimpong I, Egyam BC, Annison S, Osei-Adjei G, Antwi-Baffour S. Comparative evaluation of RT-PCR and antigen-based rapid diagnostic tests (Ag-RDTs) for SARS-CoV-2 detection: performance, variant specificity, and clinical implications. Microbiol Spectr 2024; 12:e0007324. [PMID: 38683014 DOI: 10.1128/spectrum.00073-24] [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: 01/20/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The COVID-19 pandemic has highlighted the critical need for accurate and efficient diagnostic tools for detecting severe acute respiratory coronavirus 2 (SARS-CoV-2) infections. This study presents a comparison of two diagnostic tests: RT-PCR and antigen detection rapid diagnostic tests (Ag-RDTs). This study focused on their performance, variant specificity, and their clinical implications. A simultaneous testing of 268 samples was carried out for SARS-CoV-2 using RT-PCR and Ag-RDTs [flourescence immunoassay (FIA) and lateral flow immunoassay (LFIA)]. Viral load was quantified, and variant identification was performed using a PCR-based assay. The prevalence was found to be 30.2% using reverse transcription PCR (RT-PCR), 26.5% using FIA, and 25% using LFIA. When comparing the FIA and LFIA, the overall diagnostic performance was found to be 80.25% vs 76.54%, 96.79% vs 97.33%, 91.55% vs 90.51%, and 91.88% vs 92.56% for sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), respectively. Both Ag-RDTs showed a strong agreement with RT-PCR (κ = 0.78-0.80). The overall accuracies of the FIA and LFIA were 92.41% and 92.13%, respectively. The FIA showed higher sensitivity (73.68%) and PPV (92.08%) than the LFIA (65.79% and 90.56%, respectively) in asymptomatic patients. At low Ct values (<25), both Ag-RDTs had 100% sensitivity, but the sensitivity reduced to 31.82% for FIA and 27.27% for LFIA at Ct values > 30. The diagnostic sensitivity of FIA compared to LFIA for detecting the Alpha variant was 78.85% vs. 69.23% and 72.22% vs. 83.33% for the Delta variant. Both Ag-RDTs had 100% sensitivity for detecting Omicron. Both Ag-RDTs performed well in patients with high viral loads and Omicron variant infections compared to those infected with Alpha and Delta variants. This study confirms the comparable performance of RT-PCR and Ag-RDTs, specifically FIA and LFIA, for SARS-CoV-2 detection. The FIA showed higher sensitivity and PPV in asymptomatic cases, while both Ag-RDTs exhibited strong agreement with RT-PCR results. Notably, Ag-RDTs, particularly FIA, proved effective in detecting the Omicron variant and cases with high viral loads, highlighting their potential clinical utility in managing the COVID-19 pandemic.IMPORTANCEThis study is of utmost importance in providing effective responses to manage the COVID-19 pandemic. It rigorously compares the diagnostic accuracy, variant specificity, and practical considerations of reverse transcription PCR (RT-PCR) and antigen detection rapid diagnostic tests (Ag-RDTs) for severe acute respiratory coronavirus 2 (SARS-CoV-2), answering critical questions. The results of this study will help healthcare professionals choose the appropriate testing methods, allocate resources effectively, and enhance public health strategies. Given the evolution of the virus, understanding the performance of these diagnostic tools is crucial to adapting to emerging variants. Additionally, the study provides insights into logistical challenges and accessibility issues, which will contribute to refining testing workflows, particularly in resource-limited settings. Ultimately, the study's impact extends to global healthcare, providing valuable information for policymakers, clinicians, and public health officials as they work together for mitigating the impact of the pandemic.
Collapse
Affiliation(s)
- Frank T Aboagye
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research - Water Research Institute, Accra, Ghana
| | - Lawrence Annison
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Henry Kwadwo Hackman
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Maame E Acquah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Yvonne Ashong
- Department of Parasitology, Noguchi Memorial Institute of Medical Research, College of Medical Sciences, University of Ghana, Accra, Ghana
| | - Isaac Owusu-Frimpong
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research - Water Research Institute, Accra, Ghana
| | - Bill C Egyam
- Department of Molecular Biology, MDS Lancet Laboratories Ghana Limited, Accra, Ghana
| | - Sharon Annison
- Department of Epidemiology and Disease Control, School of Public Health, University of Ghana, Accra, Ghana
| | - George Osei-Adjei
- Department of Medical Laboratory Technology, Faculty of Applied Sciences, Accra Technical University, Accra, Ghana
| | - Samuel Antwi-Baffour
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Accra, Ghana
| |
Collapse
|
3
|
Purcell‐Wiltz A, Zamuner FT, Caraballo K, De Jesus L, Miranda Y, Ortiz D, Negrón AG, Ortiz AC, Baez A, Romaguera J, Jiménez I, Ortiz A, Acevedo J, Viera L, Sidransky D, Guerrero‐Preston R. Evaluation of self-collected nasal, urine, and saliva samples for molecular detection of SARS-CoV-2 using an EUA approved RT-PCR assay and a laboratory developed LAMP SARS-CoV-2 test. Immun Inflamm Dis 2024; 12:e1285. [PMID: 38888444 PMCID: PMC11184932 DOI: 10.1002/iid3.1285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 04/23/2024] [Accepted: 05/12/2024] [Indexed: 06/20/2024] Open
Abstract
As the SARS-CoV-2 virus spread throughout the world, millions of positive cases of COVID-19 were registered and, even though there are millions of people already vaccinated against SARS-CoV-2, a large part of the global population remains vulnerable to contracting the virus. Massive nasopharyngeal sample collection in Puerto Rico at the beginning of the pandemic was limited by the scarcity of trained personnel and testing sites. To increase SARS-CoV-2 molecular testing availability, we evaluated the diagnostic accuracy of self-collected nasal, saliva, and urine samples using the TaqPath reverse transcription polymerase chain reaction (RT-PCR) COVID-19 kit to detect SARS-CoV-2. We also created a colorimetric loop-mediated isothermal amplification (LAMP) laboratory developed test (LDT) to detect SARS-CoV-2, as another strategy to increase the availability of molecular testing in community-based laboratories. Automated RNA extraction was performed in the KingFisher Flex instrument, followed by PCR quantification of SARS-CoV-2 on the 7500 Fast Dx RT-PCR using the TaqPath RT-PCR COVID-19 molecular test. Data was interpreted by the COVID-19 Interpretive Software from Applied Biosystems and statistically analyzed with Cohen's kappa coefficient (k). Cohen's kappa coefficient (k) for paired nasal and saliva samples showed moderate agreement (0.52). Saliva samples exhibited a higher viral load. We also observed 90% concordance between LifeGene-Biomarks' SARS-CoV-2 Rapid Colorimetric LAMP LDT and the TaqPath RT-PCR COVID-19 test. Our results suggest that self-collected saliva is superior to nasal and urine samples for COVID-19 testing. The results also suggest that the colorimetric LAMP LDT is a rapid alternative to RT-PCR tests for the detection of SARS-CoV-2. This test can be easily implemented in clinics, hospitals, the workplace, and at home; optimizing the surveillance and collection process, which helps mitigate global public health and socioeconomic upheaval caused by airborne pandemics.
Collapse
Affiliation(s)
- Ana Purcell‐Wiltz
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
- Internal Medicine DepartmentSan Juan Bautista School of MedicineCaguasPuerto Rico
| | - Fernando Tadeu Zamuner
- Otolaryngology Department, Head and Neck Cancer Research DivisionJohns Hopkins University, School of MedicineBaltimoreMarylandUSA
| | - Karem Caraballo
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Lorena De Jesus
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Yaima Miranda
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Denise Ortiz
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Amanda García Negrón
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
| | - Andrea Cortés Ortiz
- Biomarker Discovery and Validation Laboratory, LifeGene‐BiomarksToa BajaPuerto Rico
- Internal Medicine DepartmentSan Juan Bautista School of MedicineCaguasPuerto Rico
| | - Adriana Baez
- Otolaryngology DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Josefina Romaguera
- Obstetrics and Gynecology DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Ivonne Jiménez
- Internal Medicine DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Alberto Ortiz
- Internal Medicine DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Jorge Acevedo
- Internal Medicine DepartmentUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - Liliana Viera
- Department of SurgeryUniversity of Puerto Rico School of MedicineSan JuanPuerto Rico
| | - David Sidransky
- Otolaryngology Department, Head and Neck Cancer Research DivisionJohns Hopkins University, School of MedicineBaltimoreMarylandUSA
| | | |
Collapse
|
4
|
Bang LL, Tornby DR, Pham STD, Assing K, Möller S, Palarasah Y, Madsen LW, Thomsen KG, Johansen IS, Pedersen RM, Andersen TE. Culturing of SARS-CoV-2 from patient samples: Protocol for optimal virus recovery and assessment of infectious viral load. J Virol Methods 2024; 326:114912. [PMID: 38447645 DOI: 10.1016/j.jviromet.2024.114912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/16/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Optimal sampling, preservation, and culturing of SARS-CoV-2 from COVID-19 patients are critical for successful recovery of virus isolates and to accurately estimate contagiousness of the patient. In this study, we investigated the influence of the type of sampling media, storage time, freezing conditions, sterile filtration, and combinations of these to determine the optimal pre-analytic conditions for virus recovery and estimation of infectious viral load in COVID-19 patients. Further, we investigated the viral shedding kinetics and mucosal antibody response in 38 COVID-19 hospitalized patients. We found Universal Transport Medium (Copan) to be the most optimal medium for preservation of SARS-CoV-2 infectivity. Our data showed that the probability of a positive viral culture was strongly correlated to Ct values, however some samples did not follow the general trend. We found a significant correlation between plaque forming units and levels of mucosal antibodies and found that high levels of mucosal antibodies correlated with reduced chance of isolating the virus. Our data reveals essential parameters to consider from specimen collection over storage to culturing technique for optimal chance of isolating SARS-CoV-2 and accurately estimating patient contagiousness.
Collapse
Affiliation(s)
- Line L Bang
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ditte R Tornby
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Stephanie T D Pham
- Department of Cancer and Inflammation Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Kristian Assing
- Department of Clinical Immunology, Odense University Hospital and Research Unit for Clinical Immunology, University of Southern Denmark, Odense, Denmark
| | - Sören Möller
- Open Patient Data Explorative Network (OPEN), Department of Clinical Research, University of Southern Denmark and Odense University Hospital, Odense 5000, Denmark
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Lone W Madsen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark; Department of Regional Health Research, University of Southern Denmark, Denmark; Unit for Infectious Diseases, Department of medicine, Sygehus Lillebælt, Kolding, Denmark
| | - Karina G Thomsen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Isik S Johansen
- Department of Infectious Diseases, Odense University Hospital and Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark
| | - Rune M Pedersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Thomas E Andersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| |
Collapse
|
5
|
Zhang Z, Wang C, Li Z, Liu Y, Nie Y, Zhang J, Li D. Efficacy of respiratory rehabilitation in patients with COVID-19: a retrospective study. BMC Pulm Med 2024; 24:152. [PMID: 38532376 DOI: 10.1186/s12890-024-02969-z] [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: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
OBJECTIVE The coronavirus disease 2019 (COVID-19) pandemic has resulted in millions of confirmed cases and deaths globally. The purpose of this study was to investigate the therapeutic effect of airway clearance technology combined with prone ventilation on patients infected with COVID-19. METHODS 38 patients with COVID-19 (severe) who were treated in the intensive rehabilitation group of Shengli Oilfield Central Hospital. They were randomly divided into a control group and an observation group. The control group received prone position ventilation intervention, and the observation group received airway clearance technology combined with prone position ventilation intervention. The changes of oxygen and index, procalcitonin (PCT), interleukin-6 (IL-6) and chest X-ray image indexes were compared between the two groups. RESULT There was no significant difference in age, gender and other general data between the control group and the observation group. The results showed that oxygen index, PCT, IL-6 and chest X-ray image index in the observation group were better than that indexes in the control group. CONCLUSION Airway clearance technology combined with prone ventilation intervention in patients with COVID-19 can improve the total effective rate and oxygenation index, improve the inflammatory indicators and respiratory function of patients. And it may be widely promoted and used in the treatment of patients with COVID-19 (severe).
Collapse
Affiliation(s)
- Zhiyou Zhang
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China
| | - Congcong Wang
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China
| | - Zhendong Li
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China
| | - Yueyang Liu
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China
| | - Yutong Nie
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China
| | - Jianwei Zhang
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China
| | - Dawei Li
- Department of Neurorehabilitation, Shengli Oilfield Central Hospital, No. 31 Jinan Road, 257000, Dongying, Shandong, China.
| |
Collapse
|
6
|
Nie X, Wang D, Pan Y, Hua Y, Lü P, Yang Y. Discovery, classification and application of the CPISPR-Cas13 system. Technol Health Care 2024; 32:525-544. [PMID: 37545273 DOI: 10.3233/thc-230258] [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] [Indexed: 08/08/2023]
Abstract
BACKGROUND The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is an acquired immune system of bacteria and archaea. Continued research has resulted in the identification of other Cas13 proteins. OBJECTIVE This review briefly describes the discovery, classification, and application of the CRISPR-Cas13 system, including recent technological advances in addition to factors affecting system performance. METHODS Cas13-based molecular therapy of human, animal, and plant transcriptomes was discussed, including regulation of gene expression to combat pathogenic RNA viruses. In addition, the latest progress, potential shortcomings, and challenges of the CRISPR-Cas system for treatment of animal and plant diseases are reviewed. RESULTS The CRISPR-Cas system VI is characterized by two RNA-guided higher eukaryotes and prokaryotes nucleotide-binding domains. CRISPR RNA can cleave specific RNA through the interaction between the stem-loop rich chain of uracil residues and the Cas13a protein. The CRISPR-Cas13 system has been applied for gene editing in animal and plant cells, in addition to biological detection via accurate targeting of single-stranded RNA. CONCLUSION The CRISPR-Cas13 system offers a high-throughput and convenient technology for detection of viruses and potentially the development of anti-cancer drugs in the near future.
Collapse
Affiliation(s)
- Xiaojuan Nie
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Pan
- School of Experimental Animal Center, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| |
Collapse
|
7
|
Ray SK, Mukherjee S. Innovation and Patenting Activities During COVID-19 and Advancement of Biochemical and Molecular Diagnosis in the Post- COVID-19 Era. Recent Pat Biotechnol 2024; 18:210-226. [PMID: 37779409 DOI: 10.2174/0118722083262217230921042127] [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: 05/29/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 10/03/2023]
Abstract
The COVID-19 pandemic is to escalate globally and acquire new mutations quickly, so accurate diagnostic technologies play a vital role in controlling and understanding the epidemiology of the disease. A plethora of technologies acquires diagnosis of individuals and informs clinical management of COVID. Some important biochemical parameters for COVID diagnosis are the elevation of liver enzymes, creatinine, and nonspecific inflammatory markers such as C-reactive protein (CRP) and Interleukin 6 (IL-6). The main progression predictors are lymphopenia, elevated D-dimer, and hyperferritinemia, although it is also necessary to consider LDH, CPK, and troponin in the marker panel of diagnosis. Owing to the greater sensitivity and accuracy, molecular technologies such as conventional polymerase chain reaction (PCR), reverse transcription (RT)-PCR, nested PCR, loop-mediated isothermal amplification (LAMP), and xMAP technology have been extensively used for COVID diagnosis for some time now. To make so many diagnostics accessible to general people, many techniques may be exploited, including point of care (POC), also called bedside testing, which is developing as a portable promising tool in pathogen identification. Some other lateral flow assay (LFA)-centered techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor limited uniform detection assay (FELUDA), etc. have shown auspicious results in the rapid detection of pathogens. More recently, low-cost sequencing and advancements in big data management have resulted in a slow but steady rise of next-generation sequencing (NGS)-based approaches for diagnosis that have potential relevance for clinical purposes and may pave the way toward a better future. Due to the COVID-19 pandemic, various institutions provided free, specialized websites and tools to promote research and access to critically needed advanced solutions by alleviating research and analysis of data within a substantial body of scientific and patent literature regarding biochemical and molecular diagnosis published since January 2020. This circumstance is unquestionably unique and difficult for anyone using patent information to find pertinent disclosures at a specific date in a trustworthy manner.
Collapse
Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| |
Collapse
|
8
|
Yang C, Gan X, Zeng Y, Xu Z, Xu L, Hu C, Ma H, Chai B, Hu S, Chai Y. Advanced design and applications of digital microfluidics in biomedical fields: An update of recent progress. Biosens Bioelectron 2023; 242:115723. [PMID: 37832347 DOI: 10.1016/j.bios.2023.115723] [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: 07/05/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
Significant breakthroughs have been made in digital microfluidic (DMF)-based technologies over the past decades. DMF technology has attracted great interest in bioassays depending on automatic microscale liquid manipulations and complicated multi-step processing. In this review, the recent advances of DMF platforms in the biomedical field were summarized, focusing on the integrated design and applications of the DMF system. Firstly, the electrowetting-on-dielectric principle, fabrication of DMF chips, and commercialization of the DMF system were elaborated. Then, the updated droplets and magnetic beads manipulation strategies with DMF were explored. DMF-based biomedical applications were comprehensively discussed, including automated sample preparation strategies, immunoassays, molecular diagnosis, blood processing/testing, and microbe analysis. Emerging applications such as enzyme activity assessment and DNA storage were also explored. The performance of each bioassay was compared and discussed, providing insight into the novel design and applications of the DMF technology. Finally, the advantages, challenges, and future trends of DMF systems were systematically summarized, demonstrating new perspectives on the extensive applications of DMF in basic research and commercialization.
Collapse
Affiliation(s)
- Chengbin Yang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Xiangyu Gan
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Yuping Zeng
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Zhourui Xu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Longqian Xu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Chenxuan Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Hanbin Ma
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China; Guangdong ACXEL Micro & Nano Tech Co., Ltd, Foshan, China.
| | - Bao Chai
- Department of Dermatology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; Department of Dermatology, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.
| | - Siyi Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Yujuan Chai
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Gupta G, Hussain MS, Thapa R, Dahiya R, Mahapatra DK, Bhat AA, Singla N, Subramaniyan V, Rawat S, Jakhmola V, S R, Dua K. Hope on the horizon: Wharton's jelly mesenchymal stem cells in the fight against COVID-19. Regen Med 2023; 18:675-678. [PMID: 37554111 PMCID: PMC10411327 DOI: 10.2217/rme-2023-0077] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/19/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
- Center for Global Health research (CGHR), Saveetha Institute of Medical & Technical Science (SIMATS), Saveetha University, Chennai, India
| | - Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, Jaipur, Rajasthan, India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Rajiv Dahiya
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, Saint Augustine, Trinidad & Tobago
| | - Debarshi Kar Mahapatra
- Department of Pharmaceutical Chemistry, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, Maharashtra, India
| | - Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Neelam Singla
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Vetriselvan Subramaniyan
- Department of Pharmacology, Jeffrey Cheah School of Medicine & Health Sciences, MONASH University, Malaysia
| | - Sushama Rawat
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, Jaipur, Rajasthan, India
| | - Vikas Jakhmola
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Roshan S
- Deccan School of Pharmacy, Hyderabad, India
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary & Integrative Medicine, University of Technology, Sydney, Ultimo-NSW 2007, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, Ultimo-NSW 2007, Australia
| |
Collapse
|
11
|
Simo FBN, Burt FJ, Makoah NA. Chikungunya Virus Diagnosis: A Review of Current Antigen Detection Methods. Trop Med Infect Dis 2023; 8:365. [PMID: 37505661 PMCID: PMC10383795 DOI: 10.3390/tropicalmed8070365] [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: 05/15/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023] Open
Abstract
Chikungunya is a mosquito-borne viral disease caused by the chikungunya virus (CHIKV). CHIKV is expanding at an alarming rate, potentially spreading and establishing endemicity in new areas where competent vectors are present. The dramatic spread of CHIKV in recent years highlights the urgent need to take precautionary measures and investigate options for control. It is crucial in developing nations where diagnostic tools are limited, and symptoms are similar to other prevalent diseases such as malaria and dengue. The most reliable method for diagnosing chikungunya virus is viral gene detection by RT-PCR. Alternative methods like detecting human antibody and viral antigen can also be used, especially in areas where resources are limited. In this review, we summarize the limited data on antigen detection immunoassays. We further explain the essential structural elements of the virus to help comprehend the scientific concepts underlying the testing methods, as well as future methods and diagnostic approaches under investigation.
Collapse
Affiliation(s)
- Fredy Brice Nemg Simo
- Division of Virology, Faculty of Health Sciences, University of The Free State, Bloemfontein 9301, Free State, South Africa
| | - Felicity Jane Burt
- Division of Virology, Faculty of Health Sciences, University of The Free State, Bloemfontein 9301, Free State, South Africa
- Division of Virology, National Health Laboratory Service, Bloemfontein 9301, Free State, South Africa
| | - Nigel Aminake Makoah
- Division of Virology, Faculty of Health Sciences, University of The Free State, Bloemfontein 9301, Free State, South Africa
| |
Collapse
|
12
|
Park YS, Choi S, Jang HJ, Yoo TH. Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules. Front Bioeng Biotechnol 2023; 11:1188313. [PMID: 37456730 PMCID: PMC10343955 DOI: 10.3389/fbioe.2023.1188313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.
Collapse
Affiliation(s)
- Ye Seop Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Sunjoo Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hee Ju Jang
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
| |
Collapse
|
13
|
Farinha I, da Cunha AT, Nogueira AR, Ribeiro A, Silva C, Rua J, Trêpa J, Mateus JE, Costa F. Factors associated with non-invasive positive pressure ventilation failure in a COVID-19 intermediate care unit. Int J Emerg Med 2023; 16:36. [PMID: 37173632 PMCID: PMC10175901 DOI: 10.1186/s12245-023-00510-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The use of non-invasive positive pressure ventilation (NIPPV) in COVID-19 patients with hypoxaemia is still under debate. The aim was to evaluate the efficacy of NIPPV (CPAP, HELMET-CPAP or NIV) in COVID-19 patients treated in the dedicated COVID-19 Intermediate Care Unit of Coimbra Hospital and University Centre, Portugal, and to assess factors associated with NIPPV failure. METHODS Patients admitted from December 1st 2020 to February 28th 2021, treated with NIPPV due to COVID-19 were included. Failure was defined as orotracheal intubation (OTI) or death during hospital stay. Factors associated with NIPPV failure were included in a univariate binary logistic regression analysis; those with a significance level of p < 0.001 entered a multivariate logistic regression model. RESULTS A total of 163 patients were included, 64.4% were males (n = 105). The median age was 66 years (IQR 56-75). NIPPV failure was observed in 66 (40.5%) patients, 26 (39.4%) were intubated and 40 (60.6%) died during their hospital stay. The highest CRP (OR 1.164; 95%CI 1.036-1.308) and morphine use (OR 24.771; 95%CI 1.809-339.241) were identified as predictors of failure after applying multivariate logistic regression. Adherence to prone positioning (OR 0.109; 95%CI 0.017-0.700) and a higher value of the lowest platelet count during hospital stay (OR 0.977; 95%CI 0.960-0.994) were associated with a favorable outcome. CONCLUSIONS NIPPV was successful in over half of patients. Highest CRP during hospital stay and morphine use were predictors of failure. Adherence to prone positioning and a higher value of the lowest platelet count during hospital stay were associated with a favourable outcome.
Collapse
Affiliation(s)
- Inês Farinha
- Pulmonology Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal.
| | - Alexandra Tenda da Cunha
- Pulmonology Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - Ana Rita Nogueira
- Intensive Care Medicine Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - André Ribeiro
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- Haematology Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - Carlos Silva
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- Internal Medicine Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - João Rua
- Intensive Care Medicine Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - João Trêpa
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- Infectious Diseases Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - José Eduardo Mateus
- Intensive Care Medicine Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| | - Filipa Costa
- Pulmonology Department, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
- COVID-19 Intermediate Care Unit, Coimbra Hospital and University Centre, Praceta Prof. Mota Pinto, 3004-561, Coimbra, Portugal
| |
Collapse
|
14
|
Zhuo J, Wang K, Shi Z, Yuan C. Immunogenic cell death-led discovery of COVID-19 biomarkers and inflammatory infiltrates. Front Microbiol 2023; 14:1191004. [PMID: 37228369 PMCID: PMC10203236 DOI: 10.3389/fmicb.2023.1191004] [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: 03/21/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
Immunogenic cell death (ICD) serves a critical role in regulating cell death adequate to activate an adaptive immune response, and it is associated with various inflammation-related diseases. However, the specific role of ICD-related genes in COVID-19 remains unclear. We acquired COVID-19-related information from the GEO database and a total of 14 ICD-related differentially expressed genes (DEGs) were identified. These ICD-related DEGs were closely associated with inflammation and immune activity. Afterward, CASP1, CD4, and EIF2AK3 among the 14 DEGs were selected as feature genes based on LASSO, Random Forest, and SVM-RFE algorithms, which had reliable diagnostic abilities. Moreover, functional enrichment analysis indicated that these feature genes may have a potential role in COVID-19 by being involved in the regulation of immune response and metabolism. Further CIBERSORT analysis demonstrated that the variations in the immune microenvironment of COVID-19 patients may be correlated with CASP1, CD4, and EIF2AK3. Additionally, 33 drugs targeting 3 feature genes had been identified, and the ceRNA network demonstrated a complicated regulative association based on these feature genes. Our work identified that CASP1, CD4, and EIF2AK3 were diagnostic genes of COVID-19 and correlated with immune activity. This study presents a reliable diagnostic signature and offers an overview to investigate the mechanism of COVID-19.
Collapse
Affiliation(s)
- Jianzhen Zhuo
- Guangdong Medical University, Dongguan, Guangdong, China
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Ke Wang
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Zijun Shi
- Reproductive Medical Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Chunlei Yuan
- Guangdong Medical University, Dongguan, Guangdong, China
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| |
Collapse
|
15
|
AlMalki FA, Albukhaty S, Alyamani AA, Khalaf MN, Thomas S. The relevant information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the five-question approach (when, where, what, why, and how) and its impact on the environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:61430-61454. [PMID: 35175517 PMCID: PMC8852932 DOI: 10.1007/s11356-022-18868-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/21/2022] [Indexed: 05/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is regarded as a threat because it spreads quickly across the world without requiring a passport or establishing an identity. This tiny virus has wreaked havoc on people's lives, killed people, and created psychological problems all over the world. The viral spike protein (S) significantly contributes to host cell entry, and mutations associated with it, particularly in the receptor-binding protein (RBD), either facilitate the escape of virus from neutralizing antibodies or enhance its transmission by increasing the affinity for cell entry receptor, angiotensin-converting enzyme 2 (ACE2). The initial variants identified in Brazil, South Africa, and the UK have spread to various countries. On the other hand, new variants are being detected in India and the USA. The viral genome and proteome were applied for molecular detection techniques, and nanotechnology particles and materials were utilized in protection and prevention strategies. Consequently, the SARS-CoV-2 pandemic has resulted in extraordinary scientific community efforts to develop detection methods, diagnosis tools, and effective antiviral drugs and vaccines, where prevailing academic, governmental, and industrial institutions and organizations continue to engage themselves in large-scale screening of existing drugs, both in vitro and in vivo. In addition, COVID-19 pointed on the possible solutions for the environmental pollution globe problem. Therefore, this review aims to address SARS-CoV-2, its transmission, where it can be found, why it is severe in some people, how it can be stopped, its diagnosis and detection techniques, and its relationship with the environment.
Collapse
Affiliation(s)
- Faizah A AlMalki
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Kingdom of Saudi Arabia.
| | - Salim Albukhaty
- Deptartment of Chemistry, College of Science, University of Misan, Maysan, 62001, Iraq
| | - Amal A Alyamani
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Kingdom of Saudi Arabia
| | - Moayad N Khalaf
- Deptartment of Chemistry, College of Science, University of Basrah, Basrah, Iraq
| | - Sabu Thomas
- Centre for Nanoscience and Nanotechnology, Mahatma Gandhi University, Kottayam, Kerala, 686 560, India
| |
Collapse
|
16
|
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: 2] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
17
|
Beyranvand S, Davoodian P, Alizade H, Gouklani H, Nejatizadeh A, Eftekhar E, Nikpoor AR. Study of frequency and inheritance model of ACE1 I/D and ACE2 rs2285666 polymorphisms in COVID-19 patients with varying severity of lung involvement and its effect on serum cytokines levels. Cell Biol Int 2023; 47:731-741. [PMID: 36511187 PMCID: PMC9877702 DOI: 10.1002/cbin.11977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/15/2022] [Accepted: 12/03/2022] [Indexed: 12/15/2022]
Abstract
The angiotensin-converting enzyme (ACE) has been shown to play a role as a receptor for the COVID-19 virus. This virus usually gets into cells and infects them by attaching to their glycoprotein receptors, which are found on the ACE2 receptor. The aim of this study was to evaluate the frequency and inheritance of ACE1 I/D and ACE2 rs2285666 polymorphisms in COVID-19 patients with varying severity of lung involvement and its effect on serum cytokines levels of interleukin (IL)-1 and IL-6 and laboratory parameters. One hundred eighty-five COVID-19 patients were grouped according to the severity of lung involvement. (I/D) polymorphism of the ACE1 gene and rs2285666 polymorphism of the ACE2 gene were determined by single specific primer-polymerase chain reaction and restriction fragment length reaction-polymerase chain reaction methods, respectively. Serum levels of IL-1 and IL-6 were also measured by the enzyme linked immunosorbent assay technique. No statistically significant association of ACE2 rs2285666 polymorphism genotypes and ACE1 I/D with the severity of lung involvement was noted. However, there was a statistically significant association between I/D ACE1 polymorphism genotypes and IL-6, white blood cells (WBC), and neutrophil-to-lymphocyte ratio (NLR) levels. Also, there was no statistically significant association between rs2285666 polymorphism genotypes and patients' blood oxygen saturation level, IL-6, IL-1β, lactate dehydrogenase activity, WBC count, and NLR. In patients with COVID-19, the rs2285666 polymorphism of the ACE2 gene and the I/D polymorphism of the ACE1 gene were not significantly associated with the severity of COVID-19 disease and serum IL-6 and IL-1 cytokine levels.
Collapse
Affiliation(s)
- Shirin Beyranvand
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Parivash Davoodian
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hesam Alizade
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Azim Nejatizadeh
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ebrahim Eftekhar
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amin Reza Nikpoor
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| |
Collapse
|
18
|
Al-Azzam N, Khassawneh B, Al-Azzam S, Karasneh RA, Aldeyab MA. Acid-base imbalance as a risk factor for mortality among COVID-19 hospitalized patients. Biosci Rep 2023; 43:232681. [PMID: 36876487 PMCID: PMC10037419 DOI: 10.1042/bsr20222362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/11/2023] [Accepted: 02/17/2023] [Indexed: 03/07/2023] Open
Abstract
Severe coronavirus disease 2019 (COVID-19) infection can lead to extensive lung infiltrate, a significant increase in the respiratory rate, and respiratory failure, which can affect the acid-base balance. No research in the Middle East has previously examined acid-base imbalance in COVID-19 patients. The present study aimed to describe the acid-base imbalance in hospitalized COVID-19 patients, determine its causes, and assess its impact on mortality in a Jordanian hospital. The study divided patients into 11 groups based on arterial blood gas data. Patients in normal group were defined as having a pH of 7.35-7.45, PaCO2 of 35-45 mmHg, and HCO3- of 21-27 mEq/L. Other patients were divided into 10 additional groups: mixed acidosis and alkalosis, respiratory and metabolic acidosis with or without compensation, and respiratory and metabolic alkalosis with or without compensation. This is the first study to categorize patients in this way. The results showed that acid-base imbalance was a significant risk factor for mortality (P<0.0001). Mixed acidosis nearly quadruples the risk of death when compared with those with normal levels (OR = 3.61, P=0.05). Furthermore, the risk of death was twice as high (OR = 2) for metabolic acidosis with respiratory compensation (P=0.002), respiratory alkalosis with metabolic compensation (P=0.002), or respiratory acidosis with no compensation (P=0.002). In conclusion, acid-base abnormalities, particularly mixed metabolic and respiratory acidosis, were associated with increased mortality in hospitalized COVID-19 patients. Clinicians should be aware of the significance of these abnormalities and address their underlying causes.
Collapse
Affiliation(s)
- Nosayba Al-Azzam
- Department of Physiology and Biochemistry, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Basheer Khassawneh
- Department of Internal Medicine, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Sayer Al-Azzam
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Reema A Karasneh
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Mamoon A Aldeyab
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, U.K
| |
Collapse
|
19
|
Dong H, Zhang K, Zhang J, Xiao Y, Zhang F, Wang M, Wang H, Zhao G, Xie S, Xie X, Hu W, Yin K, Gu L. A fast RT-qPCR system significantly shortens the time for SARS-CoV-2 nucleic acid test. Drug Discov Ther 2023; 17:37-44. [PMID: 36843076 DOI: 10.5582/ddt.2022.01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to global development. Rapid and accurate diagnosis is critical for containing the pandemic and treating patients in time. As the gold standard for SARS-CoV-2 diagnosis, the qualitative reverse transcription-PCR (RT-qPCR) test has long been criticized for its long detection time. In this study, we optimized the primers and probes targeting SARS-CoV-2 ORF1ab and N gene designed by the Chinese Center for Disease Control and Preventions (CDC) to increase their Tm values to meet the optimal elongation temperature of Taq DNA polymerase, thus greatly shortened the elongation time. The higher elongation temperature in turn narrowed the temperature range of the reaction and saved more time. In addition, by shortening the distance between the fluorophore at the 5' end and the quencher in the middle we got a probe with higher signal-to-noise ratio. Finally, by using all these measures and optimized RT-qPCR program we successfully reduced the time (nucleic acid extraction step is not included) for nucleic acid test from 74 min to 26 min.
Collapse
Affiliation(s)
- Hongjie Dong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China.,Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Kundi Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Junmei Zhang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Yumeng Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Maofeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Hongwei Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Guihua Zhao
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Shiling Xie
- Shandong Shtars Medical Technology Co. Ltd, Jinan, Shandong, China
| | - Xiaohong Xie
- Shandong Shtars Medical Technology Co. Ltd, Jinan, Shandong, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Kun Yin
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| |
Collapse
|
20
|
Forero DA, Chand V. Methods in molecular biology and genetics: looking to the future. BMC Res Notes 2023; 16:26. [PMID: 36864454 PMCID: PMC9980850 DOI: 10.1186/s13104-023-06298-y] [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: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
In recent decades, advances in methods in molecular biology and genetics have revolutionized multiple areas of the life and health sciences. However, there remains a global need for the development of more refined and effective methods across these fields of research. In this current Collection, we aim to showcase articles presenting novel molecular biology and genetics techniques developed by scientists from around the world.
Collapse
Affiliation(s)
- Diego A. Forero
- grid.442076.30000 0000 9574 5136School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Vaibhav Chand
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, USA.
| |
Collapse
|
21
|
Mouliou DS. The Deceptive COVID-19: Lessons from Common Molecular Diagnostics and a Novel Plan for the Prevention of the Next Pandemic. Diseases 2023; 11:diseases11010020. [PMID: 36810534 PMCID: PMC9944891 DOI: 10.3390/diseases11010020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
The COVID-19 pandemic took place during the years 2020-2022 and the virus, named SARS-CoV-2, seems likely to have resulted in an endemic disease. Nevertheless, widespread COVID-19 has given rise to several major molecular diagnostics' facts and concerns that have emerged during the overall management of this disease and the subsequent pandemic. These concerns and lessons are undeniably critical for the prevention and control of future infectious agents. Furthermore, most populaces were introduced to several new public health maintenance strategies, and again, some critical events arose. The purpose of this perspective is to thoroughly analyze all these issues and the concerns, such as the molecular diagnostics' terminologies, their role, as well as the quantity and quality issues with a molecular diagnostics' test result. Furthermore, it is speculated that society will be more vulnerable in the future and prone to emerging infectious diseases; thus, a novel preventive medicine's plan for the prevention and control of future (re)emerging infectious diseases is presented, so as to aid the early prevention of future epidemics and pandemics.
Collapse
|
22
|
Prerana S, Ashwini P, Anupama KP, Prajna VS, Prithvisagar KS, Nayak A, Rai P, Rohit A, Karunasagar I, Karunasagar I, Maiti B. Evaluation of reverse transcriptase-polymerase spiral reaction assay for rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2. Clin Chim Acta 2023; 539:144-150. [PMID: 36528050 PMCID: PMC9750508 DOI: 10.1016/j.cca.2022.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIM Existing real-time reverse transcriptase PCR (RT-qPCR) has certain limitations for the point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since it requires sophisticated instruments, reagents and skilled laboratory personnel. In this study, we evaluated an assay termed the reverse transcriptase-polymerase spiral reaction (RT-PSR) for rapid and visual detection of SARS-CoV-2. METHODS The RT-PSR assay was optimized using RdRp gene and evaluated for the detection of SARS-CoV-2. The time of 60min and a temperature of 63°C was optimized for targeting the RNA-dependent RNA polymerase gene of SARS-CoV-2. The sensitivity of the assay was evaluated by diluting the in-vitro transcribed RNA, which amplifies as low as ten copies. RESULTS The specific primers designed for this assay showed 100% specificity and did not react when tested with other lung infection-causing viruses and bacteria. The optimized assay was validated with 190 clinical samples in two phases, using automated RTPCR based TrueNat test, and the results were comparable. CONCLUSIONS The RT-PSR assay can be considered for rapid and sensitive detection of SARS-CoV-2, particularly in resource-limited settings. To our knowledge, there is as yet no RT-PSR-based kit developed for SARS-CoV-2.
Collapse
Affiliation(s)
- Sharan Prerana
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Pai Ashwini
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Karanth Padyana Anupama
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Valakkunja Shankaranarayana Prajna
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Kattapuni Suresh Prithvisagar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Ashwath Nayak
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Praveen Rai
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India.
| | - Anusha Rohit
- Madras Medical Mission, Department of Microbiology, Dr. J. J. Nagar, Mogappair, Chennai 600037, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore 575018, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore 575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India.
| |
Collapse
|
23
|
He J, Zhu S, Zhou J, Jiang W, Yin L, Su L, Zhang X, Chen Q, Li X. Rapid detection of SARS-CoV-2: The gradual boom of lateral flow immunoassay. Front Bioeng Biotechnol 2023; 10:1090281. [PMID: 36704307 PMCID: PMC9871317 DOI: 10.3389/fbioe.2022.1090281] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is still in an epidemic situation, which poses a serious threat to the safety of people and property. Rapid diagnosis and isolation of infected individuals are one of the important methods to control virus transmission. Existing lateral flow immunoassay techniques have the advantages of rapid, sensitive, and easy operation, and some new options have emerged with the continuous development of nanotechnology. Such as lateral flow immunoassay test strips based on colorimetric-fluorescent dual-mode and gold nanoparticles, Surface Enhanced Raman Scattering, etc., these technologies have played an important role in the rapid diagnosis of COVID-19. In this paper, we summarize the current research progress of lateral flow immunoassay in the field of Severe Acute Respiratory Syndrome Coronavirus 2 infection diagnosis, analyze the performance of Severe Acute Respiratory Syndrome Coronavirus 2 lateral flow immunoassay products, review the advantages and limitations of different detection methods and markers, and then explore the competitive CRISPR-based nucleic acid chromatography detection method. This method combines the advantages of gene editing and lateral flow immunoassay and can achieve rapid and highly sensitive lateral flow immunoassay detection of target nucleic acids, which is expected to be the most representative method for community and clinical point-of-care testing. We hope that researchers will be inspired by this review and strive to solve the problems in the design of highly sensitive targets, the selection of detection methods, and the enhancement of CRISPR technology, to truly achieve rapid, sensitive, convenient, and specific detection of novel coronaviruses, thus promoting the development of novel coronavirus diagnosis and contributing our modest contribution to the world's fight against epidemics.
Collapse
|
24
|
Fulawka L, Kuzan A. Molecular Diagnostic Tools against SARS-CoV-2 in Poland in 2022. Biomedicines 2022; 10:biomedicines10123259. [PMID: 36552015 PMCID: PMC9775127 DOI: 10.3390/biomedicines10123259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The most effective way to stop the spread of COVID-19 (coronavirus disease 2019) is to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and isolate those infected as soon as possible. More than 1000 types of molecular and antigen-based immunoassay tests to detect SARS-CoV-2 are now commercially available worldwide. In this review, we present the possibilities of molecular diagnostics available in Poland in 2022. We provide a description of what samples have proven useful to confirm SARS-CoV-2 infection, we describe what methods are used, as well as what safeguards can and should be used to prevent false-negative and false-positive results, and finally we review the products that diagnostic laboratories have to choose from. We also describe diagnostic problems associated with the mutation of the virus.
Collapse
Affiliation(s)
- Lukasz Fulawka
- Molecular Pathology Centre Cellgen, 50-353 Wroclaw, Poland
| | - Aleksandra Kuzan
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, 50-367 Wroclaw, Poland
- Correspondence: ; Tel.: +48-71-784-1379
| |
Collapse
|
25
|
Ahmadi M, Alizadeh-Navaei R, Haghshenas M, Mousavi T, Saeedi M, Hedayatizadeh-Omran A, Valadan R. Differential gene expression of SARS-CoV-2 transcriptome provides insight into the design of more sensitive diagnostic tests. HUMAN GENE 2022; 34. [PMID: 37521443 PMCID: PMC9549717 DOI: 10.1016/j.humgen.2022.201116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is being addressed through RT-PCR, a frontline diagnostic technique. We evaluated gene expression patterns to improve the accuracy and sensitivity of current diagnostic tests. We downloaded relevant next-generation sequencing (NGS) data from the Sequence Read Archive (SRA) database, checked for quality, and mapped them onto the target reference sequence. It was determined that ORF1ab, N, S, and ORF8 genes are mainly expressed based on the results of the quantitative evaluation after normalization by HPRT and elimination of insufficient expression data. ORF8, ORF3a, and M genes were found to have higher expression values than the E gene as a routine RT-PCR detector gene (p*0.05). M gene expression values are also close to ORF8 values. Taking into account the importance of differential expression of genes in the design of diagnostic kits as well as the findings of from this study, it is likely that the M gene is worth further investigation due to its high expression and low mutation rate.
Collapse
Affiliation(s)
- Mohadeseh Ahmadi
- Gastrointestinal Cancer Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammadreza Haghshenas
- Department of Microbiology, Molecular and Cell-Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Tahoora Mousavi
- Molecular and Cell Biology Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences, Iran
| | - Majid Saeedi
- Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Akbar Hedayatizadeh-Omran
- Gastrointestinal Cancer Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Valadan
- Department of Immunology, Molecular and Cell Biology Research Centre, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran,Corresponding author
| |
Collapse
|
26
|
Comparative Analysis of In-House RT-qPCR Detection of SARS-CoV-2 for Resource-Constrained Settings. Diagnostics (Basel) 2022; 12:diagnostics12112883. [PMID: 36428942 PMCID: PMC9689939 DOI: 10.3390/diagnostics12112883] [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: 09/01/2022] [Revised: 10/26/2022] [Accepted: 11/11/2022] [Indexed: 11/23/2022] Open
Abstract
We developed and standardized an efficient and cost-effective in-house RT-PCR method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluated sensitivity, specificity, and other statistical parameters by different RT-qPCR methods including triplex, duplex, and simplex assays adapted from the initial World Health Organization- (WHO) recommended protocol. This protocol included the identification of the E envelope gene (E gene; specific to the Sarvecovirus genus), RdRp gene of the RNA-dependent RNA polymerase (specific for SARS-CoV-2), and RNase P gene as endogenous control. The detection limit of the E and the RdRp genes were 3.8 copies and 33.8 copies per 1 µL of RNA, respectively, in both triplex and duplex reactions. The sensitivity for the RdRp gene in the triplex and duplex RT-qPCR tests were 98.3% and 83.1%, respectively. We showed a decrease in sensitivity for the RdRp gene by 60% when the E gene acquired Ct values > 31 in the diagnostic tests. This is associated with the specific detection limit of each gene and possible interferences in the protocol. Hence, developing efficient and cost-effective methodologies that can be adapted to various health emergency scenarios is important, especially in developing countries or settings where resources are limited.
Collapse
|
27
|
Saravia-Butler AM, Schisler JC, Taylor D, Beheshti A, Butler D, Meydan C, Foox J, Hernandez K, Mozsary C, Mason CE, Meller R. Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients. iScience 2022; 25:105310. [PMID: 36246576 PMCID: PMC9540688 DOI: 10.1016/j.isci.2022.105310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/24/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
We analyzed RNA sequencing data from nasal swabs used for SARS-CoV-2 testing. 13% of 317 PCR-negative samples contained over 100 reads aligned to multiple regions of the SARS-CoV-2 genome. Differential gene expression analysis compares the host gene expression in potential false-negative (FN: PCR negative, sequencing positive) samples to subjects with multiple SARS-CoV-2 viral loads. The host transcriptional response in FN samples was distinct from true negative samples (PCR & sequencing negative) and similar to low viral load samples. Gene Ontology analysis shows viral load-dependent changes in gene expression are functionally distinct; 23 common pathways include responses to viral infections and associated immune responses. GO analysis reveals FN samples had a high overlap with high viral load samples. Deconvolution of RNA-seq data shows similar cell content across viral loads. Hence, transcriptome analysis of nasal swabs provides an additional level of identifying SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Amanda M. Saravia-Butler
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
- COVID-19 International Research Team, Medford, MA, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team, Medford, MA, USA
- McAllister Heart Institute, Department of Pharmacology, and Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deanne Taylor
- COVID-19 International Research Team, Medford, MA, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- COVID-19 International Research Team, Medford, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dan Butler
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Jonathon Foox
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Kyle Hernandez
- COVID-19 International Research Team, Medford, MA, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Center for Translational Data Science, University of Chicago, Chicago, IL, USA
| | - Chris Mozsary
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E. Mason
- COVID-19 International Research Team, Medford, MA, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA, USA
- Neuroscience Institute, Department of Neurobiology/ Department of Pharmacology and Toxicology; Morehouse School of Medicine, Atlanta, GA 30310, USA
| |
Collapse
|
28
|
Application of Nanotechnology in COVID-19 Infection: Findings and Limitations. JOURNAL OF NANOTHERANOSTICS 2022. [DOI: 10.3390/jnt3040014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is an urgent need to address the global mortality of the COVID-19 pandemic, as it reached 6.3 million as of July 2022. As such, the experts recommended the mass diagnosis of SARS-CoV-2 infection at an early stage using nanotechnology-based sensitive diagnostic approaches. The development of nanobiosensors for Point-of-Care (POC) sampling of COVID-19 could ensure mass detection without the need for sophisticated laboratories or expert personnel. The use of Artificial Intelligence (AI) techniques for POC detection was also proposed. In addition, the utilization of various antiviral nanomaterials such as Silver Nanoparticles (AgNPs) for the development of masks for personal protection mitigates viral transmission. Nowadays, nano-assisted vaccines have been approved for emergency use, but their safety and effectiveness in the mutant strain of the SARS-CoV-2 virus remain challenging. Methodology: Updated literature was sourced from various research indexing databases such as PubMed, SCOPUS, Science Direct, Research Gate and Google Scholars. Result: We presented the concept of novel nanotechnology researched discovery, including nano-devices, electrochemical biosensing, nano-assisted vaccine, and nanomedicines, for use in recent times, which could be a formidable step for future management of COVID-19.
Collapse
|
29
|
Maleki B, Hojati Z. A precise review on NAATs-based diagnostic assays for COVID-19: A motion in fast POC molecular tests. Eur J Clin Invest 2022; 52:e13853. [PMID: 35989561 PMCID: PMC9538879 DOI: 10.1111/eci.13853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Diagnosis is one of the main strategies to deal with infectious and deadly diseases such as coronavirus disease 2019 (COVID-19). The global pandemic of COVID-19 has led to an immediate need to expand rapid diagnostic techniques. New isothermal-based methods are being developed for COVID-19 detection aiming to resolve the limitations related to the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method through immediate samples processing and minimizing false-negative or ambiguous results. Advances in nucleic acid amplification techniques (NAATs) can provide affordable and easy-to-use diagnostic platforms with high sensitivity and specificity in order to be available to the public as approved commercial kits. AIMS The development of point-of-care (POC) testing can assist in rapid clinical decision-making and mitigate burdens on health care facilities. Finally, we discussed the different diagnostic methods based on NAATs for COVID-19 in detail. Comparative parameters are addressed for all assays and Emergency Use Authorizations (EUA)-approved commercial tests are cited. CONCLUSIONS Isothermal-coupled methods and LAMP-based molecular methods have been suggested as suitable portable tests with high diagnostic speed for use in POC testing.
Collapse
Affiliation(s)
- Bahareh Maleki
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| |
Collapse
|
30
|
Alamri AM, Alkhilaiwi FA, Ullah Khan N. Era of Molecular Diagnostics Techniques before and after the COVID-19 Pandemic. Curr Issues Mol Biol 2022; 44:4769-4789. [PMID: 36286040 PMCID: PMC9601158 DOI: 10.3390/cimb44100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the growth of molecular diagnosis from the era of Hippocrates, the emergence of COVID-19 is still remarkable. The previously used molecular techniques were not rapid enough to screen a vast population at home, in offices, and in hospitals. Additionally, these techniques were only available in advanced clinical laboratories.The pandemic outbreak enhanced the urgency of researchers and research and development companies to invent more rapid, robust, and portable devices and instruments to screen a vast community in a cost-effective and short time. There has been noteworthy progress in molecular diagnosing tools before and after the pandemic. This review focuses on the advancements in molecular diagnostic techniques before and after the emergence of COVID-19 and how the pandemic accelerated the implantation of molecular diagnostic techniques in most clinical laboratories towardbecoming routine tests.
Collapse
Affiliation(s)
- Ahmad M. Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61413, Saudi Arabia
- Cancer Research Unit, King Khalid University, Abha 61413, Saudi Arabia
| | - Faris A. Alkhilaiwi
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Regenerative Medicine Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Najeeb Ullah Khan
- Institute of Biotechnology and Genetic Engineering (Health Division), The University of Agriculture, Peshawar 25130, Pakistan
| |
Collapse
|
31
|
Kaushik A, Gupta S, Sood M, Steussy BW, Noll BW. Smart and connected devices in point-of-care molecular diagnostics: what role can they play in the response to COVID-19? Expert Rev Mol Diagn 2022; 22:775-781. [PMID: 36069357 DOI: 10.1080/14737159.2022.2122711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Coronavirus disease-2019 (COVID-19) has been a huge public health challenge that has led to significant morbidity and mortality across the globe. Given the high prevalence and continued circulation of SARS-CoV-2 infection globally, accurate and rapid point-of-care testing is critical. AREAS COVERED Knowledge of role of digital technology including smart and connected devices in rapid diagnosis of COVID-19 is an evolving area of scientific investigation. This review discusses the importance of rapid at-home point-of-care testing, highlighting the possible role of smart and connected device-based molecular diagnostics for COVID-19. EXPERT OPINION Accurate and rapid diagnostic modalities have the potential to improve accessibility and efficiency of diagnosis of symptomatic and asymptomatic patients and could be instrumental in timely implementation of appropriate therapeutic interventions as well as public health measures to mitigate spread of infection. With emerging challenges like newer, virulent viral variants, global vaccine shortages and vaccine hesitancy, accurate diagnostic testing with the ability to rapidly identify infection remains critical and has the potential to be pivotal in pandemic control. Digital technologies are likely to become important tools in future of healthcare and technological advancements may play a crucial role in response to COVID-19 with the goal of ultimately overcoming this pandemic.
Collapse
Affiliation(s)
- Ashlesha Kaushik
- Unity Point Health at St. Luke's Regional Medical Center.,University of Iowa Carver College of Medicine
| | - Sandeep Gupta
- Unity Point Health at St. Luke's Regional Medical Center
| | - Mangla Sood
- Indira Gandhi Medical College, Shimla, India
| | | | - Bryce W Noll
- Unity Point Health at St. Luke's Regional Medical Center
| |
Collapse
|
32
|
Fernandes RS, de Oliveira Silva J, Gomes KB, Azevedo RB, Townsend DM, de Paula Sabino A, Branco de Barros AL. Recent advances in point of care testing for COVID-19 detection. Biomed Pharmacother 2022; 153:113538. [PMID: 36076617 PMCID: PMC9371983 DOI: 10.1016/j.biopha.2022.113538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 12/23/2022] Open
Abstract
The World Health Organizations declaration of the COVID-19 pandemic was a milestone for the scientific community. The high transmission rate and the huge number of deaths, along with the lack of knowledge about the virus and the evolution of the disease, stimulated a relentless search for diagnostic tests, treatments, and vaccines. The main challenges were the differential diagnosis of COVID-19 and the development of specific, rapid, and sensitive tests that could reach all people. RT-PCR remains the gold standard for diagnosing COVID-19. However, new methods, such as other molecular techniques and immunoassays emerged. Also, the need for accessible tests with quick results boosted the development of point of care tests (POCT) that are fast, and automated, with high precision and accuracy. This assay reduces the dependence on laboratory conditions and mass testing of the population, dispersing the pressure regarding screening and detection. This review summarizes the advances in the diagnostic field since the pandemic started, emphasizing various laboratory techniques for detecting COVID-19. We reviewed the main existing diagnostic methods, as well as POCT under development, starting with RT-PCR detection, but also exploring other nucleic acid techniques, such as digital PCR, loop-mediated isothermal amplification-based assay (RT-LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and next-generation sequencing (NGS), and immunoassay tests, and nanoparticle-based biosensors, developed as portable instruments for the rapid standard diagnosis of COVID-19.
Collapse
|
33
|
Chen Y, Yang X, Liu J, Zhang D, He J, Tang L, Li J, Xiang Q. In vitro selection of a single-strand DNA aptamer targeting the receptor-binding domain of SARS-CoV-2 spike protein. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:105-118. [PMID: 35949145 DOI: 10.1080/15257770.2022.2109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Nucleic acid aptamers are developed from a pool of random oligonucleotide libraries with an in vitro selection through systematic evolution of ligands via exponential enrichment (SELEX) process, which are capable of specific and high-affinity molecular binding against targets. The receptor-binding domain (RBD) of spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is involved in the early stages of viral infection, is a promising target for aptamer selection. Currently, there are no effective approaches to prevent virus from spreading. In this study, a new ssDNA aptamer RBD/S-A1 binding to the RBD of spike protein from SARS-CoV-2 with high affinity (Kd=1.74 ± 0.2 nM) and low cross-binding activity was selected and evaluated. Although aptamers targeting the RBD of spike protein from SARS-CoV-2 have been described in a handful of previous studies, the RBD/S-A1 aptamer identified in this work may be considered as a potential supplementation for the current diagnosis and research of coronavirus SARS-CoV-2.
Collapse
Affiliation(s)
- Yongjun Chen
- Department of Neurology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Xuefeng Yang
- Department of Gastroenterology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Jian Liu
- Department of Laboratory Medicine, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Dandan Zhang
- Department of Infectious Medicine, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Jun He
- Department of Laboratory Medicine, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Liang Tang
- Academics Working Station, Changsha Medical University, Changsha, China
| | - Jianming Li
- Department of Neurology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China.,Academics Working Station, Changsha Medical University, Changsha, China
| | - Qin Xiang
- Department of Neurology, Nanhua Affiliated Hospital, Hengyang Medical College, University of South China, Hengyang, China.,Academics Working Station, Changsha Medical University, Changsha, China
| |
Collapse
|
34
|
Wu S, Hou H, Li H, Wang T, Wei W, Zhang M, Yin B, Huang M, Sun Z, Wang F. Comparison of the Performance of 24 Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Assays in the Diagnosis of Coronavirus Disease 2019 Patients. Front Microbiol 2022; 13:876227. [PMID: 36003928 PMCID: PMC9393512 DOI: 10.3389/fmicb.2022.876227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Background The accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the key to control Coronavirus Disease-2019 (COVID-19). The performance of different antibody detection methods for diagnosis of COVID-19 is inconclusive. Methods Between 16 February and 28 February 2020, 384 confirmed COVID-19 patients and 142 healthy controls were recruited. 24 different serological tests, including 4 enzyme-linked immunosorbent assays (EIAs), 10 chemiluminescent immunoassays (CLIAs), and 10 lateral flow immunoassays (LFIAs), were simultaneously performed. Results The sensitivities of anti-SARS-CoV-2 IgG and IgM antibodies with different reagents ranged from 75 to 95.83% and 46.09 to 92.45%, respectively. The specificities of both anti-SARS-CoV-2 IgG and IgM were relatively high and comparable among different reagents, ranged from 88.03 to 100%. The area under the curves (AUCs) of different tests ranged from 0.733 to 0.984, and the AUCs of EIAs or CLIAs were significantly higher than those of LFIAs. The sensitivities of both IgG and IgM gradually increased with increase of onset time. After 3–4 weeks, the sensitivities of anti-SARS-CoV-2 IgG were maintained at a certain level but the sensitivities of IgM were gradually decreased. Six COVID-19 patients who displayed negative anti-SARS-CoV-2 results were associated with the factors such as older age, having underlying diseases, and using immunosuppressant. Conclusion Besides the purpose of assessing the impact of the SARS-CoV-2 pandemic in the population, SARS-CoV-2 antibody assays may have an adjunct role in the diagnosis and exclusion of COVID-19, especially by using high-throughput technologies (EIAs or CLIAs).
Collapse
|
35
|
Qin Z, Sun Y, Zhang J, Zhou L, Chen Y, Huang C. Lessons from SARS‑CoV‑2 and its variants (Review). Mol Med Rep 2022; 26:263. [PMID: 35730623 PMCID: PMC9260876 DOI: 10.3892/mmr.2022.12779] [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: 04/17/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
COVID-19 has swept through mainland China by human-to-human transmission. The rapid spread of SARS-CoV-2 and its variants, including the currently prevalent Omicron strain, pose a serious threat worldwide. The present review summarizes epidemiological investigation and etiological analysis of genomic, epidemiological, and pathological characteristics of the original strain and its variants, as well as progress in diagnosis and treatment. Prevention and control measures used during the current Omicron pandemic are discussed to provide further knowledge of SARS-CoV-2.
Collapse
Affiliation(s)
- Ziwen Qin
- Department of Respiratory Diseases, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| | - Yan Sun
- Department of Respiratory Diseases, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Jian Zhang
- Department of Respiratory Diseases, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Ling Zhou
- Department of Respiratory Diseases, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Yujuan Chen
- Department of Respiratory Diseases, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| | - Chuanjun Huang
- Department of Respiratory Diseases, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, P.R. China
| |
Collapse
|
36
|
Evaluation and Clinical Validation of Guanidine-Based Inactivation Transport Medium for Preservation of SARS-CoV-2. Adv Pharmacol Pharm Sci 2022; 2022:1677621. [PMID: 35873075 PMCID: PMC9301760 DOI: 10.1155/2022/1677621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 12/02/2022] Open
Abstract
WHO declared the outbreak of COVID-19, caused by SARS-CoV-2, a pandemic in March 2020. More than 223 million cases and approximately 4.6 million deaths have been confirmed. Early diagnosis and immediate treatment became a priority during this pandemic. However, COVID-19 diagnostic testing resources are limited, especially early in the pandemic. Apart from being limited, the COVID-19 diagnostic tests using reverse transcription polymerase chain reaction (RT-PCR) have encountered storage, transportation, and safety issues. These problems are mainly experienced by developing poor countries, countries in the equatorial region, and archipelagic countries. VITPAD® is a guanidine-based inactivation transport medium (ITM) formulated to maintain the RNA quality of SARS-CoV-2 during transportation without cold chains. This study, conducted from September 2020 to March 2021, performed clinical validation of VITPAD® by comparing its performance with a globally commercially available ITM from the NEST brand. Its stability at room temperature, safety, and resistance at high temperatures was also tested using RT-PCR analysis. VITPAD® can reduce the infectious nature of the specimen, preserve the SARS-CoV-2 for 18 days at an ambient temperature, and resist high temperatures (40°C for 3 hours). A guanidine-based transport medium, such as VITPAD®, is compatible and recommended for RT-PCR-based molecular diagnosis of COVID-19.
Collapse
|
37
|
Mouliou DS. Managing Viral Emerging Infectious Diseases via current Molecular Diagnostics in the Emergency Department: the Tricky Cases. Expert Rev Anti Infect Ther 2022; 20:1163-1169. [PMID: 35702989 DOI: 10.1080/14787210.2022.2089653] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Emerging infectious diseases' diagnosis has been a major problem in most hospitals and other senior care facilities, especially for the current Coronavirus Disease 2019 (COVID-19). The various clinical manifestations, and the several radiology and laboratory data combined with the misleading test results for identifying the virus, are responsible for certain misdiagnoses, especially for suspected cases that visit the emergency department and require urgent management and further treatment. AREAS COVERED The major challenges for emerging infectious diseases' molecular diagnosis are being described here on a great scale, and, finally, strategies for a precise and on-the-spot molecular diagnosis are thoroughly discussed. Related literature was searched using the PubMed, Science Direct, and EMBASE databases published until May 2022 on the general information for viral infections and relevant false test results. EXPERT OPINION Emerging diseases' molecular diagnosis via current common diagnostic assays seems to be extremely tricky, and front-line physicians and other senior care facilities should be able to recognize some falsely diagnosed cases or even prevent their existence. Further biotechnologic revolution concerning viral molecular diagnostics will be evident in the near future, thus new methods' limitations should be highlighted to physicians from the very beginning of their performances and wide utilization.
Collapse
Affiliation(s)
- Dimitra S Mouliou
- Faculty of Medicine, University of Thessaly, BIOPOLIS, Larisa, Greece
| |
Collapse
|
38
|
Yang H, Liu P, Zhang Y, Du T, Zhou Y, Lu S, Peng X. Characteristic analysis of Omicron‐included SARS‐CoV‐2 variants of concern. MedComm (Beijing) 2022; 3:e129. [PMID: 35434714 PMCID: PMC8994548 DOI: 10.1002/mco2.129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
In view of the rapid development of the COVID‐19 pandemic and SARS‐CoV‐2 mutation, we characterized the emerging SARS‐CoV‐2 variants of concern (VOCs) by both bioinformatics methods and experiments. The representative genomic sequences of SARS‐CoV‐2 VOCs were first downloaded from NCBI, including the prototypic strain, Alpha (B.1.1.7) strain, Beta (B.1.351) strain, Delta (B.1.617.2), and Omicron (B1.1.529) strain. Bioinformatics analysis revealed that the D614G mutation led to formation of a protruding spike (S) in the tertiary structure of spike protein, which could be responsible for the enhanced binding to angiotensin‐converting enzyme 2 (ACE2) receptor. The epitope analysis further showed that the S protein antigenicity of the Omicron variant changed dramatically, which was possibly associated with its enhanced ability of immune escape. To verify the bioinformatics results, we performed experiments of pseudovirus infection and protein affinity assay. Notably, we found that the spike protein of Omicron variant showed the weakest infectivity and binding ability among all tested strains. Finally, we also proved this through virus infection experiments, and found that the cytotoxicity of Omicron seems to be not strong enough. The results in this study provide guidelines for prevention and control of COVID‐19.
Collapse
Affiliation(s)
- Hao Yang
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
| | - Penghui Liu
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
| | - Yong Zhang
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
| | - Tingfu Du
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
| | - Yanan Zhou
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
| | - Shuaiyao Lu
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
| | - Xiaozhong Peng
- Institute of Medical Biology Chinese Academy of Medical Sciences and Peking Union Medical College Kunming Yunnan China
- State Key Laboratory of Medical Molecular Biology Department of Molecular Biology and Biochemistry Institute of Basic Medical Sciences Medical Primate Research Center Neuroscience Center Chinese Academy of Medical Sciences School of Basic Medicine Peking Union Medical College Beijing China
| |
Collapse
|
39
|
Posteraro P, Errico FM, De Carolis A, Menchinelli G, Sanguinetti M, Posteraro B. Setting-specific variability of false-positive result rates with rapid testing for SARS-CoV-2 antigen. J Clin Virol 2022; 149:105132. [PMID: 35306232 PMCID: PMC8920111 DOI: 10.1016/j.jcv.2022.105132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 09/21/2021] [Accepted: 03/13/2022] [Indexed: 11/24/2022]
|
40
|
Morawiec N, Chyra D, Boroń A, Adamczyk B, Jaroszewicz J, Sobala-Szczygieł B, Adamczyk-Sowa M. Bilateral paralysis of peroneal nerve after COVID-19 disease: a case report. BMC Neurol 2022; 22:91. [PMID: 35287619 PMCID: PMC8919171 DOI: 10.1186/s12883-022-02613-5] [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: 04/22/2021] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
Background COVID-19, caused by a novel coronavirus SARS-CoV 2 has rapidly developed into pandemic. This infectious disease affecting mainly respiratory system may cause multiple systemic disorders. With increasing number of new infected patients there are more and more cases with neurological complications secondary to COVID-19. Case presentation Here we present a case of 67-years old Polish male with previously no comorbidities, who has developed bilateral paralysis of peroneal nerve after SARS-CoV 2 infection. Prior to the hospitalization he presented cough and fever and weakness. RT-PCR was reported positive for COVID-19 infection. Then he developed pneumonia and respiratory failure with bilateral lung consolidations on radiological examination. Laboratory findings revealed elevated levels of D-dimer, CRP, AspAT, GGTP, PCT and serum glucose. After discharge from hospital he was diagnosed with thrombophlebitis and prediabetes on follow-up visits. Due to problems with walking, numbness of toes and involuntary muscle spasms in hands, the patient went to the Neurological Outpatient Clinic. After neurological examination bilateral paralysis of peroneal nerve was revealed. Conclusions In this report we want to highlight one of the unexpected presentations of SARS-CoV 2 infection and emphasize the importance of neurological examination in COVID-19 patients.
Collapse
Affiliation(s)
- Natalia Morawiec
- Department of Neurology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. 3 Maja 13-15, 41-800, Zabrze, Poland.
| | - Daria Chyra
- Department of Neurology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. 3 Maja 13-15, 41-800, Zabrze, Poland
| | - Adrianna Boroń
- Department of Neurology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. 3 Maja 13-15, 41-800, Zabrze, Poland
| | - Bożena Adamczyk
- Department of Neurology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. 3 Maja 13-15, 41-800, Zabrze, Poland
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, ul. Aleja Legionów 49, 41-902, Bytom, Poland
| | - Barbara Sobala-Szczygieł
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, ul. Aleja Legionów 49, 41-902, Bytom, Poland
| | - Monika Adamczyk-Sowa
- Department of Neurology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, ul. 3 Maja 13-15, 41-800, Zabrze, Poland
| |
Collapse
|
41
|
Mouliou DS, Pantazopoulos I, Gourgoulianis K. COVID-19 diagnosis in the emergency department: seeing the tree but losing the forest. Emerg Med J 2022; 39:563. [DOI: 10.1136/emermed-2021-212219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2022] [Indexed: 11/04/2022]
|
42
|
Wambani J, Okoth P. SARS-CoV-2 origin, myths and diagnostic technology developments. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:42. [PMID: 37521834 PMCID: PMC8893981 DOI: 10.1186/s43042-022-00255-3] [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: 10/27/2021] [Accepted: 02/09/2022] [Indexed: 12/15/2022] Open
Abstract
Background After the first case of COVID-19 being announced in China in December 2019, various diagnostic technologies have been developed at unprecedented pace with the aim of providing a basis for accurate clinical intervention. However, some assays including CRISPR-based diagnostics and loop-mediated isothermal amplification (LAMP) have been less explored. As new COVID-19 technologies emerge, there is need for them to be assessed, validated and improved upon. Moreover, there is paucity of data on the essential factors governing the selection of an appropriate diagnostic approach within the correct timeframe. Myths and origin of SARS-CoV-2 remain to be controversial. Consequently, this review aims at exploring the current COVID-19 diagnostic technologies, performance evaluation, principles, suitability, specificity, sensitivity, successes and challenges of the technologies for laboratory and bedside testing. Main Body To date, there exist more publications on COVID-19 diagnostics as compared to the Zika virus. The SARS-CoV-2 virus genome profiles were readily available by 31st of December 2019. This was attributed to the fast-paced sharing of the epidemiological and diagnostics data of COVID-19. Timely profiling of the virus genome accelerated the development of diagnostic technologies. Furthermore, the rapid publication of studies that evaluated several diagnostic methods available provided baseline information on how the various technologies work and paved way for development of novel technologies. Conclusion Up to date, RT-PCR is the most preferred as compared to the other assays. This is despite the repeated false negatives reported in many of the study findings. Considering that COVID-19 has caused devastating effects on the economy, healthcare systems, agriculture and culture, timely and accurate detection of the virus is paramount in the provision of targeted therapy hence reducing chances of drug resistance, increased treatment costs and morbidity. However, information on the origin of SARS-CoV-2 still remains elusive. Furthermore, knowledge and perception of the patients toward management of SARS-CoV-2 are also paramount to proper diagnosis and management of the pandemic. Future implications of the misperceptions are that they may lead to increased non-compliance to SARS-CoV-2-related World Health Organization (WHO) policies and guidelines.
Collapse
Affiliation(s)
- Josephine Wambani
- KEMRI HIV Laboratory, Kenya Medical Research Institute [KEMRI]-Alupe, P. O BOX 3-50400, Busia, Kenya
| | - Patrick Okoth
- Department of Biological Sciences, School of Natural Sciences, Masinde Muliro University of Science and Technology, P. O BOX 190, Kakamega, 50100 Kenya
| |
Collapse
|
43
|
Co-Infection of COVID-19 and Pneumocystosis Following Rituximab Infusion—A Case Report. TRANSPLANTOLOGY 2022. [DOI: 10.3390/transplantology3010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Immunocompromised patients with respiratory viral infections are at increased risk of fungal superinfections, including Pneumocystosis. Within the scope of the COVID-19 pandemic, Pneumocystis jirovecii co-infections are being increasingly reported. Differential diagnosis often creates a dilemma, due to multiple overlapping clinical and radiographic features. Awareness of fungal co-infections in the context of the COVID-19 pandemic is crucial to initiate prophylactic measures, especially in high-risk individuals. We report the second case of Pneumocystis jirovecii pneumonia and COVID-19 co-infection in a renal transplant recipient in Poland.
Collapse
|
44
|
Pattnaik D, Poddar N, Pathi BK, Panigrahi K, Sabat S, Roy A, Patro ARK, Mohapatra A, Patro S, Praharaj AK. Comparative Evaluation of Cartridge-Based Abbott ID NOW Test With Probe-Based Real-Time Reverse Transcription Polymerase Chain Reaction Assay for Detection of SARS-CoV-2. Cureus 2022; 14:e22470. [PMID: 35223334 PMCID: PMC8861330 DOI: 10.7759/cureus.22470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 01/12/2023] Open
Abstract
Background: The gold standard test for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recommended by WHO is real-time reverse transcription polymerase chain reaction (RT-PCR), which has a turnaround time of five to six hours. Abbott ID NOW (Abbott Diagnostics Scarborough, Inc., Scarborough, ME, USA), the cartridge-based loop-mediated isothermal amplification (LAMP) assay, was approved by FDA for Emergency Use Authorization as rapid point of care testing. The present study was planned to evaluate the performance of the cartridge-based Abbott ID NOW test by comparing it to the currently used standard probe-based real-time RT-PCR method for detection of SARS-CoV-2. Methodology: A cross-sectional study was conducted in a tertiary care hospital in the eastern part of India after getting institutional ethics committee (IEC) approval. Two hundred fifty-nine cases of various age groups of both sexes who were advised for testing for SARS-CoV-2 were included in the study. Nasopharyngeal swabs were collected according to protocol advisory by the Indian Council of Medical Research (ICMR), India. Dry swabs were sent for Abbott ID NOW testing and swabs in viral transport medium were sent for probe-based RT-PCR assay using the CoviPath kit (Thermo Fisher Scientific, Bangalore, India). The data were collected and statistical analysis was performed using Statistical Package for Social Sciences (SPSS) (IBM Corp., Armonk, NY, USA). Sensitivity, specificity, positive and negative predictive values for ID NOW were calculated taking RT-PCR as the gold standard. Results: Out of 259 patients enrolled in the study, 49% were symptomatic for coronavirus disease 2019 (COVID-19). The prevalence rate of SARS-CoV-2 was 20.84% among the study population. Sensitivity and specificity, positive and negative predictive values of ID NOW test in comparison to RT-PCR assay was found to be 87%, 98%, 92.1% and 96.8% respectively. ID NOW detected seven out of 54 (12.9%) cases as false negative who were found to be positive with RT-PCR, with mean Ct value of the target genes >34. Conclusions: In this study the overall sensitivity for ID NOW assay was found to be lower, but specificity, positive and negative predictive values were found to be higher. It had the highest correlation to RT-PCR among symptomatic patients and at higher viral loads. Due to the ease of use and shortest result time for detecting COVID-19, ID NOW test could be used as a point-of-care test. But for all tests, the results should be interpreted according to the clinical and epidemiological context.
Collapse
|
45
|
Benevides Lima L, Mesquita FP, Brasil de Oliveira LL, Andréa da Silva Oliveira F, Elisabete Amaral de Moraes M, Souza PFN, Montenegro RC. True or False: What are the factors that influence COVID-19 diagnosis by RT-qPCR? Expert Rev Mol Diagn 2022; 22:157-167. [PMID: 35130461 PMCID: PMC8862161 DOI: 10.1080/14737159.2022.2037425] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease has had a catastrophic impact on the world resulting in several deaths. Since World Health Organization declared the pandemic status of the disease, several molecular diagnostic kits have been developed to help the tracking of viruses spread. Areas Covered This review aims to describe and evaluate the currently reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) diagnosis kit. Several processes used in COVID-19 diagnostic procedures are detailed in further depth to demonstrate optimal practices. Therefore, we debate the main factors that influence the viral detection of SARS-COV-2 and how they can affect the diagnosis of patients. Expert Opinion Here is highlighted and discussed several factors that can interfere in the RT-PCR analysis, such as the viral load of the sample, collection site, collection methodology, sample storage, transport, primer, and probe mismatch/dimerization in different brand kits. This is a pioneer study to discuss the factor that could lead to the wrong interpretation of RT-qPCR diagnosis of SARS-CoV-2. This study aimed to help the readers to understand what very likely is behind a bad result of SARS-CoV-2 detection by RT-PCR and what could be done to reach a reliable diagnosis.
Collapse
Affiliation(s)
- Luina Benevides Lima
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Felipe Pantoja Mesquita
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Lais Lacerda Brasil de Oliveira
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Francisca Andréa da Silva Oliveira
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Maria Elisabete Amaral de Moraes
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Pedro F N Souza
- Department of Biochemistry and Molecular Biology (DBBM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| | - Raquel Carvalho Montenegro
- Laboratory of Pharmacogenetics, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza, CE 60430-275, Brazil
| |
Collapse
|
46
|
Dronina J, Samukaite-Bubniene U, Ramanavicius A. Towards application of CRISPR-Cas12a in the design of modern viral DNA detection tools (Review). J Nanobiotechnology 2022; 20:41. [PMID: 35062978 PMCID: PMC8777428 DOI: 10.1186/s12951-022-01246-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Early detection of viral pathogens by DNA-sensors in clinical samples, contaminated foods, soil or water can dramatically improve clinical outcomes and reduce the socioeconomic impact of diseases such as COVID-19. Clustered regularly interspaced short palindromic repeat (CRISPR) and its associated protein Cas12a (previously known as CRISPR-Cpf1) technology is an innovative new-generation genomic engineering tool, also known as 'genetic scissors', that has demonstrated the accuracy and has recently been effectively applied as appropriate (E-CRISPR) DNA-sensor to detect the nucleic acid of interest. The CRISPR-Cas12a from Prevotella and Francisella 1 are guided by a short CRISPR RNA (gRNA). The unique simultaneous cis- and trans- DNA cleavage after target sequence recognition at the PAM site, sticky-end (5-7 bp) employment, and ssDNA/dsDNA hybrid cleavage strategies to manipulate the attractive nature of CRISPR-Cas12a are reviewed. DNA-sensors based on the CRISPR-Cas12a technology for rapid, robust, sensitive, inexpensive, and selective detection of virus DNA without additional sample purification, amplification, fluorescent-agent- and/or quencher-labeling are relevant and becoming increasingly important in industrial and medical applications. In addition, CRISPR-Cas12a system shows great potential in the field of E-CRISPR-based bioassay research technologies. Therefore, we are highlighting insights in this research direction.
Collapse
Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania.
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
| |
Collapse
|
47
|
A step toward better sample management of COVID-19: On-spot detection by biometric technology and artificial intelligence. COVID-19 AND THE SUSTAINABLE DEVELOPMENT GOALS 2022. [PMCID: PMC9334987 DOI: 10.1016/b978-0-323-91307-2.00017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
48
|
DAIA C, IONESCU A, IONESCU EV, ILIESCU MG, STANCIU LE, CAMBREA SC, ILIESCU DM, ARGHIR OC, GEORGEANU V, VOINEA F, BAZ R, PAZARA L, ONOSE G. Complex respiratory and motor rehabilitation program in a patient with post-pulmonary tuberculosis conditions and multiple sequelae after SARS-CoV-2 infection: case report. BALNEO AND PRM RESEARCH JOURNAL 2021. [DOI: 10.12680/balneo.2021.454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Introduction: A great variety of medical issues can occur after the COVID-19 infection including fatigue, muscle weakness, locomotor disability, self-care dysfunction, polyneuropathy, persistent dyspnea on exertion and a hypercoagulable state.
Materials and methods: This paper presents the case of a nonsmoker 49-year-old male with right lung lower lobe lobectomy for post tuberculosis bronchiectasis and diabetes mellitus, who developed multiple serious physicals, neurological, hematological and respiratory consequences, related to critical COVID-19 infection and prolonged hospitalization,
Results: A favorable evolution of the patient’s respiratory sequels and motor impairment on both lower limbs was noticed after a complex individualized rehabilitation program started in the post COVID-19 Rehabilitation Department of Balneal and Rehabilitation Sanatorium, Techirghiol, Romania, consisting in better functional parameters and exercise tolerance, significant improvement in daily activities, remission of exertional dyspnea, social and family reintegration.
Conclusions: multidisciplinary approach and complex individualized programs of rehabilitation is required after a critical form of COVID in a patients known with tuberculosis, and other complex pathologies, in order to restore physical function and mobility and optimize respiratory parameters.
Keywords: COVID-19, Rehabilitation, Tuberculosis,
Collapse
Affiliation(s)
- Cristina DAIA
- Department of Medical Rehabilitation, “Carol Davila” University of Medicine and Pharmacy, 041914, Bucharest, Romania
| | - Anca IONESCU
- Department of Medical Rehabilitation, “Carol Davila” University of Medicine and Pharmacy, 041914, Bucharest, Romania
| | - Elena Valentina IONESCU
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Mădălina Gabriela ILIESCU
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Liliana Elena STANCIU
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Simona Claudia CAMBREA
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Dan Marcel ILIESCU
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Oana Cristina ARGHIR
- Balneal Rehabilitation Sanatorium of Techirghiol, 900610,Techirghiol, Constanta County, Romania
| | - Vlad GEORGEANU
- Balneal Rehabilitation Sanatorium of Techirghiol, 900610,Techirghiol, Constanta County, Romania
| | - Felix VOINEA
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Radu BAZ
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Loredana PAZARA
- Faculty of Medicine, «Ovidius» University of Constanta, 1 University Alley, Campus, Corp B, 900470, Constanta, Romania
| | - Gelu ONOSE
- Department of Medical Rehabilitation, “Carol Davila” University of Medicine and Pharmacy, 041914, Bucharest, Romania
| |
Collapse
|
49
|
Varotto-Boccazzi I, Manenti A, Dapporto F, Gourlay LJ, Bisaglia B, Gabrieli P, Forneris F, Faravelli S, Bollati V, Rubolini D, Zuccotti G, Montomoli E, Epis S, Bandi C. Epidemic Preparedness- Leishmania tarentolae as an Easy-to-Handle Tool to Produce Antigens for Viral Diagnosis: Application to COVID-19. Front Microbiol 2021; 12:736530. [PMID: 34966362 PMCID: PMC8710741 DOI: 10.3389/fmicb.2021.736530] [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: 07/05/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
To detect and prevent emerging epidemics, discovery platforms are urgently needed, for the rapid development of diagnostic assays. Molecular diagnostic tests for COVID-19 were developed shortly after the isolation of SARS-CoV-2. However, serological tests based on antiviral antibody detection, revealing previous exposure to the virus, required longer testing phases, due to the need to obtain correctly folded and glycosylated antigens. The delay between the identification of a new virus and the development of reliable serodiagnostic tools limits our readiness to tackle future epidemics. We suggest that the protozoan Leishmania tarentolae can be used as an easy-to-handle microfactory for the rapid production of viral antigens to face emerging epidemics. We engineered L. tarentolae to express the SARS-CoV-2 receptor-binding domain (RBD) and we recorded the ability of the purified RBD antigen to detect SARS-CoV-2 infection in human sera, with a sensitivity and reproducibility comparable to that of a reference antigen produced in human cells. This is the first application of an antigen produced in L. tarentolae for the serodiagnosis of a Coronaviridae infection. On the basis of our results, we propose L. tarentolae as an effective system for viral antigen production, even in countries that lack high-technology cell factories.
Collapse
Affiliation(s)
- Ilaria Varotto-Boccazzi
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Biomedical and Clinical Science “L. Sacco”, University of Milan, Milan, Italy
| | | | | | | | | | - Paolo Gabrieli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Silvia Faravelli
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Water Research Institute—National Research Council of Italy, IRSA−CNR, Brugherio, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Science “L. Sacco”, University of Milan, Milan, Italy
- Pediatric CRC “Romeo ed Enrica Invernizzi”, University of Milan, Milan, Italy
| | - Emanuele Montomoli
- VisMederi Research, Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Sara Epis
- Department of Biosciences, University of Milan, Milan, Italy
- Pediatric CRC “Romeo ed Enrica Invernizzi”, University of Milan, Milan, Italy
| | - Claudio Bandi
- Department of Biosciences, University of Milan, Milan, Italy
- Pediatric CRC “Romeo ed Enrica Invernizzi”, University of Milan, Milan, Italy
| |
Collapse
|
50
|
Rodríguez-Frías F, Quer J, Tabernero D, Cortese MF, Garcia-Garcia S, Rando-Segura A, Pumarola T. Microorganisms as Shapers of Human Civilization, from Pandemics to Even Our Genomes: Villains or Friends? A Historical Approach. Microorganisms 2021; 9:2518. [PMID: 34946123 PMCID: PMC8708650 DOI: 10.3390/microorganisms9122518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Universal history is characterized by continuous evolution, in which civilizations are born and die. This evolution is associated with multiple factors, among which the role of microorganisms is often overlooked. Viruses and bacteria have written or decisively contributed to terrible episodes of history, such as the Black Death in 14th century Europe, the annihilation of pre-Columbian American civilizations, and pandemics such as the 1918 Spanish flu or the current COVID-19 pandemic caused by the coronavirus SARS-CoV-2. Nevertheless, it is clear that we could not live in a world without these tiny beings. Endogenous retroviruses have been key to our evolution and for the regulation of gene expression, and the gut microbiota helps us digest compounds that we could not otherwise process. In addition, we have used microorganisms to preserve or prepare food for millennia and more recently to obtain drugs such as antibiotics or to develop recombinant DNA technologies. Due to the enormous importance of microorganisms for our survival, they have significantly influenced the population genetics of different human groups. This paper will review the role of microorganisms as "villains" who have been responsible for tremendous mortality throughout history but also as "friends" who help us survive and evolve.
Collapse
Affiliation(s)
- Francisco Rodríguez-Frías
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Maria Francesca Cortese
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Selene Garcia-Garcia
- Clinical Biochemistry Research Group, Department of Biochemistry, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (M.F.C.); (S.G.-G.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Tomas Pumarola
- Department of Microbiology, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| |
Collapse
|