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Chavda VP, Valu DD, Parikh PK, Tiwari N, Chhipa AS, Shukla S, Patel SS, Balar PC, Paiva-Santos AC, Patravale V. Conventional and Novel Diagnostic Tools for the Diagnosis of Emerging SARS-CoV-2 Variants. Vaccines (Basel) 2023; 11:vaccines11020374. [PMID: 36851252 PMCID: PMC9960989 DOI: 10.3390/vaccines11020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Accurate identification at an early stage of infection is critical for effective care of any infectious disease. The "coronavirus disease 2019 (COVID-19)" outbreak, caused by the virus "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)", corresponds to the current and global pandemic, characterized by several developing variants, many of which are classified as variants of concern (VOCs) by the "World Health Organization (WHO, Geneva, Switzerland)". The primary diagnosis of infection is made using either the molecular technique of RT-PCR, which detects parts of the viral genome's RNA, or immunodiagnostic procedures, which identify viral proteins or antibodies generated by the host. As the demand for the RT-PCR test grew fast, several inexperienced producers joined the market with innovative kits, and an increasing number of laboratories joined the diagnostic field, rendering the test results increasingly prone to mistakes. It is difficult to determine how the outcomes of one unnoticed result could influence decisions about patient quarantine and social isolation, particularly when the patients themselves are health care providers. The development of point-of-care testing helps in the rapid in-field diagnosis of the disease, and such testing can also be used as a bedside monitor for mapping the progression of the disease in critical patients. In this review, we have provided the readers with available molecular diagnostic techniques and their pitfalls in detecting emerging VOCs of SARS-CoV-2, and lastly, we have discussed AI-ML- and nanotechnology-based smart diagnostic techniques for SARS-CoV-2 detection.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
- Correspondence: (V.P.C.); or (V.P.)
| | - Disha D. Valu
- Formulation and Drug Product Development, Biopharma Division, Intas Pharmaceutical Ltd., 3000-548 Moraiya, Ahmedabad 380054, Gujarat, India
| | - Palak K. Parikh
- Department of Pharmaceutical Chemistry and Quality Assurance, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Nikita Tiwari
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Abu Sufiyan Chhipa
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Somanshi Shukla
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
| | - Snehal S. Patel
- Department of Pharmacology, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat, India
| | - Pankti C. Balar
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, Maharashtra, India
- Correspondence: (V.P.C.); or (V.P.)
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Sharma D, Notarte KI, Fernandez RA, Lippi G, Gromiha MM, Henry BM. In silico evaluation of the impact of Omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT-qPCR assays for SARS-CoV-2 detection using whole genome sequencing. J Med Virol 2023; 95:e28241. [PMID: 36263448 PMCID: PMC9874926 DOI: 10.1002/jmv.28241] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern (VoC) Omicron (B.1.1.529) has rapidly spread around the world, presenting a new threat to global public human health. Due to the large number of mutations accumulated by SARS-CoV-2 Omicron, concerns have emerged over potentially reduced diagnostic accuracy of reverse-transcription polymerase chain reaction (RT-qPCR), the gold standard diagnostic test for diagnosing coronavirus disease 2019 (COVID-19). Thus, we aimed to assess the impact of the currently endemic Omicron sublineages BA.4 and BA.5 on the integrity and sensitivity of RT-qPCR assays used for coronavirus disease 2019 (COVID-19) diagnosis via in silico analysis. We employed whole genome sequencing data and evaluated the potential for false negatives or test failure due to mismatches between primers/probes and the Omicron VoC viral genome. METHODS In silico sensitivity of 12 RT-qPCR tests (containing 30 primers and probe sets) developed for detection of SARS-CoV-2 reported by the World Health Organization (WHO) or available in the literature, was assessed for specifically detecting SARS-CoV-2 Omicron BA.4 and BA.5 sublineages, obtained after removing redundancy from publicly available genomes from National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Avian Influenza Data (GISAID) databases. Mismatches between amplicon regions of SARS-CoV-2 Omicron VoC and primers and probe sets were evaluated, and clustering analysis of corresponding amplicon sequences was carried out. RESULTS From the 1164 representative SARS-CoV-2 Omicron VoC BA.4 sublineage genomes analyzed, a substitution in the first five nucleotides (C to T) of the amplicon's 3'-end was observed in all samples resulting in 0% sensitivity for assays HKUnivRdRp/Hel (mismatch in reverse primer) and CoremCharite N (mismatch in both forward and reverse primers). Due to a mismatch in the forward primer's 5'-end (3-nucleotide substitution, GGG to AAC), the sensitivity of the ChinaCDC N assay was at 0.69%. The 10 nucleotide mismatches in the reverse primer resulted in 0.09% sensitivity for Omicron sublineage BA.4 for Thai N assay. Of the 1926 BA.5 sublineage genomes, HKUnivRdRp/Hel assay also had 0% sensitivity. A sensitivity of 3.06% was observed for the ChinaCDC N assay because of a mismatch in the forward primer's 5'-end (3-nucleotide substitution, GGG to AAC). Similarly, due to the 10 nucleotide mismatches in the reverse primer, the Thai N assay's sensitivity was low at 0.21% for sublineage BA.5. Further, eight assays for BA.4 sublineage retained high sensitivity (more than 97%) and 9 assays for BA.5 sublineage retained more than 99% sensitivity. CONCLUSION We observed four assays (HKUnivRdRp/Hel, ChinaCDC N, Thai N, CoremCharite N) that could potentially result in false negative results for SARS-CoV-2 Omicron VoCs BA.4 and BA.5 sublineages. Interestingly, CoremCharite N had 0% sensitivity for Omicron Voc BA.4 but 99.53% sensitivity for BA.5. In addition, 66.67% of the assays for BA.4 sublineage and 75% of the assays for BA.5 sublineage retained high sensitivity. Further, amplicon clustering and additional substitution analysis along with sensitivity analysis could be used for the modification and development of RT-qPCR assays for detecting SARS-CoV-2 Omicron VoC sublineages.
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Affiliation(s)
- Divya Sharma
- Protein Bioinformatics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiTamil NaduIndia
| | - Kin Israel Notarte
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Rey Arturo Fernandez
- Ateneo de Manila University Professional SchoolsRockwell CenterMakatiPhilippines
| | - Giuseppe Lippi
- Section of Clinical BiochemistryUniversity of VeronaVeronaItaly
| | - M. Michael Gromiha
- Protein Bioinformatics Laboratory, Department of Biotechnology, Bhupat and Jyoti Mehta School of BiosciencesIndian Institute of Technology MadrasChennaiTamil NaduIndia
| | - Brandon M. Henry
- Clinical Laboratory, Division of Nephrology and HypertensionCincinnati Children's Hospital Medical CenterCincinnatiOhioUSA
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Tan C, Wang S, Yang H, Huang Q, Li S, Liu X, Ye H, Zhang G. Hydrogenated Boron Phosphide THz-Metamaterial-Based Biosensor for Diagnosing COVID-19: A DFT Coupled FEM Study. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:4024. [PMID: 36432307 PMCID: PMC9697324 DOI: 10.3390/nano12224024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Recent reports focus on the hydrogenation engineering of monolayer boron phosphide and simultaneously explore its promising applications in nanoelectronics. Coupling density functional theory and finite element method, we investigate the bowtie triangle ring microstructure composed of boron phosphide with hydrogenation based on structural and performance analysis. We determine the carrier mobility of hydrogenated boron phosphide, reveal the effect of structural and material parameters on resonance frequencies, and discuss the variation of the electric field at the two tips. The results suggest that the mobilities of electrons for hydrogenated BP monolayer in the armchair and zigzag directions are 0.51 and 94.4 cm2·V-1·s-1, whereas for holes, the values are 136.8 and 175.15 cm2·V-1·s-1. Meanwhile, the transmission spectra of the bowtie triangle ring microstructure can be controlled by adjusting the length of the bowtie triangle ring microstructure and carrier density of hydrogenated BP. With the increasing length, the transmission spectrum has a red-shift and the electric field at the tips of equilateral triangle rings is significantly weakened. Furthermore, the theoretical sensitivity of the BTR structure reaches 100 GHz/RIU, which is sufficient to determine healthy and COVID-19-infected individuals. Our findings may open up new avenues for promising applications in the rapid diagnosis of COVID-19.
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Affiliation(s)
- Chunjian Tan
- Electronic Components, Technology and Materials, Delft University of Technology, 2628 CD Delft, The Netherlands
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shaogang Wang
- Electronic Components, Technology and Materials, Delft University of Technology, 2628 CD Delft, The Netherlands
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huiru Yang
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qianming Huang
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shizhen Li
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xu Liu
- Electronic Components, Technology and Materials, Delft University of Technology, 2628 CD Delft, The Netherlands
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huaiyu Ye
- Engineering Research Center of Integrated Circuits for Next-Generation Communications, Ministry of Education, School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guoqi Zhang
- Electronic Components, Technology and Materials, Delft University of Technology, 2628 CD Delft, The Netherlands
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Bassetti M, Kanj SS, Kiratisin P, Rodrigues C, Van Duin D, Villegas MV, Yu Y. Early appropriate diagnostics and treatment of MDR Gram-negative infections. JAC Antimicrob Resist 2022; 4:dlac089. [PMID: 36111208 PMCID: PMC9469888 DOI: 10.1093/jacamr/dlac089] [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] [Indexed: 11/16/2022] Open
Abstract
The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy.
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Affiliation(s)
- Matteo Bassetti
- Department of Health Science, University of Genoa , Italy
- Infectious Diseases Clinic, Ospedale Policlinico San Martino Hospital – IRCCS , Genoa , Italy
| | - Souha S Kanj
- Division of Infectious Diseases, American University of Beirut Medical Center , Beirut , Lebanon
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre , Mumbai, Maharashtra , India
| | - David Van Duin
- Department of Medicine, University of North Carolina School of Medicine , Chapel Hill, NC , USA
| | - María Virginia Villegas
- Grupo de Investigaciones en Resistencia Antimicrobiana y Epidemiología Hospitalaria (RAEH), Universidad El Bosque , Bogotá DC , Colombia
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, Zhejiang , China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province , Hangzhou, Zhejiang , China
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SARS-CoV-2 Transmission in the Military during the Early Phase of the Pandemic-A Systematic Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19127418. [PMID: 35742662 PMCID: PMC9224230 DOI: 10.3390/ijerph19127418] [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] [Received: 05/04/2022] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023]
Abstract
Militaries worldwide have been affected by COVID-19 pandemic. However, the impact and epidemiological characteristics of transmission during the early phase of the pandemic is not well-studied. This study aims to systematically estimate the baseline incidence of COVID-19 in the military worldwide and identify the potential risk factors of transmission and clinical characteristics of the cases. English and Chinese literature reporting COVID-19 cases in military worldwide published on four electronic databases (PubMed, Scopus, EMBASE, and CKNI) through 28 May 2021 were systematically screened and synthesized qualitatively. Forty-six studies involving at least 711,408 military personnel in 17 countries were synthesized. Low incidence of cases was observed in the military with pooled COVID-19 incidence of 0.19% (95%CI: 0.00–9.18%). We observed a higher incidence among those (1) with overseas exposure (39.85%; 95%CI: 0.00–95.87%) rather than local exposure (3.03%; 95%CI: 0.00–12.53%), (2) who were on either local/overseas military deployment (26.78%; 95%CI: 0.00–71.51%) as compared to those not deployed (4.37%; 95%CI: 0.00–17.93%), and (3) on overseas military deployment (39.84%; 95%CI: 0.00–95.87%) as compared to local military deployment (3.03%; 95%CI: 2.37–3.74%). The majority of the cases were symptomatic (77.90% (95%CI: 43.91–100.00%)); hospitalization and mortality rates were low at 4.43% (95%CI: 0.00–25.34%) and 0.25% (95%CI: 0.00–0.85%), respectively; and headache, anosmia, ageusia, myalgia, nasal congestion, and cough were the most commonly observed symptoms. Overseas and local deployment were observed to have higher risk of SARS-CoV-2 transmission. Sustainable, active SARS-CoV-2 surveillance strategies are crucial to detect and contain transmission early during military deployments.
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Sengupta R, Khand H, Sarusi G. Terahertz Impedance Spectroscopy of Biological Nanoparticles by a Resonant Metamaterial Chip for Breathalyzer-Based COVID-19 Prompt Tests. ACS APPLIED NANO MATERIALS 2022; 5:5803-5812. [PMID: 37552719 PMCID: PMC9004291 DOI: 10.1021/acsanm.2c00954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 06/16/2023]
Abstract
We propose a tested, sensitive, and prompt COVID-19 breath screening method that takes less than 1 min. The method is nonbiological and is based on the detection of a shift in the resonance frequency of a nanoengineered inductor-capacitor (LC) resonant metamaterial chip, caused by viruses and mainly related exhaled particles, when performing terahertz spectroscopy. The chip consists of thousands of microantennas arranged in an array and enclosed in a plastic breathalyzer-like disposable capsule kit. After an appreciable agreement between numerical simulations (COMSOL and CST) and experimental results was reached using our metamaterial design, low-scale clinical trials were conducted with asymptomatic and symptomatic coronavirus patients and healthy individuals. It is shown that coronavirus-positive individuals are effectively screened upon observation of a shift in the transmission resonance frequency of about 1.5-9 GHz, which is diagnostically different from the resonance shift of healthy individuals who display a 0-1.5 GHz shift. The initial results of screening coronavirus patients yielded 88% agreement with the real-time quantitative polymerase chain reaction (RT-qPCR) results (performed concurrently with the breath test) with an outcome of a positive predicted value of 87% and a negative predicted value of 88%.
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Affiliation(s)
- Rudrarup Sengupta
- Department of Photonics and Electro-Optics Engineering,
School of Electrical and Computer Engineering, Ben-Gurion University of the
Negev, Beer Sheva 8410501, Israel
| | - Heena Khand
- Department of Photonics and Electro-Optics Engineering,
School of Electrical and Computer Engineering, Ben-Gurion University of the
Negev, Beer Sheva 8410501, Israel
| | - Gabby Sarusi
- Department of Photonics and Electro-Optics Engineering,
School of Electrical and Computer Engineering, Ben-Gurion University of the
Negev, Beer Sheva 8410501, Israel
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Park R, Jeon S, Jeong J, Park SY, Han DW, Hong SW. Recent Advances of Point-of-Care Devices Integrated with Molecularly Imprinted Polymers-Based Biosensors: From Biomolecule Sensing Design to Intraoral Fluid Testing. BIOSENSORS 2022; 12:bios12030136. [PMID: 35323406 PMCID: PMC8946830 DOI: 10.3390/bios12030136] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 05/11/2023]
Abstract
Recent developments of point-of-care testing (POCT) and in vitro diagnostic medical devices have provided analytical capabilities and reliable diagnostic results for rapid access at or near the patient's location. Nevertheless, the challenges of reliable diagnosis still remain an important factor in actual clinical trials before on-site medical treatment and making clinical decisions. New classes of POCT devices depict precise diagnostic technologies that can detect biomarkers in biofluids such as sweat, tears, saliva or urine. The introduction of a novel molecularly imprinted polymer (MIP) system as an artificial bioreceptor for the POCT devices could be one of the emerging candidates to improve the analytical performance along with physicochemical stability when used in harsh environments. Here, we review the potential availability of MIP-based biorecognition systems as custom artificial receptors with high selectivity and chemical affinity for specific molecules. Further developments to the progress of advanced MIP technology for biomolecule recognition are introduced. Finally, to improve the POCT-based diagnostic system, we summarized the perspectives for high expandability to MIP-based periodontal diagnosis and the future directions of MIP-based biosensors as a wearable format.
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Affiliation(s)
- Rowoon Park
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan 46241, Korea; (R.P.); (S.J.); (J.J.); (D.-W.H.)
| | - Sangheon Jeon
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan 46241, Korea; (R.P.); (S.J.); (J.J.); (D.-W.H.)
| | - Jeonghwa Jeong
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan 46241, Korea; (R.P.); (S.J.); (J.J.); (D.-W.H.)
| | - Shin-Young Park
- Department of Dental Education and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03080, Korea;
| | - Dong-Wook Han
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan 46241, Korea; (R.P.); (S.J.); (J.J.); (D.-W.H.)
- Department of Optics and Mechatronics Engineering, Pusan National University, Busan 46241, Korea
| | - Suck Won Hong
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan 46241, Korea; (R.P.); (S.J.); (J.J.); (D.-W.H.)
- Department of Optics and Mechatronics Engineering, Pusan National University, Busan 46241, Korea
- Correspondence:
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Tran NK, Albahra S, Rashidi H, May L. Innovations in infectious disease testing: Leveraging COVID-19 pandemic technologies for the future. Clin Biochem 2022; 117:10-15. [PMID: 34998789 PMCID: PMC8735816 DOI: 10.1016/j.clinbiochem.2021.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/13/2021] [Accepted: 12/30/2021] [Indexed: 12/26/2022]
Abstract
Innovations in infectious disease testing have improved our abilities to detect and understand the microbial world. The 2019 novel coronavirus infectious disease (COVID-19) pandemic introduced new innovations including non-prescription “over the counter” infectious disease tests, mass spectrometry-based detection of COVID-19 host response, and the implementation of artificial intelligence (AI) and machine learning (ML) to identify individuals infected by the severe acute respiratory syndrome - coronavirus – 2 (SARS-CoV-2). As the world recovers from the COVID-19 pandemic; these innovative solutions will give rise to a new era of infectious disease tests extending beyond the detection of SARS-CoV-2. To this end, the purpose of this review is to summarize current trends in infectious disease testing and discuss innovative applications specifically in the areas of POC testing, MS, molecular diagnostics, sample types, and AI/ML.
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Affiliation(s)
- Nam K Tran
- Dept. of Pathology and Laboratory Medicine, UC Davis School of Medicine, United States.
| | - Samer Albahra
- Dept. of Pathology and Laboratory Medicine, UC Davis School of Medicine, United States
| | - Hooman Rashidi
- Dept. of Pathology and Laboratory Medicine, UC Davis School of Medicine, United States
| | - Larissa May
- Department of Emergency Medicine, UC Davis School of Medicine, United States
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Hwang YC, Lu RM, Su SC, Chiang PY, Ko SH, Ke FY, Liang KH, Hsieh TY, Wu HC. Monoclonal antibodies for COVID-19 therapy and SARS-CoV-2 detection. J Biomed Sci 2022; 29:1. [PMID: 34983527 PMCID: PMC8724751 DOI: 10.1186/s12929-021-00784-w] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an exceptional public health crisis that demands the timely creation of new therapeutics and viral detection. Owing to their high specificity and reliability, monoclonal antibodies (mAbs) have emerged as powerful tools to treat and detect numerous diseases. Hence, many researchers have begun to urgently develop Ab-based kits for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ab drugs for use as COVID-19 therapeutic agents. The detailed structure of the SARS-CoV-2 spike protein is known, and since this protein is key for viral infection, its receptor-binding domain (RBD) has become a major target for therapeutic Ab development. Because SARS-CoV-2 is an RNA virus with a high mutation rate, especially under the selective pressure of aggressively deployed prophylactic vaccines and neutralizing Abs, the use of Ab cocktails is expected to be an important strategy for effective COVID-19 treatment. Moreover, SARS-CoV-2 infection may stimulate an overactive immune response, resulting in a cytokine storm that drives severe disease progression. Abs to combat cytokine storms have also been under intense development as treatments for COVID-19. In addition to their use as drugs, Abs are currently being utilized in SARS-CoV-2 detection tests, including antigen and immunoglobulin tests. Such Ab-based detection tests are crucial surveillance tools that can be used to prevent the spread of COVID-19. Herein, we highlight some key points regarding mAb-based detection tests and treatments for the COVID-19 pandemic.
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Affiliation(s)
- Yu-Chyi Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Ruei-Min Lu
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Chieh Su
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Pao-Yin Chiang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Shih-Han Ko
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Feng-Yi Ke
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Kang-Hao Liang
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Tzung-Yang Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan.
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Mukherjee SB, Gorohovski A, Merzon E, Levy E, Mukherjee S, Frenkel-Morgenstern M. Seasonal UV exposure and vitamin D: association with the dynamics of COVID-19 transmission in Europe. FEBS Open Bio 2021; 12:106-117. [PMID: 34608759 PMCID: PMC8653358 DOI: 10.1002/2211-5463.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/12/2021] [Accepted: 10/04/2021] [Indexed: 12/23/2022] Open
Abstract
Several recent studies have demonstrated that low plasma 25(OH) vitamin D levels are associated with the risk of COVID‐19 infection. The primary source of vitamin D production in humans is environmental UV radiation. In many viral respiratory diseases, peak infection rates are observed during winter due to reduced UV exposure and low temperatures. In Europe, the second wave of COVID‐19 began early in the winter of 2020. Investigating the impact of seasonal temperature and UV exposure on COVID‐19 transmission could thus aid in prevention and intervention. As such, we first performed a comprehensive meta‐analysis of all related published literature based on the association between vitamin D and COVID‐19, which supported the hypothesis that the low vitamin D level is a critical risk factor for COVID‐19 infection. Next, to understand the potential impact of seasonal UV and temperature levels on COVID‐19 cases, we analyzed meteorological data and daily COVID‐19 cases per million in the populations of 26 European countries. We observed that low temperature, UV index, and cloud‐free vitamin D UV dose (UVDVF) levels are negatively correlated with COVID‐19 prevalence in Europe. Furthermore, a distributed lag nonlinear model was used to assess the nonlinear delayed effects of individual seasonal factors on COVID‐19 cases. Such analysis highlighted the significantly delayed impact of UVDVF on the cumulative relative risk of COVID‐19 infection. The findings of this study suggest that low UV exposure can affect the required production of vitamin D in the body, which substantially influences the dynamics of COVID‐19 transmission and severity.
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Affiliation(s)
- Sunanda Biswas Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Alessandro Gorohovski
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Eugene Merzon
- Leumit Health Services, Tel Aviv, Israel.,Department of Family Medicine, Sackler School of Medicine, Tel Aviv University, Israel
| | - Eliad Levy
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Sumit Mukherjee
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Milana Frenkel-Morgenstern
- Cancer Genomics and BioComputing of Complex Diseases Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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Tan E, Frew E, Cooper J, Humphrey J, Holden M, Mand AR, Li J, Anderson S, Bi M, Hatler J, Person A, Mortari F, Gould K, Barry S. Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. Diagnostics (Basel) 2021; 11:1190. [PMID: 34208912 PMCID: PMC8303872 DOI: 10.3390/diagnostics11071190] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/23/2022] Open
Abstract
Identifying anti-spike antibodies that exhibit strong neutralizing activity against current dominant circulating variants, and antibodies that are escaped by these variants, has important implications in the development of therapeutic and diagnostic solutions and in improving understanding of the humoral response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We characterized seven anti-SARS-CoV-2 receptor binding domain (RBD) antibodies for binding activity, pairing capability, and neutralization activity to SARS-CoV-2 and three variant RBDs via lateral flow immunoassays. The results allowed us to group these antibodies into three distinct epitope bins. Our studies showed that two antibodies had broadly potent neutralizing activity against SARS-CoV-2 and these variant RBDs and that one antibody did not neutralize the South African (SA) and Brazilian P.1 (BR P.1) RBDs. The antibody escaped by the SA and BR P.1 RBDs retained binding activity to SA and BR P.1 RBDs but was unable to induce neutralization. We demonstrated that lateral flow immunoassay could be a rapid and effective tool for antibody characterization, including epitope classification and antibody neutralization kinetics. The potential contributions of the mutations (N501Y, E484K, and K417N/T) contained in these variants' RBDs to the antibody pairing capability, neutralization activity, and therapeutic antibody targeting strategy are discussed.
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Affiliation(s)
- Enqing Tan
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Erica Frew
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Jeff Cooper
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - John Humphrey
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Matthew Holden
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Amanda Restell Mand
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Jun Li
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Shaya Anderson
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Ming Bi
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Julia Hatler
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Anthony Person
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Frank Mortari
- Corporate Development, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA;
| | - Kevin Gould
- Diagnostic Reagents Division, Bio-Techne Corporation, San Marcos Site, San Marcos, CA 92078, USA
| | - Shelly Barry
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
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Panahi A, Sadighbayan D, Forouhi S, Ghafar-Zadeh E. Recent Advances of Field-Effect Transistor Technology for Infectious Diseases. BIOSENSORS-BASEL 2021; 11:bios11040103. [PMID: 33918325 PMCID: PMC8065562 DOI: 10.3390/bios11040103] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Field-effect transistor (FET) biosensors have been intensively researched toward label-free biomolecule sensing for different disease screening applications. High sensitivity, incredible miniaturization capability, promising extremely low minimum limit of detection (LoD) at the molecular level, integration with complementary metal oxide semiconductor (CMOS) technology and last but not least label-free operation were amongst the predominant motives for highlighting these sensors in the biosensor community. Although there are various diseases targeted by FET sensors for detection, infectious diseases are still the most demanding sector that needs higher precision in detection and integration for the realization of the diagnosis at the point of care (PoC). The COVID-19 pandemic, nevertheless, was an example of the escalated situation in terms of worldwide desperate need for fast, specific and reliable home test PoC devices for the timely screening of huge numbers of people to restrict the disease from further spread. This need spawned a wave of innovative approaches for early detection of COVID-19 antibodies in human swab or blood amongst which the FET biosensing gained much more attention due to their extraordinary LoD down to femtomolar (fM) with the comparatively faster response time. As the FET sensors are promising novel PoC devices with application in early diagnosis of various diseases and especially infectious diseases, in this research, we have reviewed the recent progress on developing FET sensors for infectious diseases diagnosis accompanied with a thorough discussion on the structure of Chem/BioFET sensors and the readout circuitry for output signal processing. This approach would help engineers and biologists to gain enough knowledge to initiate their design for accelerated innovations in response to the need for more efficient management of infectious diseases like COVID-19.
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Affiliation(s)
- Abbas Panahi
- Biologically Sensors and Actuators (BioSA) Laboratory, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada; (A.P.); (D.S.); (S.F.)
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada
| | - Deniz Sadighbayan
- Biologically Sensors and Actuators (BioSA) Laboratory, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada; (A.P.); (D.S.); (S.F.)
- Department of Biology, Faculty of Science, York University, Keel Street, Toronto, ON M3J 1P3, Canada
| | - Saghi Forouhi
- Biologically Sensors and Actuators (BioSA) Laboratory, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada; (A.P.); (D.S.); (S.F.)
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Sensors and Actuators (BioSA) Laboratory, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada; (A.P.); (D.S.); (S.F.)
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Keel Street, Toronto, ON M3J 1P3, Canada
- Department of Biology, Faculty of Science, York University, Keel Street, Toronto, ON M3J 1P3, Canada
- Correspondence: ; Tel.: +1-(416)-736-2100 (ext. 44646)
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Abstract
With the advent of the pandemic (e.g., novel corona virus disease 2019 (COVID-19)), a tremendous amount of data about individuals are collected by the health authorities on daily basis for curbing the disease’s spread. The individuals’ data collection/processing at a massive scale for community well-being with the help of digital solutions (e.g., mobile apps for mobility and proximity analysis, contact tracing through credit card usage history, facial recognition through cameras, and crowd analysis using cellular networks data etc.) raise several privacy concerns. Furthermore, the privacy concerns that are arising mainly due to the fine-grained data collection has hindered the response to tackle this pandemic in many countries. Hence, acquiring/handling individuals data with privacy protection has become a vibrant area of research in these pandemic times. This paper explains the shift in privacy paradigm due to the pandemic (e.g., COVID-19) which involves more and detailed data collection about individuals including locations and demographics. We explain technical factors due to which the people’s privacy is at higher risk in the COVID-19 time. In addition, we discuss privacy concerns in different epidemic control measures (ECMs) (e.g., contact tracing, quarantine monitoring, and symptoms reporting etc.) employed by the health authorities to tackle this disease. Further, we provide an insight on the data management in the ECMs with privacy protection. Finally, the future prospects of the research in this area tacking into account the emerging technologies are discussed. Through this brief article, we aim to provide insights about the vulnerability to user’s privacy in pandemic times, likely privacy issues in different ECMs adopted by most countries around the world, how to preserve user’s privacy effectively in all phases of the ECMs considering relevant data in loop, and conceptual foundations of ECMs to fight with future pandemics in a privacy preserving manner.
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