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Song J, Jeong S, Choi S, Oh YH, Park SJ, Chang JY, Cho Y, Byeon K, Choi JY, Lee S, Jung J, Park SM. Inverse association with COVID-19 vaccination status of the incidence of pneumonia after SARS-CoV-2 infection: A nationwide retrospective cohort study. J Infect Public Health 2024; 17:650-656. [PMID: 38430718 DOI: 10.1016/j.jiph.2024.02.005] [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: 03/12/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Although one of the characteristics of COVID-19 is accompanied by acute pneumonia immediately after infection, large-scale cohort studies focused on this issue are lacking. In addition, there is interest in how COVID-19 vaccinations reduce the incidence of acute pneumonia for people infected with different strains of SARS-CoV-2. Thus, we assess the short-term incidence of pneumonia after COVID-19 with the vaccination and SARS-CoV-2 variants. METHODS As data for 2136,751 COVID-19 patients between January 01, 2020 and February 28, 2022 was collected, they were observed for one month from the day of infection. Patients in retrospective cohort study were classified according to doses of the received vaccine and the epidemic phase when SARS-CoV-2 variants prevailed. Multivariable logistic regression analysis calculated adjusted odds ratios (aOR) and 95% confidence intervals (CIs) for the pneumonia risk. RESULTS In B.1.1.7-B.1.351, B.1.617.2, and B.1.617.2 variants, the aORs (95% CIs; p-value) for incidence of pneumonia were 0.93 (0.89-0.98; <0.001), 0.74 (0.70-0.78; <0.001), and 0.04 (0.038-0.043; <0.001), respectively, compared to the original strain. More than 80% of patients have received the second and more doses of the vaccine (average age=44.67 years). The aORs (95% CIs; p-value) for pneumonia were 0.61 (0.58-0.64; <0.001), 0.39 (0.38-0.40; <0.001), and 0.18 (0.166-0.184; <0.001) in patients who received the first (N = 68,216), second (N = 898,838), and ≥ third doses (N = 836,173), respectively, compared to unvaccinated patients. According to the received vaccine (second dose of mRNA or viral vector), those who received BNT162b2 and mRNA-1273 (N = 787,980) had lower risk of pneumonia, compared to that in those who received h ChAdOx1 nCov-19 and AD26. COV2-S (N = 89,024). CONCLUSIONS Our findings suggest that the second and ≥ third doses (61% and 82% of risk aversion effect increased, respectively) of the COVID-19 vaccine can prevent the COVID-19-related pneumonia, regardless of the variants.
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Affiliation(s)
- Jihun Song
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Seogsong Jeong
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seulggie Choi
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yun Hwan Oh
- Department of Family Medicine, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Gwangmyeong©, Republic of Korea
| | - Sun Jae Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Joo Young Chang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Yoosun Cho
- Total Healthcare Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul, Republic of Korea
| | - Kyeonghyang Byeon
- Associate Research Fellow, Big Data Department, National Health Insurance Service, Wonju, Republic of Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seju Lee
- Division of Infectious Diseases, Department of Internal Medicine, Inha University College of Medicine, Incheon, Republic of Korea
| | - Jaehun Jung
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon 21556, Republic of Korea
| | - Sang Min Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea; Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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Wani SA, Gulzar B, Khan MS, Majid S, Bhat IA. Impact of Age and Clinico-Biochemical Parameters on Clinical Severity of SARS-CoV-2 Infection. Intervirology 2023; 66:88-96. [PMID: 37263256 PMCID: PMC10353304 DOI: 10.1159/000530906] [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: 03/21/2022] [Accepted: 04/13/2023] [Indexed: 06/03/2023] Open
Abstract
INTRODUCTION The surge in novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leading to coronavirus disease-2019 (COVID-19) has overwhelmed the health system. To help health-care workers and policy makers prioritize treatment and to decrease the burden on health systems caused by COVID-19, clinical severity along with various clinico-biochemical parameters was evaluated by designing a cross-sectional study comprising 236 SARS-CoV-2-infected individuals from Kashmir Valley, India. METHODS Briefly, real-time polymerase chain reaction (RT-PCR) was used for the confirmation of SARS-CoV-2 infection. The principles of spectrophotometry and chemiluminescent microparticle immunoassay (CMIA) were employed to estimate the levels of glucose, TSH, and 25-hydroxy vitamin D levels in serum of infected patients. RESULTS A total of 236 patients infected with SARS-CoV-2 were taken for this cross-sectional study. Patients with COVID-19 had a male predominance (72.9 vs. 27.1%) and a higher prevalence of 25-hydroxy vitamin D deficiency (72.0 vs. 28.0%) with a mean 25-hydroxy vitamin D levels of 24.0 ± 13.9 in ng/mL. We observed a varied clinical spectrum of SARS-CoV-2 infection with 36.4%, 23.7%, and 29.7% patients having mild, moderate, and severe disease, respectively. We observed that severity of SARS-CoV-2 infection was significantly associated with older age group, hypertension, low TSH levels, and 25-hydroxy vitamin D deficiency. CONCLUSION We conclude that not only old age but also hypertension and low levels of TSH and 25-hydroxy vitamin D levels could significantly lead to clinical severity of SARS-CoV-2 infection.
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Affiliation(s)
- Shariq Ahmad Wani
- Department of Medicine, Government Medical College Srinagar and Associated Hospitals, Jammu and Kashmir, India
| | - Babar Gulzar
- Department of Medicine, Government Medical College Srinagar and Associated Hospitals, Jammu and Kashmir, India
| | - Mosin Saleem Khan
- Department of Biochemistry, Government Medical College Baramulla and Associated Hospitals, Jammu and Kashmir, India
| | - Sabhiya Majid
- Department of Biochemistry, Government Medical College Baramulla and Associated Hospitals, Jammu and Kashmir, India
| | - Irfan Ahmad Bhat
- Department of Medicine, Government Medical College Srinagar and Associated Hospitals, Jammu and Kashmir, India
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Filgueiras PS, Corsini CA, Almeida NBF, Pedrosa MLC, Miranda DAPD, Gomes SVC, Assis JVD, Silva RA, Medeiros MIVDARCD, Lourenço AJ, Bicalho CMF, Vilela RVR, Jeremias WDJ, Fernandes GDR, Queiroz RFGE. Rapid antigen test as a tool for the identification of SARS-CoV-2 infection and its potential as a self-testing device. Rev Soc Bras Med Trop 2023; 56:e01672022. [PMID: 37222349 DOI: 10.1590/0037-8682-0167-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 03/01/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND SARS-CoV-2 virus originated in Wuhan (China) in December (2019) and quickly spread worldwide. Antigen tests are rapid diagnostic tests (RDT) that produce results in 15-30 min and are an important tool for the scale-up of COVID-19 testing. COVID-19 diagnostic tests are authorized for self-testing at home in some countries, including Brazil. Widespread COVID-19 diagnostic testing is required to guide public health policies and control the speed of transmission and economic recovery. METHODS Patients with suspected COVID-19 were recruited at the Hospital da Baleia (Belo Horizonte, Brazil). The SARS-CoV-2 antigen-detecting rapid diagnostic tests were evaluated from June 2020 to June 2021 using saliva, nasal, and nasopharyngeal swab samples from 609 patients. Patient samples were simultaneously tested using a molecular assay (RT-qPCR). Sensitivity, specificity, accuracy, and positive and negative predictive values were determined using the statistical program, MedCalc, and GraphPad Prism 8.0. RESULTS The antigen-detecting rapid diagnostic tests displayed 98% specificity, 60% sensitivity, 96% positive predictive value, and moderate concordance with RT-qPCR. Substantial agreement was found between the two methods for patients tested < 7 days of symptom onset. CONCLUSIONS Our findings support the use of Ag-RDT as a valuable and safe diagnostic method. Ag-RDT was also demonstrated to be an important triage tool for suspected COVID-19 patients in emergencies. Overall, Ag-RDT is an effective strategy for reducing the spread of SARS-CoV-2 and contributing to COVID-19 control.
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Affiliation(s)
- Priscilla Soares Filgueiras
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Patologia, Belo Horizonte, MG, Brasil
| | - Camila Amormino Corsini
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Nathalie Bonatti Franco Almeida
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade da Geórgia, Faculdade de Medicina Veterinária, Departamento de Doenças Infecciosas, Athens, GA, Estados Unidos da América
| | - Maria Luysa Camargos Pedrosa
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Daniel Alvim Pena de Miranda
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Sarah Vieira Contin Gomes
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
| | - Jéssica Vieira de Assis
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Patologia, Belo Horizonte, MG, Brasil
| | | | | | | | | | | | - Wander de Jesus Jeremias
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Ouro Preto, Departamento de Farmácia, Ouro Preto, MG, Brasil
| | | | - Rafaella Fortini Grenfell E Queiroz
- Fundação Oswaldo Cruz, Instituto René Rachou, Diagnóstico e Terapia de Doenças Infecciosas e Câncer, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Patologia, Belo Horizonte, MG, Brasil
- Universidade da Geórgia, Faculdade de Medicina Veterinária, Departamento de Doenças Infecciosas, Athens, GA, Estados Unidos da América
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Santana PA, Álvarez CA, Valenzuela S, Manchego A, Guzmán F, Tirapegui C, Ahumada M. Stability of ACE2 Peptide Mimetics and Their Implications on the Application for SARS-CoV2 Detection. BIOSENSORS 2023; 13:bios13040473. [PMID: 37185548 PMCID: PMC10136198 DOI: 10.3390/bios13040473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
The SARS-CoV-2 worldwide outbreak prompted the development of several tools to detect and treat the disease. Among the new detection proposals, the use of peptides mimetics has surged as an alternative to avoid the use of antibodies, of which there has been a shortage during the COVID-19 pandemic. However, the use of peptides in detection systems still presents some questions to be answered, mainly referring to their stability under different environmental conditions. In this work, we synthesized an ACE2 peptide mimic and evaluated its stability in different pH, salinity, polarity, and temperature conditions. Further, the same conditions were assessed when using the ability of the peptide mimic to detect the recombinant SARS-CoV-2 spike protein in a biotin-streptavidin-enzyme-linked assay. Finally, we also tested the capacity of the peptide to detect SARS-CoV-2 from patients' samples. The results indicate that the peptide is structurally sensitive to the medium conditions, with relevance to the pH, where basic pH favored its performance when used as a SARS-CoV-2 detector. Further, the proposed peptide mimic was able to detect SARS-CoV-2 comparably to RT-qPCR results. Therefore, the present study promotes knowledge advancement, particularly in terms of stability considerations, in the application of peptide mimics as a replacement for antibodies in detection systems.
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Affiliation(s)
- Paula A Santana
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Claudio A Álvarez
- Laboratorio de Fisiología y Genética Marina, Centro de Estudios Avanzados en Zonas Áridas, Larrondo 1281, Coquimbo 1780000, Chile
- Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile
| | - Santiago Valenzuela
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Alberto Manchego
- Laboratorio de Microbiología, Facultad de Medicina Veterinaria y Parasitología Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 3673, Peru
| | - Fanny Guzmán
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Cristian Tirapegui
- Instituto de Ciencias Químicas Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, el Llano Subercaseaux 2801, San Miguel, Santiago 8910272, Chile
| | - Manuel Ahumada
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago 8910272, Chile
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Camino La Piramide 5750, Huechuraba, Santiago 8910272, Chile
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Kirub E. Re: Vitamin D deficiency predicts 30-day hospital mortality of adults with COVID-19. Clin Nutr ESPEN 2023; 54:459. [PMID: 36963895 PMCID: PMC9984282 DOI: 10.1016/j.clnesp.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023]
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6
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Musa A, Abulkhair HS, Aljuhani A, Rezki N, Abdelgawad MA, Shalaby K, El-Ghorab AH, Aouad MR. Phenylpyrazolone-1,2,3-triazole Hybrids as Potent Antiviral Agents with Promising SARS-CoV-2 Main Protease Inhibition Potential. Pharmaceuticals (Basel) 2023; 16:ph16030463. [PMID: 36986562 PMCID: PMC10051656 DOI: 10.3390/ph16030463] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
COVID-19 infection is now considered one of the leading causes of human death. As an attempt towards the discovery of novel medications for the COVID-19 pandemic, nineteen novel compounds containing 1,2,3-triazole side chains linked to phenylpyrazolone scaffold and terminal lipophilic aryl parts with prominent substituent functionalities were designed and synthesized via a click reaction based on our previous work. The novel compounds were assessed using an in vitro effect on the growth of SARS-CoV-2 virus-infested Vero cells with different compound concentrations: 1 and 10 μM. The data revealed that most of these derivatives showed potent cellular anti-COVID-19 activity and inhibited viral replication by more than 50% with no or weak cytotoxic effect on harboring cells. In addition, in vitro assay employing the SARS-CoV-2-Main protease inhibition assay was done to test the inhibitors' ability to block the common primary protease of the SARS-CoV-2 virus as a mode of action. The obtained results show that the one non-linker analog 6h and two amide-based linkers 6i and 6q were the most active compounds with IC50 values of 5.08, 3.16, and 7.55 μM, respectively, against the viral protease in comparison to data of the selective antiviral agent GC-376. Molecular modeling studies were done for compound placement within the binding pocket of protease which reveal conserved residues hydrogen bonding and non-hydrogen interactions of 6i analog fragments: triazole scaffold, aryl part, and linker. Moreover, the stability of compounds and their interactions with the target pocket were also studied and analyzed by molecular dynamic simulations. The physicochemical and toxicity profiles were predicted, and the results show that compounds behave as an antiviral activity with low or no cellular or organ toxicity. All research results point to the potential usage of new chemotype potent derivatives as promising leads to be explored in vivo that might open the door to rational drug development of SARS-CoV-2 Main protease potent medicines.
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Affiliation(s)
- Arafa Musa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Hamada S Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo 11884, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University-Egypt, International Coastal Road, New Damietta 34518, Egypt
| | - Ateyatallah Aljuhani
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
| | - Nadjet Rezki
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Khaled Shalaby
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia
| | - Ahmed H El-Ghorab
- Department of Chemistry, College of Science, Jouf University, Sakaka 72341, Saudi Arabia
| | - Mohamed R Aouad
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
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Kumar THV, Srinivasan S, Krishnan V, Vaidyanathan R, Babu KA, Natarajan S, Veerapandian M. Peptide-based direct electrochemical detection of receptor binding domains of SARS-CoV-2 spike protein in pristine samples. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 377:133052. [PMID: 36438197 PMCID: PMC9682882 DOI: 10.1016/j.snb.2022.133052] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
RNA isolation and amplification-free user-friendly detection of SARS-CoV-2 is the need of hour especially at resource limited settings. Herein, we devised the peptides of human angiotensin converting enzyme-2 (hACE-2) as bioreceptor at electrode interface for selective targeting of receptor binding domains (RBD) of SARS-CoV-2 spike protein (SP). Disposable carbon-screen printed electrode modified with methylene blue (MB) electroadsorbed graphene oxide (GO) has been constructed as cost-efficient and scalable platform for hACE-2 peptide-based SARS-CoV-2 detection. In silico molecular docking of customized 25 mer peptides with RBD of SARS-CoV-2 SP were validated by AutoDock CrankPep. N-terminal region of ACE-2 showed higher binding affinity of - 20.6 kcal/mol with 15 H-bond, 9 of which were < 3 Å. Electrochemical biosensing of different concentrations of SPs were determined by cyclic voltammetry (CV) and chronoamperometry (CA), enabling a limit of detection (LOD) of 0.58 pg/mL and 0.71 pg/mL, respectively. MB-GO devised hACE-2 peptide platform exert an enhanced current sensitivity of 0.0105 mA/pg mL-1 cm-2 (R2 = 0.9792) (CV) and 0.45 nA/pg mL-1 (R2 = 0.9570) (CA) against SP in the range of 1 pg/mL to 1 µg/mL. For clinical feasibility, nasopharyngeal and oropharyngeal swab specimens in viral transport medium were directly tested with the prepared peptide biosensor and validated with RT-PCR, promising for point-of-need analysis.
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Affiliation(s)
- T H Vignesh Kumar
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India
| | - Sowmiya Srinivasan
- Dr. A.P.J. Abdul Kalam Center of Excellence in Innovation and Entrepreneurship, Dr. M.G.R. Educational and Research Institute, Chennai 600095, Tamil Nadu, India
| | - Vinoth Krishnan
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rama Vaidyanathan
- Dr. A.P.J. Abdul Kalam Center of Excellence in Innovation and Entrepreneurship, Dr. M.G.R. Educational and Research Institute, Chennai 600095, Tamil Nadu, India
- Department of Biotechnology, Dr. M.G.R. Educational and Research Institute, Chennai 600095, Tamil Nadu, India
| | - Kannadasan Anand Babu
- Dr. A.P.J. Abdul Kalam Center of Excellence in Innovation and Entrepreneurship, Dr. M.G.R. Educational and Research Institute, Chennai 600095, Tamil Nadu, India
| | - Sudhakar Natarajan
- Department of Virology and Biotechnology, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Murugan Veerapandian
- Electrodics and Electrocatalysis Division, CSIR-Central Electrochemical Research Institute (CECRI), Karaikudi 630003, Tamil Nadu, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Çelik A, Emiralioğlu O, Yeken MZ, Çiftçi V, Özer G, Kim Y, Baloch FS, Chung YS. A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris. Front Genet 2023; 14:1136794. [PMID: 37021006 PMCID: PMC10067576 DOI: 10.3389/fgene.2023.1136794] [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: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yoonha Kim
- Laboratory of Crop Production, Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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Salman H, Al-Khero Z, Al-Aziz Yousif Z, Thanoon A. The consequences of severe acute respiratory syndrome coronavirus-2 on acute kidney injury among iraqi patients. BIOMEDICAL AND BIOTECHNOLOGY RESEARCH JOURNAL (BBRJ) 2023. [DOI: 10.4103/bbrj.bbrj_353_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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10
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Detection of Recombinant Proteins SOX2 and OCT4 Interacting in HEK293T Cells Using Real-Time Quantitative PCR. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010107. [PMID: 36676054 PMCID: PMC9862934 DOI: 10.3390/life13010107] [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: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
In vivo biotinylation using wild-type and mutants of biotin ligases is now widely applied for the study of cellular proteomes. The commercial availability of kits for the highly efficient purification of biotinylated proteins and their excellent compatibility with LC-MS/MS protocols are the main reasons for the choice of biotin ligases. Since they are all enzymes, however, just a very low expression in cells is required for experiments. Therefore, it can be difficult to perform the quantifications of these enzymes in various samples. Traditional methods, such as western blotting, are not always fit for the detection of the expression levels. Therefore, real-time qRT-PCR, a technology that is more sensitive, was used in this study to quantify the expression of BirA fusions. Using this method, we detected high expression levels of BirA fusions in models of interactions of pluripotency transcription factors to carry out their relative quantification. We also found the absence of the competing endogenous proteins SOX2 and OCT4, as well as no cross-reactivity between BAP/BirA and the endogenous biotinylation system in HEK293T cells. Thus, these data indicated that the high level of biotinylation is due to the in vivo interaction of BAP-X and BirA-Y (X,Y = SOX2, OCT4) in the cell rather than their random collision, a big difference in the expression level of BirA fusions across samples or endogenous biotinylation.
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11
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de Sousa GF, Nogueira TDS, de Sales LS, Ferreira Maissner F, Araújo de Oliveira O, Rangel HL, dos Santos DDG, Nunes-da-Fonseca R, de Souza-Menezes J, Nepomuceno-Silva JL, Mury FB, de Souza Gestinari R, Tanuri A, Ferreira Jr ODC, Monteiro-de-Barros C. The long-term dynamics of serum antibodies against SARS-CoV-2. PeerJ 2022; 10:e14547. [PMID: 36540807 PMCID: PMC9760025 DOI: 10.7717/peerj.14547] [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: 08/03/2022] [Accepted: 11/20/2022] [Indexed: 12/23/2022] Open
Abstract
Objective To analyze the long-term dynamics of antibodies against SARS-CoV-2 and understand the impact of age, gender, and viral load on patients' immunological response. Methods Serum samples were obtained from 231 COVID-19 positive patients from Macaé, in Rio de Janeiro state, in Brazil, from June 2020 until January 2021. The production of IgA, IgM, IgG, and IgE against S glycoprotein was analyzed using the S-UFRJ assay, taking into account the age, gender, and viral load. Results Analysis of antibody production over 7 months revealed that IgA positivity gradually decreased after the first month. Additionally, the highest percentage of IgM positivity occurred in the first month (97% of patients), and declined after this period, while IgG positivity remained homogeneous for all 7 months. The same analysis for IgE revealed that almost all samples were negative. The comparison of antibody production between genders showed no significant difference. Regarding the age factor and antibody production, patients aged ≥60 years produced almost twice more IgA than younger ones (17-39 years old). Finally, a relationship between viral load and antibody production was observed only for older patients. Conclusions Our work provides an overview of long-term production of antibodies against SARS-CoV-2, suggesting prolonged production of IgA and IgM antibodies for 3 months and continued IgG production for over 7 months. In addition, it identified a correlation between viral load and IgM titers in the older group and, finally, different IgA production between the age groups.
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Affiliation(s)
- Graziele Fonseca de Sousa
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Thuany da Silva Nogueira
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Lana Soares de Sales
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Fernanda Ferreira Maissner
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Odara Araújo de Oliveira
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Hellade Lopes Rangel
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Daniele das Graças dos Santos
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Jackson de Souza-Menezes
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Jose Luciano Nepomuceno-Silva
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Flávia Borges Mury
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Raquel de Souza Gestinari
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando da Costa Ferreira Jr
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cintia Monteiro-de-Barros
- Instituto de Biodiversidade e Sustentabilidade, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
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12
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Hwang CH, Lee S, Lee S, Kim H, Kang T, Lee D, Jeong KH. Highly Adsorptive Au-TiO 2 Nanocomposites for the SERS Face Mask Allow the Machine-Learning-Based Quantitative Assay of SARS-CoV-2 in Artificial Breath Aerosols. ACS APPLIED MATERIALS & INTERFACES 2022; 14:54550-54557. [PMID: 36448483 PMCID: PMC9718102 DOI: 10.1021/acsami.2c16446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Human respiratory aerosols contain diverse potential biomarkers for early disease diagnosis. Here, we report the direct and label-free detection of SARS-CoV-2 in respiratory aerosols using a highly adsorptive Au-TiO2 nanocomposite SERS face mask and an ablation-assisted autoencoder. The Au-TiO2 SERS face mask continuously preconcentrates and efficiently captures the oronasal aerosols, which substantially enhances the SERS signal intensities by 47% compared to simple Au nanoislands. The ultrasensitive Au-TiO2 nanocomposites also demonstrate the successful detection of SARS-CoV-2 spike proteins in artificial respiratory aerosols at a 100 pM concentration level. The deep learning-based autoencoder, followed by the partial ablation of nondiscriminant SERS features of spike proteins, allows a quantitative assay of the 101-104 pfu/mL SARS-CoV-2 lysates (comparable to 19-29 PCR cyclic threshold from COVID-19 patients) in aerosols with an accuracy of over 98%. The Au-TiO2 SERS face mask provides a platform for breath biopsy for the detection of various biomarkers in respiratory aerosols.
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Affiliation(s)
- Charles
S. H. Hwang
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Korea
| | - Sangyeon Lee
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Sejin Lee
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Korea
| | - Hanjin Kim
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Taejoon Kang
- Bionanotechnology
Research Center, Korea Research Institute
of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
- School
of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Doheon Lee
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Ki-Hun Jeong
- Department
of Bio and Brain Engineering, Korea Advanced
Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
- KAIST
Institute for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro,
Yuseong-gu, Daejeon 34141, Korea
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13
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Vásquez V, Orozco J. Detection of COVID-19-related biomarkers by electrochemical biosensors and potential for diagnosis, prognosis, and prediction of the course of the disease in the context of personalized medicine. Anal Bioanal Chem 2022; 415:1003-1031. [PMID: 35970970 PMCID: PMC9378265 DOI: 10.1007/s00216-022-04237-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 02/07/2023]
Abstract
As a more efficient and effective way to address disease diagnosis and intervention, cutting-edge technologies, devices, therapeutic approaches, and practices have emerged within the personalized medicine concept depending on the particular patient's biology and the molecular basis of the disease. Personalized medicine is expected to play a pivotal role in assessing disease risk or predicting response to treatment, understanding a person's health status, and, therefore, health care decision-making. This work discusses electrochemical biosensors for monitoring multiparametric biomarkers at different molecular levels and their potential to elucidate the health status of an individual in a personalized manner. In particular, and as an illustration, we discuss several aspects of the infection produced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a current health care concern worldwide. This includes SARS-CoV-2 structure, mechanism of infection, biomarkers, and electrochemical biosensors most commonly explored for diagnostics, prognostics, and potentially assessing the risk of complications in patients in the context of personalized medicine. Finally, some concluding remarks and perspectives hint at the use of electrochemical biosensors in the frame of other cutting-edge converging/emerging technologies toward the inauguration of a new paradigm of personalized medicine.
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Affiliation(s)
- Viviana Vásquez
- grid.412881.60000 0000 8882 5269Max Planck Tandem Group in Nanobioengineering, Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia, Complejo Ruta N, Calle 67 N° 52-20, Medellín, 050010 Colombia
| | - Jahir Orozco
- grid.412881.60000 0000 8882 5269Max Planck Tandem Group in Nanobioengineering, Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia, Complejo Ruta N, Calle 67 N° 52-20, Medellín, 050010 Colombia
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14
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Update on the Development of Toehold Switch-Based Approach for Molecular Diagnostic Tests of COVID-19. J Nucleic Acids 2022; 2022:7130061. [PMID: 35586794 PMCID: PMC9110250 DOI: 10.1155/2022/7130061] [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: 02/18/2022] [Accepted: 04/22/2022] [Indexed: 11/18/2022] Open
Abstract
A high volume of diagnostic tests is needed during the coronavirus disease 2019 (COVID-19) pandemic to obtain representative results. These results can help to design and implement effective policies to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis using current gold standard methods, i.e., real-time quantitative PCR (RT-qPCR), is challenging, especially in areas with limited trained personnel and health-related infrastructure. The toehold switch-based diagnostic system is a promising alternative method for detecting SARS-CoV-2 that has advantages such as inexpensive cost per testing, rapid, and highly sensitive and specific analysis. Moreover, the system can be applied to paper-based platforms, simplifying the distribution and utilization in low-resource settings. This review provides insight into the development of toehold switch-based diagnostic devices as the most recent methods for detecting SARS-CoV-2.
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15
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Choi S, Kim KW, Ku KB, Kim SJ, Park C, Park D, Kim S, Yi H. Human Alphacoronavirus Universal Primers for Genome Amplification and Sequencing. Front Microbiol 2022; 13:789665. [PMID: 35401489 PMCID: PMC8990890 DOI: 10.3389/fmicb.2022.789665] [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: 10/05/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate sequencing covering the entire genome is essential to identify genetic variations of viral pathogens. However, due to the low viral titers in clinical samples, certain amplification steps are required for viral genome sequencing. At present, there are no universal primers available for alphacoronaviruses and that, since these viruses have diverse strains, new primers specific to the target strain must be continuously developed for sequencing. Thus, in this study, we aimed to develop a universal primer set valid for all human alphacoronaviruses and applicable to samples containing trace amounts of the virus. To this aim, we designed overlapping primer pairs capable of amplifying the entire genome of all known human alphacoronaviruses. The selected primers, named the AC primer set, were composed of 10 primer pairs stretching over the entire genome of alphacoronaviruses, and produced PCR products of the expected size (3-5 kb) from both the HCoV-229E and HCoV-NL63 strains. After genome amplification, an evaluation using various sequencing platforms was carried out. The amplicon library sequencing data were assembled into complete genome sequences in all sequencing strategies examined in this study. The sequencing accuracy varied depending on the sequencing technology, but all sequencing methods showed a sequencing error of less than 0.01%. In the mock clinical specimen, the detection limit was 10-3 PFU/ml (102 copies/ml). The AC primer set and experimental procedure optimized in this study may enable the fast diagnosis of mutant alphacoronaviruses in future epidemics.
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Affiliation(s)
- Sungmi Choi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Kwan Woo Kim
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Changwoo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Dongju Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Biological Science, Chungnam National University, Daejeon, South Korea
| | - Seil Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, South Korea.,Department of Bio-Analysis Science, University of Science and Technology, Daejeon, South Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, South Korea.,School of Biosystems and Biomedical Sciences, Korea University, Seoul, South Korea
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16
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Tabilo Valenzuela PB, Flores Balter G, Saint-Pierre Contreras G, Conei Valencia D, Moreno Calderón C, Bohle Venegas C, Guajardo Rivera M, Silva Ojeda F, Vial Covarrubias MJ. Cellular Immune Response in Patients Immunized with Three Vaccine Doses of Different Vaccination Schemes Authorized by the Chilean Ministry of Health in January 2022. Life (Basel) 2022; 12:life12040534. [PMID: 35455024 PMCID: PMC9030012 DOI: 10.3390/life12040534] [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: 02/22/2022] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022] Open
Abstract
In December 2019, a case of atypical pneumonia was reported in Wuhan, China. It was named COVID-19 and caused by SARS-CoV-2. In a few months, scientific groups around the world developed vaccines to reduce the disease’s severity. The objective was to evaluate the humoral and cellular immune response post immunization with three different vaccination schedules administered in Chile until January 2022. Sixty volunteers were recruited with a three-dose schedule, who had no history of infection nor close contact with a positive patient. IgG against the spike antigenic domain was detected, and the neutralization capacity against two groups of variants, Original/Alpha and Beta/Gamma, was also measured. Finally, the cellular response with interferon release was measured through IGRA. Results showed that there were significant differences in the neutralizing antibodies for the original and alpha variant when comparing three Comirnaty doses with Coronavac and Vaxzevria. A high number of reactive subjects against the different SARS-CoV-2 variants, alpha, gamma, and delta, were observed, with no significant differences between any of the three schemes, confirming the existence of a cellular immune response against SARS-CoV-2. In conclusion, the three vaccine schemes generated a cellular immune response in these volunteers.
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Affiliation(s)
- Paz Beatriz Tabilo Valenzuela
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
- Correspondence: or ; Tel.: +56-22-2978-8070
| | - Gabriela Flores Balter
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
| | - Gustavo Saint-Pierre Contreras
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
| | - Daniel Conei Valencia
- Programa de Doctorado en Ciencias Morfológicas, Universidad de La Frontera, Temuco 4811230, Chile;
- Departamento de Ciencias de la Salud, Universidad de Aysén, Coyhaique 5951537, Chile
| | - Catalina Moreno Calderón
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
| | - Constanza Bohle Venegas
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
| | - Marcia Guajardo Rivera
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
| | - Francisco Silva Ojeda
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
| | - Maria Jesus Vial Covarrubias
- Servicio de Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile; (G.F.B.); (G.S.-P.C.); (C.M.C.); (C.B.V.); (M.G.R.); (F.S.O.); (M.J.V.C.)
- Jefe Departamento Laboratorio Clínico, Hospital Clínico Universidad de Chile, Santiago 8380000, Chile
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17
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Cha H, Kim H, Joung Y, Kang H, Moon J, Jang H, Park S, Kwon HJ, Lee IC, Kim S, Yong D, Yoon SW, Park SG, Guk K, Lim EK, Park HG, Choo J, Jung J, Kang T. Surface-enhanced Raman scattering-based immunoassay for severe acute respiratory syndrome coronavirus 2. Biosens Bioelectron 2022; 202:114008. [PMID: 35086030 PMCID: PMC8770391 DOI: 10.1016/j.bios.2022.114008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected humans worldwide for over a year now. Although various tests have been developed for the detection of SARS-CoV-2, advanced sensing methods are required for the diagnosis, screening, and surveillance of coronavirus disease 2019 (COVID-19). Here, we report a surface-enhanced Raman scattering (SERS)-based immunoassay involving an antibody pair, SERS-active hollow Au nanoparticles (NPs), and magnetic beads for the detection of SARS-CoV-2. The selected antibody pair against the SARS-CoV-2 antigen, along with the magnetic beads, facilitates the accurate direct detection of the virus. The hollow Au NPs exhibit strong, reproducible SERS signals, allowing sensitive quantitative detection of SARS-CoV-2. This assay had detection limits of 2.56 fg/mL for the SARS-CoV-2 antigen and 3.4 plaque-forming units/mL for the SARS-CoV-2 lysates. Furthermore, it facilitated the identification of SARS-CoV-2 in human nasopharyngeal aspirates and diagnosis of COVID-19 within 30 min using a portable Raman device. Thus, this assay can be potentially used for the diagnosis and prevention of COVID-19.
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Affiliation(s)
- Hyunjung Cha
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyeran Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Younju Joung
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyunju Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jeong Moon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sohyun Park
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - In-Chul Lee
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Jinju, 52828, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sun-Woo Yoon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sung-Gyu Park
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, 51508, Republic of Korea
| | - Kyeonghye Guk
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
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18
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Zhang D, Duran SSF, Lim WYS, Tan CKI, Cheong WCD, Suwardi A, Loh XJ. SARS-CoV-2 in wastewater: From detection to evaluation. MATERIALS TODAY. ADVANCES 2022; 13:100211. [PMID: 35098102 PMCID: PMC8786653 DOI: 10.1016/j.mtadv.2022.100211] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/16/2022] [Accepted: 01/21/2022] [Indexed: 05/07/2023]
Abstract
SARS-CoV-2 presence in wastewater has been reported in several studies and has received widespread attention among the Wastewater-based epidemiology (WBE) community. Such studies can potentially be used as a proxy for early warning of potential COVID-19 outbreak, or as a mitigation measure for potential virus transmission via contaminated water. In this review, we summarized the latest understanding on the detection, concentration, and evaluation of SARS-CoV-2 in wastewater. Importantly, we discuss factors affecting the quality of wastewater surveillance ranging from temperature, pH, starting concentration, as well as the presence of chemical pollutants. These factors greatly affect the reliability and comparability of studies reported by various communities across the world. Overall, this review provides a broadly encompassing guidance for epidemiological study using wastewater surveillance.
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Affiliation(s)
- Danwei Zhang
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
| | - Solco S Faye Duran
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
| | - Wei Yang Samuel Lim
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
| | - Chee Kiang Ivan Tan
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
| | - Wun Chet Davy Cheong
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
| | - Ady Suwardi
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
| | - Xian Jun Loh
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Agency for Science, Technology and Research, Singapore, 138634
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19
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Aljuhani A, Ahmed HEA, Ihmaid SK, Omar AM, Althagfan SS, Alahmadi YM, Ahmad I, Patel H, Ahmed S, Almikhlafi MA, El-Agrody AM, Zayed MF, Turkistani SA, Abulkhair SH, Almaghrabi M, Salama SA, Al-Karmalawy AA, Abulkhair HS. In vitro and computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M Pro inhibitors. RSC Adv 2022; 12:26895-26907. [PMID: 36320844 PMCID: PMC9494209 DOI: 10.1039/d2ra04015h] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
An essential target for COVID-19 is the main protease of SARS-CoV-2 (Mpro). With the objective of targeting this receptor, a novel set of pyrido[1,2-a]pyrrolo[2,3-d]pyrimidines with terminal carboxamide fragments was designed, synthesized, and considered as an initial motif for the creation of effective pan-coronavirus inhibitors. Accordingly, nine derivatives (21–29) have been introduced for in vitro assay to evaluate their antiviral activity and cytotoxicity effect against COVID-19 virus using Vero cells. The obtained data revealed that the majority of these derivatives showed potent cellular anti-COVID-19 activity and prevent viral growth by more than 90% at two different concentrations with weak or even no detectable cytotoxic effect on Vero cells. Extensive molecular docking simulations highlighted proper non-covalent interaction of new compounds within the binding pocket of Mpro as a potential target for their antiviral activity. In vitro assay for all the synthesized derivatives against the viral Mpro target indicated that compounds 25 and 29 have promising inhibitory activity with IC50 values at low micromolar concentrations. The molecular dynamic simulation results predicted the stability of compound 29 in the binding cavity of SARS-CoV-2 Mpro and hence supported the high inhibitory activity shown by the In vitro assay. These results suggested that compounds 25 and 29 merit further investigations as promising drug candidates for the management of SARS-CoV-2. An essential target for COVID-19 is the main protease of SARS-CoV-2 (Mpro).![]()
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Affiliation(s)
- Ateyatallah Aljuhani
- Chemistry Department, College of Sciences, Taibah University, Al-Madinah Al-Munawarah 41477, Saudi Arabia
| | - Hany E. A. Ahmed
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Saleh K. Ihmaid
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Jadara University, Irbid, Jordan
| | - Abdelsattar M. Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Sultan S. Althagfan
- Clinical and Hospital Pharmacy Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Yaser M. Alahmadi
- Clinical and Hospital Pharmacy Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Sahar Ahmed
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assuit, Egypt
| | - Mohannad A. Almikhlafi
- Pharmacology and Toxicology Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Ahmed M. El-Agrody
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, Egypt
| | - Mohamed F. Zayed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
- Pharmaceutical Sciences Department, Fakeeh College for Medical Sciences, Jeddah 21461, Saudi Arabia
| | | | - Shorouk H. Abulkhair
- Department of Biochemistry, Faculty of Medicine, Al-Azhar University (Girls), Nasr City 11754, Cairo, Egypt
| | - Mohammed Almaghrabi
- Pharmacognosy and Pharmaceutical Chemistry Department, College of Pharmacy, Taibah University, Al-Madinah Al-Munawarah, Saudi Arabia
| | - Samir A. Salama
- Division of Biochemistry, Department of Pharmacology, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed A. Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University – Egypt, International Coastal Road, New Damietta 34518, Egypt
| | - Hamada S. Abulkhair
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City 11884, Cairo, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Horus University – Egypt, International Coastal Road, New Damietta 34518, Egypt
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20
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Abstract
In the past few years, the CRISPR (clustered regularly interspaced short palindromic repeats) applications in medicine and molecular biology have broadened. CRISPR has also been integrated with microfluidic-based biosensors to enhance the sensitivity and selectivity of medical diagnosis due to its great potentials. The CRISPR-powered microfluidics can help quantify DNAs and RNAs for different diseases such as cancer, and viral or bacterial diseases among others. Here in this review, we discussed the main applications of such tools along with their advantages and limitations.
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21
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Hossain ME, Rahman MM, Alam MS, Sarmin M, Karim Y, Hasan M, Hoque AF, Hasan MM, Rahman MZ, Chisti MJ, Rahman M. A Case Report: Genetically Distinct Severe Acute Respiratory Syndrome Coronavirus-2 Variant Causing Reinfection. Front Microbiol 2021; 12:792514. [PMID: 34956160 PMCID: PMC8696118 DOI: 10.3389/fmicb.2021.792514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022] Open
Abstract
Background: The emergence of novel variants has been a great deal of international concern since the recently published data suggest that previous infections with SARS-CoV-2 may not protect an individual from new variants. We report a patient had two distinct episodes of COVID-19 with different variants of SARS-CoV-2. Methods: The nasopharyngeal samples collected from the two episodes were subjected to whole-genome sequencing and comparative genome analysis. Results: The first infection presented with mild symptoms, while the second infection presented with severe outcomes which occurred 74 days after the patient recovered from the first episode. He had elevated C-reactive protein, ferritin, and bilateral consolidation as a sign of acute infection. Genome analysis revealed that the strains from the first and second episodes belonged to two distinct Nexstrain clades 20B and 20I and Pangolin lineages B.1.1.25 and B.1.1.7, respectively. A total of 36 mutations were observed in the episode-2 strain when compared with the reference strain Wuhan-Hu-1. Among them, eight mutations were identified in the receptor-binding domain (RBD). Conclusion: Our findings concern whether the immunity acquired by natural infection or mass vaccination could confer adequate protection against the constantly evolving SARS-CoV-2. Therefore, continuous monitoring of genetic variations of SARS-CoV-2 strains is crucial for interventions such as vaccine and drug designs, treatment using monoclonal antibodies, and patient management.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mustafizur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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22
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Lee CJ, Shin W, Mun S, Yu M, Choi YB, Kim DH, Han K. Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19. Genes Genomics 2021; 43:1277-1288. [PMID: 34524612 PMCID: PMC8441239 DOI: 10.1007/s13258-021-01162-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Background Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, first discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence. Objective We aimed to evaluate the diagnostic competency and efficiency with the Allplex™ 2019-nCoV Assay kit and the Dr. PCR 20 K COVID-19 Detection kit, designed based on the qRT-PCR and dPCR technologies, respectively. Methods A total of 30 negative and 20 COVID-19 positive specimens were assigned to the diagnostic test by using different COVID-19 diagnosis kits. Diagnostic accuracy was measured by statistical testing with sensitivity, specificity, and co-efficiency calculations. Results Comparing both diagnostic kits, we confirmed that the diagnostic results of 30 negative and 20 positive cases were the same pre-diagnostic results. The diagnostic statistics test results were perfectly matched with value (1). Cohen’s Kappa coefficient was demonstrated that the given kits in two different ways were “almost perfect” with value (1). In evaluating the detection capability, the dilutional linearity experiments substantiate that the Dr. PCR 20 K COVID-19 Detection kit could detect SARS-CoV-2 viral load at a concentration ten times lower than that of the Allplex™ 2019-nCoV Assay kit. Conclusions In this study, we propose that the dPCR diagnosis using LOAA dPCR could be a powerful method for COVID-19 point-of-care tests requiring immediate diagnosis in a limited time and space through the advantages of relatively low sample concentration and small equipment size compared to conventional qRT-PCR. Supplementary Information The online version contains supplementary material available at 10.1007/s13258-021-01162-4.
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Affiliation(s)
- Cherl-Joon Lee
- Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea
| | - Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.,DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea
| | - Minjae Yu
- DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea.,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Young-Bong Choi
- Department of Chemistry, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Dong Hee Kim
- Department of Anesthesiology and Pain Management, Dankook University College of Medicine, Cheonan, 31116, Republic of Korea.
| | - Kyudong Han
- Department of Bio-Convergence Engineering, Dankook University, Jukjeon, 16890, Republic of Korea. .,NGS Clinical Laboratory, Dankook University Hospital, Cheonan, 31116, Republic of Korea. .,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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