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Onozuka D, Takatera S, Matsuo H, Yoshida H, Hamaguchi S, Yamamoto S, Sada RM, Suzuki K, Konishi K, Kutsuna S. Oral mouthwashes for asymptomatic to mildly symptomatic adults with COVID-19 and salivary viral load: a randomized, placebo-controlled, open-label clinical trial. BMC Oral Health 2024; 24:491. [PMID: 38664718 PMCID: PMC11044332 DOI: 10.1186/s12903-024-04246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Recent randomized clinical trials suggest that the effect of using cetylpyridinium chloride (CPC) mouthwashes on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load in COVID-19 patients has been inconsistent. Additionally, no clinical study has investigated the effectiveness of on-demand aqueous chlorine dioxide mouthwash against COVID-19. METHODS We performed a randomized, placebo-controlled, open-label clinical trial to assess for any effects of using mouthwash on the salivary SARS-CoV-2 viral load among asymptomatic to mildly symptomatic adult COVID-19-positive patients. Patients were randomized to receive either 20 mL of 0.05% CPC, 10 mL of 0.01% on-demand aqueous chlorine dioxide, or 20 mL of placebo mouthwash (purified water) in a 1:1:1 ratio. The primary endpoint was the cycle threshold (Ct) values employed for SARS-CoV-2 salivary viral load estimation. We used linear mixed-effects models to assess for any effect of the mouthwashes on SARS-CoV-2 salivary viral load. RESULTS Of a total of 96 eligible participants enrolled from November 7, 2022, to January 19, 2023, 90 were accepted for the primary analysis. The use of 0.05% CPC mouthwash was not shown to be superior to placebo in change from baseline salivary Ct value at 30 min (difference vs. placebo, 0.640; 95% confidence interval [CI], -1.425 to 2.706; P = 0.543); 2 h (difference vs. placebo, 1.158; 95% CI, -0.797 to 3.112; P = 0.246); 4 h (difference vs. placebo, 1.283; 95% CI, -0.719 to 3.285; P = 0.209); 10 h (difference vs. placebo, 0.304; 95% CI, -1.777 to 2.385; P = 0.775); or 24 h (difference vs. placebo, 0.782; 95% CI, -1.195 to 2.759; P = 0.438). The use of 0.01% on-demand aqueous chlorine dioxide mouthwash was also not shown to be superior to placebo in change from baseline salivary Ct value at 30 min (difference vs. placebo, 0.905; 95% CI, -1.079 to 2.888; P = 0.371); 2 h (difference vs. placebo, 0.709; 95% CI, -1.275 to 2.693; P = 0.483); 4 h (difference vs. placebo, 0.220; 95% CI, -1.787 to 2.226; P = 0.830); 10 h (difference vs. placebo, 0.198; 95% CI, -1.901 to 2.296; P = 0.854); or 24 h (difference vs. placebo, 0.784; 95% CI, -1.236 to 2.804; P = 0.447). CONCLUSIONS In asymptomatic to mildly symptomatic adults with COVID-19, compared to placebo, the use of 0.05% CPC and 0.01% on-demand aqueous chlorine dioxide mouthwash did not lead to a significant reduction in SARS-CoV-2 salivary viral load. Future studies of the efficacy of CPC and on-demand aqueous chlorine dioxide mouthwash on the viral viability of SARS-CoV-2 should be conducted using different specimen types and in multiple populations and settings.
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Affiliation(s)
- Daisuke Onozuka
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan.
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan.
| | - Satoko Takatera
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
| | - Hiroo Matsuo
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
| | - Hisao Yoshida
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
| | - Shigeto Hamaguchi
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
- Department of Transformative Analysis for Human Specimen, Graduate School of Medicine, Osaka University, Osaka, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Shungo Yamamoto
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
- Department of Transformative Protection to Infectious Disease, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryuichi Minoda Sada
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
- Department of Transformative Protection to Infectious Disease, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Osaka, Japan
| | - Keiji Konishi
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan
| | - Satoshi Kutsuna
- Department of Oral Microbe Control, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan.
- Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Osaka, 565-0871, Osaka, Japan.
- Department of Transformative Analysis for Human Specimen, Graduate School of Medicine, Osaka University, Osaka, Japan.
- Division of Fostering Required Medical Human Resources, Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan.
- Department of Transformative Protection to Infectious Disease, Graduate School of Medicine, Osaka University, Osaka, Japan.
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Chakraborty C, Bhattacharya M, Lee SS. Regulatory role of miRNAs in the human immune and inflammatory response during the infection of SARS-CoV-2 and other respiratory viruses: A comprehensive review. Rev Med Virol 2024; 34:e2526. [PMID: 38446531 DOI: 10.1002/rmv.2526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/11/2024] [Accepted: 02/22/2024] [Indexed: 03/07/2024]
Abstract
miRNAs are single-stranded ncRNAs that act as regulators of different human body processes. Several miRNAs have been noted to control the human immune and inflammatory response during severe acute respiratory infection syndrome (SARS-CoV-2) infection. Similarly, many miRNAs were upregulated and downregulated during different respiratory virus infections. Here, an attempt has been made to capture the regulatory role of miRNAs in the human immune and inflammatory response during the infection of SARS-CoV-2 and other respiratory viruses. Firstly, the role of miRNAs has been depicted in the human immune and inflammatory response during the infection of SARS-CoV-2. In this direction, several significant points have been discussed about SARS-CoV-2 infection, such as the role of miRNAs in human innate immune response; miRNAs and its regulation of granulocytes; the role of miRNAs in macrophage activation and polarisation; miRNAs and neutrophil extracellular trap formation; miRNA-related inflammatory response; and miRNAs association in adaptive immunity. Secondly, the miRNAs landscape has been depicted during human respiratory virus infections such as human coronavirus, respiratory syncytial virus, influenza virus, rhinovirus, and human metapneumovirus. The article will provide more understanding of the miRNA-controlled mechanism of the immune and inflammatory response during COVID-19, which will help more therapeutics discoveries to fight against the future pandemic.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, India
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
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3
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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Leong NKC, Gu H, Ng DYM, Chang LDJ, Krishnan P, Cheng SSM, Peiris M, Poon LLM. Development of multiplex RT-ddPCR assays for detection of SARS-CoV-2 and other common respiratory virus infections. Influenza Other Respir Viruses 2022; 17:e13084. [PMID: 36517993 PMCID: PMC9835441 DOI: 10.1111/irv.13084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Measures for mitigation of Coronavirus Disease 2019 (COVID-19) were set to reduce the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 and other respiratory viruses share similar transmission routes and some common clinical manifestations. Co-circulation of SARS-CoV-2 and other common respiratory viruses is imminent. Therefore, development of multiplex assays for detecting these respiratory viruses is essential for being prepared for future outbreaks of respiratory viruses. METHODS A panel of three reverse transcription droplet digital PCR (RT-ddPCR) assays were developed to detect 15 different human respiratory viruses. Evaluations of its performance were demonstrated. A total of 100 local and 98 imported COVID-19 cases in Hong Kong were screened for co-infection with other common respiratory viruses. RESULTS All detected viral targets showed distinct signal clusters using the multiplex RT-ddPCR assays. These assays have a broad range of linearity and good intra-/inter-assay reproducibility for each target. The lower limits of quantification for all targets were ≤46 copies per reaction. Six imported cases of COVID-19 were found to be co-infected with other respiratory viruses, whereas no local case of co-infection was observed. CONCLUSIONS The multiplex RT-ddPCR assays were demonstrated to be useful for screening of respiratory virus co-infections. The strict preventive measures applied in Hong Kong may be effective in limiting the circulation of other human respiratory viruses. The multiplex assays developed in this study can achieve a robust detection method for clinical and research purposes.
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Affiliation(s)
- Nathaniel K. C. Leong
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Haogao Gu
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Daisy Y. M. Ng
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Lydia D. J. Chang
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Samuel S. M. Cheng
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Malik Peiris
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong,Centre for Immunology and InfectionHong Kong Science and Technology ParkHong Kong,HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
| | - Leo L. M. Poon
- School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong,Centre for Immunology and InfectionHong Kong Science and Technology ParkHong Kong,HKU‐Pasteur Research Pole, School of Public Health, LKS Faculty of MedicineThe University of Hong KongHong Kong
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5
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Validation of SARS-CoV-2 pooled testing for surveillance using the Panther Fusion® system: Impact of pool size, automation, and assay chemistry. PLoS One 2022; 17:e0276729. [PMID: 36342921 PMCID: PMC9639840 DOI: 10.1371/journal.pone.0276729] [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: 07/29/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
Combining diagnostic specimens into pools has been considered as a strategy to augment throughput, decrease turnaround time, and leverage resources. This study utilized a multi-parametric approach to assess optimum pool size, impact of automation, and effect of nucleic acid amplification chemistries on the detection of SARS-CoV-2 RNA in pooled samples for surveillance testing on the Hologic Panther Fusion® System. Dorfman pooled testing was conducted with previously tested SARS-CoV-2 nasopharyngeal samples using Hologic’s Aptima® and Panther Fusion® SARS-CoV-2 Emergency Use Authorization assays. A manual workflow was used to generate pool sizes of 5:1 (five samples: one positive, four negative) and 10:1. An automated workflow was used to generate pool sizes of 3:1, 4:1, 5:1, 8:1 and 10:1. The impact of pool size, pooling method, and assay chemistry on sensitivity, specificity, and lower limit of detection (LLOD) was evaluated. Both the Hologic Aptima® and Panther Fusion® SARS-CoV-2 assays demonstrated >85% positive percent agreement between neat testing and pool sizes ≤5:1, satisfying FDA recommendation. Discordant results between neat and pooled testing were more frequent for positive samples with CT>35. Fusion® CT (cycle threshold) values for pooled samples increased as expected for pool sizes of 5:1 (CT increase of 1.92–2.41) and 10:1 (CT increase of 3.03–3.29). The Fusion® assay demonstrated lower LLOD than the Aptima® assay for pooled testing (956 vs 1503 cp/mL, pool size of 5:1). Lowering the cut-off threshold of the Aptima® assay from 560 kRLU (manufacturer’s setting) to 350 kRLU improved the assay sensitivity to that of the Fusion® assay for pooled testing. Both Hologic’s SARS-CoV-2 assays met the FDA recommended guidelines for percent positive agreement (>85%) for pool sizes ≤5:1. Automated pooling increased test throughput and enabled automated sample tracking while requiring less labor. The Fusion® SARS-CoV-2 assay, which demonstrated a lower LLOD, may be more appropriate for surveillance testing.
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Zhang X, Meng H, Liu H, Ye Q. Advances in laboratory detection methods and technology application of SARS-CoV-2. J Med Virol 2022; 94:1357-1365. [PMID: 34854101 PMCID: PMC9015480 DOI: 10.1002/jmv.27494] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023]
Abstract
At present, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raging worldwide, and the coronavirus disease 2019 outbreak caused by SARS-CoV-2 seriously threatens the life and health of all humankind. There is no specific medicine for novel coronavirus yet. So, laboratory diagnoses of novel coronavirus as soon as possible and isolation of the source of infection play a vital role in preventing and controlling the epidemic. Therefore, selecting appropriate detection techniques and methods is particularly important to improve the efficiency of disease diagnosis and treatment and to curb the outbreak of infectious diseases. In this paper, virus nucleic acid, protein, and serum immunology were reviewed to provide a reference for further developing virus detection technology to provide better prevention and treatment strategies and research ideas for clinicians and researchers.
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Affiliation(s)
- Xiucai Zhang
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Hanyan Meng
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Huihui Liu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
| | - Qing Ye
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child HealthNational Children's Regional Medical CenterHangzhouChina
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7
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Chow YP, Chin BHZ, Loo JM, Moorthy LR, Jairaman J, Tan LH, Tay WWY. Clinical and epidemiological characteristics of patients seeking COVID-19 testing in a private centre in Malaysia: Is there a role for private healthcare in battling the outbreak? PLoS One 2021; 16:e0258671. [PMID: 34648575 PMCID: PMC8516249 DOI: 10.1371/journal.pone.0258671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/03/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE This cross-sectional observational study summarized the baseline characteristics of subjects who underwent COVID-19 molecular testing in a private medical centre located in the state of Selangor in Malaysia between 1 Oct 2020 and 31 Jan 2021. We compared the baseline characteristics between subjects who were tested positive and negative of SARS-CoV-2 infection, and identified risk factors which may be predictive of SARS-CoV-2 positivity. METHODS AND FINDINGS A total of 36603 subjects who were tested for COVID-19 infection via molecular assays at Sunway Medical Centre between Oct 1, 2020 and Jan 31, 2021, and consented to participate in this observation study were included for analysis. Descriptive statistics was used to summarize the study cohort, whereas logistic regression analysis was used to identify risk factors associated with SARS-CoV-2 positivity. Among the reasons listed for COVID-19 screening were those who needed clearance for travelling, clearance to return to work, or clearance prior to hospital admission. They accounted for 67.7% of tested subjects, followed by the self-referred group (27.3%). Most of the confirmed cases were asymptomatic (62.6%), had no travel history (99.6%), and had neither exposure to SARS-CoV-2 confirmed cases (61.9%) nor exposure to patients under investigation (82.7%) and disease clusters (89.2%). Those who presented with loss of smell or taste (OR: 26.91; 95% CI: 14.81-48.92, p<0.001), fever (OR:3.97; 95% CI: 2.54-6.20, p<0.001), running nose (OR: 1.75; 95% CI:1.10-2.79, p = 0.019) or other symptoms (OR: 5.63; 95% CI:1.68-18.91, p = 0.005) were significantly associated with SARS-CoV-2 positivity in the multivariate logistic regression analysis. CONCLUSION Our study showed that majority of patients seeking COVID-19 testing in a private healthcare setting were mainly asymptomatic with low epidemiological risk. Consequently, the average positivity rate was 1.2% compared to the national cumulative positivity rate of 4.65%. Consistent with other studies, we found that loss of smell or taste, fever and running nose were associated with SARS-CoV-2 positivity. We believe that strengthening the capacity of private health institutions is important in the national battle against the COVID-19 pandemic, emphasizing the importance of public-private partnership to improve the quality of clinical care.
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Affiliation(s)
- Yock Ping Chow
- Clinical Research Centre, Sunway Medical Centre, Selangor Darul Ehsan, Malaysia
| | | | - Jin Ming Loo
- Department of Information & Communication Technologies, Sunway Medical Centre, Selangor Darul Ehsan, Malaysia
| | - Loshini R. Moorthy
- Clinical Research Centre, Sunway Medical Centre, Selangor Darul Ehsan, Malaysia
| | - Jamuna Jairaman
- Department of Diagnostic Laboratory, Sunway Medical Centre, Selangor Darul Ehsan, Malaysia
| | - Lian Huat Tan
- Department of Medicine, Sunway Medical Centre, Selangor Darul Ehsan, Malaysia
| | - Wendy Wan Ying Tay
- Clinical Research Centre, Sunway Medical Centre, Selangor Darul Ehsan, Malaysia
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Köksaldı İÇ, Köse S, Ahan RE, Hacıosmanoğlu N, Şahin Kehribar E, Güngen MA, Baştuğ A, Dinç B, Bodur H, Özkul A, Şeker UÖŞ. SARS-CoV-2 Detection with De Novo-Designed Synthetic Riboregulators. Anal Chem 2021; 93:9719-9727. [PMID: 34192453 PMCID: PMC8265535 DOI: 10.1021/acs.analchem.1c00886] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 is a human pathogen and the main cause of COVID-19 disease, announced as a global pandemic by the World Health Organization. COVID-19 is characterized by severe conditions, and early diagnosis can make dramatic changes for both personal and public health. Low-cost, easy-to-use diagnostic capabilities can have a very critical role in controlling the transmission of the disease. Here, we are reporting a state-of-the-art diagnostic tool developed with an in vitro synthetic biology approach by employing engineered de novo riboregulators. Our design coupled with a home-made point-of-care device can detect and report the presence of SARS-CoV-2-specific genes. The presence of SARS-CoV-2-related genes triggers the translation of sfGFP mRNAs, resulting in a green fluorescence output. The approach proposed here has the potential of being a game changer in SARS-CoV-2 diagnostics by providing an easy-to-run, low-cost diagnostic capability.
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Affiliation(s)
- İlkay Çisil Köksaldı
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Sıla Köse
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Recep Erdem Ahan
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Nedim Hacıosmanoğlu
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Ebru Şahin Kehribar
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Murat Alp Güngen
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
| | - Aliye Baştuğ
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Bedia Dinç
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Hürrem Bodur
- Department of Infectious Diseases and Clinical
Microbiology, Health Science University Turkey, Ankara City
Hospital, 06800 Ankara, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of
Virology, Ankara University, 06110 Ankara,
Turkey
- Biotechnology Institute, Ankara
University, 06135 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM—National Nanotechnology Research Center,
Bilkent University, 06800 Ankara,
Turkey
- Institute of Materials Science and Nanotechnology,
Bilkent University, 06800 Ankara,
Turkey
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9
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Dierks S, Bader O, Schwanbeck J, Groß U, Weig MS, Mese K, Lugert R, Bohne W, Hahn A, Feltgen N, Torkieh S, Denker FR, Lauermann P, Storch MW, Frickmann H, Zautner AE. Diagnosing SARS-CoV-2 with Antigen Testing, Transcription-Mediated Amplification and Real-Time PCR. J Clin Med 2021; 10:jcm10112404. [PMID: 34072381 PMCID: PMC8199284 DOI: 10.3390/jcm10112404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 11/18/2022] Open
Abstract
This study was performed as a head-to-head comparison of the performance characteristics of (1) two SARS-CoV-2-specific rapid antigen assays with real-time PCR as gold standard as well as (2) a fully automated high-throughput transcription-mediated amplification (TMA) assay and real-time PCR in a latent class analysis-based test comparison without a gold standard with several hundred samples in a low prevalence "real world" setting. Recorded sensitivity and specificity of the NADAL and the LumiraDx antigen assays and the Hologic Aptima SARS-CoV-2 TMA assay were 0.1429 (0.0194, 0.5835), 0.7644 (0.7016, 0.8174), and 0.7157 (0, 1) as well as 0.4545 (0.2022, 0.7326), 0.9954 (0.9817, 0.9988), and 0.9997 (not estimable), respectively. Agreement kappa between the positive results of the two antigen-based assays was 0.060 (0.002, 0.167) and 0.659 (0.492, 0.825) for TMA and real-time PCR. Samples with low viral load as indicated by cycle threshold (Ct) values > 30 were generally missed by both antigen assays, while 1:10 pooling suggested higher sensitivity of TMA compared to real-time PCR. In conclusion, both sensitivity and specificity speak in favor of the use of the LumiraDx rather than the NADAL antigen assay, while TMA results are comparably as accurate as PCR, when applied in a low prevalence setting.
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Affiliation(s)
- Sascha Dierks
- Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Julian Schwanbeck
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Michael S. Weig
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Kemal Mese
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Raimond Lugert
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Wolfgang Bohne
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
| | - Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.)
| | - Nicolas Feltgen
- Department of Ophthalmology, University Medical Center Göttingen, 37075 Göttingen, Germany; (N.F.); (S.T.); (F.R.D.); (P.L.); (M.W.S.)
| | - Setare Torkieh
- Department of Ophthalmology, University Medical Center Göttingen, 37075 Göttingen, Germany; (N.F.); (S.T.); (F.R.D.); (P.L.); (M.W.S.)
| | - Fenja R. Denker
- Department of Ophthalmology, University Medical Center Göttingen, 37075 Göttingen, Germany; (N.F.); (S.T.); (F.R.D.); (P.L.); (M.W.S.)
| | - Peer Lauermann
- Department of Ophthalmology, University Medical Center Göttingen, 37075 Göttingen, Germany; (N.F.); (S.T.); (F.R.D.); (P.L.); (M.W.S.)
| | - Marcus W. Storch
- Department of Ophthalmology, University Medical Center Göttingen, 37075 Göttingen, Germany; (N.F.); (S.T.); (F.R.D.); (P.L.); (M.W.S.)
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany; (A.H.); (H.F.)
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
| | - Andreas Erich Zautner
- Institute for Medical Microbiology, University Medical Center Göttingen, 37075 Göttingen, Germany; (O.B.); (J.S.); (U.G.); (M.S.W.); (K.M.); (R.L.); (W.B.)
- Correspondence: ; Tel.: +49-551-39-65927
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10
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Yadav R, Chaudhary JK, Jain N, Chaudhary PK, Khanra S, Dhamija P, Sharma A, Kumar A, Handu S. Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells 2021; 10:cells10040821. [PMID: 33917481 PMCID: PMC8067447 DOI: 10.3390/cells10040821] [Citation(s) in RCA: 230] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10-20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5' end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
- Correspondence: ; Tel.: +91-94-1415-3849
| | | | - Neeraj Jain
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India;
| | - Pankaj Kumar Chaudhary
- Molecular Biology & Proteomics Laboratory, Department of Biotechnology, Indian Institute of Technology (IIT), Roorkee 247667, India;
| | - Supriya Khanra
- Uttaranchal Institute of Pharmaceutical Sciences, Dehradun 248007, India;
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
| | - Ambika Sharma
- Department of Biochemistry, U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University, Mathura 281001, India;
| | - Ashish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
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