101
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Chiara M, D’Erchia AM, Gissi C, Manzari C, Parisi A, Resta N, Zambelli F, Picardi E, Pavesi G, Horner DS, Pesole G. Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Brief Bioinform 2021; 22:616-630. [PMID: 33279989 PMCID: PMC7799330 DOI: 10.1093/bib/bbaa297] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our 'vademecum' for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.
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Affiliation(s)
- Matteo Chiara
- molecular biology and bioinformatics at the University of Milan
| | - Anna Maria D’Erchia
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Carmela Gissi
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Antonio Parisi
- Genetic and Molecular Epidemiology Laboratory at the Experimental Zooprophylactic Institute of Apulia and Basilicata
| | - Nicoletta Resta
- Medical Genetics at the University of Bari. She heads the Laboratory Unit of Medical Genetics and the School of Specialization in Medical Genetics
| | | | - Ernesto Picardi
- molecular biology and bioinformatics at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Giulio Pavesi
- Associate Professor of bioinformatics at the University of Milan (Italy)
| | - David S Horner
- molecular biology and bioinformatics at the University of Milan
| | - Graziano Pesole
- molecular biology at the University of Bari and Research Associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
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102
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Ertas YN, Mahmoodi M, Shahabipour F, Jahed V, Diltemiz SE, Tutar R, Ashammakhi N. Role of biomaterials in the diagnosis, prevention, treatment, and study of corona virus disease 2019 (COVID-19). EMERGENT MATERIALS 2021; 4:35-55. [PMID: 33748672 PMCID: PMC7962632 DOI: 10.1007/s42247-021-00165-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
Recently emerged novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting corona virus disease 2019 (COVID-19) led to urgent search for methods to prevent and treat COVID-19. Among important disciplines that were mobilized is the biomaterials science and engineering. Biomaterials offer a range of possibilities to develop disease models, protective, diagnostic, therapeutic, monitoring measures, and vaccines. Among the most important contributions made so far from this field are tissue engineering, organoids, and organ-on-a-chip systems, which have been the important frontiers in developing tissue models for viral infection studies. Also, due to low bioavailability and limited circulation time of conventional antiviral drugs, controlled and targeted drug delivery could be applied alternatively. Fortunately, at the time of writing this paper, we have two successful vaccines and new at-home detection platforms. In this paper, we aim to review recent advances of biomaterial-based platforms for protection, diagnosis, vaccination, therapeutics, and monitoring of SARS-CoV-2 and discuss challenges and possible future research directions in this field.
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Affiliation(s)
- Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Mahboobeh Mahmoodi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Fahimeh Shahabipour
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
- Skin Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Vahid Jahed
- Biomedical Engineering Division, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Rumeysa Tutar
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpasa, Avcilar, Istanbul, Turkey
| | - Nureddin Ashammakhi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI USA
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103
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Zhang W, He H, Zhu L, Liu G, Wu L. Food Safety in Post-COVID-19 Pandemic: Challenges and Countermeasures. BIOSENSORS 2021; 11:71. [PMID: 33806704 PMCID: PMC8000942 DOI: 10.3390/bios11030071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022]
Abstract
Understanding food safety hazard risks is essential to avoid potential negative heath impacts in the food supply chain in a post-COVID-19 pandemic era. Development of strategies for virus direction in foods plays an important role in food safety and verification. Early warning, tracing, and detection should be implemented as an integrated system in order to mitigate thecoronavirus disease 2019 (COVID-19) outbreak, in which the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical as it not only concerns screening of populations but also monitoring of possible contaminated sources such as the food supply chain. In this review, we point out the consequences in different aspects of our daily life in the post-COVID-19 pandemic from the perspective of the food supply chain and the food industry. We summarize the possible transmission routes of COVID-19 in the food supply chain before exploring the development of corresponding detection tools of SARS-CoV-2. Accordingly, we compare different detection methods for the virus in foods, including different pretreatments of food matrices in the virus detection. Finally, the future perspectives are proposed.
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Affiliation(s)
- Weimin Zhang
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China;
| | - Huiyu He
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (H.H.); (L.Z.)
| | - Lin Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (H.H.); (L.Z.)
| | - Guozhen Liu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China;
| | - Long Wu
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, College of Food Science and Engineering, Hainan University, Haikou 570228, China;
- Key Laboratory of Fermentation Engineering (Ministry of Education), National “111” Center for Cellular Regulation and Molecular Pharmaceutics, College of Bioengineering and Food, Hubei University of Technology, Wuhan 430068, China
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104
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Konwarh R, Cho WC. Fortifying the diagnostic-frontiers with nanoscale technology amidst the COVID-19 catastrophe. Expert Rev Mol Diagn 2021; 21:131-135. [PMID: 33470125 DOI: 10.1080/14737159.2021.1878879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rocktotpal Konwarh
- Division of Nanobiomaterials and Nanomedicine, Uniglobe Scientific Pvt. Ltd., 7/9, Kishan Garh, Vasant Kunj, New Delhi, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, SAR, China
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105
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Husain A. A novel approach to minimize the false negative COVID-19 diagnosis by inclusion of specific cell markers and multiple sample collection. MethodsX 2021; 8:101270. [PMID: 33614422 PMCID: PMC7881297 DOI: 10.1016/j.mex.2021.101270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/08/2021] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 pandemic has caused unpredictable mortality and economic losses globally. With no approved drug for the treatment, the accurate diagnosis of COVID-19 becomes essential. RNA based test takes several hours and require extensive human intervention for RNA extraction and RT-PCR, but it is preferred over the antibody-based detection as the latter does not detect the early stage infections. The RT-PCR being a gold standard of COVID-19 diagnosis offers highly standardized detection of the SARS-CoV-2 RNA, still vulnerable for false-negative diagnosis due to absence of infected cells in the sample or inaccurate RNA extraction. Hence there is a need to develop alternative protocols and methods for the accurate COVID-19 diagnosis. Here we propose two additional steps in RT-PCR based COVID-19 diagnosis to minimize false-negative detection. The first step involves collection of four samples from an individual. Each sample should be collected from nasopharyngeal and oropharyngeal regions on day 01, mixed together followed by RNA extraction and then repeating the same exercise on day 03. The RNA extracted on day 01 and day 03 must be pooled together to be used in the RT-PCR. Second, we propose the inclusion of the control marker genes specific to nasal goblet cell, type-II pneumocyte and absorptive enterocytes to ensure the specificity of the RNA source. Overall, these additional steps in the proposed method would increase the chances of SARS-CoV-2 detection in the infected population and would limit the false-negative diagnosis of COVID-19 and hence the spread of this disease.•RT-PCR based COVID-19 diagnosis is vulnerable to the false-negative results due to inaccurate sample isolation or RNA extraction.•RNA pool of multiple samples from an individual improves the chances of detection of SARS-CoV-2 by RT-PCR.•Inclusion of specific marker genes would ensure the right RNA source from the desired cell.
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Affiliation(s)
- Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research (IISER) Bhopal, MP, India.,Innovation and Incubation Centre for Entrepreneurship, Indian Institute of Science Education and Research (IISER) Bhopal, MP, India
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106
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Prasetyoputri A. Detection of Bacterial Coinfection in COVID-19 Patients Is a Missing Piece of the Puzzle in the COVID-19 Management in Indonesia. ACS Infect Dis 2021; 7:203-205. [PMID: 33502840 PMCID: PMC7860142 DOI: 10.1021/acsinfecdis.1c00006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Indexed: 01/08/2023]
Abstract
Bacterial coinfection in COVID-19 patients has the potential to complicate treatments and accelerate the development of antibiotic resistance in the clinic due to the widespread use of broad-spectrum antibiotics, including in Indonesia. The surge of COVID-19 patients may worsen antibiotic overuse; therefore, information on the actual extent of bacterial coinfection in COVID-19 patients in Indonesia is crucial to inform appropriate treatment. This Viewpoint elaborates on a nascent research project focused on sequencing of swab samples to detect bacterial coinfection in COVID-19 patients in Indonesia. Supported by a L'Oréal-UNESCO For Women in Science National Fellowship, it is designed to inform better clinical management of COVID-19 in Indonesia.
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Affiliation(s)
- Anggia Prasetyoputri
- Research Centre for Biotechnology, Indonesian
Institute of Sciences (LIPI), Cibinong 16911,
Indonesia
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107
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Ortega MA, Fraile-Martínez O, García-Montero C, García-Gallego S, Sánchez-Trujillo L, Torres-Carranza D, Álvarez-Mon MÁ, Pekarek L, García-Honduvilla N, Bujan J, Álvarez-Mon M, Asúnsolo Á, De La Torre B. An integrative look at SARS‑CoV‑2 (Review). Int J Mol Med 2021; 47:415-434. [PMID: 33416095 PMCID: PMC7797443 DOI: 10.3892/ijmm.2020.4828] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
SARS‑CoV‑2 is a newly discovered member of the betacoronaviruses and the etiological agent of the disease COVID‑19. SARS‑CoV‑2 is responsible for the worldwide pandemic which has been taking place in 2020, and is causing a markedly higher number of infections and deaths compared to previous coronaviruses, such as SARS‑CoV or MERS‑CoV. Based on updated scientific literature, the present review compiles the most relevant knowledge of SARS‑CoV‑2, COVID‑19 and the clinical and typical responses that patients have exhibited against this virus, discussing current and future therapies, and proposing strategies with which to combat the disease and prevent a further global threat. The aggressiveness of SARS‑CoV‑2 arises from its capacity to infect, and spread easily and rapidly through its tight interaction with the human angiotensin‑converting enzyme 2 (ACE‑2) receptor. While not all patients respond in a similar manner and may even be asymptomatic, a wide range of manifestations associated with COVID‑19 have been described, particularly in vulnerable population groups, such as the elderly or individuals with other underlying conditions. The proper function of the immune system plays a key role in an individual's favorable response to SARS‑CoV‑2 infection. A hyperactivated response, on the contrary, could account for the more severe cases of COVID‑19, and this may finally lead to respiratory insufficiency and other complications, such as thrombotic or thromboembolic events. The development of novel therapies and vaccines designed to control and regulate a proper immune system response will be key to clinical management, prevention measures and effective population screening to attenuate the transmission of this novel RNA virus.
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Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
- Tumor Registry, Pathological Anatomy Service, Prince of Asturias University Hospital, Alcalá de Henares, 28801 Madrid
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
| | - Cielo García-Montero
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
| | - Sandra García-Gallego
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
- Department of Organic and Inorganic Chemistry, 'Andrés M. del Río' Institute of Chemistry (IQAR), University of Alcalá, CIBER-BBN, 28805 Madrid
| | - Lara Sánchez-Trujillo
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
- Tumor Registry, Pathological Anatomy Service, Prince of Asturias University Hospital, Alcalá de Henares, 28801 Madrid
| | | | - Miguel Ángel Álvarez-Mon
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
- Department of Psychiatry and Medical Psychology, Infanta Leonor University Hospital, 28031 Madrid
| | - Leonel Pekarek
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
| | - Julia Bujan
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialties, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
- Internal Medicine Service, Prince of Asturias University Hospital, CIBEREHD, Alcalá de Henares, 28805 Madrid
| | - Ángel Asúnsolo
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
- Preventive Medicine and Public Health Area, Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid, Spain
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, New York University, New York, NY 10027, USA
| | - Basilio De La Torre
- Ramón y Cajal Health Research Institute (IRYCIS), 28034 Madrid
- Preventive Medicine and Public Health Area, Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, Alcalá de Henares, 28801 Madrid, Spain
- Traumatology Service, Ramón y Cajal University Hospital, 28034 Madrid, Spain
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108
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Jing R, Kudinha T, Zhou ML, Xiao M, Wang H, Yang WH, Xu YC, Hsueh PR. Laboratory diagnosis of COVID-19 in China: A review of challenging cases and analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:17-26. [PMID: 33153907 PMCID: PMC7568515 DOI: 10.1016/j.jmii.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/10/2020] [Indexed: 12/24/2022]
Abstract
Since the initial emergence of coronavirus disease 2019 (COVID-19) in Wuhan, Hubei province, China, a rapid spread of the disease occurred around the world, rising to become an international global health concern at pandemic level. In the face of this medical challenge threatening humans, the development of rapid and accurate methods for early screening and diagnosis of COVID-19 became crucial to containing the emerging public health threat, and prevent further spread within the population. Despite the large number of COVID-19 confirmed cases in China, some problematic cases with inconsistent laboratory testing results, were reported. Specifically, a high false-negative rate of 41% on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse transcription-polymerase chain reaction (qRT-PCR) assays was observed in China. Although serological testing has been applied worldwide as a complementary method to help identify SARS-CoV-2, several limitations on its use have been reported in China. Therefore, the use of both qRT-PCR and serological testing in the diagnosis of COVID-19 in China and elsewhere, presented considerable challenges, but when used in combination, can be valuable tools in the fight against COVID-19. In this review, we give an overview of the advantages and disadvantages of different molecular techniques for SARS-CoV-2 detection that are currently used in several labs, including qRT-PCR, gene sequencing, loop-mediated isothermal amplification (LAMP), nucleic acid mass spectrometry (MS), and gene editing technique based on clustered regularly interspaced short palindromic repeats (CRISPR/Cas13) system. Then we mainly review and analyze some causes of false-negative qRT-PCR results, and how to resolve some of the diagnostic dilemma.
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Affiliation(s)
- Ran Jing
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Leeds Parade, Orange, NSW, 2800, Australia; NSW Health Pathology, Orange Pathology Lab, Orange, NSW, 2800, Australia.
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - He Wang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wen-Hang Yang
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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109
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Xiong E, Jiang L, Tian T, Hu M, Yue H, Huang M, Lin W, Jiang Y, Zhu D, Zhou X. Simultaneous Dual-Gene Diagnosis of SARS-CoV-2 Based on CRISPR/Cas9-Mediated Lateral Flow Assay. Angew Chem Int Ed Engl 2021; 60:5307-5315. [PMID: 33295064 DOI: 10.1002/anie.202014506] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Few methods for the detection of SARS-CoV-2 currently have the capability to simultaneously detect two genes in a single test, which is a key measure to improve detection accuracy, as adopted by the gold standard RT-qPCR method. Developed here is a CRISPR/Cas9-mediated triple-line lateral flow assay (TL-LFA) combined with multiplex reverse transcription-recombinase polymerase amplification (RT-RPA) for rapid and simultaneous dual-gene detection of SARS-CoV-2 in a single strip test. This assay is characterized by the detection of envelope (E) and open reading frame 1ab (Orf1ab) genes from cell-cultured SARS-CoV-2 and SARS-CoV-2 viral RNA standards, showing a sensitivity of 100 RNA copies per reaction (25 μL). Furthermore, dual-gene analysis of 64 nasopharyngeal swab samples showed 100 % negative predictive agreement and 97.14 % positive predictive agreement. This platform will provide a more accurate and convenient pathway for diagnosis of COVID-19 or other infectious diseases in low-resource regions.
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Affiliation(s)
- Erhu Xiong
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Ling Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Menglu Hu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huahua Yue
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Mengqi Huang
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wei Lin
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yongzhong Jiang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry, South China Normal University, Guangzhou, 510006, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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110
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Xiong E, Jiang L, Tian T, Hu M, Yue H, Huang M, Lin W, Jiang Y, Zhu D, Zhou X. Simultaneous Dual‐Gene Diagnosis of SARS‐CoV‐2 Based on CRISPR/Cas9‐Mediated Lateral Flow Assay. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014506] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Erhu Xiong
- School of Life Sciences South China Normal University Guangzhou 510631 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
| | - Ling Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
| | - Tian Tian
- School of Life Sciences South China Normal University Guangzhou 510631 China
| | - Menglu Hu
- School of Life Sciences South China Normal University Guangzhou 510631 China
| | - Huahua Yue
- School of Life Sciences South China Normal University Guangzhou 510631 China
| | - Mengqi Huang
- School of Life Sciences South China Normal University Guangzhou 510631 China
| | - Wei Lin
- School of Life Sciences South China Normal University Guangzhou 510631 China
| | - Yongzhong Jiang
- Hubei Provincial Center for Disease Control and Prevention Wuhan 430079 China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine School of Chemistry South China Normal University Guangzhou 510006 China
| | - Xiaoming Zhou
- School of Life Sciences South China Normal University Guangzhou 510631 China
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111
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Yüce M, Filiztekin E, Özkaya KG. COVID-19 diagnosis -A review of current methods. Biosens Bioelectron 2021; 172:112752. [PMID: 33126180 PMCID: PMC7584564 DOI: 10.1016/j.bios.2020.112752] [Citation(s) in RCA: 360] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/01/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023]
Abstract
A fast and accurate self-testing tool for COVID-19 diagnosis has become a prerequisite to comprehend the exact number of cases worldwide and to take medical and governmental actions accordingly. SARS-CoV-2 (formerly, 2019-nCoV) infection was first reported in Wuhan (China) in December 2019, and then it has rapidly spread around the world, causing ~14 million active cases with ~582,000 deaths as of July 2020. The diagnosis tools available so far have been based on a) viral gene detection, b) human antibody detection, and c) viral antigen detection, among which the viral gene detection by RT-PCR has been found as the most reliable technique. In this report, the current SARS-CoV-2 detection kits, exclusively the ones that were issued an "Emergency Use Authorization" from the U.S. Food and Drug Administration, were discussed. The key structural components of the virus were presented to provide the audience with an understanding of the scientific principles behind the testing tools. The methods that are still in the early research state were also reviewed in a subsection based on the reports available so far.
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Affiliation(s)
- Meral Yüce
- SUNUM Nanotechnology Research and Application Centre, Sabanci University, 34956, Orhanli, Tuzla, Istanbul, Turkey.
| | - Elif Filiztekin
- Faculty of Engineering and Natural Sciences and, Sabanci University, 34956, Orhanli, Tuzla, Istanbul, Turkey
| | - Korin Gasia Özkaya
- Faculty of Engineering and Natural Sciences and, Sabanci University, 34956, Orhanli, Tuzla, Istanbul, Turkey
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Jayamohan H, Lambert CJ, Sant HJ, Jafek A, Patel D, Feng H, Beeman M, Mahmood T, Nze U, Gale BK. SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations. Anal Bioanal Chem 2021; 413:49-71. [PMID: 33073312 PMCID: PMC7568947 DOI: 10.1007/s00216-020-02958-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.
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Affiliation(s)
- Harikrishnan Jayamohan
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Christopher J Lambert
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Himanshu J Sant
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Alexander Jafek
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Dhruv Patel
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Haidong Feng
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Michael Beeman
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Tawsif Mahmood
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ugochukwu Nze
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Bruce K Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
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113
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Zhang Y, Xi H, Juhas M. Biosensing Detection of the SARS-CoV-2 D614G Mutation. Trends Genet 2020; 37:299-302. [PMID: 33402270 PMCID: PMC7758719 DOI: 10.1016/j.tig.2020.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 02/02/2023]
Abstract
The emergence of a mutant strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with an amino acid change from aspartate to a glycine residue at position 614 (D614G) has been reported and this mutant appears to be now dominant in the pandemic. Efficient detection of the SARS-CoV-2 D614G mutant by biosensing technologies is therefore crucial for the control of the pandemic.
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Affiliation(s)
- Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China.
| | - Hui Xi
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
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114
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Mukherjee S, Mazumder P, Joshi M, Joshi C, Dalvi SV, Kumar M. Biomedical application, drug delivery and metabolic pathway of antiviral nanotherapeutics for combating viral pandemic: A review. ENVIRONMENTAL RESEARCH 2020; 191:110119. [PMID: 32846177 PMCID: PMC7443328 DOI: 10.1016/j.envres.2020.110119] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/19/2020] [Accepted: 08/12/2020] [Indexed: 05/20/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a neoteric virus belonging to the beta coronavirus class has created a global health concern, responsible for an outbreak of severe acute respiratory illness, the COVID-19 pandemic. Infected hosts exhibit diverse clinical features, ranging from asymptomatic to severe symptoms in their genital organs, respiratory, digestive, and circulatory systems. Considering the high transmissibility (R0: ≤6.0) compared to Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV, the quest for the clinical development of suitable antiviral nanotherapeutics (NTPs) is incessant. We are presenting a systematic review of the literature published between 2003 and 2020 to validate the hypothesis that the pharmacokinetics, collateral acute/chronic side effects of nano drugs and spike proteins arrangement of coronaviruses can revolutionize the therapeutic approach to cure COVID-19. Our aim is also to critically assess the slow release kinetics and specific target site chemical synthesis influenced competence of NTPs and nanotoxicity based antiviral actions, which are commonly exploited in the synthesis of modulated nanomedicines. The pathogenesis of novel virulent pathogens at the cellular and molecular levels are also considered, which is of utmost importance to characterize the emerging nano-drug agents as diagnostics or therapeutics or viral entry inhibitors. Such types of approaches trigger the scientists and policymakers in the development of a conceptual framework of nano-biotechnology by linking nanoscience and virology to present a smart molecular diagnosis/treatment for pandemic viral infections.
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Affiliation(s)
- Santanu Mukherjee
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, 382355, India
| | - Payal Mazumder
- Centre for the Environment, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Gujarat, 382016, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Gujarat, 382016, India
| | - Sameer V Dalvi
- Chemical Engineering, Indian Institute of Technology Gandhinagar, 382355, India
| | - Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, 382355, India.
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115
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Sheikhzadeh E, Eissa S, Ismail A, Zourob M. Diagnostic techniques for COVID-19 and new developments. Talanta 2020; 220:121392. [PMID: 32928412 PMCID: PMC7358765 DOI: 10.1016/j.talanta.2020.121392] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/23/2022]
Abstract
COVID-19 pandemic is a serious global health issue today due to the rapid human to human transmission of SARS-CoV-2, a new type of coronavirus that causes fatal pneumonia. SARS -CoV-2 has a faster rate of transmission than other coronaviruses such as SARS and MERS and until now there are no approved specific drugs or vaccines for treatment. Thus, early diagnosis is crucial to prevent the extensive spread of the disease. The reverse transcription-polymerase chain reaction (RT-PCR) is the most routinely used method until now to detect SARS-CoV-2 infections. However, several other faster and accurate assays are being developed for the diagnosis of COVID-19 aiming to control the spread of infection through the identification of patients and immediate isolation. In this review, we will discuss the various detection methods of the SARS-CoV-2 virus including the recent developments in immunological assays, amplification techniques as well as biosensors.
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Affiliation(s)
- Elham Sheikhzadeh
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia16150 Kubang Kerian, Kelantan, Malaysia
| | - Shimaa Eissa
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia16150 Kubang Kerian, Kelantan, Malaysia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia; King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh, 12713, Saudi Arabia.
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116
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Hosseini A, Pandey R, Osman E, Victorious A, Li F, Didar T, Soleymani L. Roadmap to the Bioanalytical Testing of COVID-19: From Sample Collection to Disease Surveillance. ACS Sens 2020; 5:3328-3345. [PMID: 33124797 PMCID: PMC7605339 DOI: 10.1021/acssensors.0c01377] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022]
Abstract
The disease caused by SARS-CoV-2, coronavirus disease 2019 (COVID-19), has led to a global pandemic with tremendous mortality, morbidity, and economic loss. The current lack of effective vaccines and treatments places tremendous value on widespread screening, early detection, and contact tracing of COVID-19 for controlling its spread and minimizing the resultant health and societal impact. Bioanalytical diagnostic technologies have played a critical role in the mitigation of the COVID-19 pandemic and will continue to be foundational in the prevention of the subsequent waves of this pandemic along with future infectious disease outbreaks. In this Review, we aim at presenting a roadmap to the bioanalytical testing of COVID-19, with a focus on the performance metrics as well as the limitations of various techniques. The state-of-the-art technologies, mostly limited to centralized laboratories, set the clinical metrics against which the emerging technologies are measured. Technologies for point-of-care and do-it-yourself testing are rapidly emerging, which open the route for testing in the community, at home, and at points-of-entry to widely screen and monitor individuals for enabling normal life despite of an infectious disease pandemic. The combination of different classes of diagnostic technologies (centralized and point-of-care and relying on multiple biomarkers) are needed for effective diagnosis, treatment selection, prognosis, patient monitoring, and epidemiological surveillance in the event of major pandemics such as COVID-19.
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Affiliation(s)
- Amin Hosseini
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Richa Pandey
- Department of Engineering Physics,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Enas Osman
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Amanda Victorious
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Feng Li
- Department of Chemistry,
Brock University, St. Catharines, ON
L2S 3A1, Canada
- Key Laboratory of Green Chemistry and
Technology of Ministry of Education, College of Chemistry,
Sichuan University, Chengdu, Sichuan
610065, China
| | - Tohid Didar
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
- Department of Mechanical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
- Department of Engineering Physics,
McMaster University, Hamilton, ON L8S
4L8, Canada
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117
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Abstract
The COVID-19 caused by a novel coronavirus, named Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken a great toll of life affecting lakhs of people around the globe. It was detected initially in Wuhan, China and has spread rapidly to more than 208 countries to date. A range of molecular and immunoassay-based techniques ranging from central laboratory testing to point-of-care tests is urgently needed for the diagnosis and management of COVID-19 patients. Intensive research is going on for the rapid and highly sensitive detection of COVID 19 using varied approach. Hence, this review will focus on the structure of SARS-CoV-2 and recent progress of different detection tool for the detection of COVID-19. This review will also stimulate academics and researcher to update their current technology. Additionally, we also state about the future revolving around the detection of the novel coronavirus. Lately, the way ahead for better management are also put forward.
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Affiliation(s)
- Nidhi Verma
- Department of Engineering and Physical Sciences, Institute of Advanced Research, Gandhinagar, Gujarat, 382426, India
| | - Dhaval Patel
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gujarat, 382426, India
| | - Alok Pandya
- Department of Engineering and Physical Sciences, Institute of Advanced Research, Gandhinagar, Gujarat, 382426, India.
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118
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Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ. Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients. mBio 2020; 11:e01969-20. [PMID: 33219095 PMCID: PMC7686804 DOI: 10.1128/mbio.01969-20] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.
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Affiliation(s)
- Heba H Mostafa
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John A Fissel
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Yehudit Bergman
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rita R Colwell
- CosmosID, Inc., Rockville, Maryland, USA
- University of Maryland College Park, Institute for Advanced Computer Studies, College Park, Maryland, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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119
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Khan S, Tombuloglu H, Hassanein SE, Rehman S, Bozkurt A, Cevik E, Abdel-Ghany S, Nabi G, Ali A, Sabit H. Coronavirus diseases 2019: Current biological situation and potential therapeutic perspective. Eur J Pharmacol 2020; 886:173447. [PMID: 32763302 PMCID: PMC7403098 DOI: 10.1016/j.ejphar.2020.173447] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/19/2020] [Accepted: 07/29/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) caused by a Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was first reported in Wuhan, China at the end of December 2019. SARS-CoV-2 is a highly pathogenic zoonotic virus and closely related to the Severe Acute Respiratory Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). The COVID-19 was declared as a global pandemic due to its high infectiousness, and worldwide morbidities and mortalities. The Chinese scientists at the start of the outbreak reported genome sequences, which made the characterization of glycoproteins and other structural proteins possible. Moreover, researchers across the world have widely focused on understanding basic biology, developing vaccines, and therapeutic drugs against the COVID-19. However, until now, no promising treatment options, as well as vaccines, are available. In this review, we have described SARS-CoV-2's genome, transmission, and pathogenicity. We also discussed novel potential therapeutic agents that can help to treat the COVID-19 patients.
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Affiliation(s)
- Suliman Khan
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Huseyin Tombuloglu
- Department of Genetics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Sameh E. Hassanein
- Bioinformatics Dept., Agricultural Genetic Engineering Research Institute (AGERI), Bioinformatics and Functional Genomics Dept., College of Biotechnology, Misr University for Science and Technology, P. O. Box 77, Giza, Egypt
| | - Suriya Rehman
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Ayhan Bozkurt
- Department of Physics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, P. O. Box: 1982, 31441, Dammam, Saudi Arabia
| | - Emre Cevik
- Department of Genetics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Shaimaa Abdel-Ghany
- Department of Environmental Biotechnology, College of Biotechnology, Misr University for Science and Technology, P. O. Box 77, Giza, Egypt
| | - Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, PR China
| | - Ashaq Ali
- Wuhan Institute of Virology, Chinese Academy of Sciences Xiao Hong Shan No.44, Wuhan, PR China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hussein Sabit
- Department of Genetics, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441, Saudi Arabia,Corresponding author
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120
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Li C, Zhao C, Bao J, Tang B, Wang Y, Gu B. Laboratory diagnosis of coronavirus disease-2019 (COVID-19). Clin Chim Acta 2020; 510:35-46. [PMID: 32621814 PMCID: PMC7329657 DOI: 10.1016/j.cca.2020.06.045] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The outbreak of Coronavirus Disease-2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has threatened health worldwide. As of the end of 2020, there were nearly 10 million confirmed cases and nearly 5 million deaths associated with COVID-19. Rapid and early laboratory diagnosis of COVID-19 is the main focus of treatment and control. Molecular tests are the basis for confirmation of COVID-19, but serological tests for SARS-CoV-2 are widely available and play an increasingly important role in understanding the epidemiology of the virus and in identifying populations at higher risk for infection. Point-of-care tests have the advantage of rapid, accurate, portable, low cost and non-specific device requirements, which provide great help for disease diagnosis and detection. This review will discuss the performance of different laboratory diagnostic tests and platforms, as well as suitable clinical samples for testing, and related biosafety protection. This review shall guide for the diagnosis of COVID-19 caused by SARS-CoV-2.
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Affiliation(s)
- Chenxi Li
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China
| | - Chengxue Zhao
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China
| | - Jingfeng Bao
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China
| | - Bo Tang
- Nanjing Vazyme Medical Technology Co. Ltd., Nanjing 210046, China
| | - Yunfeng Wang
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, USA.
| | - Bing Gu
- Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou 221004, China; Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221006, China.
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121
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Kim Y, Yaseen AB, Kishi JY, Hong F, Saka SK, Sheng K, Gopalkrishnan N, Schaus TE, Yin P. Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.08.17.20177006. [PMID: 32839783 PMCID: PMC7444299 DOI: 10.1101/2020.08.17.20177006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the single-strand Recombinase Polymerase Amplification (ssRPA) method, which merges the fast, isothermal amplification of RPA with subsequent rapid conversion of the double-strand DNA amplicon to single strands, and hence enables facile hybridization-based, high-specificity readout. We demonstrate the utility of ssRPA for sensitive and rapid (4 copies per 50 μL reaction within 10 min, or 8 copies within 8 min) visual detection of SARS-CoV-2 RNA spiked samples, as well as clinical saliva and nasopharyngeal swabs in VTM or water, on lateral flow devices. The ssRPA method promises rapid, sensitive, and accessible RNA detection to facilitate mass testing in the COVID-19 pandemic.
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Affiliation(s)
- Youngeun Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Adam B. Yaseen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Fan Hong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Sinem K. Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Nikhil Gopalkrishnan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Thomas E. Schaus
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
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122
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Wu K, Saha R, Su D, Krishna VD, Liu J, Cheeran MCJ, Wang JP. Magnetic-Nanosensor-Based Virus and Pathogen Detection Strategies before and during COVID-19. ACS APPLIED NANO MATERIALS 2020; 3:9560-9580. [PMID: 37556271 PMCID: PMC7526334 DOI: 10.1021/acsanm.0c02048] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/22/2020] [Indexed: 05/02/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is a threat to the global healthcare system and economic security. As of July 2020, no specific drugs or vaccines are yet available for COVID-19; a fast and accurate diagnosis for SARS-CoV-2 is essential in slowing the spread of COVID-19 and for efficient implementation of control and containment strategies. Magnetic nanosensing is an emerging topic representing the frontiers of current biosensing and magnetic areas. The past decade has seen rapid growth in applying magnetic tools for biological and biomedical applications. Recent advances in magnetic nanomaterials and nanotechnologies have transformed current diagnostic methods to nanoscale and pushed the detection limit to early-stage disease diagnosis. Herein, this review covers the literature of magnetic nanosensors for virus and pathogen detection before COVID-19. We review popular magnetic nanosensing techniques including magnetoresistance, magnetic particle spectroscopy, and nuclear magnetic resonance. Magnetic point-of-care diagnostic kits are also reviewed aiming at developing plug-and-play diagnostics to manage the SARS-CoV-2 outbreak as well as preventing future epidemics. In addition, other platforms that use magnetic nanomaterials as auxiliary tools for enhanced pathogen and virus detection are also covered. The goal of this review is to inform the researchers of diagnostic and surveillance platforms for SARS-CoV-2 and their performances.
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Affiliation(s)
- Kai Wu
- Department of Electrical and Computer
Engineering, University of Minnesota,
Minneapolis, Minnesota 55455, United States
| | - Renata Saha
- Department of Electrical and Computer
Engineering, University of Minnesota,
Minneapolis, Minnesota 55455, United States
| | - Diqing Su
- Department of Chemical Engineering and
Material Science, University of Minnesota,
Minneapolis, Minnesota 55455, United States
| | - Venkatramana D. Krishna
- Department of Veterinary Population
Medicine, University of Minnesota, St.
Paul, Minnesota 55108, United States
| | - Jinming Liu
- Department of Electrical and Computer
Engineering, University of Minnesota,
Minneapolis, Minnesota 55455, United States
| | - Maxim C.-J. Cheeran
- Department of Veterinary Population
Medicine, University of Minnesota, St.
Paul, Minnesota 55108, United States
| | - Jian-Ping Wang
- Department of Electrical and Computer
Engineering, University of Minnesota,
Minneapolis, Minnesota 55455, United States
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Tang Z, Kong N, Zhang X, Liu Y, Hu P, Mou S, Liljeström P, Shi J, Tan W, Kim JS, Cao Y, Langer R, Leong KW, Farokhzad OC, Tao W. A materials-science perspective on tackling COVID-19. NATURE REVIEWS. MATERIALS 2020; 5:847-860. [PMID: 33078077 PMCID: PMC7556605 DOI: 10.1038/s41578-020-00247-y] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/14/2020] [Indexed: 05/08/2023]
Abstract
The ongoing SARS-CoV-2 pandemic highlights the importance of materials science in providing tools and technologies for antiviral research and treatment development. In this Review, we discuss previous efforts in materials science in developing imaging systems and microfluidic devices for the in-depth and real-time investigation of viral structures and transmission, as well as material platforms for the detection of viruses and the delivery of antiviral drugs and vaccines. We highlight the contribution of materials science to the manufacturing of personal protective equipment and to the design of simple, accurate and low-cost virus-detection devices. We then investigate future possibilities of materials science in antiviral research and treatment development, examining the role of materials in antiviral-drug design, including the importance of synthetic material platforms for organoids and organs-on-a-chip, in drug delivery and vaccination, and for the production of medical equipment. Materials-science-based technologies not only contribute to the ongoing SARS-CoV-2 research efforts but can also provide platforms and tools for the understanding, protection, detection and treatment of future viral diseases.
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Affiliation(s)
- Zhongmin Tang
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Xingcai Zhang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Yuan Liu
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Ping Hu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China
| | - Shan Mou
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peter Liljeström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jianlin Shi
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | | | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Langer
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY USA
| | - Omid C. Farokhzad
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
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124
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Chang JJM, Ip YCA, Ng CSL, Huang D. Takeaways from Mobile DNA Barcoding with BentoLab and MinION. Genes (Basel) 2020; 11:E1121. [PMID: 32987804 PMCID: PMC7598690 DOI: 10.3390/genes11101121] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for species identification and discovery, yet the existing sample capability is limited (n ≤ 10). Here, we assembled a portable sequencing setup comprising the BentoLab and MinION and developed a workflow capable of processing 32 samples simultaneously. We demonstrated this enhanced capability out at sea, where we collected samples and barcoded them onboard a dive vessel moored off Sisters' Islands Marine Park, Singapore. In under 9 h, we generated 105 MinION barcodes, of which 19 belonged to fresh metazoans processed immediately after collection. Our setup is thus viable and would greatly fortify existing portable DNA barcoding capabilities. We also tested the performance of the newly released R10.3 nanopore flow cell for DNA barcoding, and showed that the barcodes generated were ~99.9% accurate when compared to Illumina references. A total of 80% of the R10.3 nanopore barcodes also had zero base ambiguities, compared to 50-60% for R9.4.1, suggesting an improved homopolymer resolution and making the use of R10.3 highly recommended.
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Affiliation(s)
- Jia Jin Marc Chang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Yin Cheong Aden Ip
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
| | - Chin Soon Lionel Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Y.C.A.I.); (C.S.L.N.)
- Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore 119227, Singapore
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125
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Chen Q, He Z, Mao F, Pei H, Cao H, Liu X. Diagnostic technologies for COVID-19: a review. RSC Adv 2020; 10:35257-35264. [PMID: 35515699 PMCID: PMC9056975 DOI: 10.1039/d0ra06445a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/12/2020] [Indexed: 01/08/2023] Open
Abstract
Since the outbreak of COVID-19 in December 2019, the highly contagious SARS-CoV-2 virus has spread rapidly worldwide. Although the governments across the world have adopted different preventative measures, the spread of the virus still cannot be effectively controlled, and the number of infections and deaths continues to grow. Early diagnosis of COVID-19 is one of the key measures to control the spread of the pandemic and timely treatment of infected people. This review summarizes current COVID-19 diagnostic techniques based on virology, serology, and imaging diagnostics and discusses their advantages and limitations with the aim of providing a reference for rapid and accurate diagnosis of COVID-19.
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Affiliation(s)
- Qi Chen
- College of Food Science and Engineering, Hainan University Haikou 570228 China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province Haikou 570228 China
| | - Zhenyun He
- Hainan Institute for Food Control Haikou 570314 China
| | - Fujing Mao
- College of Food Science and Engineering, Hainan University Haikou 570228 China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province Haikou 570228 China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University Haikou 570311 China
| | - Hongmei Cao
- College of Food Science and Engineering, Hainan University Haikou 570228 China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province Haikou 570228 China
| | - Xing Liu
- College of Food Science and Engineering, Hainan University Haikou 570228 China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province Haikou 570228 China
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Campos EVR, Pereira AES, de Oliveira JL, Carvalho LB, Guilger-Casagrande M, de Lima R, Fraceto LF. How can nanotechnology help to combat COVID-19? Opportunities and urgent need. J Nanobiotechnology 2020; 18:125. [PMID: 32891146 PMCID: PMC7474329 DOI: 10.1186/s12951-020-00685-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Incidents of viral outbreaks have increased at an alarming rate over the past decades. The most recent human coronavirus known as COVID-19 (SARS-CoV-2) has already spread around the world and shown R0 values from 2.2 to 2.68. However, the ratio between mortality and number of infections seems to be lower in this case in comparison to other human coronaviruses (such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV)). These outbreaks have tested the limits of healthcare systems and have posed serious questions about management using conventional therapies and diagnostic tools. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis and treatment of COVID-19 and other viral infections. In this review, we discuss the use of nanotechnology for COVID-19 virus management by the development of nano-based materials, such as disinfectants, personal protective equipment, diagnostic systems and nanocarrier systems, for treatments and vaccine development, as well as the challenges and drawbacks that need addressing.
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Affiliation(s)
- Estefânia V R Campos
- Human and Natural Sciences Center, Federal University of ABC. Av. dos Estados, 5001. Bl. A, T3 Lab. 503-3. Bangú, Santo André, SP, Brazil
| | - Anderson E S Pereira
- São Paulo State University-UNESP, Institute of Science and Technology, Sorocaba, SP, Brazil
| | | | | | | | - Renata de Lima
- Universidade de Sorocaba, Rodovia Raposo Tavares km 92,5, Sorocaba, São Paulo, Brazil.
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127
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King J, Harder T, Beer M, Pohlmann A. Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses. BMC Infect Dis 2020; 20:648. [PMID: 32883215 PMCID: PMC7468549 DOI: 10.1186/s12879-020-05367-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Due to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, the MinION sequencing device (Oxford Nanopore Technologies) has become a serious competitor for routine whole-genome sequencing. Here, we established a novel, rapid and high-throughput MinION multiplexing workflow based on a universal RT-PCR. METHODS Twelve representative influenza A virus samples of multiple subtypes were universally amplified in a one-step RT-PCR and subsequently sequenced on the MinION instrument in conjunction with a barcoding library preparation kit from the rapid family and the MinIT performing live base-calling. The identical PCR products were sequenced on an IonTorrent platform and, after final consensus assembly, all data was compared for validation. To prove the practicability of the MinION-MinIT method in human and veterinary diagnostics, we sequenced recent and historical influenza strains for further benchmarking. RESULTS The MinION-MinIT combination generated over two million reads for twelve samples in a six-hour sequencing run, from which a total of 72% classified as quality screened, trimmed and mapped influenza reads to produce full genome sequences. Identities between the datasets of > 99.9% were achieved, with 100% coverage of all segments alongside a sufficient confidence and 4492fold mean depth. From RNA extraction to finished sequences, only 14 h were required. CONCLUSIONS Overall, we developed and validated a novel and rapid multiplex workflow for influenza A virus sequencing. This protocol suits both clinical and academic settings, aiding in real time diagnostics and passive surveillance.
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Affiliation(s)
- Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany.
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128
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Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection. mSphere 2020; 5:5/4/e00808-20. [PMID: 32848011 PMCID: PMC7449630 DOI: 10.1128/msphere.00808-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We developed a visual and rapid reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assay targeting the S gene for SARS-CoV-2 infection. The strength of our study was that we validated the RT-LAMP assay using 481 clinical respiratory samples from two prospective cohorts of suspected COVID-19 patients and on the serial samples from an asymptomatic carrier. The developed RT-LAMP approach showed an increased sensitivity (88.89%) and high consistency (kappa, 0.92) compared with those of reverse transcription-quantitative PCR (RT-qPCR) for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection, facilitating SARS-CoV-2 screening in well-equipped labs as well as in the field. The time required for RT-LAMP was less than 1 h from sample preparation to the result (more than 2 h for RT-qPCR). This study showed that the RT-LAMP assay was a simple, rapid, and sensitive approach for SARS-CoV-2 infection and can facilitate COVID-19 diagnosis, especially in resource-poor settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak urgently necessitates sensitive and convenient COVID-19 diagnostics for the containment and timely treatment of patients. We aimed to develop and validate a novel reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assay to detect SARS-CoV-2. Patients with suspected COVID-19 and close contacts were recruited from two hospitals between 26 January and 8 April 2020. Respiratory samples were collected and tested using RT-LAMP, and the results were compared with those obtained by reverse transcription-quantitative PCR (RT-qPCR). Samples yielding inconsistent results between these two methods were subjected to next-generation sequencing for confirmation. RT-LAMP was also applied to an asymptomatic COVID-19 carrier and patients with other respiratory viral infections. Samples were collected from a cohort of 129 cases (329 nasopharyngeal swabs) and an independent cohort of 76 patients (152 nasopharyngeal swabs and sputum samples). The RT-LAMP assay was validated to be accurate (overall sensitivity and specificity of 88.89% and 99.00%, respectively) and diagnostically useful (positive and negative likelihood ratios of 88.89 and 0.11, respectively). RT-LAMP showed increased sensitivity (88.89% versus 81.48%) and high consistency (kappa, 0.92) compared to those of RT-qPCR for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection. The time required for RT-LAMP was less than 1 h from sample preparation to the result. In addition, RT-LAMP was feasible for use with asymptomatic patients and did not cross-react with other respiratory pathogens. The developed RT-LAMP assay offers rapid, sensitive, and straightforward detection of SARS-CoV-2 infection and may aid the expansion of COVID-19 testing in the public domain and hospitals. IMPORTANCE We developed a visual and rapid reverse transcription–loop-mediated isothermal amplification (RT-LAMP) assay targeting the S gene for SARS-CoV-2 infection. The strength of our study was that we validated the RT-LAMP assay using 481 clinical respiratory samples from two prospective cohorts of suspected COVID-19 patients and on the serial samples from an asymptomatic carrier. The developed RT-LAMP approach showed an increased sensitivity (88.89%) and high consistency (kappa, 0.92) compared with those of reverse transcription-quantitative PCR (RT-qPCR) for SARS-CoV-2 screening while requiring only constant-temperature heating and visual inspection, facilitating SARS-CoV-2 screening in well-equipped labs as well as in the field. The time required for RT-LAMP was less than 1 h from sample preparation to the result (more than 2 h for RT-qPCR). This study showed that the RT-LAMP assay was a simple, rapid, and sensitive approach for SARS-CoV-2 infection and can facilitate COVID-19 diagnosis, especially in resource-poor settings.
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129
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Xu M, Wang D, Wang H, Zhang X, Liang T, Dai J, Li M, Zhang J, Zhang K, Xu D, Yu X. COVID-19 diagnostic testing: Technology perspective. Clin Transl Med 2020; 10:e158. [PMID: 32898340 PMCID: PMC7443140 DOI: 10.1002/ctm2.158] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023] Open
Abstract
The corona virus disease 2019 (COVID-19) is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 18 million people were infected with a total of 0.7 million deaths in ∼188 countries. Controlling the spread of SARS-CoV-2 is therefore inherently dependent on identifying and isolating infected individuals, especially since COVID-19 can result in little to no symptoms. Here, we provide a comprehensive review of the different primary technologies used to test for COVID-19 infection, discuss the advantages and disadvantages of each technology, and highlight the studies that have employed them. We also describe technologies that have the potential to accelerate SARS-CoV-2 detection in the future, including digital PCR, CRISPR, and microarray. Finally, remaining challenges in COVID-19 diagnostic testing are discussed, including (a) the lack of universal standards for diagnostic testing; (b) the identification of appropriate sample collection site(s); (c) the difficulty in performing large population screening; and (d) the limited understanding of SARS-COV-2 viral invasion, replication, and transmission.
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Affiliation(s)
- Meng Xu
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjingChina
| | - Dan Wang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Hongye Wang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Xiaomei Zhang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Te Liang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Jiayu Dai
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Meng Li
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Jiahui Zhang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Kai Zhang
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjingChina
| | - Xiaobo Yu
- State Key Laboratory of ProteomicsBeijing Proteome Research CenterNational Center for Protein SciencesBeijing Institute of LifeomicsBeijingChina
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Sivasankarapillai VS, Pillai AM, Rahdar A, Sobha AP, Das SS, Mitropoulos AC, Mokarrar MH, Kyzas GZ. On Facing the SARS-CoV-2 (COVID-19) with Combination of Nanomaterials and Medicine: Possible Strategies and First Challenges. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E852. [PMID: 32354113 PMCID: PMC7712148 DOI: 10.3390/nano10050852] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/24/2020] [Accepted: 04/25/2020] [Indexed: 02/07/2023]
Abstract
Global health is facing the most dangerous situation regarding the novel severe acute respiratory syndrome called coronavirus 2 (SARS-CoV-2), which is widely known as the abbreviated COVID-19 pandemic. This is due to the highly infectious nature of the disease and its possibility to cause pneumonia induced death in approximately 6.89% of infected individuals (data until 27 April 2020). The pathogen causing COVID-19 is called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is believed to be originated from the Wuhan Province in China. Unfortunately, an effective and approved vaccine for SARS-CoV-2 virus is still not available, making the situation more dangerous and currently available medical care futile. This unmet medical need thus requires significant and very urgent research attention to develop an effective vaccine to address the SARS-CoV-2 virus. In this review, the state-of-the-art drug design strategies against the virus are critically summarized including exploitations of novel drugs and potentials of repurposed drugs. The applications of nanochemistry and general nanotechnology was also discussed to give the status of nanodiagnostic systems for COVID-19.
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Affiliation(s)
| | - Akhilash M. Pillai
- Department of Chemistry, University College, Thiruvananthapuram, Kerala 695034, India;
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol 98615538, Iran
| | - Anumol P. Sobha
- Department of Biochemistry, University of Kerala, Thiruvananthapuram, Kerala 695581, India;
| | - Sabya Sachi Das
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India;
| | | | | | - George Z. Kyzas
- Department of Chemistry, International Hellenic University, 65404 Kavala, Greece;
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Baldi P, La Porta N. Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry. FRONTIERS IN PLANT SCIENCE 2020; 11:570862. [PMID: 33193502 PMCID: PMC7655913 DOI: 10.3389/fpls.2020.570862] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/29/2020] [Indexed: 05/14/2023]
Abstract
Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.
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Affiliation(s)
- Paolo Baldi
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- *Correspondence: Paolo Baldi,
| | - Nicola La Porta
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- The EFI Project Centre on Mountain Forests (MOUNTFOR), San Michele a/Adige, Trento, Italy
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