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Ganesh PS, Elugoke SE, Lee SH, Kim SY, Ebenso EE. Smart and emerging point of care electrochemical sensors based on nanomaterials for SARS-CoV-2 virus detection: Towards designing a future rapid diagnostic tool. CHEMOSPHERE 2024; 352:141269. [PMID: 38307334 DOI: 10.1016/j.chemosphere.2024.141269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
In the recent years, researchers from all over the world have become interested in the fabrication of advanced and innovative electrochemical and/or biosensors for respiratory virus detection with the use of nanotechnology. These fabricated sensors demonstrated a number of benefits, including precision, affordability, accessibility, and miniaturization which makes them a promising test method for point-of-care (PoC) screening for SARS-CoV-2 viral infection. In order to comprehend the principles of electrochemical sensing and the role of various types of sensing interfaces, we comprehensively explored the underlying principles of electroanalytical methods and terminologies related to it in this review. In addition, it is addressed how to fabricate electrochemical sensing devices incorporating nanomaterials as graphene, metal/metal oxides, metal organic frameworks (MOFs), MXenes, quantum dots, and polymers. We took an effort to carefully compile current developments, advantages, drawbacks, possible solutions in nanomaterials based electrochemical sensors.
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Affiliation(s)
- Pattan Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Saheed Eluwale Elugoke
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa
| | - Seok-Han Lee
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Eno E Ebenso
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa.
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Saravanan KA, Panigrahi M, Kumar H, Rajawat D, Nayak SS, Bhushan B, Dutt T. Role of genomics in combating COVID-19 pandemic. Gene 2022; 823:146387. [PMID: 35248659 PMCID: PMC8894692 DOI: 10.1016/j.gene.2022.146387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022]
Abstract
The coronavirus disease 2019 (COVID-19) quickly swept over the world, becoming one of the most devastating outbreaks in human history. Being the first pandemic in the post-genomic era, advancements in genomics contributed significantly to scientific understanding and public health response to COVID-19. Genomic technologies have been employed by researchers all over the world to better understand the biology of SARS-CoV-2 and its origin, genomic diversity, and evolution. Worldwide genomic resources have greatly aided in the investigation of the COVID-19 pandemic. The pandemic has ushered in a new era of genomic surveillance, wherein scientists are tracking the changes of the SARS-CoV-2 genome in real-time at the international and national levels. Availability of genomic and proteomic information enables the rapid development of molecular diagnostics and therapeutics. The advent of high-throughput sequencing and genome editing technologies led to the development of modern vaccines. We briefly discuss the impact of genomics in the ongoing COVID-19 pandemic in this review.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Deval H, Nyayanit DA, Mishra SK, Yadav PD, Zaman K, Shankar P, Misra BR, Behera SP, Kumar N, Kumar A, Bhardwaj P, Dwivedi GR, Singh R, Shete AM, Pandit P, Pandey AK, Yadav GK, Gupta S, Kumar M, Kavathekar A, Singh RS, Prajapati S, Kant R. Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Front Med (Lausanne) 2022; 8:781287. [PMID: 35071267 PMCID: PMC8777020 DOI: 10.3389/fmed.2021.781287] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022] Open
Abstract
Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes-49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.
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Affiliation(s)
- Hirawati Deval
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Shailendra Kumar Mishra
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Pragya D. Yadav
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Kamran Zaman
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Prem Shankar
- All India Institute of Medical Sciences, Gorakhpur, India
| | - Brij R. Misra
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Sthita Pragnya Behera
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Niraj Kumar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Abhinendra Kumar
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Pooja Bhardwaj
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Gaurav Raj Dwivedi
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Rajeev Singh
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Anita M. Shete
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Priyanka Pandit
- Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India
| | - Ashok K. Pandey
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Girijesh Kumar Yadav
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Shashi Gupta
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Manoj Kumar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Asif Kavathekar
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Ravi Shankar Singh
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Sanjay Prajapati
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
| | - Rajni Kant
- Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India
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Shen X, Wang J, Li J, He A, Liu H, Ma X. Field Validation of a Rapid Recombinase Aided Amplification Assay for SARS-CoV-2 RNA at Customs - Zhejiang Province, China, January 2021. China CDC Wkly 2021; 3:973-976. [PMID: 34804630 PMCID: PMC8598545 DOI: 10.46234/ccdcw2021.236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
Introduction The best approach to preventing the importation of coronavirus disease 2019 (COVID-19) is enhancing the detection capacity at customs. The rapid detection is of utmost importance and therefore highly demanded. Methods We conducted a field validation study of a duplex real-time reverse transcription recombinase-aided amplification (RT-RAA) assay in Zhoushan and Hangzhou customs, in Zhejiang Province, China. The reverse transcriptase polymerase chain reaction (RT-PCR) assay kit routinely used at customs was used in parallel, and the duration the two methods took to complete a specific number of samples was compared. Results Among 506 samples collected, RT-RAA results were consistent with the RT-PCR results. The sensitivity and specificity were 100%, the total coincidence rate was 100%, and the Kappa value was 1 (P<0.05) for both methods. The RT-RAA kit took a significantly shorter time in testing the 20-200 samples than the RT-PCR kit. Discussion The RT-RAA detection method is more efficient and suitable for use at customs than RT-PCR assay to realize rapid customs clearance of 200 or fewer samples.
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Affiliation(s)
- Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinrong Wang
- Shijiazhuang People's Hospital, Shijiazhuang, Hebei, China
| | - Jingyi Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Anna He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Liu
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
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