|
1
|
Jiang S, Qian S, Zhu S, Lu J, Hu Y, Zhang C, Geng Y, Chen X, Guo Y, Chen Z, Pu J, Guo Z, Liu S. A Point-of-Care Testing Device Utilizing Graphene-Enhanced Fiber Optic SPR Sensor for Real-Time Detection of Infectious Pathogens. Biosensors (Basel) 2023; 13:1029. [PMID: 38131789 PMCID: PMC10741924 DOI: 10.3390/bios13121029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Timely detection of highly infectious pathogens is essential for preventing and controlling public health risks. However, most traditional testing instruments require multiple tedious steps and ultimately testing in hospitals and third-party laboratories. The sample transfer process significantly prolongs the time to obtain test results. To tackle this aspect, a portable fiber optic surface plasmon resonance (FO-SPR) device was developed for the real-time detection of infectious pathogens. The portable device innovatively integrated a compact FO-SPR sensing component, a signal acquisition and processing system, and an embedded power supply unit. A gold-plated fiber is used as the FO-SPR sensing probe. Compared with traditional SPR sensing systems, the device is smaller size, lighter weight, and higher convenience. To enhance the detection capacity of pathogens, a monolayer graphene was coated on the sensing region of the FO-SPR sensing probe. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used to evaluate the performance of the portable device. The device can accurately detect the SARS-CoV-2 spike S1 protein in phosphate-buffered saline (PBS) and artificial saliva within just 20 min, and the device successfully detected cultured SARS-CoV-2 virus. Furthermore, the FO-SPR probe has long-term stability, remaining stable for up to 8 days. It could distinguish between the SARS-CoV-2 spike protein and the MERS-CoV spike protein. Hence, this FO-SPR device provides reliable, rapid, and portable access to test results. It provides a promising point-of-care testing (POCT) tool for on-site screening of infectious pathogens.
Collapse
Affiliation(s)
- Shiyu Jiang
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Siyu Qian
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Shunning Zhu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Jinxin Lu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Yunxin Hu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Cheng Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Yikai Geng
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Xuefeng Chen
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Ying Guo
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| | - Zhaoliang Chen
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Jie Pu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Zhendong Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China; (C.Z.); (Z.C.); (J.P.); (Z.G.)
| | - Shengchun Liu
- Heilongjiang Provincial Key Laboratory of Metamaterials Physics and Device, Heilongjiang University, Harbin 150080, China; (S.J.); (S.Z.); (J.L.); (Y.H.); (Y.G.); (X.C.); (Y.G.)
| |
Collapse
|
|
2
|
Desai S, Rashmi S, Rane A, Dharavath B, Sawant A, Dutt A. An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Brief Bioinform 2021; 22:1065-1075. [PMID: 33479725 PMCID: PMC7929363 DOI: 10.1093/bib/bbaa437] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The analysis of the SARS-CoV-2 genome datasets has significantly advanced our understanding of the biology and genomic adaptability of the virus. However, the plurality of advanced sequencing datasets-such as short and long reads-presents a formidable computational challenge to uniformly perform quantitative, variant or phylogenetic analysis, thus limiting its application in public health laboratories engaged in studying epidemic outbreaks. We present a computational tool, Infectious Pathogen Detector (IPD), to perform integrated analysis of diverse genomic datasets, with a customized analytical module for the SARS-CoV-2 virus. The IPD pipeline quantitates individual occurrences of 1060 pathogens and performs mutation and phylogenetic analysis from heterogeneous sequencing datasets. Using IPD, we demonstrate a varying burden (5.055-999655.7 fragments per million) of SARS-CoV-2 transcripts across 1500 short- and long-read sequencing SARS-CoV-2 datasets and identify 4634 SARS-CoV-2 variants (~3.05 variants per sample), including 449 novel variants, across the genome with distinct hotspot mutations in the ORF1ab and S genes along with their phylogenetic relationships establishing the utility of IPD in tracing the genome isolates from the genomic data (as accessed on 11 June 2020). The IPD predicts the occurrence and dynamics of variability among infectious pathogens-with a potential for direct utility in the COVID-19 pandemic and beyond to help automate the sequencing-based pathogen analysis and in responding to public health threats, efficaciously. A graphical user interface (GUI)-enabled desktop application is freely available for download for the academic users at http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html and for web-based processing at http://ipd.actrec.gov.in/ipdweb/ to generate an automated report without any prior computational know-how.
Collapse
Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | | | | | - Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Aniket Sawant
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
| | - Amit Dutt
- Corresponding author: Dr Amit Dutt, Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Tata Memorial Centre, Maharashtra, Navi Mumbai 410210, India. Tel.: +91-22-27405056/30435056; E-mail:
| |
Collapse
|