Rapid Nanoplasmonic-Enhanced Detection of SARS-CoV-2 and Variants on DNA Aptamer Metasurfaces
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Abstract
Since the discovery of coronavirus disease 2019 (COVID-19) in December 2019, it has been mainly diagnosed with quantitative reverse transcription polymerase chain reaction (PCR) of nasal swabs in clinics. A very sensitive and rapid detection technique using easily collected fluids such as saliva is needed for safer and more practical, precise mass testing. Here, we introduce a computationally screened gold-nanopatterned metasurface platform out of a pattern space of 2 100 combinations for strongly enhanced light–virus interaction using a genetic algorithm and apply them to investigate the presence and concentration of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In our approach, the gold metasurface with the nanopattern that provides the highest plasmonic enhancement is modified with the primary DNA aptamer for COVID-19 sensing from unprocessed saliva. A fluorescently tagged secondary aptamer was used to bind the virus that was then captured on the surface with the primary aptamer. By incorporating machine learning to identify the virus from Raman spectra, we achieved 95.2% sensitivity and specificity on 36 SARS-CoV-2 PCR-positive and 33 SARS-CoV-2 PCR-negative samples collected in the clinics. In addition, we demonstrated that our nanoplasmonic aptasensor could distinguish wild-type, Alpha, and Beta variants through the machine learning analysis of their spectra. Our results may help pave the way for effective, safe, and quantitative preventive screening and identification of variants.
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SciScore for 10.1101/2021.08.07.21261749: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Vero CCL-81 cells grown in Dulbecco minimal essential medium (DMEM) supplemented with antibiotic/antimycotic (GIBCO) and heat-inactivated fetal bovine serum (5% or 10%) were used for SARS-CoV-2 isolation and first passage. Vero CCL-81suggested: NoneThen, 100 μl of Vero cell suspension was added on to serial dilutions of the clinical samples. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Virus inactivation was confirmed by the absence of cytopathic effect in two consecutive passages in the VeroE6 cell lines and the inability to demonstrate amplification by quantitative … SciScore for 10.1101/2021.08.07.21261749: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Vero CCL-81 cells grown in Dulbecco minimal essential medium (DMEM) supplemented with antibiotic/antimycotic (GIBCO) and heat-inactivated fetal bovine serum (5% or 10%) were used for SARS-CoV-2 isolation and first passage. Vero CCL-81suggested: NoneThen, 100 μl of Vero cell suspension was added on to serial dilutions of the clinical samples. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Virus inactivation was confirmed by the absence of cytopathic effect in two consecutive passages in the VeroE6 cell lines and the inability to demonstrate amplification by quantitative RT-PCR. VeroE6suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)Software and Algorithms Sentences Resources Poor-quality bases found in the raw data were removed using Trimmomatic 0.36 (-phred33, LEADING:20, TRAILING:20, SLID INGWINDOW:4:20, MINLEN:40) Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)Lumerical FDTD and MATLAB were used for implementing and running the electromagnetic and genetic algorithm models, respectively. MATLABsuggested: (MATLAB, RRID:SCR_001622)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32 and 6. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a protocol registration statement.
Results from scite Reference Check: We found no unreliable references.
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