A Tri‐Channel Oxide Transistor Concept for the Rapid Detection of Biomolecules Including the SARS‐CoV‐2 Spike Protein

In this paper, a highly sensitive graphene-based multiple-layer (BK7/Au/PtSe2/Graphene) coated surface plasmon resonance (SPR) biosensor is proposed for the rapid detection of the novel Coronavirus (COVID-19). The proposed sensor was modeled on the basis of the total internal reflection (TIR) technique for real-time detection of ligand-analyte immobilization in the sensing region. The refractive index (RI) of the sensing region is changed due to the interaction of different concentrations of the ligand-analyte, thus impacting surface plasmon polaritons (SPPs) excitation of the multi-layer sensor interface. The performance of the proposed sensor was numerically investigated by using the transfer matrix method (TMM) and the finite-difference time-domain (FDTD) method. The proposed SPR biosensor provides fast and accurate early-stage diagnosis of the COVID-19 virus, which is crucial in limiting the spread of the pandemic. In addition, the performance of the proposed sensor was investigated numerically with different ligand-analytes: (i) the monoclonal antibodies (mAbs) as ligand and the COVID-19 virus spike receptor-binding domain (RBD) as analyte, (ii) the virus spike RBD as ligand and the virus anti-spike protein (IgM, IgG) as analyte and (iii) the specific probe as ligand and the COVID-19 virus single-standard ribonucleic acid (RNA) as analyte. After the investigation, the sensitivity of the proposed sensor was found to provide 183.33°/refractive index unit (RIU) in SPR angle (θSPR) and 833.33THz/RIU in SPR frequency (SPRF) for detection of the COVID-19 virus spike RBD; the sensitivity obtained 153.85°/RIU in SPR angle and 726.50THz/RIU in SPRF for detection of the anti-spike protein, and finally, the sensitivity obtained 140.35°/RIU in SPR angle and 500THz/RIU in SPRF for detection of viral RNA. It was observed that whole virus spike RBD detection sensitivity is higher than that of the other two detection processes. Highly sensitive two-dimensional (2D) materials were used to achieve significant enhancement in the Goos-Hänchen (GH) shift detection sensitivity and plasmonic properties of the conventional SPR sensor. The proposed sensor successfully senses the COVID-19 virus and offers additional (1 + 0.55) × L times sensitivity owing to the added graphene layers. Besides, the performance of the proposed sensor was analyzed based on detection accuracy (DA), the figure of merit (FOM), signal-noise ratio (SNR), and quality factor (QF). Based on its performance analysis, it is expected that the proposed sensor may reduce lengthy procedures, false positive results, and clinical costs, compared to traditional sensors. The performance of the proposed sensor model was checked using the TMM algorithm and validated by the FDTD technique.

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Importance of mutations in amino acid 484 of the Spike protein of SARS-CoV-2: rapid detection by restriction enzyme analysis

Investigación Clínica ◽

10.22209/ic.v62s2a02 ◽

2021 ◽

Vol 62 ◽

pp. 18-26

Author(s):

Rossana C Jaspe ◽

Yoneira Sulbarn ◽

Carmen L Loureiro ◽

Pierina D´Angelo ◽

Lieska Rodríguez ◽

...

Keyword(s):

Amino Acid ◽

Restriction Enzyme ◽

Rapid Detection ◽

Neutralizing Antibodies ◽

Spike Protein ◽

Enzyme Analysis ◽

Restriction Enzyme Analysis ◽

Spike Gene ◽

Detection Of Mutations ◽

Viral Isolates

Variants of Concern of SARS-CoV-2 (VOCs), the new coronavirus responsible for COVID-19, have emerged in several countries. Mutations in the amino acid 484 of the Spike protein are particularly important and associated with some of these variants: E484K or E484Q. These mutations have been associated with evasion to neutralizing antibodies. Restriction enzyme analysis is proposed as a rapid method to detect these mutations. A search on GISAID was performed in April 2021 to detect the frequency of these two mutations in the sequence available and their association with other lineages. E484K, present in some VOCs, has emerged in several other lineages and is frequently found in recent viral isolates. A small amplicon from the Spike gene was digested with two enzymes: HpyAV, and MseI. The use of these two enzymes allows the detection of mutations at position 484, and to differentiate between these three conditions: non-mutated, and the presence of E484K or E484Q. A 100% correlation was observed with sequencing results. The proposed methodology, which allows for the screening of a great number of samples, will probably help to provide more information on the prevalence and epidemiology of these mutations worldwide, to select the candidates for whole-genome sequencing.

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Importance of E484K and N501Y mutations in SARS-CoV-2 for genomic surveillance: rapid detection by restriction enzyme analysis

10.1101/2021.05.04.21256650 ◽

2021 ◽

Author(s):

Rossana C Jaspe ◽

Yoneira Sulbaran ◽

Carmen L Loureiro ◽

Pierina D Angelo ◽

Lieska Rodriguez ◽

...

Keyword(s):

Genome Sequencing ◽

Restriction Enzyme ◽

Viral Genome ◽

Rapid Detection ◽

Spike Protein ◽

Enzyme Analysis ◽

Restriction Enzyme Analysis ◽

Whole Genome ◽

Spike Gene ◽

Gene Coding

Introduction: Variants of Concern of SARS-CoV-2 (VOCs), the new coronavirus responsible for COVID-19, have emerged in several countries. Two mutations in the gene coding for the Spike protein of the viral genome are particularly important and associated with some of these variants: E484K and N501Y. Restriction enzyme analysis is proposed as a rapid method to detect these two mutations. Methodology: A search on GISAID was performed in April 2021 to detect the frequency of these two mutations in the sequence available and their association with other lineages. A small amplicon from the Spike gene was digested with two enzymes: HpyAV, which allows detecting E484K mutation, and MseI, for detecting the N501Y one. Results: The mutations E484K and N501Y, associated with VOCs, have emerged in several other lineages, particularly E484K. A 100% correlation was observed with sequencing results. Conclusions: The proposed methodology, which allows screening a great number of samples, will probably help to provide more information on the prevalence and epidemiology of these mutations worldwide, to select the candidates for whole-genome sequencing.

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Development of a rapid diagnostic test for the detection of antibodies or antigens to Coronavirus (COVID-19)

Fields journal of Huddersfield student research ◽

10.5920/fields.978 ◽

2021 ◽

Author(s):

James Elliff

Keyword(s):

Low Income ◽

Rapid Detection ◽

Spike Protein ◽

Low Income Countries ◽

Health Crisis ◽

Significant Difference ◽

Specific Antigens ◽

Microscope Slides ◽

Glass Microscope ◽

Control Samples

Theglobal health crisis caused by COVID-19 has overwhelmed both healthcaresettings and economies globally. Whilst mass population testing has improveddrastically, recent reviews of existing methods have highlighted variousshortcomings with these methods. Theaim of this project was to investigate whether the LAA could be modified andutilised as rapid detection test which either matched or exceeded the existingsensitivity and specificity values.   TheLAA investigated whether the COVID-19 spike protein could be detected insamples. COVID-19 specific IgM and IgG were used in conjunction with a seriesof non-specific antigens. Control or AG containing samples weremixed with AB-microsphere complexes on glass microscope slides. Manualvisualisation identified various levels of agglutination. Light microscopy andspectrophotometry at 405nm determined that the LAA could detect at least 2.3ngof spike protein.  Theparticle counting tool of ImageJ was utilised to obtain a dataset which wassubjected to statistical analysis which indicated that there was a significantdifference between control samples and live tests, P = 0.000102 for the spikeprotein assay and P = 0.254 for the non-specific assay respectively. Theresults obtained fell in line with a similar study conducted by Buffin et al in2018. Theanalytical methods used in this project twinned with data obtained in previousstudies supports the significant difference between control values and livetest values. The LAA is easier, quicker to use (results in ≤ 30 minutes) andcheaper, with potentially better sensitivity to existing methods. This couldbenefit high and low-income countries alike upon further research andoptimisation. 

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