PCR-Free Innovative Strategies for SARS-CoV-2 Detection

Unraveling the Amplification-Free Quantitative Detection of Viral RNA in Nasopharyngeal Swab Samples Using a Compact Electrochemical Rapid Test Device

Providing viral load numbers of infection events aids in the identification of disease severity and in the effective overall patient management. Gold-standard polymerase chain reaction (PCR) techniques make this possible but cannot be applied at the point of need and in low-resource settings. Here, we report on the development of a compact analytical platform that can detect a conserved sequence of the RNA of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in 40 min in nasopharyngeal swab samples without the need for any previous purification or gene amplification steps. It combines electrochemical and paper fluidic approaches together with a sandwich hybridization assay performed on magnetic nanoparticles (MNPs) modified with a tailor-designed capture DNA hairpin. The device proves to quantitatively detect viral RNA in a retrospective study carried out with nasopharyngeal swab samples. A sensitivity of 100% and a specificity of 93% were estimated by the receiver operating characteristic (ROC) analysis. However, although molar concentration values of the target RNA sequence are provided, these estimates do not fully correlate with the viral load numbers estimated by RT-qPCR over the whole Ct sample range. Empirical studies have been carried out that have provided clear insights into this hurdle and simple solutions to overcome it, without depriving the device of the features required for potential use in a point-of-care (PoC) environment.

Antibody screening-assisted multichannel nanoplasmonic sensing chip based on SERS for viral screening and variants identification

The Omicron variants of SARS-CoV-2 have been spreading globally and have never disappeared from our sight, indicating that their coexistence with humans has become a fact, and monitoring its evolution and spread remains a current task. Although polymerase chain reaction (PCR) is the most commonly used virus detection method, it requires labor-intensive and time-consuming procedures in a laboratory setting. Herein, a multichannel nanoplasmonic sensing chip based on surface enhanced Raman spectroscopy (SERS) was developed for detecting N and S proteins, as well as IgG and IgM, related to SARS-CoV-2 Omicron variants. Through a self-screening process, specific antibodies for on-site and rapid identification of important variants of concern (VoCs) were obtained, and their binding was confirmed by protein structure analysis. The use of these S protein specific antibodies can accurately identify Omicron VoCs (BA. 5, BF.7，XBB.1.5) with the detection limit (LoD) of 0.16 pg/mL. Then, the proposed SERS array chip was integrated with a hand-held Raman spectrometer to successfully detect the Omicron subvariants in real saliva samples within only 20 min, greatly reducing the detection time of PCR. This sensing technology will provide a powerful and rapid point-of-care testing (POCT) method for virus diagnosis, subtype identification, and post-infection antibody level monitoring.

Au@Pt@Pd nanozymes based lateral flow immunoassay for quantitative detection of SARS-CoV-2 nucleocapsid protein in nasal swab samples

Three-metal-core-shell nanoparticles (Au@Pt@PdNPs) providing excellent peroxidase-like activity were applied in lateral flow immunoassay (LFIA), designated as Au@Pt@Pd-LFIA, for detecting the nucleocapsid protein (NP) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). An Au@Pt@Pd-LFIA was developed for quantitatively testing of SARS-CoV-2 NP with a range 0.12-31.25 ng/mL. The limit of detection (LOD) of Au@Pt@Pd-LFIA strip was 0.06 ng/mL, which was 16-fold or eightfold more sensitive than that of the gold lateral flow immunoassay (Au-LFIA) and the gold flower flow immunoassay (AF-LFIA) strips, respectively. For detection of clinical samples from nasal swabs using test strips, Au@Pt@Pd-LFIA had 84.09% sensitivity, 100% specificity, and 92.55% accuracy. In terms of detection time, the testing of Au@Pt@Pd-LFIA strip was 16 min similar to Au-LFIA (15 min) and AF-LFIA (10 min), but much shorter than ELISA (2 h). In conclusion, Au@Pt@Pd-LFIA is a sensitive, rapid, and simple test for quantitative detection of SARS-CoV-2 NP in nasal swab samples.

Weak-cooperative binding of a long single-stranded DNA chain on a surface

Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.

PCR Independent Strategy-Based Biosensors for RNA Detection

RNA is an important information and functional molecule. It can respond to the regulation of life processes and is also a key molecule in gene expression and regulation. Therefore, RNA detection technology has been widely used in many fields, especially in disease diagnosis, medical research, genetic engineering and other fields. However, the current RT-qPCR for RNA detection is complex, costly and requires the support of professional technicians, resulting in it not having great potential for rapid application in the field. PCR-free techniques are the most attractive alternative. They are a low-cost, simple operation method and do not require the support of large instruments, providing a new concept for the development of new RNA detection methods. This article reviews current PCR-free methods, overviews reported RNA biosensors based on electrochemistry, SPR, microfluidics, nanomaterials and CRISPR, and discusses their challenges and future research prospects in RNA detection.

Development of Detection Antibody Targeting the Linear Epitope in SARS-CoV-2 Nucleocapsid Protein with Ultra-High Sensitivity

The COVID-19 pandemic caused by SARS-CoV-2 highlighted the importance of reliable detection methods for disease control and surveillance. Optimizing detection antibodies by rational screening antigens would improve the sensitivity and specificity of antibody-based detection methods such as colloidal gold immunochromatography. In this study, we screened three peptide antigens with conserved sequences in the N protein of SARS-CoV-2 using bioinformatical and structural biological analyses. Antibodies that specifically recognize these peptides were prepared. The epitope of the peptide that had the highest binding affinity with its antibody was located on the surface of the N protein, which was favorable for antibody binding. Using the optimal antibody that can recognize this epitope, we developed colloidal gold immunochromatography, which can detect the N protein at 10 pg/mL. Importantly, this antibody could effectively recognize both the natural peptide antigen and mutated peptide antigen in the N protein, showing the feasibility of being applied in the large-scale population testing of SARS-CoV-2. Our study provides a platform with reference significance for the rational screening of detection antibodies with high sensitivity, specificity, and reliability for SARS-CoV-2 and other pathogens.

FlashPCR: Revolutionising qPCR by Accelerating Amplification through Low ∆T Protocols

Versatility, sensitivity, and accuracy have made the real-time polymerase chain reaction (qPCR) a crucial tool for research, as well as diagnostic applications. However, for point-of-care (PoC) use, traditional qPCR faces two main challenges: long run times mean results are not available for half an hour or more, and the requisite high-temperature denaturation requires more robust and power-demanding instrumentation. This study addresses both issues and revises primer and probe designs, modified buffers, and low ∆T protocols which, together, speed up qPCR on conventional qPCR instruments and will allow for the development of robust, point-of-care devices. Our approach, called "FlashPCR", uses a protocol involving a 15-second denaturation at 79 °C, followed by repeated cycling for 1 s at 79 °C and 71 °C, together with high Tm primers and specific but simple buffers. It also allows for efficient reverse transcription as part of a one-step RT-qPCR protocol, making it universally applicable for both rapid research and diagnostic applications.