Discovery and Characterization of Spike N‐Terminal Domain‐Binding Aptamers for Rapid SARS‐CoV‐2 Detection

Microfluidic Enrichment of Intact SARS-CoV-2 Viral Particles by Stoichiometric Balanced DNA Computation

Health diagnostic tools for community safety and environmental monitoring require selective and quantitatively accurate active viral load assessment. Herein, we report a microfluidic enrichment strategy to separate intact SARS-CoV-2 particles by AND logic gate with inputs of cholesterol oligonucleotides for the envelope and aptamers for the spike viral proteins. Considering the unequal quantity of endogenous spikes and lipid membranes on SARS-CoV-2, a dual-domain binding strategy, with two aptamers targeting different spike domains, was applied to balance the spike-envelope stoichiometric ratio. By balancing the stoichiometric with DNA computation and promoting microscale mass transfer of the herringbone chip, the developed strategy enabled high sensitivity detection of pseudotyped SARS-CoV-2 with a limit of detection as low as 37 active virions/μL while distinguishing it from inactive counterparts, other nontarget viruses, and free spike protein. Moreover, the captured viral particles can be released through DNase I treatment with up to 90% efficiency, which is fully compatible with virus culture and sequencing. Overall, the developed strategy not only identified SARS-CoV-2-infected patients (n = 14) with 100% identification from healthy donors (n = 8) but also provided a fresh perspective on the regulation of stoichiometric ratio to achieve a more biologically relevant DNA computation.

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.

Rolosense: Mechanical detection of SARS-CoV-2 using a DNA-based motor

Assays detecting viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here we present Rolosense, a virus sensing platform that transduces the motion of synthetic DNA-based motors transporting 5-micron particles on RNA fuel chips. Motors and chips are modified with virus-binding aptamers that lead to stalling of motion. Therefore, motors perform a "mechanical test" of viral target and stall in the presence of whole virions which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as we demonstrated one-pot detection of influenza A and SARS-CoV-2. As a proof-of-concept, we show readout can be achieved using a smartphone camera in as little as 15 mins without any sample preparation steps. Taken together, mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost, point-of-care screening of circulating viruses.

Aptamer-based biosensors for virus protein detection

Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.

Fluorescence-Linked Aptamer Assay for SARS-CoV-2 Spike-Protein: A Step-by-Step Performance Analysis in Clinical Samples

The COVID-19 pandemic has been a main concern over the last two years and has become one of the most important crises in the history of human health. Today, there is still a need for affordable and reliable diagnostic tests for massive disease monitoring. Previously, a set of highly specific DNA-aptamers (C7/C9) binding to the SARS-CoV-2 Spike (S) protein were isolated but its performance in clinical samples remained to be tested. Here, 242 samples were collected through three different methods and subjected to florescence-linked aptamer assays (FLAA) based on C7/C9 aptamers through two readout protocols. Then, a step-by-step statistical approach which included agreement tests, proportion comparisons and binomial and multinomial logistic regressions was used to predict optimal conditions for the novel C7/C9 FLAA test. RTqPCR threshold cycles, symptoms onset and processing time were influential factors on FLAA test results. Naturally occurring mutations on S were also detected and analyzed. Aminoacidic substitutions D614G and T732A appeared relevant for aptamer recognition although further studies are necessary. The methodology presented here is the first step to determine the performance and diagnosis across a range of clinical contexts and it might serve as a base for a complete analysis applicable to other designs of new diagnostic tests.

Enzyme linked oligonucleotide assay for the sensitive detection of SARS-CoV-2 variants

The exponential spread of COVID-19 has prompted the need to develop a simple and sensitive diagnostic tool. Aptamer-based detection assays like ELONA are promising since they are inexpensive and sensitive. Aptamers have advantages over antibodies in wide modification, small size, in vitro selection, and stability under stringent conditions, which aid in scalable and reliable detection. In this work, we used aptamers against SARS-CoV-2 RBD S protein to design a simple and sensitive ELONA detection tool. Screening CoV2-RBD-1C and CoV2-RBD-4C aptamers and optimizing assay conditions led to the development of a direct ELONA that can detect SARS-CoV-2 RBD S glycoprotein in buffer solution and 0.1 % human nasal fluid with a detection limit of 2.16 ng/mL and 1.02 ng/mL, respectively. We detected inactivated Alpha, Wuhan, and Delta variants of SARS-CoV-2 with the detection limit of 3.73, 5.72, and 6.02 TCID₅₀/mL, respectively. Using the two aptamers as capture and reporter elements, we designed a more sensitive sandwich assay to identify the three SARS-CoV-2 variants employed in this research. As predicted, a lower detection limit was obtained. Sandwich assay LOD was 2.31 TCID₅₀/mL for Alpha, 1.15 TCID₅₀/mL for Wuhan, and 2.96 TCID₅₀/mL for Delta. The sensitivity of sandwich ELONA was validated using Alpha and Wuhan variants spiked in 0.1% human nasal fluid sample condition and were detected in 1.41 and 1.79 TCID₅₀/mL LOD, respectively. SEM was used to visualize the presence of viral particles in the Delta variant sample. The effective detection of SARS-CoV-2 in this study confirms the potential of our aptamer-based technique as a screening tool.

SCORe: SARS-CoV-2 Omicron Variant RBD-Binding DNA Aptamer for Multiplexed Rapid Detection and Pseudovirus Neutralization

During the COVID-19 (coronavirus disease 2019) pandemic, several SARS-CoV-2 variants of concern emerged, including the Omicron variant, which has enhanced infectivity and immune invasion. Many antibodies and aptamers that bind the spike (S) of previous strains of SARS-CoV-2 either do not bind or bind with low affinity to Omicron S. In this study, we report a high-affinity SARS-CoV-2 Omicron RBD-binding aptamer (SCORe) that binds Omicron BA.1 and BA.2 RBD with nanomolar KD1. We employ aptamers SCORe.50 and SNAP4.74 in a multiplexed lateral flow assay (LFA) to distinguish between Omicron and wild-type S at concentrations as low as 100 pM. Finally, we show that SCORe.50 and its dimerized form SCOReD can neutralize Omicron S-pseudotyped virus infection of ACE2-overexpressing cells by >70%. SCORe therefore has potential applications in COVID-19 rapid diagnostics as well as in viral neutralization.

SARS-CoV-2 virus label-free electrochemical nanohybrid MIP-aptasensor based on Ni3(BTC)2 MOF as a high-performance surface substrate

A dual recognition biosensor was developed via introducing aptamer strings and molecular imprinting polymer (MIP) for the selective detection of intact SARS-CoV-2 virus based on screen printed carbon electrode (SPCE) modified with nickel-benzene tricarboxylic acid-metal–organic framework (Ni₃(BTC)₂ MOF) synthesized by in situ growth method, SARS-CoV-2 S protein-specific amino-aptamer and electropolymerization of dopamine (ePDA). The proposed biosensor showed an excellent linear relationship between charge transfer resistance (R_ct) and increase in virus concentration in the range 10 to 10⁸ plaque-forming units/mL (PFU/mL) with a low detection limit of 3.3 ± 0.04 PFU/mL and response time of 20 min. Compared with single-element sensors (aptamer or MIP), it showed higher selectivity for  the SARS-CoV-2 virus and facilitated detection in real samples.

Label-free electrochemical aptasensor for rapid detection of SARS-CoV-2 spike glycoprotein based on the composite of Cu(OH)2 nanorods arrays as a high-performance surface substrate

The development of advanced electrode materials and the combination of aptamer with them have improved dramatically the performance of aptasensors. Herein, a new architecture based on copper hydroxide nanorods (Cu(OH)₂ NRs) are directly grown on the surface of screen printed carbon electrode (SPCE) using a two-step in situ, very simple and fast strategy and was used as a high-performance substrate for immobilization of aptamer strings, as well as an electrochemical probe to development a label-free electrochemical aptasensor for SARS-CoV-2 spike glycoprotein measurement. The Cu(OH)₂ NRs was characterized using X-ray Diffraction (XRD) and electron microscopy (FESEM). In the presence of SARS-CoV-2 spike glycoprotein, a decrease in Cu(OH)₂ NRs-associated peak current was observed that can be owing to the target-aptamer complexes formation and thus blocking the electron transfer of Cu(OH)₂ NRs on the surface of electrode. This strategy exhibited wide dynamic range in of 0.1 fg mL⁻¹ to 1.2 µg mL⁻¹ and with a high sensitivity of 1974.43 μA mM⁻¹ cm⁻² and low detection limit of 0.03 ± 0.01 fg mL⁻¹ of SARS-CoV-2 spike glycoprotein deprived of any cross-reactivity in the presence of possible interference species. In addition, the good reproducibility, repeatability, high stability and excellent feasibility in real samples of saliva and viral transport medium (VTM) were found from the provided aptasensor. Also, the aptasensor efficiency was evaluated by real samples of sick and healthy individuals and compared with the standard polymerase chain reaction (PCR) method and acceptable results were observed.

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS‐CoV‐2 Variants of Concern

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS‐CoV‐2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one‐round SELEX experiments using five different trimeric spike proteins from variants, followed by high‐throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K_d values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS‐CoV‐2 with K_d values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well‐suited for molecular recognition of rapidly evolving targets such as those found in SARS‐CoV‐2.