Review of analytical performance of COVID-19 detection methods

Novel Lateral Flow-Based Assay for Simple and Visual Detection of SARS-CoV-2 Mutations

Identification of the main SARS-CoV-2 variants in real time is of interest to control the virus and to rapidly devise appropriate public health responses. The RT-qPCR is currently considered to be the reference method to screen SARS-CoV-2 mutations, but it has some limitations. The multiplexing capability is limited when the number of markers to detect increases. Moreover, the performance of this allele-specific method may be impacted in the presence of new mutations. Herein, we present a proof-of-concept study of a simple molecular assay to detect key SARS-CoV-2 mutations. The innovative features of the assay are the multiplex asymmetric one-step RT-PCR amplification covering different regions of SARS-CoV-2 S gene and the visual detection of mutations on a lateral flow DNA microarray. Three kits (Kit 1: N501Y, E484K; Kit 2: L452R, E484K/Q; Kit 3: K417N, L452R, E484K/Q/A) were developed to match recommendations for surveillance of SARS-CoV-2 variants between January and December 2021. The clinical performance was assessed using RNA extracts from 113 SARS-CoV-2-positive samples with cycle thresholds <30, and results demonstrated that our assay allows specific and sensitive detection of mutations, with a performance comparable to that of RT-qPCR. The VAR-CoV assay detected four SARS-CoV-2 targets and achieved specific and sensitive screening of spike mutations associated with the main variants of concern, with a performance comparable to that of RT-qPCR. With well-defined virus sequences, this assay can be rapidly adapted to other emerging mutations; it is a promising tool for variant surveillance.

Development and evaluation of time-resolved fluorescent immunochromatographic assay for quantitative detection of SARS-CoV-2 spike antigen

BACKGROUND

The spread of COVID-19 worldwide caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has necessitated efficient, sensitive diagnostic methods to identify infected people. We report on the development of a rapid 15-minute time-resolved fluorescent (TRF) lateral flow immunochromatographic assay for the quantitative detection of the SARS-CoV-2 spike protein receptor-binding domain (S1-RBD).

OBJECTIVES

Our objective was to develop an efficient method of detecting SARS-CoV-2 within 15 min of sample collection.

METHODS

We constructed and evaluated a portable, disposable lateral flow device, which detected the S1-RBD protein directly in nasopharyngeal swab samples. The device emits a fluorescent signal in the presence of S1-RBD, which can be captured by an automated TRF instrument.

RESULTS

The TRF lateral flow assay signal was linear from 0 to 20 ng/ml and demonstrated high accuracy and reproducibility. When evaluated with clinical nasopharyngeal swabs, the assay was performed at >80% sensitivity, >84% specificity, and > 82% accuracy for detection of the S1-RBD antigen.

CONCLUSION

The new S1-RBD antigen test is a rapid (15 min), sensitive, and specific assay that requires minimal sample preparation. Critically, the assay correlated closely with PCR-based methodology in nasopharyngeal swab samples, showing that the detected S1-RBD antigen levels correlate with SARS-CoV-2 virus load. Therefore, the new TRF lateral flow test for S1-RBD has potential application in point-of-care settings.

Systematic Approach to Address Early Pandemic's Diagnostic Unmet Needs

During the first few months of the global Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic, the medical research community had to expeditiously develop, select, and deploy novel diagnostic methods and tools to address the numerous testing challenges presented by the novel virus. Integrating a systematic approach to diagnostic selection with a rapid validation protocol in a clinical setting can shorten the timeline to bring new technologies to practice. In response to the urgent need to provide tools for identifying SARS-CoV-2-positive individuals, we developed a framework for assessing technologies against a set of prioritized performance metrics to guide device selection. We also developed and proposed clinical validation frameworks for the rapid screening of new technologies. The rubric described here represents a versatile approach that can be extended to future technology assessments and can be implemented in preparation for future emerging pathogens.

SARS-CoV-2 Detection Methods

A fast and highly specific detection of COVID-19 infections is essential in managing the virus dissemination networks. The most relevant technologies developed for SARS-CoV-2 detection, along with their advantages and limitations, will be presented and fully explored. Additionally, some of the newest and emerging COVID-19 diagnosis tools, such as biosensing platforms, will also be introduced. Considering the extreme relevance that all these technologies assume in pandemic control, it is of the utmost relevance to have an intrinsic knowledge of the parameters that need to be taken into consideration before choosing the most adequate test for a particular situation. Moreover, the new variants of the virus and their potential impact on the detection method’s effectiveness will be discussed. In order to better manage the pandemic, it is essential to maintain continuous research into the SARS-CoV-2 genome and updated genomic surveillance at the global level. This will allow for timely detection of new mutations and viral variants, which may affect the performance of COVID-19 detection tests.

Strategies for Scaling up SARS-CoV-2 Molecular Testing Capacity

Scaling up SARS-CoV-2 testing during the COVID-19 pandemic was critical to maintaining clinical operations and an open society. Pooled testing and automation were two critical strategies used by laboratories to meet the unprecedented demand. Here, we review these and other cutting-edge strategies that sought to expand SARS-CoV-2 testing capacity while maintaining high individual test performance.

Effect and Prognosis Factors of Combining Laparoscopic Radical Resection of Colon Adenocarcinoma with Docetaxel Therapy in Treating Middle and Advanced Colon Adenocarcinoma

Objective. The aim of the study is to explore the clinical efficacy and prognosis factors of joint application of laparoscopic radical resection of colon adenocarcinoma (COAD) and docetaxel therapy in treating COAD of middle and advanced stages. Methods. The clinical data of 103 COAD patients of middle and advanced stages treated in our hospital from July 2016 to July 2018 were selected for the retrospective analysis, all patients received the treatment scheme of combining laparoscopic radical resection of COAD with docetaxel therapy for the observation of short-term efficacy, follow-up was conducted to record their 3-year survival, and relevant factors affecting patient prognosis were analyzed by the logistic regression model. Results. After treatment, the total remission rate of patients was 75.73% (78/103), the total incidence rate of adverse reactions was 16.50% (17/103); patients’ level values of various serum tumor markers after treatment were significantly lower than those before treatment ( $P<0.001$ ); according to the univariate analysis results, for COAD patients with different tumor diameters, differentiated degrees, TNM stages, perineural invasion degrees, pathological types, and depths of invasion, their modality rates were statistically different ( $P<0.05$ ); and the logistic regression analysis showed that tumor diameter ≥5 cm, poor differentiation, TNM stage IV, perineural invasion, pathologically signet-ring cell carcinoma, and T3-invasion were the independent risk factors affecting patient prognosis ( $P<0.05$ ). Conclusion. Combining laparoscopic radical resection of COAD with docetaxel therapy in treating COAD of middle and advanced stages achieves affirmed short-term efficacy, which can reduce patients’ level of serum tumor markers and ensure high safety and good survival prognosis. Tumor diameter, differentiated degree, TNM stage, perineural invasion, pathological type, and T3-invasion are the relevant factors affecting the prognosis of middle and advanced COAD.

Rapid identification of SARS-CoV-2 in the point-of-care using digital PCR-based Dr. PCR™ Di20K COVID-19 Detection Kit without viral RNA extraction

BACKGROUND

Since COVID-19 was declared the pandemic by the WHO, it has continued to spread. There is a need for rapid, efficient, and accurate diagnostic kits and techniques to control its spread.

OBJECTIVE

The diagnostic capability of the qRT-PCR-based Real-Q 2019-nCoV Detection Kit and dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit was compared and evaluated.

METHODS

Diagnostic tests for COVID-19 were performed using two different COVID-19 kits and 301 individual specimens with confirmed COVID-19 positive/negative at the government-accredited medical institution. Assessment of diagnostic capability was measured through diagnostic sensitivity, specificity, Cohen's Kappa coefficient, and dilutional linearity tests.

RESULTS

The COVID-19 diagnostic test results using two kits and 301 individual specimens perfectly matched the pre-diagnosis results of the medical institution. In addition, the measurement results of diagnostic sensitivity and specificity were "1", indicating high diagnostic capability. Cohen's Kappa coefficient value is "1", which means that the diagnosis concordance between the two kits is "Almost Perfect". As a result of dilutional linearity tests to evaluate their detection capability, both kits were measured with very high detection reliability.

CONCLUSION

Here, we propose that the dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit has the advantages of the dPCR method reported in the previous study and is suitable for point-of-care testing (POCT) by overcoming the limitations of space, test time, cross-over contamination, and biosafety due to omitting RNA extraction process.

Microfluidics Technology in SARS-CoV-2 Diagnosis and Beyond: A Systematic Review

With the progression of the COVID-19 pandemic, new technologies are being implemented for more rapid, scalable, and sensitive diagnostics. The implementation of microfluidic techniques and their amalgamation with different detection techniques has led to innovative diagnostics kits to detect SARS-CoV-2 antibodies, antigens, and nucleic acids. In this review, we explore the different microfluidic-based diagnostics kits and how their amalgamation with the various detection techniques has spearheaded their availability throughout the world. Three other online databases, PubMed, ScienceDirect, and Google Scholar, were referred for articles. One thousand one hundred sixty-four articles were determined with the search algorithm of microfluidics followed by diagnostics and SARS-CoV-2. We found that most of the materials used to produce microfluidics devices were the polymer materials such as PDMS, PMMA, and others. Centrifugal force is the most commonly used fluid manipulation technique, followed by electrochemical pumping, capillary action, and isotachophoresis. The implementation of the detection technique varied. In the case of antibody detection, spectrometer-based detection was most common, followed by fluorescence-based as well as colorimetry-based. In contrast, antigen detection implemented electrochemical-based detection followed by fluorescence-based detection, and spectrometer-based detection were most common. Finally, nucleic acid detection exclusively implements fluorescence-based detection with a few colorimetry-based detections. It has been further observed that the sensitivity and specificity of most devices varied with implementing the detection-based technique alongside the fluid manipulation technique. Most microfluidics devices are simple and incorporate the detection-based system within the device. This simplifies the deployment of such devices in a wide range of environments. They can play a significant role in increasing the rate of infection detection and facilitating better health services.

An isothermal amplification-coupled dipstick for the rapid detection of COVID-19

Early detection of coronavirus disease 2019 (COVID-19) is critical for both initiating appropriate treatment and preventing the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent. A simple and rapid diagnostic test that can be performed without any expensive equipment would be valuable for clinicians working in a low-resource setting. Here, we report a point-of-care detection technique for COVID-19 that combines the power of isothermal amplification (reverse transcription helicase-dependent amplification, RT-HDA) and dipstick technologies. The limit of detection of this diagnostic test is six copies of SARS-CoV-2 µl^-1 in clinical specimens. Of the 22 clinical specimens tested, RT-HDA-coupled dipstick correctly identified all positive and negative specimens. The RT-HDA can be performed over a heating block and the results can be interpreted visually with the dipstick technology without any specialized equipment. Furthermore, the RT-HDA-coupled dipstick could be performed in a short turnaround time of ~2 h. Thus, the RT-HDA-coupled dipstick could serve as a point-of-care diagnostic test for COVID-19 in a low-resource environment.

Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output

The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)-based methods and rapid-antigen tests rose to the occasion, the analytical challenge of rapid and sequence-specific nucleic acid-sensing at a point-of-care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA-templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an SN Ar that simultaneously transfers biotin from one Peptide Nucleic Acid (PNA) strand to another PNA strand, enabling LFA detection while uncaging a coumarin for fluorescence readout. This methodology has been applied to the detection of a DNA or RNA sequence uniquely attributed to the SARS-CoV-2.

Sensitive and specific serological ELISA for the detection of SARS-CoV-2 infections

Background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered the worldwide coronavirus disease 2019 (COVID-19) pandemic. Serological assays for the detection of SARS-CoV-2 infections are important to understand the immune response in patients and to obtain epidemiological data about the number of infected people, especially to identify asymptomatic persons not aware of a past infection.

Methods

We recombinantly produced SARS-CoV-2 nucleocapsid (N)-protein in Escherichia coli. We used the purified protein to develop an indirect enzyme-linked immunosorbent assay (ELISA) for the detection of SARS-CoV-2 specific antibodies. This ELISA method was optimized and validated with serum samples collected from 113 patients with RT-PCR-confirmed SARS-CoV-2 infections including hospitalized COVID-19 patients and 1500 control sera mostly collected before 2015 with different clinical background.

Results

The optimized N-protein-ELISA provided a sensitivity of 89.7% (n = 68) for samples collected from patients with confirmed SARS-CoV-2 infections and mild to severe symptoms more than 14 days after symptom onset or a positive PCR test. The antibody levels remained low for serum samples collected in the first six days (n = 23) and increased in the second week (n = 22) post symptom onset or PCR confirmation. At this early phase, the ELISA provided a sensitivity of 39.1% and 86.4%, respectively, reflecting the time of an IgG immune response against pathogens. The assay specificity was 99.3% (n = 1500; 95% CI 0.995–0.999). Serum samples from persons with confirmed antibody titers against human immunodeficiency viruses 1/2, parvovirus B19, hepatitis A/B virus, cytomegalovirus, Epstein Barr virus, and herpes simplex virus were tested negative.

Conclusions

We conclude that the N-protein-based ELISA developed here is well suited for the sensitive and specific serological detection of SARS-CoV-2 specific IgG antibodies in human serum for symptomatic infections. It may also prove useful to identify previous SARS-CoV-2 infections in vaccinated people, as all currently approved vaccines rely on the SARS-CoV-2 spike (S-) protein.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01768-4.

Assessment of the feasibility of pool testing for SARS-CoV-2 infection screening

BACKGROUND

SARS-CoV-2 pandemic represented a huge challenge for national health systems worldwide. Pooling nasopharyngeal (NP) swabs seems to be a promising strategy, saving time and resources, but it could reduce the sensitivity of the RT-PCR and exacerbate samples management in terms of automation and tracing. In this study, taking advantage of the routine implementation of a screening plan on health workers, we evaluated the feasibility of pool testing for SARS-CoV-2 infection diagnosis in the presence of low viral load samples.

METHOD

Pools were prepared with an automated instrument, mixing 4, 6 or 20 NP specimens, including one, two or none positive samples. Ct values of positive samples were on average about 35 for the four genes analyzed.

RESULTS

The overall sensitivity of 4-samples and 6-samples pools was 93.1 and 90.0%, respectively. Focussing on pools including one sample with Ct value ≥35 for all analyzed genes, sensitivity decreased to 77.8 and 75.0% for 4- and 6-samples, respectively; pools including two positive samples, resulted positive in any size as well as pools including positive samples with Ct values <35.

CONCLUSION

Pool testing strategy should account the balance between cost-effectiveness, dilution effect and prevalence of the infection. Our study demonstrated the good performances in terms of sensitivity and saving resources of pool testing mixing 4 or 6 samples, even including low viral load specimens, in a real screening context possibly affected by prevalence fluctuation. In conclusion, pool testing strategy represents an efficient and resources saving surveillance and tracing tool, especially in specific context like schools, even for monitoring changes in prevalence associated to vaccination campaign.

Computational design of a thermolabile uracil-DNA glycosylase of Escherichia coli

Polymerase chain reaction (PCR) is a powerful tool to diagnose infectious diseases. Uracil DNA glycosylase (UDG) is broadly used to remove carryover contamination in PCR. However, UDG can contribute to false negative results when not inactivated completely, leading to DNA degradation during the amplification step. In this study, we designed novel thermolabile UDG derivatives by supercomputing molecular dynamic simulations and residual network analysis. Based on enzyme activity analysis, thermolability, thermal stability, and biochemical experiments of Escherichia coli-derived UDG and 22 derivatives, we uncovered that the UDG D43A mutant eliminated the false negative problem, demonstrated high efficiency, and offered great benefit for use in PCR diagnosis. We further obtained structural and thermodynamic insights into the role of the D43A mutation, including perturbed protein structure near D43; weakened pairwise interactions of D43 with K42, N46, and R80; and decreased melting temperature and native fraction of the UDG D43A mutant compared with wild-type UDG.

Detection of SARS-CoV-2 in COVID-19 Patient Nasal Swab Samples Using Signal Processing

This work presents an opto-electrical method that measures the viral nucleocapsid protein and anti-N antibody interactions to differentiate between SARS-CoV-2 negative and positive nasal swab samples. Upon light exposure of the patient nasal swab sample mixed with the anti-N antibody, charge transfer (CT) transitions within the altered protein folds are initiated between the charged amino acids side chain moieties and the peptide backbone that play the role of donor and acceptor groups. A Figure of Merit (FOM) was introduced to correlate the relative variations of the samples with and without antibody at two different voltages. Empirically, SARS-CoV-2 in patient nasal swab samples was detected within two minutes, if an extracted FOM threshold of >1 was achieved; otherwise, the sample wasconsidered negative.

Performance of RT-qPCR detection of SARS-CoV-2 in unextracted nasopharyngeal samples using the Seegene AllplexTM 2019-nCoV protocol

The rapid spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led the world to a pandemic. Therefore, rapid, sensitive, and reproducible diagnostic tests are essential to indicate which measures should be taken during pandemics. We retrospectively tested unextracted nasopharyngeal samples from consecutive patients with suspected SARS-CoV-2 infection (n = 334), and compared two different Ct cut-off values for interpretation of results using a modified Allplex protocol. Its performance was evaluated using the USA Centers for Disease Control and Prevention (CDC) as reference. The reduction on Ct cut-off to 35 increased the test NPA from 79.65 to 88.00 %, reducing the number of false positives, from 10.48 to 6.29 %, resulting in an almost perfect agreement between the Allplex and the CDC protocol (Cohen's Kappa coefficient = 0.830 ± 0.032). This study demonstrates that the Seegene Allplex™ 2019-nCoV protocol skipping the viral RNA extraction step using the Ct cut-off of 35 is a rapid and efficient method to detect SARS-CoV-2 in nasopharyngeal samples.

Designing isolation guidelines for COVID-19 patients utilizing rapid antigen tests: a simulation study using viral dynamics models

Appropriate isolation guidelines for COVID-19 patients are warranted. Currently, isolating for fixed time is adapted in most countries. However, given the variability in viral dynamics between patients, some patients may no longer be infectious by the end of isolation (thus they are redundantly isolated), whereas others may still be infectious. Utilizing viral test results to determine ending isolation would minimize both the risk of ending isolation of infectious patients and the burden due to redundant isolation of noninfectious patients. In our previous study, we proposed a computational framework using SARS-CoV-2 viral dynamics models to compute the risk and the burden of different isolation guidelines with PCR tests. In this study, we extend the computational framework to design isolation guidelines for COVID-19 patients utilizing rapid antigen tests. Time interval of tests and number of consecutive negative tests to minimize the risk and the burden of isolation were explored. Furthermore, the approach was extended for asymptomatic cases. We found the guideline should be designed considering various factors: the infectiousness threshold values, the detection limit of antigen tests, symptom presence, and an acceptable level of releasing infectious patients. Especially, when detection limit is higher than the infectiousness threshold values, more consecutive negative results are needed to ascertain loss of infectiousness. To control the risk of releasing of infectious individuals under certain levels, rapid antigen tests should be designed to have lower detection limits than infectiousness threshold values to minimize the length of prolonged isolation, and the length of prolonged isolation increases when the detection limit is higher than the infectiousness threshold values, even though the guidelines are optimized for given conditions.

User experience of home-based AbC-19 SARS-CoV-2 antibody rapid lateral flow immunoassay test

The urgent need to scale up testing capacity during the COVID-19 pandemic has prompted the rapid development of point-of-care diagnostic tools such as lateral flow immunoassays (LFIA) for large-scale community-based rapid testing. However, studies of how the general public perform when using LFIA tests in different environmental settings are scarce. This user experience (UX) study of 264 participants in Northern Ireland aimed to gather a better understanding of how self-administered LFIA tests were performed by the general public at home. The UX performance was assessed via analysis of a post-test questionnaire including 30 polar questions and 11 7-point Likert scale questions, which covers the multidimensional aspects of UX in terms of ease of use, effectiveness, efficiency, accuracy and satisfaction. Results show that 96.6% of participants completed the test with an overall average UX score of 95.27% [95% confidence interval (CI) 92.71–97.83%], which suggests a good degree of user experience and effectiveness. Efficiency was assessed based on the use of physical resources and human support received, together with the mental effort of self-administering the test measured via NASA Task Load Index (TLX). The results for six TLX subscales show that the participants scored the test highest for mental demand and lowest for physical demand, but the average TLX score suggests that the general public have a relatively low level of mental workload when using LFIA self-testing at home. Five printed LFIA testing results (i.e. the ‘simulated’ results) were used as the ground truth to assess the participant’s performance in interpreting the test results. The overall agreement (accuracy) was 80.63% [95% CI 75.21–86.05%] with a Kappa score 0.67 [95% CI 0.58–0.75] indicating substantial agreement. The users scored lower in confidence when interpreting test results that were weak positive cases (due to the relatively low signal intensity in the test-line) compared to strong positive cases. The end-users also found that the kit was easier to use than they expected (p < 0.001) and 231 of 264 (87.5%) reported that the test kit would meet their requirements if they needed an antibody testing kit. The overall findings provide an insight into the opportunities for improving the design of self-administered SARS-CoV-2 antibody testing kits for the general public and to inform protocols for future UX studies of LFIA rapid test kits.

SARS-CoV-2 Detection Using Optical Fiber Based Sensor Method

The SARS-CoV-2 Coronavirus disease, also known as the COVID-19 pandemic, has engendered the biggest challenge to human life for the last two years. With a rapid increase in the spread of the Omicron variant across the world, and to contain the spread of COVID-19 in general, it is crucial to rapidly identify this viral infection with minimal logistics. To achieve this, a novel plastic optical fiber (POF) U-shaped probe sensing method is presented for accurate detection of SARS-CoV-2, commonly known as the COVID-19 virus, which has the capability to detect new variants such as Omicron. The sample under test can be taken from oropharyngeal or nasopharyngeal via specific POF U-shaped probe with one end that is fed with a laser source while the other end is connected to a photodetector to receive the response and postprocess for decision-making. The study includes detection comparison with two types of POF with diameters of 200 and 500 µm. Results show that detection is better when a smaller-diameter POF is used. It is also seen that the proposed test bed and its envisaged prototype can detect the COVID-19 variants within 15 min of the test. The proposed approach will make the clinical diagnosis faster, cheaper and applicable to patients in remote areas where there are no hospitals or clinical laboratories due to poverty, geographic obstacles, or other factors.

Movable Layer Device for Rapid Detection of Influenza a H1N1 Virus Using Highly Bright Multi-Quantum Dot-Embedded Particles and Magnetic Beads

Preventing the rapid spread of viral infectious diseases has become a major concern for global health. In this study, we present a microfluidic platform that performs an immunoassay of viral antigens in a simple, automated, yet highly sensitive manner. The device uses silica particles embedded with highly bright quantum dots (QD2) and performs the immunoassay with a vertically movable top layer and a rotating bottom layer. Through the motion of the layers and the surface tension in the liquids, reagents move from top chambers to bottom chambers and mix homogeneously. A tip in the top layer with a mobile permanent magnet moves the immune complexes comprising the magnetic beads, virus particles, and QD2 between the bottom chambers. In this way, our automated device achieves a highly sensitive magnetic bead-based sandwich immunoassay for the influenza A H1N1 virus within 32.5 min. The detection limit of our method is 5.1 × 10-4 hemagglutination units, which is 2 × 103 times more sensitive than that of the conventional hemagglutination method and is comparable to PCR. Our device is useful for the rapid and sensitive detection of infectious diseases in point-of-care applications and resource-limited environments.

Precise RNA Quantification by Counting Individual RNA Molecules Using High-Sensitivity Capillary Flow Cytometry

Precise determination of ribonucleic acid (RNA) concentration without the need for calibration was pursued by sequence-specific counting of individual RNA molecules. This approach eliminates the reverse transcription (RT) step required for polymerase chain reaction (PCR)-based quantification, which may hamper accurate measurements owing to uncertain yields of RT reactions. Target RNAs were tagged with a number of fluorescent oligonucleotide probes with complementary sequences. Tagged RNAs were exhaustively counted one by one using a high-sensitivity capillary-based flow cytometric setup. MS2 viral RNA was quantified as a model RNA for which essential parameters, including probe numbers, probe concentration, and hybridization conditions, were optimized for the best performance. Using 70 oligonucleotide probes, MS2 RNA was quantified with 2.0% relative standard deviation, and its validity was assessed by comparison with other RNA quantification methods such as droplet digital PCR and UV spectrophotometry. The observed comparability indicated that the proposed method is unlikely to have a substantial bias. It works for a substantially lower-level RNA than UV and avoids the potential variability in the yield of the RT reaction of RT-qPCR. Therefore, the proposed method could be a valuable addition to current methods and could be further developed as a standard reference method for RNA quantification.

Clinical validation of engineered CRISPR/Cas12a for rapid SARS-CoV-2 detection

Background

The coronavirus disease (COVID-19) caused by SARS-CoV-2 has swept through the globe at an unprecedented rate. CRISPR-based detection technologies have emerged as a rapid and affordable platform that can shape the future of diagnostics.

Methods

We developed ENHANCEv2 that is composed of a chimeric guide RNA, a modified LbCas12a enzyme, and a dual reporter construct to improve the previously reported ENHANCE system. We validated both ENHANCE and ENHANCEv2 using 62 nasopharyngeal swabs and compared the results to RT-qPCR. We created a lyophilized version of ENHANCEv2 and characterized its detection capability and stability.

Results

Here we demonstrate that when coupled with an RT-LAMP step, ENHANCE detects COVID-19 samples down to a few copies with 95% accuracy while maintaining a high specificity towards various isolates of SARS-CoV-2 against 31 highly similar and common respiratory pathogens. ENHANCE works robustly in a wide range of magnesium concentrations (3 mM-13 mM), allowing for further assay optimization. Our clinical validation results for both ENHANCE and ENHANCEv2 show 60/62 (96.7%) sample agreement with RT-qPCR results while only using 5 µL of sample and 20 minutes of CRISPR reaction. We show that the lateral flow assay using paper-based strips displays 100% agreement with the fluorescence-based reporter assay during clinical validation. Finally, we demonstrate that a lyophilized version of ENHANCEv2 shows high sensitivity and specificity for SARS-CoV-2 detection while reducing the CRISPR reaction time to as low as 3 minutes while maintaining its detection capability for several weeks upon storage at room temperature.

Conclusions

CRISPR-based diagnostic platforms offer many advantages as compared to conventional qPCR-based detection methods. Our work here provides clinical validation of ENHANCE and its improved form ENHANCEv2 for the detection of COVID-19.

Nguyen et al. describe the clinical validation of the ENHANCE system, a method to detect SARS-CoV-2 based on engineered crRNAs for Cas12a and preceded by an RT-LAMP amplification step. Authors also describe the development and clinical validation of a version of this system, ENHANCEv2, that can be lyophilized and that uses another mutated Cas12a for further signal amplification.

The COVID-19 pandemic has underscored the need for rapid and accurate tests to detect SARS-CoV-2 infection. The tests commonly used have limitations, and a detection system based on CRISPR technology could offer a useful alternative. CRISPR is a technology derived from bacteria that can specifically detect pieces of DNA. We have previously developed ENHANCE, a detection system that converts the SARS-CoV-2 genetic material into DNA that is then detected by an engineered CRISPR technology. Here, we develop an improved version of this method, ENHANCEv2, that has an extended shelf life and less need for refrigeration, facilitating transportation of the components required for the test and its use. We show that both ENHANCE and ENHACEv2 can quickly and accurately detect SARS-CoV-2 in swabs from infected people. This is a step towards having more versatile tools to detect SARS-CoV-2 infection quickly and accurately.

Analytical and Clinical Evaluation of the Semiquantitative Elecsys Anti-SARS-CoV-2 Spike Protein Receptor Binding Domain Antibody Assay on the Roche cobas e602 Analyzer

Objectives

To analytically and clinically evaluate the semiquantitative Elecsys anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein antibody (S-Ab) assay on the Roche cobas e602 analyzer.

Methods

The S-Ab assay is a 1-step, double-antigen sandwich electrochemiluminescent immunoassay that semiquantitatively measures total IgG, IgM, and IgA antibodies specific for the receptor binding domain of SARS-CoV-2 spike protein in serum or plasma. The S-Ab assay was evaluated for precision, linearity, interference (by hemoglobin, bilirubin, triglycerides, and biotin), cross-reactivity, and clinical performance, and was compared to the qualitative Elecsys anti-nucleocapsid (N-Ab) immunoassay, a lateral flow device that qualitatively detects S-Ab and N-Ab, and an anti-spike enzyme-linked immunosorbent assay (ELISA).

Results

S-Ab assay is precise, exhibits linearity from 0.4 to 250 U/mL, is unaffected by significant cross-reactivity or interferences, and qualitatively demonstrates greater than 90% concordance with N-Ab assay and lateral flow device. Readouts of S-Ab assay correlate with ELISA, which in turn correlates strongly with SARS-CoV-2 virus neutralization assay, and exhibit 100% sensitivity and specificity for COVID-19 patient samples obtained at or more than 14 days after PCR positivity.

Conclusions

The S-Ab assay is a robust clinical test for qualitative and semiquantitative detection of seropositivity following SARS-CoV-2 infection or spike-encoding mRNA COVID-19 vaccination.

COVID-19: Clinical laboratory diagnosis and monitoring of novel coronavirus infected patients using molecular, serological and biochemical markers: A review

COVID-19, a novel coronavirus disease, has provoked a variety of health and safety concerns, and socioeconomic challenges around the globe. The laboratory diagnosis of SARS-CoV-2 was quickly established utilizing nucleic acid amplification techniques (NAAT) after the disease causing virus has been identified, and its genetic sequence has been determined. In addition to NAAT, serological tests based on antibodies testing against SARS-CoV-2 were introduced for diagnostic and epidemiologic studies. Other biochemical investigations include monitoring of peripheral blood cells count, platelets/lymphocyte ratio, coagulation profile, cardiac, and inflammatory markers such as cytokines storm are also crucial in combating COVID-19 pandemic. Further, accurate and reliable laboratory results for SARS-CoV-2 play very important role in the initiation of early treatment and timely management of COVID-19 patients, provide support in clinical decision-making process to control infection, and detection of asymptomatic cases. The Task Force on Coronavirus-19 constituted by International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has recognized informational framework for epidemiology, pathogenesis, and recommended the PCR-based analysis, serological and biochemical assays for analysis, monitoring, and management of disease. This literature review provides an overview of the currently used diagnostic techniques in clinical laboratories for the diagnosis, treatment monitoring, and management of COVID-19 patients. We concluded that each assays differ in their performance characteristics and the utilization of multiple techniques is necessary for the accurate diagnosis and management of SARS-CoV-2 infection.

Deep Learning Hybrid Models for COVID-19 Prediction

COVID-19 is a highly contagious virus. Blood test is one of effective method for COVID-19 diagnosis. However, the issues of blood test are time-consuming and lack of medical staffs. In this paper, four deep learning hybrid models are proposed to address these issues, i.e., CNN+GRU, CNN+Bi-RNN, CNN+Bi-LSTM, CNN+Bi-GRU. Besides, two best models CNN and CNN+LSTM from Turabieh et al. and Alakus et al. are implemented, respectively. Blood test data from Hospital Israelita Albert Einstein is used to train and test six models. The proposed best model CNN+Bi-GRU is accuracy of 0.9415, precision of 0.9417, recall of 0.9417, F1-score of 0.9417, AUC of 0.91, which outperforms the best models from Turabieh et al. and Alakus et al. Furthermore, the proposed model can help patients to get blood test results faster than traditional manual tests, and do not have errors caused by fatigue. We can envisage a wide deployment of proposed model in hospitals to alleviate the testing pressure from medical workers, especially in developing and underdeveloped countries.

Lab-on-paper based devices for COVID-19 sensors

In December 2019, a disease linked to the coronavirus (CoV) was identified in the capital of China’s Wuhan. When seen under an electron microscope, CoVs, which are enveloped positive-sense RNA viruses, appear like crown-shaped viruses. There are four subtypes of CoVs such as (a) alpha, (b) beta, (c) delta, (d) gamma CoV. Coronavirus disease is caused by the extreme acute respiratory syndrome coronavirus 2, which is caused by a beta coronavirus (-CoVs or Beta-CoVs) (SARS-CoV-2). Infected people may have fever of 38°C, cough, and shortness of breath. WHO officially called COVID-19, an abbreviated form of coronavirus disease 2019, on February 12, 2020.

The role of the surface ligand on the performance of electrochemical SARS-CoV-2 antigen biosensors

Point-of-care (POC) technologies and testing programs hold great potential to significantly improve diagnosis and disease surveillance. POC tests have the intrinsic advantage of being able to be performed near the patient or treatment facility, owing to their portable character. With rapid results often in minutes, these diagnostic platforms have a high positive impact on disease management. POC tests are, in addition, advantageous in situations of a shortage of skilled personnel and restricted availability of laboratory-based analytics. While POC testing programs are widely considered in addressing health care challenges in low-income health systems, the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections could largely benefit from fast, efficient, accurate, and cost-effective point-of-care testing (POCT) devices for limiting COVID-19 spreading. The unrestrained availability of SARS-CoV-2 POC tests is indeed one of the adequate means of better managing the COVID-19 outbreak. A large number of novel and innovative solutions to address this medical need have emerged over the last months. Here, we critically elaborate the role of the surface ligands in the design of biosensors to cope with the current viral outbreak situation. Their notable effect on electrical and electrochemical sensors' design will be discussed in some given examples. Graphical abstract.

Identification of SARS-CoV-2 Proteins from Nasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem Mass Spectrometry

Numerous reverse transcription polymerase chain reaction (RT-PCR) tests have emerged over the past year as the gold standard for detecting millions of cases of SARS-CoV-2 reported daily worldwide. However, problems with critical shortages of key reagents such as PCR primers and RNA extraction kits and unpredictable test reliability related to high viral replication cycles have triggered the need for alternative methodologies to PCR to detect specific COVID-19 proteins. Several authors have developed methods based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) to confirm the potential of the technique to detect two major proteins, the spike and the nucleoprotein, of COVID-19. In the present work, an S-Trap mini spin column digestion protocol was used for sample preparation prodromal to LC-MS/MS analysis in multiple reactions monitoring ion mode (MRM) to obtain a comprehensive method capable of detecting different viral proteins. The developed method was applied to n. 81 oro/nasopharyngeal swabs submitted in parallel to quantitative reverse transcription PCR (RT-qPCR) assays to detect RdRP, the S and N genes specific for COVID-19, and the E gene for all Sarbecoviruses, including SARS-CoV-2 (with cycle negativity threshold set to 40). A total of 23 peptides representative of the six specific viral proteins were detected in the monitoring of 128 transitions found to have good ionic currents extracted in clinical samples that reacted differently to the PCR assay. The best instrumental response came from the FLPFQFGR sequence of spike [558-566] peptide used to test the analytical performance of the method that has good sensitivity with a low false-negative rate. Transition monitoring using a targeted MS approach has the great potential to detect the fragmentation reactions of any peptide molecularly defined by a specific amino acid sequence, offering the extensibility of the approach to any viral sequence including derived variants and thus providing insights into the development of new types of clinical diagnostics.

Aptamer-Functionalized Nanochannels for One-Step Detection of SARS-CoV-2 in Samples from COVID-19 Patients

With the outbreak of COVID-19, which is fast transmitting and highly contagious, the development of rapid, highly specific, and sensitive detection kits has become a research hotspot. The existing assay methods for SARS-CoV-2 are mainly based on enzymatic reactions, which require expensive reagents, hindering popular use, especially in resource-constrained areas. Herein, we propose an aptamer-based method for the assay of SARS-CoV-2 via binding of the spike protein using functionalized biomimetic nanochannels. To get the analogous effect of human ACE2, a receptor for the spike protein, the aptamer to bind to the spike S1 protein has been first screened by a SELEX technique and then immobilized on the previously prepared nanochannels. In the presence of SARS-CoV-2, the changes in steric hindrance and charge density on the surface of the nanochannels will affect the ion transport, along with a rapid electrochemical response. Our method has been successfully applied to detect the viral particles in clinical pharyngeal swab specimens in one step without sample treatment. We expect this rapid, reagent-free, and sensitive assay method to be developed as a useful tool for diagnosing COVID-19.

Challenges and emerging perspectives of an international SARS-CoV-2 epidemiological surveillance in wastewater

SARS-CoV-2 is a new type of coronavirus capable to infect humans and cause the severe acute respiratory syndrome COVID-19, a disease that has been causing huge impacts across the Earth. COVID-19 patients, including mild, pre-symptomatic and asymptomatic cases, were often seen to contain infectious fragments of SARS-CoV-2 in feces and urine samples. Therefore, studies to detect the new coronavirus in wastewater, which collect and concentrate human excreta, have been extremely useful as a viral tracking tool in communities. This type of monitoring, in addition to serve as a non-invasive early warning of COVID-19 outbreaks, would provide better predictions about the SARS-CoV-2 spread and strongly contribute to maintenance the global health. Although current methods to detect viruses in wastewater, based on molecular RT-PCR and RT-qPCR techniques, were considered as reliable and provided accurate qualitative and quantitative results, they have been facing considerable challenges concerning the SARS-CoV-2 surveillance. In this review, the methods used to detect the SARS-CoV-2 in wastewater and the challenges to implement an international viral monitoring network were described. The article also addressed the emerging perspectives associated with the SARS-CoV-2 epidemiological surveillance in this environment and the importance of a worldwide collaboration to generate and disseminate the detection results.

Fluorescence immunoassay rapid detection of 2019-nCoV antibody based on the fluorescence resonance energy transfer between graphene quantum dots and Ag@Au nanoparticle

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has dramatically changed the world, is a highly contagious virus. The timely and accurate diagnosis of SARS-CoV-2 infections is vital for disease control and prevention. Here in this work, a fluorescence immunoassay was developed to detect 2019 Novel Coronavirus antibodies (2019-nCoV mAb). Fluorescent graphene quantum dots (GQDs) and Ag@Au nanoparticles (Ag@AuNPs) were successfully synthesized and characterized. Fluorescence resonance energy transfer (FRET) enables effective quenching of GQDs fluorescence by Ag@AuNPs. With the presence of 2019-nCoV mAb, a steric hindrance was observed between the Ag@AuNPs-NCP (2019-nCoV antigen) complex and GQDs, which reduced the FRET efficiency and restored the fluorescence of GQDs. The fluorescence enhancement efficiency has a satisfactory linear relationship with the logarithm of the 2019-nCoV mAb in a concentration range of 0.1 pg mL⁻¹–10 ng mL⁻¹, and the limit of detection was 50 fg mL⁻¹. The method has good selectivity. When the serum sample was spiked with 2019-nCoV mAb, the recovery rate was between 90.8% and 103.3%. The fluorescence immunosensor demonstrates the potential to complement the existing serological assays for COVID-19 diagnosis.

A novel G-quadruplex aptamer-based spike trimeric antigen test for the detection of SARS-CoV-2

The recent SARS-CoV-2 outbreak has been declared a global health emergency. It will take years to vaccinate the whole population to protect them from this deadly virus, hence the management of SARS-CoV-2 largely depends on the widespread availability of an accurate diagnostic test. Toward addressing the unmet need of a reliable diagnostic test in the current work by utilizing the power of Systematic Evolution of Ligands by EXponential enrichment, a 44-mer G-quadruplex-forming DNA aptamer against spike trimer antigen of SARS-CoV-2 was identified. The lead aptamer candidate (S14) was characterized thoroughly for its binding, selectivity, affinity, structure, and batch-to-batch variability by utilizing various biochemical, biophysical, and in silico techniques. S14 has demonstrated a low nanomolar KD, confirming its tight binding to a spike antigen of SARS-CoV-2. S14 can detect as low as 2 nM of antigen. The clinical evaluation of S14 aptamer on nasopharyngeal swab specimens (n = 232) has displayed a highly discriminatory response between SARS-CoV-2 infected individuals from the non-infected one with a sensitivity and specificity of ∼91% and 98%, respectively. Importantly, S14 aptamer-based test has evinced a comparable performance with that of RT-PCR-based assay. Altogether, this study established the utility of aptamer technology for the detection of SARS-CoV-2.

Performance Validation of COVID-19 Self-Conduct Buccal and Nasal Swabs RTK-Antigen Diagnostic Kit

The antigen rapid diagnostic test (Ag-RDT) is an immunodiagnostic test that detects the presence of viral proteins (antigens) expressed by the COVID-19 virus in a sample from a patient's respiratory tract. This study focused on evaluating the performance of self-conduct buccal and nasal swabs RTK-antigen test compared to nasopharyngeal swab RTK-based COVID-19 diagnostic assays, Panbio™ COVID-19 Ag Rapid Test Device (Nasopharyngeal) (Abbott Rapid Diagnostics Jena GmbH, Jena, Germany) used in hospitals for first-line screening. The sensitivity and specificity of the paired RTK-Ag test in detecting the an-tigen were calculated at 96.4% and 100%, respectively. Fisher exact tests showed the association between nasopharyngeal swabs RTK-Ag assay and buccal-nasal swabs RTK-Ag from ProdetectTM is significant (p-values < 0.001). The result showed that a self-conducted buccal and nasal RTK-antigen rapid test by the patients is comparable to the results obtained from a rapid test device conducted by trained medical personnel using a nasopharyngeal swab.

Aptamer-based biosensors and their implications in COVID-19 diagnosis

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel infectious member of the coronavirus family, has caused millions of cases of infection and deaths all over the world, and been declared a pandemic by the World Health Organization. Conventional laboratory-based diagnostic testing has faced extreme difficulties in meeting the overwhelming demand for testing worldwide, and this has brought about a pressing need for cost-effective rapid diagnosis. There has been a surge in the number of prototypes of diagnostic kits developed, although many of these have been found to be lacking in terms of their accuracy and sensitivity. One type of chip-based diagnostic platform is the aptamer-based biosensor. Aptamers are artificially synthesized oligonucleotides that are capable of specifically binding to a target antigen. As of now, some aptamers have been reported for SARS-CoV-2. Although many ultrasensitive aptasensors have been developed for viruses, few have been successfully adapted for SARS-CoV-2 detection. Our review discusses the recent developments in the domain of SARS-CoV-2 specific aptamer isolation, the design of electrochemical and optical aptasensors, and the implications of aptasensor-based COVID-19 diagnosis.

Paper-Based Biosensors for COVID-19: A Review of Innovative Tools for Controlling the Pandemic

The appearance and quick spread of the new severe acute respiratory syndrome coronavirus disease, COVID-19, brought major societal challenges. Importantly, suitable medical diagnosis procedures and smooth clinical management of the disease are an emergent need, which must be anchored on novel diagnostic methods and devices. Novel molecular diagnostic tools relying on nucleic acid amplification testing have emerged globally and are the current gold standard in COVID-19 diagnosis. However, the need for widespread testing methodologies for fast, effective testing in multiple epidemiological scenarios remains a crucial step in the fight against the COVID-19 pandemic. Biosensors have previously shown the potential for cost-effective and accessible diagnostics, finding applications in settings where conventional, laboratorial techniques may not be readily employed. Paper- and cellulose-based biosensors can be particularly relevant in pandemic times, for the renewability, possibility of mass production with sustainable methodologies, and safe environmental disposal. In this review, paper-based devices and platforms targeting SARS-CoV-2 are showcased and discussed, as a means to achieve quick and low-cost PoC diagnosis, including detection methodologies for viral genomic material, viral antigen detection, and serological antibody testing. Devices targeting inflammatory markers relevant for COVID-19 are also discussed, as fast, reliable bedside diagnostic tools for patient treatment and follow-up.

Development and Characterization of Magnetic SARS-CoV-2 Peptide-Imprinted Polymers

The development of new methods for the rapid, sensitive, and selective detection of SARS-CoV-2 is a key factor in overcoming the global pandemic that we have been facing for over a year. In this work, we focused on the preparation of magnetic molecularly imprinted polymers (MMIPs) based on the self-polymerization of dopamine at the surface of magnetic nanoparticles (MNPs). Instead of using the whole SARS-CoV-2 virion as a template, a peptide of the viral spike protein, which is present at the viral surface, was innovatively used for the imprinting step. Thus, problems associated with the infectious nature of the virus along with its potential instability when used as a template and under the polymerization conditions were avoided. Dopamine was selected as a functional monomer following a rational computational screening approach that revealed not only a high binding energy of the dopamine–peptide complex but also multi-point interactions across the entire peptide template surface as opposed to other monomers with similar binding affinity. Moreover, variables affecting the imprinting efficiency including polymerization time and amount of peptide and dopamine were experimentally evaluated. Finally, the selectivity of the prepared MMIPs vs. other peptide sequences (i.e., from Zika virus) was evaluated, demonstrating that the developed MMIPs were only specific for the target SARS-CoV-2 peptide.

The role of chest imaging in the diagnosis, management, and monitoring of coronavirus disease 2019 (COVID-19)

Coronavirus disease 2019 (COVID-19) pandemic has posed a major public health crisis all over the world. The role of chest imaging, especially computed tomography (CT), has evolved during the pandemic paralleling the accumulation of scientific evidence. In the early stage of the pandemic, the performance of chest imaging for COVID-19 has widely been debated especially in the context of comparison to real-time reverse transcription polymerase chain reaction. Current evidence is against the use of chest imaging for routine screening of COVID-19 contrary to the initial expectations. It still has an integral role to play, however, in its work up and staging, especially when assessing complications or disease progression. Chest CT is gold standard imaging modality for COVID-19 pneumonia; in some situations, chest X-ray or ultrasound may be an effective alternative. The most important role of radiologists in this context is to be able to identify those patients at greatest risk of imminent clinical decompensation by learning to stratify cases of COVID-19 on the basis of radiologic imaging in the most efficient and timely fashion possible. The present availability of multiple and more refined CT grading systems and classification is now making this task easier and thereby contributing to the recent improvements achieved in COVID-19 treatment and outcomes. In this article, evidence of chest imaging regarding diagnosis, management and monitoring of COVID-19 will be chronologically reviewed.

COVID-19 Diagnostics: Past, Present, and Future

In winter of 2020, SARS-CoV-2 emerged as a global threat, impacting not only health but also financial and political stability. To address the societal need for monitoring the spread of SARS-CoV-2, many existing diagnostic technologies were quickly adapted to detect SARS-CoV-2 RNA and antigens as well as the immune response, and new testing strategies were developed to accelerate time-to-decision. In parallel, the infusion of research support accelerated the development of new spectroscopic methods. While these methods have significantly reduced the impact of SARS-CoV-2 on society when coupled with behavioral changes, they also lay the groundwork for a new generation of platform technologies. With several epidemics on the horizon, such as the rise of antibiotic-resistant bacteria, the ability to quickly pivot the target pathogen of this diagnostic toolset will continue to have an impact.

Plasmonic Fiberoptic Absorbance Biosensor (P-FAB) for Rapid Detection of SARS-CoV-2 Nucleocapsid Protein

SARS-CoV-2 nucleocapsid protein-based COVID-19 diagnosis is a promising alternative to the high-priced, time-consuming, and labor-intensive RT-PCR tests. Here, we developed a rapid, dip-type, wash-free plasmonic fiber optic absorbance biosensor (P-FAB) strategy for the point-of-care detection of SARS-CoV-2 N-protein, expressed abundantly during the infection. P-FAB involves a sandwich assay with plasmonic labels on the surface of a U-bent fiber optic sensor probe with a high evanescent wave absorbance (EWA) sensitivity. The SARS-CoV-2 N-protein is quantified in terms of the change in the intensity of the light propagating through the U-bent sensor probe coupled to a green LED and a photodetector. Firstly, the optical fiber material (silica vs. polymeric optical fiber), was evaluated to realize a sensitive sensor platform. The optimal size of AuNP labels (20, 40, and 60 nm) to achieve high sensitivity and a lower limit of detection (LoD) was investigated. Following the P-FAB strategy, fused silica/glass optical fiber (GOF) U-bent senor probe and citrate-capped AuNP labels (size ~40 nm) gave rise to an LoD down to ~2.5 ng/mL within 10 mins of read-out time. Further, studies on development and validation of a point of care (PoC) read-out device, and preclinical studies are in progress.

Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an In Silico Proteomics Approach

Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human SARS-CoV-2-infected cell lines and samples from COVID-19 patients. Initially, 129 unique peptides were identified, which were rigorously evaluated for repeats, disorders, polymorphisms, antigenicity, immunogenicity, toxicity, allergens, sequence similarity to human proteins, and contributions from other potential cross-reacting pathogenic species or the human saliva microbiome. We also screened SARS-CoV-2-infected NBHE and A549 cell lines for presence of antigenic peptides, and identified paratope peptides from crystal structures of SARS-CoV-2 antigen-antibody complexes. We then selected four antigen peptides for docking with known viral unbound T-cell receptor (TCR), class I and II peptide major histocompatibility complex (pMHC), and identified paratope sequences. We also tested the paratope binding affinity of SARS-CoV T- and B-cell peptides that had been previously experimentally validated. The resultant antigenic peptides have high potential for generating SARS-CoV-2-specific antibodies, and the paratope peptides can be directly used to develop a COVID-19 diagnostics assay. The presented genomics and proteomics-based in-silico approaches have apparent utility for identifying new diagnostic peptides that could be used to fight SARS-CoV-2.

Factors that Influence the Reported Sensitivity of Rapid Antigen Testing for SARS-CoV-2

Tests that detect the presence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) antigen in clinical specimens from the upper respiratory tract can provide a rapid means of coronavirus disease 2019 (COVID-19) diagnosis and help identify individuals who may be infectious and should isolate to prevent SARS-CoV-2 transmission. This systematic review assesses the diagnostic accuracy of SARS-CoV-2 antigen detection in COVID-19 symptomatic and asymptomatic individuals compared to quantitative reverse transcription polymerase chain reaction (RT-qPCR) and summarizes antigen test sensitivity using meta-regression. In total, 83 studies were included that compared SARS-CoV-2 rapid antigen-based lateral flow testing (RALFT) to RT-qPCR for SARS-CoV-2. Generally, the quality of the evaluated studies was inconsistent; nevertheless, the overall sensitivity for RALFT was determined to be 75.0% (95% confidence interval: 71.0-78.0). Additionally, RALFT sensitivity was found to be higher for symptomatic vs. asymptomatic individuals and was higher for a symptomatic population within 7 days from symptom onset compared to a population with extended days of symptoms. Viral load was found to be the most important factor for determining SARS-CoV-2 antigen test sensitivity. Other design factors, such as specimen storage and anatomical collection type, also affect the performance of RALFT. RALFT and RT-qPCR testing both achieve high sensitivity when compared to SARS-CoV-2 viral culture.

COVID-19 rhapsody: Rage towards advanced diagnostics and therapeutic strategy

The deadly global outbreak of coronavirus disease-2019 (COVID-19) has forged an unrivaled threat to human civilization. Contemplating its profuse impact, initial risk management and therapies are needed, as well as rapid detection strategies alongside treatments with existing drugs or traditional treatments to provide better clinical support for critical patients. Conventional detection techniques have been considered but do not sufficiently meet the current challenges of effective COVID-19 diagnosis. Therefore, several modern techniques including point-of-care diagnosis with a biosensor, clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins that function as nuclease (Cas) technology, next-generation sequencing, serological, digital, and imaging approaches have delivered improved and noteworthy success compared to that using traditional strategies. Conventional drug treatment, plasma therapy, and vaccine development are also ongoing. However, alternative medicines including Ayurveda, herbal drugs, homeopathy, and Unani have also been enlisted as prominent treatment strategies for developing herd immunity and physical defenses against COVID-19. All considered, this review can help develop rapid and simplified diagnostic strategies, as well as advanced evidence-based modern therapeutic approaches that will aid in combating the global pandemic.

Monitoring changes in COVID-19 infection using wastewater-based epidemiology: A South African perspective

Monitoring of COVID-19 infections within communities via wastewater-based epidemiology could provide a cost-effective alternative to clinical testing. This approach, however, still requires improvement for its efficient application. In this paper, we present the use of wastewater-based epidemiology in monitoring COVID-19 infection dynamics in the KwaZulu-Natal province of South Africa, focusing on four wastewater treatment plants for 14 weeks. The SARS-CoV-2 viral load in influent wastewater was determined using droplet digital PCR, and the number of people infected was estimated using published models as well as using a modified model to improve efficiency. On average, viral loads ranged between 0 and 2.73 × 105 copies/100 ml, 0-1.52 × 105 copies/100 ml, 3 × 104-7.32 × 105 copies/100 ml and 1.55 × 104-4.12 × 105 copies/100 ml in the four wastewater treatment plants studied. The peak in viral load corresponded to the reported COVID-19 infections within the districts where these catchments are located. In addition, we also observed that easing of lockdown restrictions by authorities corresponded with an increase in viral load in the untreated wastewater. Estimation of infection numbers based on the viral load showed that a higher number of people could potentially be infected, compared to the number of cases reported based on clinical testing. The findings reported in this paper contribute to the field of wastewater-based epidemiology for COVID-19 surveillance, whilst highlighting some of the challenges associated with this approach, especially in developing countries.

Self-Powered Respiration Monitoring Enabled By a Triboelectric Nanogenerator

In mammals, physiological respiration involves respiratory cycles of inhaled and exhaled breaths, which has traditionally been an underutilized resource potentially encompassing a wealth of physiologically relevant information as well as clues to potential diseases. Recently, triboelectric nanogenerators (TENGs) have been widely adopted for self-powered respiration monitoring owing to their compelling features, such as decent biocompatibility, wearing comfort, low-cost, and high sensitivity to respiration activities in the aspect of low frequency and slight amplitude body motions. Physiological respiration behaviors and exhaled chemical regents can be precisely and continuously monitored by TENG-based respiration sensors for personalized health care. This article presents an overview of TENG enabled self-powered respiration monitoring, with a focus on the working principle, sensing materials, functional structures, and related applications in both physical respiration motion detection and chemical breath analysis. Concepts and approaches for acquisition of physical information associated with respiratory rate and depth are covered in the first part. Then the sensing mechanism, theoretical modeling, and applications related to detection of chemicals released from breathing gases are systemically summarized. Finally, the opportunities and challenges of triboelectric effect enabled self-powered respiration monitoring are comprehensively discussed and criticized.

Revisiting the guidelines for ending isolation for COVID-19 patients

Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0-6.6%). However, this policy entails lengthy unnecessary isolations (4.8-8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.

A comprehensive review on current COVID-19 detection methods: From lab care to point of care diagnosis

Without a doubt, the current global pandemic affects all walks of our life. It affected almost every age group all over the world with a disease named COVID-19, declared as a global pandemic by WHO in early 2020. Due to the high transmission and moderate mortality rate of this virus, it is also regarded as the panic-zone virus. This potentially deadly virus has pointed up the significance of COVID-19 research. Due to the rapid transmission of COVID-19, early detection is very crucial. Presently, there are different conventional techniques are available for coronavirus detection like CT-scan, PCR, Sequencing, CRISPR, ELISA, LFA, LAMP. The urgent need for rapid, accurate, and cost-effective detection and the requirement to cut off shortcomings of traditional detection methods, make scientists realize to advance new technologies. Biosensors are one of the reliable platforms for accurate, early diagnosis. In this article, we have pointed recent diagnosis approaches for COVID-19. The review includes basic virology of SARS-CoV-2 mainly clinical and pathological features. We have also briefly discussed different types of biosensors, their working principles, and current advancement for COVID-19 detection and prevention.

COVID-19 Biomarkers and Advanced Sensing Technologies for Point-of-Care (POC) Diagnosis

COVID-19, also known as SARS-CoV-2 is a novel, respiratory virus currently plaguing humanity. Genetically, at its core, it is a single-strand positive-sense RNA virus. It is a beta-type Coronavirus and is distinct in its structure and binding mechanism compared to other types of coronaviruses. Testing for the virus remains a challenge due to the small market available for at-home detection. Currently, there are three main types of tests for biomarker detection: viral, antigen and antibody. Reverse Transcription-Polymerase Chain Reaction (RT-PCR) remains the gold standard for viral testing. However, the lack of quantitative detection and turnaround time for results are drawbacks. This manuscript focuses on recent advances in COVID-19 detection that have lower limits of detection and faster response times than RT-PCR testing. The advancements in sensing platforms have amplified the detection levels and provided real-time results for SARS-CoV-2 spike protein detection with limits as low as 1 fg/mL in the Graphene Field Effect Transistor (FET) sensor. Additionally, using multiple biomarkers, detection levels can achieve a specificity and sensitivity level comparable to that of PCR testing. Proper biomarker selection coupled with nano sensing detection platforms are key in the widespread use of Point of Care (POC) diagnosis in COVID-19 detection.

The Hologic Aptima SARS-CoV-2 assay enables high ratio pooling saving reagents and improving turnaround time

BACKGROUND

The Hologic Aptima™ TMA SARS-CoV-2 assay was employed to test pooled nasopharyngeal (NP) samples to evaluate the performance of pooled sample testing and characterize variables influencing results.

METHODS

Results on 1033 previously tested NP samples were retrieved to characterize the relative light units (RLU) of SARS-CoV-2-positive samples in the tested population. The pooling strategy of combining 10 SARS-CoV-2 samples into one pool (10/1) was used in this study. The results were compared with neat sample testing using the same Aptima™ TMA SARS-CoV-2 assay and also the CDC RT-PCR and the Cepheid SARS-CoV-2 assays.

RESULTS

The Aptima assay compares favorably with both CDC RT-PCR and the Cepheid SARS-CoV-2 assays. Once samples are pooled 10 to 1 as in our experiments, the resulting signal strength of the assay suffers. A divide opens between pools assembled from strong-positive versus only weak-positive samples. Pools of the former can be reliably detected with positive percent agreement (PPA) of 95.2%, while pools of the latter are frequently misclassified as negative with PPA of 40%. When the weak-positive samples with kRLU value lower than 1012 constitute 3.4% of the total sample profile, the assay PPA approaches 93.4% suggesting that 10/1 pooled sample testing by the Aptima assay is an effective screening tool for SARS-CoV-2.

CONCLUSION

Performing pooled testing, one should monitor the weak positives with kRLU lower than 1012 or quantification cycle (Cq) value higher than 35 on an ongoing basis and adjust pooling approaches to avoid reporting false negatives.

Structure-based Design of a Specific, Homogeneous Luminescence Enzyme Reporter Assay for SARS-CoV-2

Recombinant antibodies (Abs) against the SARS-CoV-2 virus hold promise for treatment of COVID-19 and high sensitivity and specific diagnostic assays. Here, we report engineering principles and realization of a Protein-fragment Complementation Assay (PCA) detector of SARS-CoV-2 antigen by coupling two Abs to complementary N- and C-terminal fragments of the reporter enzyme Gaussia luciferase (Gluc). Both Abs display comparably high affinities for distinct epitopes of viral Spike (S)-protein trimers. Gluc activity is reconstituted when the Abs are simultaneously bound to S-protein bringing the Ab-fused N- and C-terminal fragments close enough together (8 nm) to fold. We thus achieve high specificity both by requirement of simultaneous binding of the two Abs to the S-protein and also, in a steric configuration in which the two Gluc complementary fragments can fold and thus reconstitute catalytic activity. Gluc activity can also be reconstituted with virus-like particles that express surface S-protein with detectable signal over background within 5 min of incubation. Design principles presented here can be readily applied to develop reporters to virtually any protein with sufficient available structural details. Thus, our results present a general framework to develop reporter assays for COVID-19, and the strategy can be readily deployed in response to existing and future pathogenic threats and other diseases.

Rapid detection of SARS-CoV-2 viral nucleic acids based on surface enhanced infrared absorption spectroscopy

Efficient point-of-care diagnosis of severe acute respiratory syndrome-corovavirus-2 (SARS-CoV-2) is crucial for the early control of novel coronavirus infections. At present, polymerase chain reaction (PCR) is primarily used to detect SARS-CoV-2. Despite the high sensitivity, the PCR process is time-consuming and complex which limits its applicability for rapid testing of large-scale outbreaks. Here, we propose a rapid and easy-to-implement approach for SARS-CoV-2 detection based on surface enhanced infrared absorption (SEIRA) spectroscopy. The evaporated gold nano-island films are used as SEIRA substrates which are functionalized with the single-stranded DNA probes for specific binding to selected SARS-CoV-2 genomic sequences. The infrared absorption spectra are analyzed using the principal component analysis method to identify the key characteristic differences between infected and control samples. The SEIRA-based biosensor demonstrates rapid detection of SARS-CoV-2, completing the detection of 1 μM viral nucleic acids within less than 5 min without any amplification. When combined with the recombinase polymerase amplification treatment, the detection capability of 2.98 copies per μL (5 aM) can be completed within 30 min. This approach provides a simple and economical alternative for COVID-19 diagnosis, which can be potentially useful in monitoring and controlling future pandemics in a timely manner.