In vitro diagnostics of coronavirus disease 2019: Technologies and application

Detection of the SARS-CoV-2 nucleoprotein by electrochemical biosensor based on molecularly imprinted polypyrrole formed on self-assembled monolayer

Herein, we report the development and characterisation of an electrochemical biosensor with a polypyrrole (Ppy)-based molecularly imprinted polymer (MIP) for the serological detection of the recombinant nucleocapsid protein of SARS-CoV-2 (rN). The electrochemical biosensor utilises a Ppy-based MIP formed on a self-assembled monolayer (SAM) at the gold interface to enhance Ppy layer stability on the screen-printed electrode (SPE). Electrochemical impedance spectroscopy (EIS) and square wave voltammetry (SWV) were employed for the electrochemical characterisation of screen-printed gold electrodes (SPGEs) modified with MIP or non-imprinted polymer (NIP) layers. Removing the rN protein template from the MIP layer increased electron transfer and decreased impedance, indicating the specificity of molecular imprinting. The electrochemical biosensor with a Ppy-based MIP exhibited higher sensitivity than the NIP counterpart, demonstrating its potential for selective rN protein detection. The limit of detection 0.4 nM and 0.2 nM and the limit of quantification 1.3 nM and 0.66 nM values obtained through SWV and EIS, respectively, highlight the biosensor's ability to detect low target protein concentrations. The specificity test confirmed minimal nonspecific binding, reinforcing the reliability of the novel electrochemical sensor with a Ppy-based MIP.

Characterization of CRISPR-Cas Systems in Shewanella algae and Shewanella haliotis: Insights into the Adaptation and Survival of Marine Pathogens

CRISPR-Cas systems are adaptive immune mechanisms present in most prokaryotes that play an important role in the adaptation of bacteria and archaea to new environments. Shewanella algae is a marine zoonotic pathogen with worldwide distribution, which accounts for the majority of clinical cases of Shewanella infections. However, the characterization of Shewanella algae CRISPR-Cas systems has not been well investigated yet. Through whole genome sequence analysis, we characterized the CRISPR-Cas systems in S. algae. Our results indicate that CRISPR-Cas systems are prevalent in S. algae, with the majority of strains containing the Type I-F system. This study provides new insights into the diversity and function of CRISPR-Cas systems in S. algae and highlights their potential role in the adaptation and survival of these marine pathogens.

Ultrasensitive Electrochemical Immunosensor for Multiplex Sandwich Bioassaying Based on the Functional Antibodies

In vitro diagnostics (IVDs) based on electrochemical immunosensors are crucial for disease screening, diagnosis, prognosis, and treatment monitoring. However, label-free electrochemical immunosensors commonly suffer from poor specificity, leading to false positives. To address this issue, we propose a highly sensitive and precise electrochemical immunosensor for protein marker detection. This approach involves directly labeling the detection antibodies (Ab2) with thionine (Thi). The Ab2 labeled by Thi exhibits a distinct redox peak upon targeted voltage stimulation, enabling accurate quantification of protein biomarkers. Thi-modified antibodies provide significant advantages over traditional antibody modification methods, such as enhanced detection sensitivity, improved accuracy, and specificity in protein marker identification. The method is straightforward and efficient, ensuring specific analyte detection while minimizing interference from other substances in the sample. Additionally, a multielectrode detection method was employed, achieving remarkably low limits of detection (LoDs) for tumor necrosis factor-alpha (TNF-alpha), cardiac troponin I (cTnI), and interleukin-6 (IL-6), with LoDs of 9.38 fg/mL, 1.70 fg/mL, and 8.14 fg/mL, respectively. The proposed electrochemical immunosensor also exhibited high selectivity and repeatability, with relative standard deviations (RSD) of 6.39% for TNF-alpha, 2.42% for cTnI, and 2.72% for IL-6 (n = 5). Moreover, it demonstrated high sensitivity and was evaluated for serum detection using the standard addition method. The results highlight the great potential of the proposed electrochemical immunosensor for clinical applications, offering a novel approach for future utilization in clinical settings.

Disease diagnosis and application analysis of molecularly imprinted polymers (MIPs) in saliva detection

Saliva has significantly evolved as a diagnostic fluid in recent years, giving a non-invasive alternative to blood analysis. A high protein concentration in saliva is delivered directly from the bloodstream, making it a "human mirror" that reflects the body's physiological state. It plays an essential role in detecting diseases in biomedical and fitness monitoring. Molecularly imprinted polymers (MIPs) are biomimetic materials with custom-designed synthetic recognition sites that imitate biological counterparts renowned for sensitive analyte detection. This paper reviews the progress made in research about MIP biosensors for detecting saliva biomarkers. Specifically, we investigate the link between saliva biomarkers and various diseases, providing detailed insights into the corresponding biosensors. Furthermore, we discuss the principles of molecular imprinting for disease diagnostics and application analysis, including recent advances in integrated MIP-sensor technologies for high-affinity analyte detection in saliva. Notably, these biosensors exhibit high discrimination, allowing for the detection of saliva biomarkers linked explicitly to chronic stress disorders, diabetes, cancer, bacterial or viral-induced illnesses, and exposure to illicit toxic substances or tobacco smoke. Our findings indicate that MIP-based biosensors match and perhaps surpass their counterparts featuring integrated natural antibodies in terms of stability, signal-to-noise ratios, and detection limits. Additionally, we highlight the design of MIP coatings, strategies for synthesizing polymers, and the integration of advanced biodevices. These tailored biodevices, designed to assess various salivary biomarkers, are emerging as promising screening or diagnostic tools for real-time monitoring and self-health management, improving quality of life.

Performance evaluation of the cobas SARS-CoV-2 Duo, a novel qualitative and quantitative assay, for the detection of SARS-CoV-2 RNA

IMPORTANCE

Quantitative SARS-CoV-2 tests for viral load are necessary to guide patient treatment, as well as to determine infection control measures and policies. Although the real-time RT-PCR assays can report the Ct value to estimate the viral load, there are several serious concerns regarding the use of Ct values. Importantly, Ct values can vary significantly among between- and within-run methods. The diagnostic performance of the cobas SARS-CoV-2 Duo is appropriate. It is a precise, accurate, and sensitive method for the detection of SARS-CoV-2 RNA and is comparable to two qualitative assays (the cobas SARS-CoV-2 and the Liat cobas SARS-CoV-2 and Inf A/B). In contrast, using the Ct value to estimate viral load is not reliable, and utilization of a quantitative detection test, such as the cobas SARS-CoV-2 Duo, to accurately measure the viral load is needed.

Evaluation of the performance of Abbott Panbio™ COVID-19 antigen rapid diagnostic test for the detection of severe acute respiratory syndrome coronavirus 2 at Harar, Eastern Ethiopia

Background

Rapid antigen tests can help in the effective isolation of symptomatic cases and the systematic tracing of close contacts. However, their reliability must be validated before implementing them widely.

Methods

A cross-sectional study was conducted on 236 COVID-19-suspected patients visiting four different health institutions in Harari Regional State, Harar, Eastern Ethiopia, from June to July 2021. Two nasopharyngeal samples were collected and processed by the Panbio™ Ag-RDT kit and qRT-PCR. The collected data were analyzed using SPSS version 25.0.

Results

The Panbio tests had a sensitivity of 77.5% (95% CI: 61.6-89.2%) and a specificity of 98.5% (95% CI: 95.6-99.7%). It also had a positive predictive value of 91.2% (95% CI: 76.9-96.9%), a negative predictive value of 95.5% (95% CI: 92.3-97.4%), and a kappa of 0.81 (95% CI: 0.7-0.9). The test had a sensitivity of 94.4%, 100%, 100%, and 90% in the samples collected from patients within the 1-5 days post-onset of COVID-19 signs and symptoms, of age group ≤18 years old, with cycle threshold values of <20, and with household contact, respectively.

Conclusion

This test can be used as point-of-care testing for the diagnosis of symptomatic patients with short clinical courses and contact with patients in households.

At-Home COVID-19 Rapid Antigen Test Down to 0.03 pg mL-1 of Nucleocapsid Protein

Rapid and ultra-sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for early screening and management of COVID-19. Currently, the real-time reverse transcription polymerase chain reaction (rRT-PCR) is the primary laboratory method for diagnosing SARS-CoV-2. It is not suitable for at-home COVID-19 diagnostic test due to the long operating time, specific equipment, and professional procedures. Here an all-printed photonic crystal (PC) microarray with portable device for at-home COVID-19 rapid antigen test is reported. The fluorescence-enhanced effect of PC amplifies the fluorescence intensity of the labeled probe, achieving detection of nucleocapsid (N-) protein down to 0.03 pg mL^-1 . A portable fluorescence intensity measurement instrument gives the result (negative or positive) by the color of the indicator within 5 s after inserting the reacted PC microarray test card. The N protein in inactivated virus samples (with cycle threshold values of 26.6-40.0) can be detected. The PC microarray provides a general and easy-to-use method for the timely monitoring and eventual control of the global coronavirus pandemic.

Diagnostic Sensitivity of Saliva and Other Respiratory Tract Samples of SARS-CoV-2 Variants in Patients with COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge during the ongoing coronavirus disease 2019 (COVID-19) pandemic. Contrasting studies on the omicron variant have demonstrated higher viral loads in different clinical specimens, which is consistent with its high transmissibility. We investigated the viral load in clinical specimens that were infected with the SARS-CoV-2 wild-type, delta, and omicron variants, and we analyzed the diagnostic accuracy of upper and lower respiratory specimens for these variants. We performed nested reverse transcription (RT)-polymerase chain reaction (PCR), targeting the spike gene and sequencing for variant classification. RT-PCR was performed using upper and lower respiratory specimens, including saliva from 78 COVID-19 patients (wild-type, delta, and omicron variants). A comparison of the sensitivity and specificity, using the area under the receiver operating characteristic curve (AUC) values from the N gene, showed that the omicron variant saliva samples had a higher sensitivity (AUC = 1.000) than did the delta (AUC = 0.875) and the wild-type (AUC = 0.878) variant samples. The sensitivity of the omicron saliva samples was greater than that of the wild-type nasopharynx and sputum samples (P < 0.001). The viral loads of the saliva samples containing the wild-type, delta, and omicron variants were 8.18 × 105, 2.77 × 106, and 5.69 × 105, respectively, which did not differ significantly (P = 0.610). Statistically significant differences were not observed in the saliva viral loads between vaccinated and nonvaccinated patients who were infected with the omicron variant (P = 0.120). In conclusion, omicron saliva samples had higher sensitivity than did wild-type and delta samples, and the viral load did not significantly differ between vaccinated and nonvaccinated patients. Further research is necessary to elucidate the mechanisms underlying the sensitivity differences. IMPORTANCE Owing to the vast heterogeneity of the studies focused on the correlation between the SARS-CoV-2 omicron variant and COVID-19, accurate comparisons of the specificity and sensitivity of samples and associated outcomes are still inconclusive. Moreover, limited information is available on the leading causes of infection and the factors that are associated with the conditions that underlie the spread of infection. Although several studies have contributed important knowledge regarding infectious specimens, the impact of saliva samples remains unknown. This study showed that the sensitivity of the omicron variant saliva samples was higher than that of the wild-type nasopharyngeal and sputum samples. Moreover, neither vaccinated nor nonvaccinated patients who were infected with the omicron variant showed any significant differences in SARS-CoV-2 viral loads. Hence, this study is an important step toward understanding how saliva sample results are correlated with other specimen results, regardless of the vaccination status of patients who are infected with the SARS-CoV-2 omicron variant.

PCR-like performance of rapid test with permselective tunable nanotrap

Highly sensitive rapid testing for COVID-19 is essential for minimizing virus transmission, especially before the onset of symptoms and in asymptomatic cases. Here, we report bioengineered enrichment tools for lateral flow assays (LFAs) with enhanced sensitivity and specificity (BEETLES2), achieving enrichment of SARS-CoV-2 viruses, nucleocapsid (N) proteins and immunoglobulin G (IgG) with 3-minute operation. The limit of detection is improved up to 20-fold. We apply this method to clinical samples, including 83% with either intermediate (35%) or low viral loads (48%), collected from 62 individuals (n = 42 for positive and n = 20 for healthy controls). We observe diagnostic sensitivity, specificity, and accuracy of 88.1%, 100%, and 91.9%, respectively, compared with commercial LFAs alone achieving 14.29%, 100%, and 41.94%, respectively. BEETLES2, with permselectivity and tunability, can enrich the SARS-CoV-2 virus, N proteins, and IgG in the nasopharyngeal/oropharyngeal swab, saliva, and blood serum, enabling reliable and sensitive point-of-care testing, facilitating fast early diagnosis.

COVID-19 Pandemic Control Measures and Their Impact on University Students and Family Members in a Central Region of Spain

The first waves of the COVID-19 pandemic were times of great change in the lives of university students and their families in Spain. The aim of this study was to explore the psychosocial aspects and preventive measures carried out during the COVID-19 pandemic by students and family members of the nursing degree students of the University of Valladolid (Spain). The number of people surveyed was 877, by means of an ad hoc questionnaire. Relationships between variables were established by means of the Chi-square test and Student's t-test. In addition, multivariate logistic regression was generated. The significance level used was 0.05. Students and family members maintained preventive measures= such as hand washing, correct use of masks =in closed places, avoiding crowds and maintaining social distance, but at low rates (close to 20% in all cases). Regarding psychosocial aspects, 41.07% of the participants suffered from anxiety and loneliness, while 5.2% needed to take drugs to reduce anxiety or sleep and 66.07% were dependent on technology. Suicidal behavior is related to stress, anxiety, loneliness, poor family relationships, psychotropic drug use and technology abuse. The pandemic has caused life changes in university students and their families at the psychosocial level, generating high figures of suicidal ideation regardless of age. Preventive measures adopted to control the pandemic have not been followed for the most part.

Affordable on-site COVID-19 test using non-powered preconcentrator

A simple, affordable point of care test (POCT) is necessary for on-site detection of coronavirus disease 2019 (COVID-19). The lateral flow assay (LFA) has great potential for use in POCT mainly because of factors such as low time consumption, low cost, and ease of use. However, it lacks sensitivity and limits of detection (LOD), which are essential for early diagnostics. In this study, we proposed a non-powered preconcentrator (NPP) based on nanoelectrokinetics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Antigen (Ag) lateral flow assay. The non-powered preconcentrator is composed of glass fiber-based composite paper and ion permselective material, and it can be simply operated by force balancing gravitational, capillary, and depletion-induced forces. The proposed approach helps enrich the SARS-CoV-2 viral nucleocapsid (N) proteins based on a 10-min operation, and it improved the LOD by up to 10-fold. The corresponding virus enrichment, which was evaluated using the reverse-transcriptase polymerase chain reaction (RT-PCR), revealed an improvement in ΔCt values > 3. We successfully demonstrated the enhancement of the NPP-assisted LFA, we extended to applying it to clinical samples. Further, we demonstrated an affordable, easy-to-implement form of LFA by simply designing NPP directly on the LFA buffer tube.

Label-free electrochemical aptasensor for the detection of SARS-CoV-2 spike protein based on carbon cloth sputtered gold nanoparticles

The proliferation and transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or the (COVID-19) disease, has become a threat to worldwide biosecurity. Therefore, early diagnosis of COVID-19 is crucial to combat the ongoing infection spread. In this study we propose a flexible aptamer-based electrochemical sensor for the rapid, label-free detection of SARS-CoV-2 spike protein (SP). A platform made of a porous and flexible carbon cloth, coated with gold nanoparticles, to increase the conductivity and electrochemical performance of the material, was assembled with a thiol functionalized DNA aptamer via S-Au bonds, for the selective recognition of the SARS-CoV-2 SP. The various steps for the sensor preparation were followed by using scanning electron microscopy, cyclic voltammetry and differential pulse voltammetry (DPV). The proposed platform displayed good mechanical stability, revealing negligible changes on voltammetric responses to bending at various angles. Quantification of SARS-CoV-2 SP was performed by DPV and chronopotentiometry (CP), exploiting the changes of the electrical signals due the [Fe(CN)₆]^3-/4- redox probe, when SARS-CoV-2 SP binds to the aptamer immobilized on the electrode surface. Current density, in DPV, and square root of the transition time, in CP, varied linearly with the log[ SARS-CoV-2 SP], providing lower limits of detection (LOD) of 0.11 ng/mL and 37.8 ng/mL, respectively. The sensor displayed good selectivity, repeatability, and was tested in diluted human saliva, spiked with different SARS-CoV-2 SP concentrations, providing LODs of 0.167 ng/mL and 46.2 ng/mL for DPV and CP, respectively.

Multicenter study evaluating novel multi-specimen pooling assay for the detection of SARS-CoV-2: High sensitivity and high throughput testing

BACKGROUND/PURPOSE

Mass screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important to prevent the spread of coronavirus disease 2019 (COVID-19). Pooling samples can increase the number of tests processed. LabTurbo AIO 48 is an automated platform that allows ribonucleic acid extraction and sample analysis on the same instrument. We created a novel pooling assay on this platform for SARS-CoV-2 detection and demonstrated that the pooling strategy increases testing capacity without affecting accuracy and sensitivity.

METHODS

Comparative limit of detection (LoD) assessment was performed on the LabTurbo AIO 48 platform and the current standard detection system based on real-time reverse transcription polymerase chain reaction (rRT-PCR) using 55 clinically positive samples. An additional 330 primary clinical samples were assessed.

RESULTS

Six samples pooled into one reaction tube were detected in approximately 2.5 h using the World Health Organization rRT-PCR protocol. LabTurbo AIO 48 also demonstrated a higher throughput than our reference rRT-PCR assay, with an LoD of 1000 copies/mL. The overall percentage agreement between the methods for the 330 samples was 100%.

CONCLUSION

We created a novel multi-specimen pooling assay using LabTurbo AIO 48 for the robust detection of SARS-CoV-2, allowing high-throughput results; this assay will aid in better control and prevention of COVID-19. The diagnostic assay was cost-effective and time-efficient; thus, the pooling strategy is a practical and effective method for diagnosing large quantities of specimens without compromising precision.

Hosseini I, Lu Y, Yedire SG, Mahshid SS, Tabatabaiefar MA, Liang C, Mahshid S. A Versatile Biomimic Nanotemplating Fluidic Assay for Multiplex Quantitative Monitoring of Viral Respiratory Infections and Immune Responses in Saliva and Blood

The last pandemic exposed critical gaps in monitoring and mitigating the spread of viral respiratory infections at the point-of-need. A cost-effective multiplexed fluidic device (NFluidEX), as a home-test kit analogous to a glucometer, that uses saliva and blood for parallel quantitative detection of viral infection and body's immune response in an automated manner within 11 min is proposed. The technology integrates a versatile biomimetic receptor based on molecularly imprinted polymers in a core-shell structure with nano gold electrodes, a multiplexed fluidic-impedimetric readout, built-in saliva collection/preparation, and smartphone-enabled data acquisition and interpretation. NFluidEX is validated with Influenza A H1N1 and SARS-CoV-2 (original strain and variants of concern), and achieves low detection limit in saliva and blood for the viral proteins and the anti-receptor binding domain (RBD) Immunoglobulin G (IgG) and Immunoglobulin M (IgM), respectively. It is demonstrated that nanoprotrusions of gold electrodes are essential for the fine templating of antibodies and spike proteins during molecular imprinting, and differentiation of IgG and IgM in whole blood. In the clinical setting, NFluidEX achieves 100% sensitivity and 100% specificity by testing 44 COVID-positive and 25 COVID-negative saliva and blood samples on par with the real-time quantitative polymerase chain reaction (p < 0.001, 95% confidence) and the enzyme-linked immunosorbent assay.

Microbiological and Clinical Findings of SARS-CoV-2 Infection after 2 Years of Pandemic: From Lung to Gut Microbiota

Early recognition and prompt management are crucial for improving survival in COVID-19 patients, and after 2 years of the pandemic, many efforts have been made to obtain an early diagnosis. A key factor is the use of fast microbiological techniques, considering also that COVID-19 patients may show no peculiar signs and symptoms that may differentiate COVID-19 from other infective or non-infective diseases. These techniques were developed to promptly identify SARS-CoV-2 infection and to prevent viral spread and transmission. However, recent data about clinical, radiological and laboratory features of COVID-19 at time of hospitalization could help physicians in early suspicion of SARS-CoV-2 infection and distinguishing it from other etiologies. The knowledge of clinical features and microbiological techniques will be crucial in the next years when the endemic circulation of SARS-CoV-2 will be probably associated with clusters of infection. In this review we provide a state of the art about new advances in microbiological and clinical findings of SARS-CoV-2 infection in hospitalized patients with a focus on pulmonary and extrapulmonary characteristics, including the role of gut microbiota.

Verification and Comparison of Qualitative Serological Assays for Anti-SARS-COV-2 IgM and IgG Antibodies Detection

Background

Due to their wide application in the SARS-CoV-2 pandemic, we verified and compared three qualitative serological methods in order to select the most optimal that will best serve its purpose under laboratory conditions.

Methods

We assessed the diagnostic characteristics of two automated serological methods (Roche Elecsys^® Anti-SARS-CoV-2 and Abbott SARS-CoV-2 IgG) and a POCT test (Colloidal Gold Method SARS-CoV-2 IgM/IgG Antibody Assay Kit). In the process of verification, analytical precision was also assessed for the automated assays.

Results

Diagnostic characteristics were determined by measuring antibodies against SARS-CoV-2 in 91 RT-PCR-negative and 60 RT-PCR-positive samples. The POCT test gave the highest number of false positive cases (8.61%). Roche Elecsys^® Anti-SARS-CoV-2 gave only 2.65% false positivity and showed the highest diagnostic sensitivity of 98.33% (95% CI: 91.06-99.96), while Abbott SARS-CoV-2 IgG method showed 100.00% (95% CI: 96.03-100.00) diagnostic specificity and an almost perfect agreement with Roche Elecsys^® Anti-SARS-CoV-2. When assessing the precision of the automated methods, we observed some variability in the positive control samples, but the values did not affect clinical interpretation.

Conclusion

Both automated methods demonstrate superior diagnostic characteristics compared to the Colloidal Gold Method, and this POCT test is not considered as an appropriate choice for routine testing. The two automated methods showed low variability without altering the results and their interpretation.

COVID-19 diagnostic methods in developing countries

COVID-19 has become one of the few leading causes of death and has evolved into a pandemic that disrupts everyone's routine, and balanced way of life worldwide, and will continue to do so. To bring an end to this pandemic, scientists had put their all effort into discovering the vaccine for SARS-CoV-2 infection. For their dedication, now, we have a handful of COVID-19 vaccines. Worldwide, millions of people are at risk due to the current pandemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). Despite the lack of clinically authorized antiviral medications and vaccines for COVID-19, clinical trials of many recognized antiviral agents, their combination, and vaccine development in patients with confirmed COVID-19 are still ongoing. This discovery gave us a chance to get immune to this disease worldwide and end the pandemic. However, the unexpected capacity of mutation of the SARS-CoV-2 virus makes it difficult, like the recent SAS-CoV-2 Omicron variant. Therefore, there is a great necessity to spread the vaccination programs and prevent the spread of this dreadful epidemic by identifying and isolating afflicted patients. Furthermore, several COVID-19 tests are thought to be expensive, time-consuming, and require the use of adequately qualified persons to be carried out efficiently. In addition, we also conversed about how the various COVID-19 testing methods can be implemented for the first time in a developing country and their cost-effectiveness, accuracy, human resources requirements, and laboratory facilities.

Sensitive and specific clinically diagnosis of SARS-CoV-2 employing a novel biosensor based on boron nitride quantum dots/flower-like gold nanostructures signal amplification

The sudden increase of the COVID-19 outbreak and its continued growth with mutations in various forms has created a global health crisis as well as devastating social and economic effects over the past two years. In this study, a screen-printed carbon electrode reinforced with boron nitride quantum dots/flower-like gold nanostructures (BNQDs/FGNs/SPCE) and functionalized by highly specific antisense DNA oligonucleotide presents an alternative and promising solution for targeting SARS-CoV-2 RNA without nucleic acid amplification. The platform was tested on 120 SARS-CoV-2 RNA isolated from real clinical samples (60 positive and 60 negative confirmed by conventional RT-PCR method). Based on obtained quantitative results and statistical analysis (box-diagram, cutoff value, receiver operating characteristic curve, and t-test), the biosensor revealed a significant difference between the two positive and negative groups with 100% sensitivity and 100% specificity. To evaluate the quantitation capacity and detection limit of the biosensor for clinical trials, the detection performance of the biosensor for continuously diluted RNA isolated from SARS-CoV-2-confirmed patients was compared to those obtained by RT-PCR, demonstrating that the detection limit of the biosensor is lower than or comparable to that of RT-PCR. The ssDNA/BNQDs/FGNs/SPCE showed negligible cross-reactivity with RNA fragments isolated from Influenza A (IAV) clinical samples and also remained stable for up to 14 days. In conclusion, the fabricated biosensor may serve as a promising tool for point-of-care applications.

A novel colorimetric biosensor for detecting SARS-CoV-2 by utilizing the interaction between nucleocapsid antibody and spike proteins

SARS-CoV-2 is a pandemic coronavirus that causes severe respiratory disease (COVID-19) in humans and is responsible for millions of deaths around the world since early 2020. The virus affects the human respiratory cells through its spike (S) proteins located at the outer shell. To monitor the rapid spreading of SARS-CoV-2 and to reduce the deaths from the COVID-19, early detection of SARS-CoV-2 is of utmost necessity. This report describes a flexible colorimetric biosensor capable of detecting the S protein of SARS-CoV-2. The colorimetric biosensor is made of polyurethane (PU)-polydiacetylene (PDA) nanofiber composite that was chemically functionalized to create a binding site for the receptor molecule-nucleocapsid antibody (anti-N) protein of SARS-CoV-2. After the anti-N protein conjugation to the functionalized PDA fibers, the PU-PDA-NHS-anti fiber was able to detect the S protein of SARS-CoV-2 at room temperature via a colorimetric transition from blue to red. The PU-PDA nanofiber-based biosensors are flexible and lightweight and do not require a power supply such as a battery when the colorimetric detection to S protein occurs, suggesting a sensing platform of wearable devices and personal protective equipment such as face masks and medical gowns for real-time monitoring of virus contraction and contamination. The wearable biosensors could significantly power mass surveillance technologies to fight against the COVID-19 pandemic.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s44164-022-00022-z.

Performance study of the anterior nasal AMP SARS-CoV-2 rapid antigen test in comparison with nasopharyngeal rRT-PCR

Introduction.

The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is real-time reverse transcription PCR (rRT-PCR), which is expensive, has a long turnaround time and requires special equipment and trained personnel. Nasopharyngeal swabs are uncomfortable, not suitable for certain patient groups and do not allow self-testing. Convenient, well-tolerated rapid antigen tests (RATs) for SARS-CoV-2 detection are called for.

Gap statement.

More real-life performance data on anterior nasal RATs are required.

Aim.

We set out to evaluate the anterior nasal AMP RAT in comparison with rRT-PCR in a hospital cohort.

Methodology.

The study included 175 patients, either hospitalized in a coronavirus disease 2019 (COVID-19) ward or screened in a preadmittance outpatient clinic. Two swabs were collected per patient: an anterior nasal one for the RAT and a combined naso-/oropharyngeal one for the rRT-PCR. Sixty-five patients (37%) were rRT-PCR-positive [cycle threshold (C_t) <40].

Results.

The anterior nasal AMP RAT showed an overall sensitivity and specificity of 29.2 % (18.6–41.8, 95 % CI) and 100.0 % (96.7–100.0, 95 % CI) respectively. In patients with a C_t value <25, <30 and <33, higher sensitivities were observed. Time since symptom onset was significantly higher in patients with a false-negative RAT (P=0.02).

Conclusion.

The anterior nasal AMP RAT showed low sensitivities in this cohort, especially in patients with a longer time since symptom onset. Further knowledge concerning the viral load and antigen expression over time and in different swabbing locations is needed to outline the usage time frame for SARS-CoV-2 RAT.

Developing novel liquid biopsy by selective capture of viral RNA on magnetic beads to detect COVID-19

Objectives

Early, specific, and sensitive detection methods of COVID-19 are essential for force stopping its worldwide infection. Although CT images of the lung and/or viral RNA extraction followed by real-time reverse-transcriptase-polymerase chain reaction (rRT-PCR) are widely used; they have some limitations. Here, we developed a highly sensitive magnetic bead-based viral RNA extraction assay followed by rRT-PCR.

Materials and Methods

Case group included oropharyngeal/nasopharyngeal and blood samples from 30 patients diagnosed positive by PCR test for COVID-19 and control group included 30 same samples from COVID-19 negative PCR test individuals. RNA was extracted, using viral RNA extraction kit as well as using our hand-made capture bead-based technique. A one-step cDNA synthesis and Real Time PCR was conducted. A two-step comparison of the different viral RNA extraction methods for oropharyngeal/nasopharyngeal and blood samples was performed. Student t-test was applied with a P<0.05 considered statistically significant.

Results

In the case group, all 30 mucosal samples extracted either with viral RNA extraction kit or with beads-based assay were COVID-19 positive although in the latter category, Cqs were much lower. Although 43% of plasma samples extracted by bead-based method were found to be positive but no plasma samples extracted with column-based kit were detected positive by Real Time PCR.

Conclusion

Bead-based RNA extraction method can reduce RNA loss by its single-tube performance and enhance the test sensitivity. It is also more sensitive to lower viral loads as shown in the detection of blood samples and the lower Cqs of mucosal samples.

Assessment of the Diagnostic Performance of a Novel SARS-CoV-2 Antigen Sealing Tube Test Strip (Colloidal Gold) as Point-of-Care Surveillance Test

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant outbreaks have highlighted the need of antigen-detecting rapid diagnostic tests (Ag-RDTs) that can be used at the point-of-care (POC). Although many Ag-RDTs have been approved for SARS-CoV-2 detection, studies demonstrating the clinical performance of Ag-RDTs against variants of concern, especially the new Omicron variant, are limited. The aim of this study was to evaluate the diagnostic sensitivity and specificity of the AMAZING COVID-19 Antigen Sealing Tube Test Strip (Colloidal Gold) in 584 early symptomatic and asymptomatic participants (age range 0–90 years). The performance of this Ag-RDT was assessed by comparing its results with reverse transcription RT-PCR (rRT-PCR). One hundred twenty positive samples were also analyzed with rRT-PCR to discriminate Omicron and Delta/Kappa variants (72.50% Omicron; 27.50% Delta/Kappa). Overall, the Ag-RDT showed high positive and negative percent values of 92.52% (95% CI, 86.61–95.95%) and 98.05% (95% CI, 96.41–98.95%), respectively, as well as an overall diagnostic accuracy of 96.92% (95% CI, 95.17–98.16%). Taken together, these data indicate that this inexpensive and simple-to-use Ag-RDT presents excellent analytical performance and can reliably detect Omicron and Delta/Kappa variants.

Controlled, partially exfoliated, self-supported functionalized flexible graphitic carbon foil for ultrasensitive detection of SARS-CoV-2 spike protein

This paper reports on an ultrasensitive and label-free electrochemical immunosensor for monitoring the SARS-CoV-2 spike protein (SARS-CoV-2 SP). A self-supported electrode, which can simultaneously serve as an antibody immobilization matrix and electron transport channel, was initially fabricated by a controlled partial exfoliation of a flexible graphitic carbon foil (GCF). Mild acidic treatment enabled the partial oxidation and exfoliation (down to a few layers) of the flexible GCF; this also provided a high percentage of oxygen functionality and an enhanced surface roughness. The substrate electrode was further functionalized with ethylenediamine (EDA) to provide a suitable platform with even a higher surface roughness, for the covalent immobilization of an anti-SARS-CoV-2 antibody. The change in the current response for the [Fe(CN)6]3-/4- redox couple, induced by the binding of SARS-CoV-2 SP to the antibody immobilized on the electrode surface, was used to determine the SARS-CoV-2 SP concentration. The immunosensor thus prepared could detect SARS-CoV-2 SP within 30 min with high reproducibility and specificity over a wide concentration range (0.2-100 ng/mL). Detection limits of 25 pg/mL and 27 pg/mL were found in a phosphate buffer solution (pH 7.4), and diluted blood plasma, respectively. The immunosensor was also employed to detect SARS-CoV-2 SP in artificial human saliva.

Research progress in laboratory detection of SARS-CoV-2

BACKGROUND

Nucleic acid testing is a reliable method for diagnosing viral infection in clinical samples. However, when the number of cases is huge and there are individual differences in the virus itself, the probability of false-negative results increases. With the advancement in research on the new coronavirus, new detection technologies that use serum-specific antibodies as detection targets have been developed. These detection technologies have high efficiency and shorter turnaround time, which ultimately shortens the time required for diagnosis. This article summarizes the methods that have been reported to date for the detection of the new coronavirus and discusses their principles and technical characteristics.

AIMS

Compare the advantages and disadvantages of various SARS-CoV-2 detection methods and analyze their principles.

METHODS

Searched reports on SARS-CoV-2 detection methods published so far, extracted the data and analyzed them. Use the primer blast function of NCBI to analyze the primers used in qRT-PCR detection.

RESULTS

The detection sensitivity was the highest when nucleocapsid protein gene was used as the target, reaching 96.6%. The detection efficiency of the remaining targets ranged from 66.7% to 96.0%. Various new detection methods, like Serum specific antibody detection, can speed up the test time. However, due to the complexity of the method and higher testing requirements, it seems that it cannot be used as a complete replacement for qRT-PRC testing.

CONCLUSIONS

With the advancement of technology and the improvement of methods, the detection methods of SARSCoV-2 have become more mature. These advances provided great help to the detection of SARS-CoV-2.

Accuracy of Real-Time Polymerase Chain Reaction in COVID-19 Patients

Coronavirus disease 2019 (COVID-19) is a mild to severe respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnostic accuracy of the Centers for Disease Control and Prevention (CDC)- or World Health Organization (WHO)-recommended real-time PCR (RT-qPCR) primers in clinical practice remains unproven. We conducted a prospective study on the accuracy of RT-qPCR using an in-house-designed primer set (iNP) targeting the nucleocapsid protein as well as various recommended and commercial primers. The accuracy was assessed by culturing or seroconversion. We enrolled 12 confirmed COVID-19 patients with a total of 590 clinical samples. When a cutoff value of the cycle threshold (C_t) was set to 35, RT-qPCRs with WHO RdRp primers and CDC N1, N2, and N3 primers showed sensitivity of 42.1% to 63.2% and specificity of 90.5% to 100% in sputum, and sensitivity of 65.2% to 69.6% and specificity of 65.2% to 69.6% in nasopharyngeal samples. The sensitivity and specificity of iNP RT-qPCR in sputum and nasopharyngeal samples were 94.8%/100% and 69.6%/100%, respectively. Sputum testing had the highest sensitivity, followed by nasopharyngeal testing (P = 0.0193); self-collected saliva samples yielded better characteristics than oropharyngeal samples (P = 0.0032). Our results suggest that iNP RT-qPCR has better sensitivity and specificity than RT-PCR with WHO (P < 0.0001) or CDC (N1: P = 0.0012, N2: P = 0.0013, N3: P = 0.0012) primers. Sputum RT-qPCR analysis has the highest sensitivity, followed by nasopharyngeal, saliva, and oropharyngeal assays. Our study suggests that considerable improvement is needed for the RT-qPCR WHO and CDC primer sets for detecting SARS-CoV-2. IMPORTANCE Numerous research campaigns have addressed the vast majority of clinical and diagnostic specificity and sensitivity of various primer sets of SARS-CoV2 viral detection. Despite the impressive progress made to resolve the pandemic, there is still a need for continuous and active improvement of primers used for diagnosis in clinical practice. Our study significantly exceeds the scale of previously published research on the specificity and sensitivity of different primers comparing with different specimens and is the most comprehensive to date in terms of constant monitoring of primer sets of current usage. Henceforth, our results suggest that sputum samples sensitivity is the highest, followed by nasopharyngeal, saliva, and oropharyngeal samples. The CDC recommends the use of oropharyngeal specimens, leading to certain discrepancy between the guidelines set forth by the CDC and IDSA. We proved that the oropharyngeal samples demonstrated the lowest sensitivity for the detection of SARS-CoV-2.

SARS-CoV-2 and Variant Diagnostic Testing Approaches in the United States

Purpose of Review Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2 and its associated variants including Omicron (B.1.1.529), many options are available to diagnose infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents. Recent Findings Additional testing platforms continue to be developed, including those to detect specific variants, but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain has improved, and more established companies are providing materials to support these testing efforts. In the United States (U.S.), the need for rapid assay development and subsequent approval through the attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. Through these efforts, the U.S. has been able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges still remain due to the diversity of the performance characteristics of tests being utilized and newly discovered viral variants. Summary This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology, variants and antibody responses that are available to diagnose infection in the U.S.

Seroprevalence of Unidentified SARS-CoV-2 Infection in Hong Kong During 3 Pandemic Waves

IMPORTANCE

Seroprevalence studies inform the extent of infection and assist evaluation of mitigation strategies for the COVID-19 pandemic.

OBJECTIVE

To estimate the prevalence of unidentified SARS-CoV-2 infection in the general population of Hong Kong.

DESIGN, SETTING, AND PARTICIPANTS

A prospective cross-sectional study was conducted in Hong Kong after each major wave of the COVID-19 pandemic (April 21 to July 7, 2020; September 29 to November 23, 2020; and January 15 to April 18, 2021). Adults (age ≥18 years) who had not been diagnosed with COVID-19 were recruited during each period, and their sociodemographic information, symptoms, travel, contact, quarantine, and COVID-19 testing history were collected.

MAIN OUTCOMES AND MEASURES

The main outcome was prevalence of SARS-CoV-2 infection. SARS-CoV-2 IgG antibodies were detected by an enzyme-linked immunosorbent assay based on spike (S1/S2) protein, followed by confirmation with a commercial electrochemiluminescence immunoassay based on the receptor binding domain of spike protein.

RESULTS

The study enrolled 4198 participants (2539 [60%] female; median age, 50 years [IQR, 25 years]), including 903 (22%), 1046 (25%), and 2249 (53%) during April 21 to July 7, 2020; during September 29 to November 23, 2020; and during January 15 to April 18, 2021, respectively. The numbers of participants aged 18 to 39 years, 40 to 59 years, and 60 years or older were 1328 (32%), 1645 (39%), and 1225 (29%), respectively. Among the participants, 2444 (58%) stayed in Hong Kong since November 2019 and 2094 (50%) had negative SARS-CoV-2 RNA test results. Only 170 (4%) reported ever having contact with individuals with confirmed cases, and 5% had been isolated or quarantined. Most (2803 [67%]) did not recall any illnesses, whereas 737 (18%), 212 (5%), and 385 (9%) had experienced respiratory symptoms, gastrointestinal symptoms, or both, respectively, before testing. Six participants were confirmed to be positive for anti-SARS-CoV-2 IgG; the adjusted prevalence of unidentified infection was 0.15% (95% CI, 0.06%-0.32%). Extrapolating these findings to the whole population, there were fewer than 1.9 unidentified infections for every recorded confirmed case. The overall prevalence of SARS-CoV-2 infection in Hong Kong before the roll out of vaccination was less than 0.45%.

CONCLUSIONS AND RELEVANCE

In this cross-sectional study of participants from the general public in Hong Kong, the prevalence of unidentified SARS-CoV-2 infection was low after 3 major waves of the pandemic, suggesting the success of the pandemic mitigation by stringent isolation and quarantine policies even without complete city lockdown. More than 99.5% of the general population of Hong Kong remain naive to SARS-CoV-2, highlighting the urgent need to achieve high vaccine coverage.

Investigating SARS-CoV-2 persistent contamination in different indoor environments

Environmental contamination caused by COVID-19 patients could be a medium of transmission. Previous reports of SARS-CoV-2 in environmental surfaces were about short-term contamination. This study investigated SARS-CoV-2 RNA existence in room-temperature and low-temperature environments long after exposure (>28 days). A department store, where a COVID-19 outbreak was occurred in January 2020 (the epicenter of 43 COVID-19 patients), and a patient's apartment were included as room-temperature environments after being blocked for 57 days and 48 days, respectively. Seven cold storages and imported frozen foods inside were included as low-temperature environments (under -18 °C). Twenty food markets with potential contamination of imported frozen foods were also included to study the consecutive contamination. Information about temperature, relative humidity, and the number of days of environmental samples since the last exposure was collected and analyzed. In sum, 11,808 swab samples were collected before disinfection, of which 35 samples were positive. Persistent contamination of SARS-CoV-2 RNA was identified in the apartment (6/19), the department store (3/50), food packages in cold storages (23/1360), environmental surfaces of cold storages (2/345), and a package in the food market (1/10,034). Two positive samples were isolated from the bathroom of the apartment (66.7 %, 2/3), and doorknobs were proved with contamination in the apartment (40 %, 2/5) and cold storage (33.3 %, 1/3). The epidemiology information and environmental contamination results of an imported frozen food related COVID-19 case (138th COVID-19 patient in Tianjin) were analyzed. Based on the Ct values, the number of copies of two target genes was calculated by standard curves and linear regressions. In conclusion, SARS-CoV-2 RNA can be detected in room-temperature environments at least 57 days after the last exposure, much longer than previous reports. Based on the results of this study and previous studies, infectious SARS-CoV-2 could exist for at least 60 days on the surface of cold-chain food packages. Doorknobs and toilets (bathrooms) were important positions in COVID-19 control. High-risk populations of cold-chain-related logistic operations, such as porters, require strict prevention and high-level personal protection.

Diagnostic Testing for SARS-CoV-2 Infection

PURPOSE OF REVIEW

Given the rapid development of diagnostic approaches to test for and diagnose infection with SARS-CoV-2, many options are available to assess infection. Multiple established diagnostic companies are now providing testing platforms whereas initially, testing was being performed with simple PCR-based tests using standard laboratory reagents.

RECENT FINDINGS

Additional testing platforms continue to be developed but challenges with testing, including obtaining testing reagents and other related supplies, are frequently encountered. With time, the testing supply chain will improve and more companies will be providing materials to support these testing efforts. In the USA, the need for rapid assay development and subsequent approval through attainment of emergency use authorization (EUA) has superseded the traditional arduous diagnostic testing approval workflow mandated by the FDA. It is anticipated that the USA will be able to continue to significantly increase its testing capabilities to address this pandemic; however, challenges remain due to the diversity of the performance characteristics of tests being utilized.

SUMMARY

This review provides an overview of the current diagnostic testing landscape, with pertinent information related to SARS-CoV-2 virology and antibody responses, that is available to diagnose infection.

Evaluation of the clinical performance of a magnetic force-assisted electrochemical immunoassay for the detection of SARS-CoV-2 antigens

Rapid antigen (Ag) tests for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provide quick results, do not require specialized technical skills or infrastructure, and can be used as a point-of-care method to prevent the spread of coronavirus disease (COVID-19). The performance of a magnetic force-assisted electrochemical immunoassay-based test, namely the MARK-B COVID-19 Ag test (BBB, Sungnam, Republic of Korea), was evaluated using 170 nasopharyngeal swab specimens and compared to that of RT-PCR and commercial rapid Ag test (STANDARD Q COVID-19 Ag Test, SD Biosensor, Suwon-si, Republic of Korea). The overall sensitivity and specificity of the MARK-B test were 90.0% (95% CI 79.4%–96.2%) and 99.0% (95% CI 95.0%–99.9%), respectively, with a kappa coefficient of 0.908. The correlations between the electrical current values of MARK-B and the Ct values of RT-PCR were −0.898 (E gene, 95% CI −0.938 to −0.834) and −0.914 (RdRp gene, 95% CI −0.948 to −0.860), respectively. The limit of detection of the MARK-B was measured using the viral culture reference samples and found to be 1 x 10² pfu/mL. The magnetic force-assisted electrochemical immunoassay-based Ag test can be used to rapidly detect SARS-CoV-2 infections, and the corresponding fully automated portable device can provide easy readability and semi-quantitative results.

Comparative study of SmartAmp assay and reverse transcription-polymerase chain reaction by saliva specimen for the diagnosing COVID-19

INTRODUCTION

The pandemic of a novel coronavirus disease 2019 (COVID-19) caused by a severe acute respiratory coronavirus 2 (SARS-CoV-2) infection has been problematic worldwide. A new SARS-CoV-2 diagnostic test (SmartAmp) was licensed in Japan in July 2021. This method, which enables us to diagnose COVID-19 as well as a gene mutation on the virus, is promising to reduce medical costs and staff labor.

PATIENTS AND METHODS

To analyze the diagnostic accuracy of the SmartAmp assay for diagnosing COVID-19, we performed this retrospective study at our institute during April and May 2021. We compared the results of the SmartAmp assay and real-time reverse transcription-polymerase chain reaction (rRT-PCR) using a saliva sample from individuals suspected as having COVID-19.

RESULTS

Out of 70 samples tested, the SmartAmp assay had 50 (71%) positive and 20 (29%) negative results. Using rRT-PCR as a reference, the diagnostic accuracy displayed a sensitivity of 84%, a specificity of 95%, a positive predictive value of 97.7%, and a negative predictive value of 70.4%. On the other hand, false-negative cases were found in 7 (10%), and there was no significant difference of Ct-value between true positive and false negative cases (Mean Ct-value 25.2 vs. 27.5 cycles, p = 0.226 by Mann-Whitney U test).

CONCLUSION

The SmartAmp assay is a valuable method to diagnose COVID-19 rapidly. However, the negative predictive value is not high enough to diagnose the disease, so that negative results should be considered for rRT-PCR testing if patients are suspected of having COVID-19.

Adoption of improved neural network blade pattern recognition in prevention and control of corona virus disease-19 pandemic

To explore the adoption effect of improved neural network blade pattern in corona virus disease (COVID)-19, comparative analysis is implemented. First, the following hypotheses are proposed. I: in addition to the confirmed cases and deaths, people suspected of being infected are also involved in the spread of the epidemic. II: patients who have been cured may also develop secondary infections, so it is considered that there is still a link between cured cases and the spread of the epidemic. III: only the relevant data of the previous day is used to predict the epidemic prevention and control of the next day. Then, the epidemic data from February 1st to February 15th in X province were selected as the control. The combined neural network model is used for prevention and control prediction, and the prediction results of the traditional neural network model are compared. The results show that the predictions of the daily new cases by the five neural network models have little difference with the actual value, and the trend is basically consistent. However, there are still differences in some time nodes. The errors of neural network 1 on the 6th and network 3 on the 13th are large. The accuracy of the combined neural network prediction model is high, and there is little difference between the result and the actual value at each time node. The prediction of the cumulative number of diagnoses per day of the five neural network models is also analyzed, and the results are relatively ideal. In addition, the accuracy of the combined neural network prediction model is high, and the difference between the result and the actual value at each time node is relatively small. It is found that the standard deviations of neural networks 2 and 3 are relatively high through the comparison of the deviations. The deviation means of the five models were all relatively low, and the mean deviation and standard deviation of the combined neural network model are the lowest. It is found that the accuracy of prediction on the epidemic spread in this province is good by comparing the performance of each neural network model. Regarding various indicators, the prediction accuracy of the combined neural network model is higher than that of the other four models, and its performance is also the best. Finally, the MSE of the improved neural network model is lower compared with the traditional neural network model. Moreover, with the change of learning times, the change trend of MSE is constant (P < 0.05 for all). In short, the improved neural network blade model has better performance compared with that of the traditional neural network blade model. The prediction results of the epidemic situation are accurate, and the application effect is remarkable, so the proposed model is worthy of further promotion and application in the medical field.

Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19

Background

Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, first discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence.

Objective

We aimed to evaluate the diagnostic competency and efficiency with the Allplex™ 2019-nCoV Assay kit and the Dr. PCR 20 K COVID-19 Detection kit, designed based on the qRT-PCR and dPCR technologies, respectively.

Methods

A total of 30 negative and 20 COVID-19 positive specimens were assigned to the diagnostic test by using different COVID-19 diagnosis kits. Diagnostic accuracy was measured by statistical testing with sensitivity, specificity, and co-efficiency calculations.

Results

Comparing both diagnostic kits, we confirmed that the diagnostic results of 30 negative and 20 positive cases were the same pre-diagnostic results. The diagnostic statistics test results were perfectly matched with value (1). Cohen’s Kappa coefficient was demonstrated that the given kits in two different ways were “almost perfect” with value (1). In evaluating the detection capability, the dilutional linearity experiments substantiate that the Dr. PCR 20 K COVID-19 Detection kit could detect SARS-CoV-2 viral load at a concentration ten times lower than that of the Allplex™ 2019-nCoV Assay kit.

Conclusions

In this study, we propose that the dPCR diagnosis using LOAA dPCR could be a powerful method for COVID-19 point-of-care tests requiring immediate diagnosis in a limited time and space through the advantages of relatively low sample concentration and small equipment size compared to conventional qRT-PCR.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13258-021-01162-4.

Impact of COVID-19 Infection on the Outcome of Patients With Ischemic Stroke

Supplemental Digital Content is available in the text.

We evaluated whether stroke severity, functional outcome, and mortality are different in patients with ischemic stroke with or without coronavirus disease 2019 (COVID-19) infection.

A dried blood spot protocol for high throughput analysis of SARS-CoV-2 serology based on the Roche Elecsys anti-N assay

BACKGROUND

Since 2020 SARS-CoV-2 spreads pandemically, infecting more than 119 million people, causing >2·6 million fatalities. Symptoms of SARS-CoV-2 infection vary greatly, ranging from asymptomatic to fatal. Different populations react differently to the disease, making it very hard to track the spread of the infection in a population. Measuring specific anti-SARS-CoV-2 antibodies is an important tool to assess the spread of the infection or successful vaccinations. To achieve sufficient sample numbers, alternatives to venous blood sampling are needed not requiring medical personnel or cold-chains. Dried-blood-spots (DBS) on filter-cards have been used for different studies, but not routinely for serology.

METHODS

We developed a semi-automated protocol using self-sampled DBS for SARS-CoV-2 serology. It was validated in a cohort of matched DBS and venous-blood samples (n = 1710). Feasibility is demonstrated with two large serosurveys with 10247 company employees and a population cohort of 4465 participants.

FINDINGS

Sensitivity and specificity reached 99·20% and 98·65%, respectively. Providing written instructions and video tutorials, 99·87% (4465/4471) of the unsupervised home sampling DBS cards could be analysed.

INTERPRETATION

DBS-sampling is a valid and highly reliable tool for large scale serosurveys. We demonstrate feasibility and accuracy with a large validation cohort including unsupervised home sampling. This protocol might be of big importance for surveillance in resource-limited settings, providing low-cost highly accurate serology data.

FUNDING

Provided by Bavarian State Ministry of Science and the Arts, LMU University-Hospital; Helmholtz-Centre-Munich, German Ministry for Education and Research (project01KI20271); University of Bonn; University of Bielefeld; the Medical Biodefense Research Program of Bundeswehr-Medical-Service; Euroimmun, RocheDiagnostics provided discounted kits and machines.

SARS-CoV-2 PCR positivity rate and seroprevalence of related antibodies among a sample of patients in Cairo: Pre-wave 2 results of a screening program in a university hospital

BACKGROUND

Research has revealed that asymptomatic and pre-symptomatic infections are important contributors to the transmission of SARS-CoV-2 in populations. In Egypt, the true prevalence of infections is veiled due to the low number of screening tests. The aim of this study was to determine the SARS-CoV-2 PCR positivity rate as well the seroprevalence of the SARS-CoV-2 antibodies before the ultimate development of a second wave of the epidemic in Cairo, Egypt.

METHODS

Our study was carried out between May 5 and the end of October 2020. It included all patients requiring admission to Ain Shams University hospitals. An interview questionnaire was used to collect demographic and clinical data. Laboratory tests for all participants included RT-PCR and total antibody assay for SARS-CoV-2.

RESULTS

A total of 4,313 subjects were enrolled in our study, with females representing 56% of the sample. Adults and middle-aged individuals represented around 60% of the study sample. The positivity rate of SARS-CoV-2 PCR was 3.84% (95% CI 3.29-4.48), and the SARS-CoV-2 antibody seroprevalence was 29.82% (95% CI: 28.16-31.51). Males showed a higher risk for getting the COVID-19 infection, while middle-age group had significantly higher antibody seroprevalence rates.

CONCLUSION

SARS-CoV-2 infection imposes a high burden on the community as detected by high seroprevalence rates.

Evaluation of the AMP SARS-CoV-2 rapid antigen test in a hospital setting

OBJECTIVES

Quick and inexpensive SARS-CoV-2 screening and frontline testing are in growing demand. Our study aimed to evaluate the performance of the immunochromatographic AMP rapid antigen test (AMP RAT) compared to the gold-standard real-time reverse transcription PCR (rRT-PCR) in a hospital cohort.

METHODS

A total of 392 patients, who presented consecutively with COVID-19 symptoms in our emergency department, were included in this retrospective study. Two swabs were collected per patient: a nasopharyngeal for the RAT and a combined naso- and oropharyngeal for the rRT-PCR. A positive rRT-PCR (defined as cycle threshold (Ct) < 40) was found in 94 (24%) patients.

RESULTS

In our cohort with a median patient age of 70, overall sensitivity and specificity of the AMP RAT was 69.2% (58.8-78.3, 95% CI) and 99.7% (98.1-100.0, 95% CI), respectively. In patients with a Ct value < 25 and < 30, higher sensitivities of 100.0% (89.4-100.0, 95% CI) and 91.8% (81.9-97.3%, 95% CI) were observed.

CONCLUSIONS

The AMP RAT showed a high sensitivity in patients with a Ct value < 25 and < 30 and might be helpful for frontline testing whenever rRT-PCR is not readily available.

A single snapshot multiplex immunoassay platform utilizing dense test lines based on engineered beads

Co-circulation of coronavirus disease 2019 (COVID-19) and dengue fever has been reported. Accurate and timely multiplex diagnosis is required to prevent future pandemics. Here, we developed an innovative microfluidic chip that enables a snapshot multiplex immunoassay for timely on-site response and offers unprecedented multiplexing capability with an operating procedure similar to that of lateral flow assays. An open microchannel assembly of individually engineered microbeads was developed to construct nine high-density test lines, which can be imaged in a 1 mm² field-of-view. Thus, simultaneous detection of multiple antibodies would be achievable in a single high-resolution snapshot. Next, we developed a novel pixel intensity-based imaging process to distinguish effective and non-specific fluorescence signals, thereby improving the reliability of this fluorescence-based immunoassay. Finally, the chip specifically identified and classified random combinations of arbovirus (Zika, dengue, and chikungunya viruses) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies within 30 min. Therefore, we believe that this snapshot multiplex immunoassay chip is a powerful diagnostic tool to control current and future pandemics.

SARS-CoV-2 RNA Quantification Using Droplet Digital RT-PCR

Quantitative viral load assays have transformed our understanding of viral diseases. They hold similar potential to advance COVID-19 control and prevention, but SARS-CoV-2 viral load tests are not yet widely available. SARS-CoV-2 molecular diagnostic tests, which typically employ real-time RT-PCR, yield semiquantitative results only. Droplet digital RT-PCR (RT-ddPCR) offers an attractive platform for SARS-CoV-2 RNA quantification. Eight primer/probe sets originally developed for real-time RT-PCR–based SARS-CoV-2 diagnostic tests were evaluated for use in RT-ddPCR; three were identified as the most efficient, precise, and sensitive for RT-ddPCR–based SARS-CoV-2 RNA quantification. For example, the analytical efficiency for the E-Sarbeco primer/probe set was approximately 83%, whereas assay precision, measured as the coefficient of variation, was approximately 2% at 1000 input copies/reaction. Lower limits of quantification and detection for this primer/probe set were 18.6 and 4.4 input SARS-CoV-2 RNA copies/reaction, respectively. SARS-CoV-2 RNA viral loads in a convenience panel of 48 COVID-19–positive diagnostic specimens spanned a 6.2log₁₀ range, confirming substantial viral load variation in vivo. RT-ddPCR–derived SARS-CoV-2 E gene copy numbers were further calibrated against cycle threshold values from a commercial real-time RT-PCR diagnostic platform. This log-linear relationship can be used to mathematically derive SARS-CoV-2 RNA copy numbers from cycle threshold values, allowing the wealth of available diagnostic test data to be harnessed to address foundational questions in SARS-CoV-2 biology.

Seroprevalence Surveys for Anti-SARS-CoV-2 Antibody in Different Populations in Taiwan With Low Incidence of COVID-19 in 2020 and Severe Outbreaks of SARS in 2003

Accurate detection of anti-SARS-CoV-2 antibodies provides a more accurate estimation of incident cases, epidemic dynamics, and risk of community transmission. We conducted a cross-sectional seroprevalence study specifically targeting different populations to examine the performance of pandemic control in Taiwan: symptomatic patients with epidemiological risk and negative qRT-PCR test (Group P), frontline healthcare workers (Group H), healthy adult citizens (Group C), and participants with prior virologically-confirmed severe acute respiratory syndrome (SARS) infection in 2003 (Group S). The presence of anti-SARS-CoV-2 total and IgG antibodies in all participants were determined by Roche Elecsys® Anti-SARS-CoV-2 test and Abbott SARS-CoV-2 IgG assay, respectively. Sera that showed positive results by the two chemiluminescent immunoassays were further tested by three anti-SARS-CoV-2 lateral flow immunoassays and line immunoassay (MIKROGEN recomLine SARS-CoV-2 IgG). Between June 29 and July 25, 2020, sera of 2,115 participates, including 499 Group P participants, 464 Group H participants, 1,142 Group C participants, and 10 Group S participants, were tested. After excluding six false-positive samples, SARS-CoV-2 seroprevalence were 0.4, 0, and 0% in Groups P, H, and C, respectively. Cross-reactivity with SARS-CoV-2 antibodies was observed in 80.0% of recovered SARS participants. Our study showed that rigorous exclusion of false-positive testing results is imperative for an accurate estimate of seroprevalence in countries with previous SARS outbreak and low COVID-19 prevalence. The overall SARS-CoV-2 seroprevalence was extremely low among populations of different exposure risk of contracting SARS-CoV-2 in Taiwan, supporting the importance of integrated countermeasures in containing the spread of SARS-CoV-2 before effective COVID-19 vaccines available.

Safety and Effectiveness of an In-Hospital Screening Station for Coronavirus Disease 2019 in Response to the Massive Community Outbreak

Purpose

To evaluate the results of operating an in-hospital coronavirus disease 2019 screening station on an outpatient basis and to identify the effectiveness and necessity of such a screening station.

Patients and Methods

This cross-sectional study included 1345 individuals who were tested for COVID-19 using real-time reverse transcription polymerase chain reaction (RT-PCR) at an in-hospital screening station on an outpatient basis. The subjects were healthcare workers (HCWs) with suspected COVID-19 symptoms or exposure to patients with confirmed COVID-19, caregivers at the hospital for complete enumeration, and patients who were scheduled to be admitted to a nonrestricted area in the hospital or to visit for outpatient treatment, but had suspected COVID-19 symptoms. The subjects were divided and compared as follows: HCW versus non-HCW groups and RT-PCR positive versus negative groups.

Results

A total of 140 had symptoms, 291 wanted to be tested, and 664 were asymptomatic but were screened. Seven subjects had positive results for COVID-19. Compared with the non-HCWs, the HCWs were younger and had a lower rate of underlying medical conditions. In addition, there were more women, individuals with exposure to confirmed cases, and individuals with symptoms or those who just wanted to be tested. The frequency of all symptoms was high among the HCWs. The results of the logistic regression analysis showed that the HCWs were significantly associated with the presence of symptoms, having an odds ratio of 23.317 (confidence interval, 15.142-35.907L; P < 0.001). The positive group had a high rate of exposure to patients with confirmed COVID-19 and had more subjects with symptoms or those who wanted to be tested.

Conclusion

In-hospital screening stations are a relatively safe way to protect and support HCWs and to reduce and manage the spread of infection within the hospital effectively during an outbreak in the community.

High Seroprevalence of SARS-CoV-2 among Healthcare Workers in a North Italy Hospital

Background: Healthcare workers (HCWs) have been the key players in the fight against the coronavirus disease 2019 (COVID-19) pandemic. The aim of our study was to evaluate the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG anti-bodies. Methods: We conducted a cross-sectional study among workers of two hospitals and Territorial Medical and Administrative services in Northern Italy. From 8 May to 3 June 2020, 2252 subjects were tested. Seroprevalence and 95% confidence interval (CI) were calculated for all individuals who were stratified by job title, COVID-19 risk of exposure, direct contact with patients, unit ward, and intensity of care. Results: Median age was 50 years, and 72% of subjects were female. The overall seroprevalence was 17.11% [95% CI 15.55–18.67]. Around 20% of healthcare assistants were seropositive, followed by physicians and nurses (16.89% and 15.84%, respectively). HCWs with high risk of exposure to COVID-19 were more frequently seropositive (28.52%) with respect to those with medium and low risks (16.71% and 12.76%, respectively). Moreover, personnel in direct contact had higher prevalence (18.32%) compared to those who did not (10.66%). Furthermore, the IgG were more frequently detected among personnel of one hospital (19.43%). Conclusion: The high seroprevalence observed can be partially explained by the timing and the population seroprevalence; the study was conducted in an area with huge spread of the infection.

Increased antimicrobial resistance during the COVID-19 pandemic

In addition to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection itself, an increase in the incidence of antimicrobial resistance poses collateral damage to the current status of the COVID-19 (coronavirus disease 2019) pandemic. There has been a rapid increase in multidrug-resistant organisms (MDROs), including extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae, carbapenem-resistant New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales, Acinetobacter baumannii, methicillin-resistant Staphylococcus aureus (MRSA), pan-echinocandin-resistant Candida glabrata and multi-triazole-resistant Aspergillus fumigatus. The cause is multifactorial and is particularly related to high rates of antimicrobial agent utilisation in COVID-19 patients with a relatively low rate of co- or secondary infection. Appropriate prescription and optimised use of antimicrobials according to the principles of antimicrobial stewardship as well as quality diagnosis and aggressive infection control measures may help prevent the occurrence of MDROs during this pandemic.

Point-of-care test system for detection of immunoglobulin-G and -M against nucleocapsid protein and spike glycoprotein of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) epidemic continues to ravage the world. In epidemic control, dealing with a large number of samples is a huge challenge. In this study, a point-of-care test (POCT) system was successfully developed and applied for rapid and accurate detection of immunoglobulin-G and -M against nucleocapsid protein (anti-N IgG/IgM) and receptor-binding domain in spike glycoprotein (anti-S-RBD IgG/IgM) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Any one of the IgG/IgM found in a sample was identified as positive. The POCT system contains colloidal gold-based lateral flow immunoassay test strips, homemade portable reader, and certified reference materials, which detected anti-N and anti-S-RBD IgG/IgM objectively in serum within 15 min. Receiver operating characteristic curve analysis was used to determine the optimal cutoff values, sensitivity, and specificity. It exhibited equal to or better performances than four approved commercial kits. Results of the system and chemiluminescence immunoassay kit detecting 108 suspicious samples had high consistency with kappa coefficient at 0.804 (P < 0.001). Besides, the levels and alterations of the IgG/IgM in an inpatient were primarily investigated by the POCT system. Those results suggested the POCT system possess the potential to contribute to rapid and accurate serological diagnosis and epidemiological survey of COVID-19.

Point-of-care test system for detection of immunoglobulin-G and -M against nucleocapsid protein and spike glycoprotein of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) epidemic continues to ravage the world. In epidemic control, dealing with a large number of samples is a huge challenge. In this study, a point-of-care test (POCT) system was successfully developed and applied for rapid and accurate detection of immunoglobulin-G and -M against nucleocapsid protein (anti-N IgG/IgM) and receptor-binding domain in spike glycoprotein (anti-S-RBD IgG/IgM) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Any one of the IgG/IgM found in a sample was identified as positive. The POCT system contains colloidal gold-based lateral flow immunoassay test strips, homemade portable reader, and certified reference materials, which detected anti-N and anti-S-RBD IgG/IgM objectively in serum within 15 min. Receiver operating characteristic curve analysis was used to determine the optimal cutoff values, sensitivity, and specificity. It exhibited equal to or better performances than four approved commercial kits. Results of the system and chemiluminescence immunoassay kit detecting 108 suspicious samples had high consistency with kappa coefficient at 0.804 (P < 0.001). Besides, the levels and alterations of the IgG/IgM in an inpatient were primarily investigated by the POCT system. Those results suggested the POCT system possess the potential to contribute to rapid and accurate serological diagnosis and epidemiological survey of COVID-19.

Detection of SARS-CoV-2-specific antibodies via rapid diagnostic immunoassays in COVID-19 patients

BACKGROUND

Efficient monitoring and control of coronavirus disease 2019 (COVID-19) require access to diagnostic tests, and serological diagnostic testing is desirable. In the current study, antibodies were investigated in patients recently diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

METHODS

Cross-sectional data were obtained from 245 patients in whom SARS-CoV-2 infection had been confirmed via real-time reverse transcriptase-polymerase chain reaction between March and October 2020. Serum samples were acquired between 2 and 60 days following the onset of COVID-19 symptoms or the first detection of SARS-CoV-2 in asymptomatic patients. All specimens were tested simultaneously using an IgM/IgG rapid diagnostic test (RDT), IgG nucleocapsid protein-based chemiluminescent microparticle immunoassay (CMIA), IgG, and IgA spike protein-based enzyme-linked immunosorbent assays (ELISAs). Blood donor samples obtained in 2018 were used as negative controls.

RESULTS

The sensitivity and specificity of the RDT IgG were compared with the IgG immunoassays as standards. The RDT IgG exhibited 97.5% sensitivity and 89.4% specificity compared with a CMIA IgG, 98.4% sensitivity, and 78.8% specificity compared with an ELISA IgG. IgM, IgG, and IgA seropositivity rates were low between 1 and 2 weeks after COVID-19 symptom onset or the detection of SARS-CoV-2 RNA. IgM seropositivity rate began decreasing after 4 weeks, whereas IgG and IgA seropositivity rate remained at appreciable levels over the 8-week study period. No cross-reactivity with seasonal coronaviruses was detected.

CONCLUSIONS

IgG RDT alone or combined with molecular diagnostic tests may be useful for identifying recent SARS-CoV-2 infection.

Development and validation of viral load assays to quantitate SARS-CoV-2

SARS-CoV-2 has infected more than 30 million persons throughout the world. A subset of patients suffer serious consequences that require hospitalization and ventilator support. Current tests for SARS-CoV-2 generate qualitative results and are vital to make a diagnosis of the infection. However, they are not helpful to follow changes in viral loads after diagnosis. The ability to quantitatively assess viral levels is necessary to determine the effectiveness of therapy with anti-viral or immune agents. Viral load analysis is also necessary to determine the replicative potential of strains with different mutations, emergence of resistance to anti-viral agents and the stability of viral nucleic acid and degree of RT-PCR inhibition in different types of collection media. Quantitative viral load analysis in body fluids, plasma and tissue may be helpful to determine the effects of the infection in various organ systems. To address these needs, we developed two assays to quantitate SARS-CoV-2. The assays target either the S or E genes in the virus, produce comparable viral load results, are highly sensitive and specific and have a wide range of quantitation. We believe that these assays will be helpful to manage the clinical course of infected patients and may also help to better understand the biology of infection with SARS-CoV-2.

Development of a portable MIP-based electrochemical sensor for detection of SARS-CoV-2 antigen

The current COVID-19 pandemic caused by SARS-CoV-2 coronavirus is expanding around the globe. Hence, accurate and cheap portable sensors are crucially important for the clinical diagnosis of COVID-19. Molecularly imprinted polymers (MIPs) as robust synthetic molecular recognition materials with antibody-like ability to bind and discriminate between molecules can perfectly serve in building selective elements in such sensors. Herein, we report for the first time on the development of a MIP-based electrochemical sensor for detection of SARS-CoV-2 nucleoprotein (ncovNP). A key element of the sensor is a disposable sensor chip - thin film electrode - interfaced with a MIP-endowed selectivity for ncovNP and connected with a portable potentiostat. The resulting ncovNP sensor showed a linear response to ncovNP in the lysis buffer up to 111 fM with a detection and quantification limit of 15 fM and 50 fM, respectively. Notably, the sensor was capable of signaling ncovNP presence in nasopharyngeal swab samples of COVID-19 positive patients. The presented strategy unlocks a new route for the development of rapid COVID-19 diagnostic tools.