Molecular Diagnosis of COVID-19: Challenges and Research Needs

Wastewater-Based Epidemiology for Community Monitoring of SARS-CoV-2: Progress and Challenges

Wastewater-based epidemiology (WBE) is useful for the surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in communities, complementing clinical diagnostic testing of individuals. In this Review, we summarize recent progress and highlight remaining challenges in monitoring SARS-CoV-2 RNA in wastewater systems for community and environmental surveillance. Very low concentrations of viral particles and RNA present in the complicated wastewater and sewage sample matrix require efficient sample processing and sensitive detection. We discuss advantages and limitations of available methods for wastewater sample processing, including collection, separation, enrichment, RNA extraction, and purification. Efficient extraction of the viral RNA and removal of interfering sample matrices are critical to the subsequent reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for sensitive detection of SARS-CoV-2 in wastewater. We emphasize the importance of implementing appropriate controls and method validation, which include the use of surrogate viruses for assessing extraction efficiency and normalization against measurable chemical and biological components in wastewater. Critical analysis of the published studies reveals imperative research needs for the development, validation, and standardization of robust and sensitive methods for quantitative detection of viral RNA and proteins in wastewater for WBE.

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.

CRISPR/Cas-powered nanobiosensors for diagnostics

CRISPR diagnostics (CRISPR-Dx) offer a wide range of enhancements compared to traditional nanobiosensors by taking advantage of the excellent trans-cleavage activity of the CRISPR/Cas systems. However, the single-stranded DNA/RNA reporters of the current CRISPR-Dx suffer from poor stability and limited sensitivity, which make their application in complex biological environments difficult. In comparison, nanomaterials, especially metal nanoparticles, exhibits robust stability and desirable optical and electrocatalytical properties, which make them ideal as reporter molecules. Therefore, biosensing research is moving towards the use of the trans-cleavage activity of CRISPR/Cas effectors on metal nanoparticles and apply the new phenomenon to develop novel nanobiosensors to target various targets such as viral infections, genetic mutations and tumor biomarkers, by using different sensing methods, including, but not limited to fluorescence, luminescence resonance, colorimetric and electrochemical signal readout. In this review, we explore some of the most recent advances in the field of CRISPR-powered nanotechnological biosensors. Demonstrating high accuracy, sensitivity, selectivity and versatility, nanobiosensors along with CRISPR/Cas technology offer tremendous potential for next-generation diagnostics of multiple targets, especially at the point of care and without any target amplification.

2D MOF-Based Photoelectrochemical Aptasensor for SARS-CoV-2 Spike Glycoprotein Detection

A reliable and sensitive detection approach for SARS-CoV 2 is essential for timely infection diagnosis and transmission prevention. Here, a two-dimensional (2D) metal-organic framework (MOF)-based photoelectrochemical (PEC) aptasensor with high sensitivity and stability for SARS-CoV 2 spike glycoprotein (S protein) detection was developed. The PEC aptasensor was constructed by a plasmon-enhanced photoactive material (namely, Au NPs/Yb-TCPP) with a specific DNA aptamer against S protein. The Au NPs/Yb-TCPP fabricated by in situ growth of Au NPs on the surface of 2D Yb-TCPP nanosheets showed a high electron-hole (e-h) separation efficiency due to the enhancement effect of plasmon, resulting in excellent photoelectric performance. The modified DNA aptamer on the surface of Au NPs/Yb-TCPP can bind with S protein with high selectivity, thus decreasing the photocurrent of the system due to the high steric hindrance and low conductivity of the S protein. The established PEC aptasensor demonstrated a highly sensitive detection for S protein with a linear response range of 0.5-8 μg/mL with a detection limit of 72 ng/mL. This work presented a promising way for the detection of SARS-CoV 2, which may conduce to the impetus of clinic diagnostics.

Diagnostic value of chest computed tomography imaging for COVID-19 based on reverse transcription-polymerase chain reaction: a meta-analysis

Background

The computed tomography (CT) diagnostic value of COVID-19 is controversial. We summarized the value of chest CT in the diagnosis of COVID-19 through a meta-analysis based on the reference standard.

Methods

All Chinese and English studies related to the diagnostic value of CT for COVID-19 across multiple publication platforms, was searched for and collected. Studies quality evaluation and plotting the risk of bias were estimated. A heterogeneity test and meta-analysis, including plotting sensitivity (Sen), specificity (Spe) forest plots, pooled positive likelihood ratio (+LR), negative likelihood ratio (-LR), dignostic odds ratio (DOR) values and 95% confidence interval (CI), were estimated. If there was a threshold effect, summary receiver operating characteristic curves (SROC) was further plotted. Pooled area under the receiver operating characteristic curve (AUROC) and 95% CI were also calculated.

Results

Twenty diagnostic studies that represented a total of 9004 patients were included from 20 pieces of literatures after assessing all the aggregated studies. The reason for heterogeneity was caused by the threshold effect, so the AUROC = 0.91 (95% CI: 0.89–0.94) for chest CT of COVID-19. Pooled sensitivity, specificity, +LR, -LR from 20 studies were 0.91 (95% CI: 0.88–0.94), 0.71 (95% CI: 0.59–0.80), 3.1(95% CI: 2.2–4.4), 0.12 (95% CI: 0.09–0.17), separately. The I² was 85.6% (P = 0.001) by Q-test.

Conclusions

The results of this study showed that CT diagnosis of COVID-19 was close to the reference standard. The diagnostic value of chest CT may be further enhanced if there is a unified COVID-19 diagnostic standard. However, please pay attention to rational use of CT.

Graphic Abstract

Sensitive and rapid on-site detection of SARS-CoV-2 using a gold nanoparticle-based high-throughput platform coupled with CRISPR/Cas12-assisted RT-LAMP

The outbreak of corona virus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a global pandemic. The high infectivity of SARS-CoV-2 highlights the need for sensitive, rapid and on-site diagnostic assays of SARS-CoV-2 with high-throughput testing capability for large-scale population screening. The current detection methods in clinical application need to operate in centralized labs. Though some on-site detection methods have been developed, few tests could be performed for high-throughput analysis. We here developed a gold nanoparticle-based visual assay that combines with CRISPR/Cas12a-assisted RT-LAMP, which is called Cas12a-assisted RT-LAMP/AuNP (CLAP) assay for rapid and sensitive detection of SARS-CoV-2. In optimal condition, we could detect down to 4 copies/μL of SARS-CoV-2 RNA in 40 min. by naked eye. The sequence-specific recognition character of CRISPR/Cas12a enables CLAP a superior specificity. More importantly, the CLAP is easy for operation that can be extended to high-throughput test by using a common microplate reader. The CLAP assay holds a great potential to be applied in airports, railway stations, or low-resource settings for screening of suspected people. To the best of our knowledge, this is the first AuNP-based colorimetric assay coupled with Cas12 and RT-LAMP for on-site diagnosis of COVID-19. We expect CLAP assay will improve the current COVID-19 screening efforts, and make contribution for control and mitigation of the pandemic.

Sensitive and rapid on-site detection of SARS-CoV-2 using a gold nanoparticle-based high-throughput platform coupled with CRISPR/Cas12-assisted RT-LAMP

The outbreak of corona virus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a global pandemic. The high infectivity of SARS-CoV-2 highlights the need for sensitive, rapid and on-site diagnostic assays of SARS-CoV-2 with high-throughput testing capability for large-scale population screening. The current detection methods in clinical application need to operate in centralized labs. Though some on-site detection methods have been developed, few tests could be performed for high-throughput analysis. We here developed a gold nanoparticle-based visual assay that combines with CRISPR/Cas12a-assisted RT-LAMP, which is called Cas12a-assisted RT-LAMP/AuNP (CLAP) assay for rapid and sensitive detection of SARS-CoV-2. In optimal condition, we could detect down to 4 copies/μL of SARS-CoV-2 RNA in 40 min. by naked eye. The sequence-specific recognition character of CRISPR/Cas12a enables CLAP a superior specificity. More importantly, the CLAP is easy for operation that can be extended to high-throughput test by using a common microplate reader. The CLAP assay holds a great potential to be applied in airports, railway stations, or low-resource settings for screening of suspected people. To the best of our knowledge, this is the first AuNP-based colorimetric assay coupled with Cas12 and RT-LAMP for on-site diagnosis of COVID-19. We expect CLAP assay will improve the current COVID-19 screening efforts, and make contribution for control and mitigation of the pandemic.

SenSARS: A Low-Cost Portable Electrochemical System for Ultra-Sensitive, Near Real-Time, Diagnostics of SARS-CoV-2 Infections

A critical path to solving the SARS-CoV-2 pandemic, without further socioeconomic impact, is to stop its spread. For this to happen, pre- or asymptomatic individuals infected with the virus need to be detected and isolated opportunely. Unfortunately, there are no current ubiquitous (i.e., ultra-sensitive, cheap, and widely available) rapid testing tools capable of early detection of SARS-CoV-2 infections. In this article, we introduce an accurate, portable, and low-cost medical device and bio-nanosensing electrode dubbed SenSARS and its experimental validation. SenSARS' device measures the electrochemical impedance spectra of a disposable bio-modified screen-printed carbon-based working electrode (SPCE) to the changes in the concentration of SARS-CoV-2 antigen molecules ("S" spike proteins) contained within a sub-microliter fluid sample deposited on its surface. SenSARS offers real-time diagnostics and viral load tracking capabilities. Positive and negative control tests were performed in phosphate-buffered saline (PBS) at different concentrations (between 1 and 50 fg/mL) of SARS-CoV-2(S), Epstein-Barr virus (EBV) glycoprotein gp350, and Influenza H1N1 M1 recombinant viral proteins. We demonstrate that SenSARS is easy to use, with a portable and lightweight (< 200 g) instrument and disposable test electrodes ( Collapse

Key Words

• Biosensors
• SARS-CoV-2
• electrochemical biosensors
• electrochemical impedance spectroscopy (EIS)

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MESH Headings Collapse

Grants

• Colombian Ministry of Science, Innovation, and Technology, through the Mincienciatón health emergency

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Affiliation(s)

Sammy A. Perdomo Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Viviana Ortega Facultad de Ciencias Naturales y ExactasUniversidad del ValleCali760032Colombia
Andres Jaramillo-Botero Chemistry and Chemical Engineering DivisionCalifornia Institute of TechnologyPasadenaCA91125USA Omicas ProgramPontificia Universidad JaverianaCali760031Colombia
Nelson Mancilla Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
José Hernando Mosquera-DeLaCruz Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Drochss Pettry Valencia Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Mauricio Quimbaya Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Juan David Contreras Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Gabriel Esteban Velez Facultad de Ciencias NaturalesUniversidad ICESICali760031Colombia
Oscar A. Loaiza Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Adriana Gómez Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia
Jhonattan de la Roche Facultad de Ingeniería y CienciasPontificia Universidad JaverianaCali760031Colombia

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Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size

Rapid and accurate detection of nucleic acids is of paramount importance in many fields, including medical diagnosis, gene therapy and virus identification. In this work, by taking advantage of two DNA hybridization probes, one of which was immobilized on the surface of gold nanoparticles, while the other was free in solution, detection of short length nucleic acids was successfully achieved using a large size (20 nm tip diameter) polyethylene terephythalate (PET) nanopore. The sensor was sensitive and selective: DNA samples with concentrations at as low as 0.5 nM could be detected within minutes and the number of mismatches can be discerned from the translocation frequency. Furthermore, the nanopore can be repeatedly used many times. Our developed large-size nanopore sensing platform offers the potential for fieldable/point-of-care diagnostic applications.

CRISPR/Cas-New Molecular Scissors in Diagnostics and Therapeutics of COVID-19

The current pandemic of COVID-19, with its climbing number of cases and deaths, has us searching for tools for rapid, reliable, and affordable methods of detection on one hand, and novel, improved therapeutic strategies on the other. The currently employed RT-PCR method, despite its all-encompassing utility, has its shortcomings. Newer diagnostic tools, based on the Clustered Regularly Interspaced Short Palindromic Repeats/Cas(CRISPR-Cas) system, with its better diagnostic accuracy measures, have come up to fill that void. These assay platforms are expected to slowly take up the place of COVID-19 diagnostics. Further, the current therapeutic options focus mainly on counteracting the viral proteins and components and their entry into host cells. The CRISPR-based system, especially through the RNA-guided Cas13 approach, can identify the genomic characteristics of SARS-CoV-2 and provide a novel inhibition strategy for coronaviruses. In this mini-review, we have discussed the available and upcoming CRISPR-based diagnostic assays and the potential of the CRISPR/Cas system as a therapeutic or prevention strategy in COVID-19. CRISPR-Cas system shows promise in both diagnostics as well as therapeutics and may as well change the face of molecular diagnosis and precision medicine.

Challenges to detect SARS-CoV-2 on environmental media, the need and strategies to implement the detection methodologies in wastewaters

Understanding risks, putting in place preventative methods to seamlessly continue daily activities are essential tools to fight a pandemic. All social, commercial and leisure activities have an impact on the environmental media. Therefore, to accurately predict the fate and behavior of viruses in the environment, it is necessary to understand and analyze available detection methods, possible transmission pathways and preventative techniques. The aim of this review is to critically analyze and summarize the research done regarding SARS-COV-2 virus detection, focusing on sampling and laboratory detection methods in environmental media. Special attention will be given to wastewater and sewage sludge. This review has summarized the survival of the virus on surfaces to estimate the risk carried by different environmental media (water, wastewater, air and soil) in order to explain which communities are under higher risk. The critical analysis concludes that the detection of SARS-CoV-2 with current technologies and sampling strategies would reveal the presence of the virus. This information could be used to design systematic sampling points throughout the sewage systems when available, taking into account peak flows and more importantly economic factors on when to sample. Such approaches will provide clues for potential future viral outbreak, saving financial resources by reducing testing necessities for viral detection, hence contributing for more appropriate confinement policies by governments and could be further used to define more precisely post-pandemic or additional waves measures if/ when needed.

False-Negative RT-PCR Findings and Double Mutant Variant as Factors of an Overwhelming Second Wave of COVID-19 in India: an Emerging Global Health Disaster

RT-PCR is considered to be the standard gold diagnostic test for detecting COVID-19 causing SARS-CoV-2. Recent reports and recent pieces of evidence from scientific literature, however, tell a different story. There have been speculations of SARS-CoV-2 escaping the RT-PCR because of the series of mutations it has gone through. It is possible that host-dependent RNA editing and high person-to-person transmission have equipped the virus with mutations enabling it to spread faster and even evade the RT-PCR. Added to this is burnout among healthcare workers and technicians handling the RT-PCR machines and sampling. All of these factors may be working in unison to result in the deluge of false-negative cases India is facing during the second COVID-19 wave. The mutant strains are spreading to other parts, posing challenges to the whole world. These circumstances warrant supplementary diagnostic tests such as serological and radiological findings to deal with cases of high clinical suspicion. Even one misdiagnosed COVID-19 patient poses a risk to hundreds of others in the vicinity. Healthcare workers' burnout also has to be dealt with. Erroneous staff should be re-trained.

MALDI-ToF protein profiling as a potential rapid diagnostic platform for COVID-19

More than a year after the COVID-19 pandemic was declared, the need still exists for accurate, rapid, inexpensive and non-invasive diagnostic methods that yield high specificity and sensitivity towards the current and newly emerging SARS-CoV-2 strains. Compared to the nasopharyngeal swabs, several studies have established saliva as a more amenable specimen type for early detection of SARS-CoV-2. Considering the limitations and high demand for COVID-19 testing, we employed MALDI-ToF mass spectrometry in the analysis of 60 gargle samples from human donors and compared the resultant spectra against COVID-19 status. Several standards, including isolated human serum immunoglobulins, and controls, such as pre-COVID-19 saliva and heat inactivated SARS-CoV-2 virus, were simultaneously analyzed to provide a relative view of the saliva and viral proteome as they would appear in this workflow. Five potential biomarker peaks were established that demonstrated high concordance with COVID-19 positive individuals. Overall, the agreement of these results with RT-qPCR testing on nasopharyngeal swabs was ≥90% for the studied cohort, which consisted of young and largely asymptomatic student athletes. From a clinical standpoint, the results from this pilot study suggest that MALDI-ToF could be used to develop a relatively rapid and inexpensive COVID-19 assay.

SARS-CoV-2 Point-of-Care (POC) Diagnosis Based on Commercial Pregnancy Test Strips and a Palm-Size Microfluidic Device

Coronavirus diseases such as the coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), pose serious threats. Portable and accurate nucleic acid detection is still an urgent need to achieve on-site virus screening and timely infection control. Herein, we have developed an on-site, semiautomatic detection system, aiming at simultaneously overcoming the shortcomings suffered by various commercially available assays, such as low accuracy, poor portability, instrument dependency, and labor intensity. Ultrasensitive isothermal amplification [i.e., reverse transcription loop-mediated isothermal amplification (RT-LAMP)] was applied to generate intensified SARS-CoV-2 RNA signals, which were then transduced to portable commercial pregnancy test strips (PTSs) via ultraspecific human chorionic gonadotropin (hCG)-conjugated toehold-mediated strand exchange (TMSE) probes (hCG-P). The entire detection was integrated into a four-channel, palm-size microfluidic device, named the microfluidic point-of-care (POC) diagnosis system based on the PTS (MPSP) detection system. It provides rapid, cost-effective, and sensitive detection, of which the lowest concentration of detection was 0.5 copy/μL of SARS-CoV-2 RNA, regardless of the presence of other similar viruses, even highly similar severe acute respiratory syndrome coronavirus (SARS-CoV). The successful detection of the authentic samples from different resources evaluated the practical application. The commercial PTS provides a colorimetric visible signal, which is instrument- and optimization-free. Therefore, this MPSP system can be immediately used for SARS-CoV-2 emergency detection, and it is worthy of further optimization to achieve full automation and detection for other infectious diseases.

Direct Comparison of N-Glycans and Their Isomers Derived from Spike Glycoprotein 1 of MERS-CoV, SARS-CoV-1, and SARS-CoV-2

The emergence of COVID-19 pandemic has engaged the scientific community around the globe in the rapid development of effective therapeutics and vaccines. Owing to its crucial role in the invasion of the host cell, spike (S) glycoprotein is one of the major targets in these studies. The S1 subunit of the S protein (S1 protein) accommodates the receptor-binding domain, which enables the initial binding of the virus to the host cell. Being a heavily glycosylated protein, numerous studies have investigated its glycan composition. However, none of the studies have explored the isomeric glycan distribution of this protein. Furthermore, this isomeric glycan distribution has never been compared to that in S1 proteins of other coronaviruses, severe acute respiratory syndrome coronavirus 1 and Middle East respiratory syndrome coronavirus, which were responsible for past epidemics. This study explores the uncharted territory of the isomeric glycan distribution in the coronaviruses' S1 protein using liquid chromatography coupled to tandem mass spectrometry. We believe that our data would facilitate future investigations to study the role of isomeric glycans in coronavirus viral pathogenesis.

Molecular diagnostics in the era of COVID-19

As the COVID-19 pandemic continues to escalate globally and acquires new mutations, accurate diagnostic technologies continue to play a vital role in controlling and understanding the epidemiology of this disease. A plethora of technologies have enabled the diagnosis of individuals, informed clinical management, aided population-wide screening to determine transmission rates and identified cases within the wider community and high-risk settings. This review explores the application of molecular diagnostics technologies in controlling the spread of COVID-19, and the key factors that affect the sensitivity and specificity of the tests used.

Association between SARS-CoV-2 exposure and antibody status among healthcare workers in two London hospitals: a cross-sectional study

BACKGROUND

Patient-facing (frontline) health-care workers (HCWs) are at high risk of repeated exposure to SARS-CoV-2.

AIM

We sought to determine the association between levels of frontline exposure and likelihood of SARS-CoV-2 seropositivity amongst HCW.

METHODS

A cross-sectional study was undertaken using purposefully collected data from HCWs at two hospitals in London, United Kingdom (UK) over eight weeks in May-June 2020. Information on sociodemographic, clinical and occupational characteristics was collected using an anonymised questionnaire. Serology was performed using split SARS-CoV-2 IgM/IgG lateral flow immunoassays. Exposure risk was categorised into five pre-defined ordered grades. Multivariable logistic regression was used to examine the association between being frontline and SARS-CoV-2 seropositivity after controlling for other risks of infection.

FINDINGS

615 HCWs participated in the study. 250/615 (40.7%) were SARS-CoV-2 IgM and/or IgG positive. After controlling for other exposures, there was non-significant evidence of a modest association between being a frontline HCW (any level) and SARS-CoV-2 seropositivity compared to non-frontline status (OR 1.39, 95% CI 0.84-2.30, P=0.200). There was 15% increase in the odds of SARS-CoV-2 seropositivity for each step along the frontline exposure gradient (OR 1.15, 95% CI 1.00-1.32, P=0.043).

CONCLUSION

We found a high SARS-CoV-2 IgM/IgG seropositivity with modest evidence for a dose-response association between increasing levels of frontline exposure risk and seropositivity. Even in well-resourced hospital settings, appropriate use of personal protective equipment, in addition to other transmission-based precautions for inpatient care of SARS-CoV-2 patients could reduce the risk of hospital-acquired SARS-CoV-2 infection among frontline HCW.

Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants

Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.

Coronavirus in water media: Analysis, fate, disinfection and epidemiological applications

Considerable attention has been recently given to possible transmission of SARS-CoV-2 via water media. This review addresses this issue and examines the fate of coronaviruses (CoVs) in water systems, with particular attention to the recently available information on the novel SARS-CoV-2. The methods for the determination of viable virus particles and quantification of CoVs and, in particular, of SARS-CoV-2 in water and wastewater are discussed with particular regard to the methods of concentration and to the emerging methods of detection. The analysis of the environmental stability of CoVs, with particular regard of SARS-CoV-2, and the efficacy of the disinfection methods are extensively reviewed as well. This information provides a broad view of the state-of-the-art for researchers involved in the investigation of CoVs in aquatic systems, and poses the basis for further analyses and discussions on the risk associated to the presence of SARS-CoV-2 in water media. The examined data indicates that detection of the virus in wastewater and natural water bodies provides a potentially powerful tool for quantitative microbiological risk assessment (QMRA) and for wastewater-based epidemiology (WBE) for the evaluation of the level of circulation of the virus in a population. Assays of the viable virions in water media provide information on the integrity, capability of replication (in suitable host species) and on the potential infectivity. Challenges and critical issues relevant to the detection of coronaviruses in different water matrixes with both direct and surrogate methods as well as in the implementation of epidemiological tools are presented and critically discussed.

A Novel Saliva RT-LAMP Workflow for Rapid Identification of COVID-19 Cases and Restraining Viral Spread

Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP (reverse transcription loop-mediated isothermal amplification) workflow for viral detection in saliva, and to provide more information regarding its potential in curbing COVID-19 transmission. Clinical and contrived specimens were used to optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate the clinical performance of the test and to characterize saliva based on age, gender and time from onset of symptoms. Our workflow achieved an overall sensitivity of 77.2% (n = 90), with 93.2% sensitivity, 97% specificity, and 0.895 Kappa for specimens containing >102 copies/μL (n = 77). Further analyses in saliva showed that viral load peaks in the first days of symptoms and decreases afterwards, and that viral load is ~10 times lower in females compared to males, and declines following symptom onset. NOP RT-PCR data did not yield relevant associations. This work suggests that saliva reflects the transmission dynamics better than NOP specimens, and reveals gender differences that may reflect higher transmission by males. This saliva RT-LAMP workflow can be applied to track viral spread and, to maximize detection, testing should be performed immediately after symptoms are presented, especially in females.

Current state of diagnostic, screening and surveillance testing methods for COVID-19 from an analytical chemistry point of view

Since December 2019, we have been in the battlefield with a new threat to the humanity known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this review, we describe the four main methods used for diagnosis, screening and/or surveillance of SARS-CoV-2: Real-time reverse transcription polymerase chain reaction (RT-PCR); chest computed tomography (CT); and different complementary alternatives developed in order to obtain rapid results, antigen and antibody detection. All of them compare the highlighting advantages and disadvantages from an analytical point of view. The gold standard method in terms of sensitivity and specificity is the RT-PCR. The different modifications propose to make it more rapid and applicable at point of care (POC) are also presented and discussed. CT images are limited to central hospitals. However, being combined with RT-PCR is the most robust and accurate way to confirm COVID-19 infection. Antibody tests, although unable to provide reliable results on the status of the infection, are suitable for carrying out maximum screening of the population in order to know the immune capacity. More recently, antigen tests, less sensitive than RT-PCR, have been authorized to determine in a quicker way whether the patient is infected at the time of analysis and without the need of specific instruments.

Sensitive quantitative detection of SARS-CoV-2 in clinical samples using digital warm-start CRISPR assay

Quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is crucial for early diagnosis and timely medical treatment of coronavirus disease 2019. Here, we describe a digital warm-start CRISPR (dWS-CRISPR) assay for sensitive quantitative detection of SARS-CoV-2 in clinical samples. The dWS-CRISPR assay is initiated at above 50 °C and overcomes undesired premature target amplification at room temperature, enabling accurate and reliable digital quantification of SARS-CoV-2. By targeting SARS-CoV-2's nucleoprotein gene, the dWS-CRISPR assay is able to detect down to 5 copies/μl SARS-CoV-2 RNA in the chip. It is clinically validated by quantitatively determining 32 clinical swab samples and three clinical saliva samples. Moreover, it has been demonstrated to directly detect SARS-CoV-2 in heat-treated saliva samples without RNA extraction. Thus, the dWS-CRISPR method, as a sensitive and reliable CRISPR assay, facilitates accurate SARS-CoV-2 detection toward digitized quantification.

Can a field molecular diagnosis be accurate? A performance evaluation of colorimetric RT-LAMP for the detection of SARS-CoV-2 in a hospital setting

SARS-CoV-2 currently represents a serious global public health problem. Non-pharmaceutical intervention measures (NPIs) have been widely adopted, and the testing strategy since the beginning of the infection is the most effective tool for tracking, isolating, and minimizing transmission. The high operating costs and the need for sophisticated instrumentation related to gold standard diagnostic for COVID-19, Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR), have highlighted the urgency and importance of developing and applying new diagnostic techniques, especially in places with scarce resources. Thus, alternative molecular tests, such as Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP), based on isothermal amplification have been used to detect SARS-CoV-2 using different protocols. The potential for field application of RT-LAMP is due to the lower cost and time and not requiring high-cost instrumentation. Here, we evaluate the colorimetric RT-LAMP to detect SARS-CoV-2 in a hospital environment and correlate its performance with tests performed in a reference laboratory. The analysis performed at the hospital showed high sensitivity (88.89%), specificity (98.55%), accuracy (95.83%), and a Cohen's kappa of 0.895. However, we achieved 100% of agreement when comparing the RT-LAMP results with the gold standard (qRT-PCR) results for samples with Ct < 30 in the hospital-based test. In addition, a similar performance was found in the field compared to the reference laboratory, corroborating the proposal to apply the test directly at point-of-care.

Translating daily COVID-19 screening into a simple glucose test: a proof of concept study

Home testing is an attractive emerging strategy to combat the COVID-19 pandemic and prevent overloading of healthcare resources through at-home isolation, screening and monitoring of symptoms. However, current diagnostic technologies of SARS-CoV-2 still suffer from some drawbacks because of the tradeoffs between sensitivity, usability and costs, making the test unaffordable to most users at home. To address these limitations, taking advantage of clustered regularly interspaced short palindromic repeats (CRISPRs) and a portable glucose meter (PGM), we present a proof-of-concept demonstration of a target-responsive CRISPR-PGM system for translating SARS-CoV-2 detection into a glucose test. Using this system, a specific N gene, N protein, and pseudo-viruses of SARS-CoV-2 have been detected quantitatively with a PGM. Given the facile integration of various bioreceptors into the CRISPR-PGM system, the proposed method provides a starting point to provide patients with a single-device solution that can quantitatively monitor multiple COVID-19 biomarkers at home.

Hairpin-Spherical Nucleic Acids for Diagnosing COVID-19: a Simple Method to Generalize the Conventional PCR for Molecular Assays

The COVID-19 pandemic revealed during the first global wave of this infectious disease that mass diagnostic testing was necessary to more rapidly detect infection in patients and control the pandemic. Therefore, extra research efforts to develop reliable and more accessible techniques for disease diagnosis are of supreme importance. Here, a target-responsive assembly of gold nanoparticle-core hairpin-spherical nucleic acids (AuNP-core H-SNAs) was implemented to modify the conventional polymerase chain reaction (PCR) assay for the "naked-eye" colorimetric detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Two hairpin DNA ligands are designed based on the two highly conserved regions within N and E genes of SARS-CoV-2 RNA by positioning two short palindromic arms (stem) on either side of a recognition sequence (loop). In the presence of a sequence-specific probe (activator), hairpin DNAs anchored to the surface of AuNPs unfold and expose the palindromic ends to the DNA-directed assembly of AuNPs. The sequence of the activator probes was chosen to be identical to the TaqMan probe in a real-time reverse transcription PCR (RT-PCR) assay for specifically targeting the N and E genes of SARS-CoV-2 RNA. They may either be degraded by the 5'-exonuclease activity of DNA polymerase during PCR cycles or stay intact depending on the presence or absence of the target template in the sample, respectively. Post-addition of H-SNA solutions to the final PCR products of some preconfirmed clinical samples for COVID-19 generated naked-eye-observable red and blue colors for positive and negative cases, respectively, with similar sensitivity to that of the real-time RT-PCR method.

Antiviral Activity of Metabolites from Peruvian Plants against SARS-CoV-2: An In Silico Approach

(1) Background: The COVID-19 pandemic lacks treatments; for this reason, the search for potential compounds against therapeutic targets is still necessary. Bioinformatics tools have allowed the rapid in silico screening of possible new metabolite candidates from natural resources or repurposing known ones. Thus, in this work, we aimed to select phytochemical candidates from Peruvian plants with antiviral potential against three therapeutical targets of SARS-CoV-2. (2) Methods: We applied in silico technics, such as virtual screening, molecular docking, molecular dynamics simulation, and MM/GBSA estimation. (3) Results: Rutin, a compound present in Peruvian native plants, showed affinity against three targets of SARS-CoV-2. The molecular dynamics simulation demonstrated the high stability of receptor-ligand systems during the time of the simulation. Our results showed that the Mpro-Rutin system exhibited higher binding free energy than PLpro-Rutin and N-Rutin systems through MM/GBSA analysis. (4) Conclusions: Our study provides insight on natural metabolites from Peruvian plants with therapeutical potential. We found Rutin as a potential candidate with multiple pharmacological properties against SARS-CoV-2.

Rapid Point-of-Care COVID-19 Diagnosis with a Gold-Nanoarchitecture-Assisted Laser-Scribed Graphene Biosensor

The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has revealed the urgent need for accurate, rapid, and affordable diagnostic tests for epidemic understanding and management by monitoring the population worldwide. Though current diagnostic methods including real-time polymerase chain reaction (RT-PCR) provide sensitive detection of SARS-CoV-2, they require relatively long processing time, equipped laboratory facilities, and highly skilled personnel. Laser-scribed graphene (LSG)-based biosensing platforms have gained enormous attention as miniaturized electrochemical systems, holding an enormous potential as point-of-care (POC) diagnostic tools. We describe here a miniaturized LSG-based electrochemical sensing scheme for coronavirus disease 2019 (COVID-19) diagnosis combined with three-dimensional (3D) gold nanostructures. This electrode was modified with the SARS-CoV-2 spike protein antibody following the proper surface modifications proved by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) characterizations as well as electrochemical techniques. The system was integrated into a handheld POC detection system operated using a custom smartphone application, providing a user-friendly diagnostic platform due to its ease of operation, accessibility, and systematic data management. The analytical features of the electrochemical immunoassay were evaluated using the standard solution of S-protein in the range of 5.0-500 ng/mL with a detection limit of 2.9 ng/mL. A clinical study was carried out on 23 patient blood serum samples with successful COVID-19 diagnosis, compared to the commercial RT-PCR, antibody blood test, and enzyme-linked immunosorbent assay (ELISA) IgG and IgA test results. Our test provides faster results compared to commercial diagnostic tools and offers a promising alternative solution for next-generation POC applications.

A critical review on SARS-CoV-2 infectivity in water and wastewater. What do we know?

The COVID-19 outbreak circulating the world is far from being controlled, and possible contamination routes are still being studied. There are no confirmed cases yet, but little is known about the infection possibility via contact with sewage or contaminated water as well as with aerosols generated during the pumping and treatment of these aqueous matrices. Therefore, this article presents a literature review on the detection of SARS-CoV-2 in human excreta and its pathways through the sewer system and wastewater treatment plants until it reaches the water bodies, highlighting their occurrence and infectivity in sewage and natural water. Research lines are still indicated, which we believe are important for improving the detection, quantification, and mainly the infectivity analyzes of SARS-CoV-2 and other enveloped viruses in sewage and natural water. In fact, up till now, no case of transmission via contact with sewage or contaminated water has been reported and the few studies conducted with these aqueous matrices have not detected infectious viruses. On the other hand, studies are showing that SARS-CoV-2 can remain viable, i.e., infectious, for up to 4.3 and 6 days in sewage and water, respectively, and that other species of coronavirus may remain viable in these aqueous matrices for more than one year, depending on the sample conditions. These are strong pieces of evidence that the contamination mediated by contact with sewage or contaminated water cannot be ruled out, even because other more resistant and infectious mutations of SARS-CoV-2 may appear.

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers' effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment.

Detection of COVID-19 Virus on Surfaces Using Photonics: Challenges and Perspectives

The propagation of viruses has become a global threat as proven through the coronavirus disease (COVID-19) pandemic. Therefore, the quick detection of viral diseases and infections could be necessary. This study aims to develop a framework for virus diagnoses based on integrating photonics technology with artificial intelligence to enhance healthcare in public areas, marketplaces, hospitals, and airfields due to the distinct spectral signatures from lasers' effectiveness in the classification and monitoring of viruses. However, providing insights into the technical aspect also helps researchers identify the possibilities and difficulties in this field. The contents of this study were collected from six authoritative databases: Web of Science, IEEE Xplore, Science Direct, Scopus, PubMed Central, and Google Scholar. This review includes an analysis and summary of laser techniques to diagnose COVID-19 such as fluorescence methods, surface-enhanced Raman scattering, surface plasmon resonance, and integration of Raman scattering with SPR techniques. Finally, we select the best strategies that could potentially be the most effective methods of reducing epidemic spreading and improving healthcare in the environment.

Droplet Cas12a Assay Enables DNA Quantification from Unamplified Samples at the Single-Molecule Level

DNA quantification is important for biomedical research, but the routinely used techniques rely on nucleic acid amplification which have inherent issues like cross-contamination risk and quantification bias. Here, we report a CRISPR-Cas12a-based molecular diagnostic technique for amplification-free and absolute quantification of DNA at the single-molecule level. To achieve this, we first screened out the optimal reaction parameters for high-efficient Cas12a assay, yielding over 50-fold improvement in sensitivity compared with the reported Cas12a assays. We further leveraged the microdroplet-enabled confinement effect to perform an ultralocalized droplet Cas12a assay, obtaining excellent specificity and single-molecule sensitivity. Moreover, we demonstrated its versatility and quantification capability by direct counting of diverse virus's DNAs (African swine fever virus, Epstein-Barr virus, and Hepatitis B virus) from clinical serum samples with a wide range of viral titers. Given the flexible programmability of crRNA, we envision this amplification-free technique as a versatile and quantitative platform for molecular diagnosis.

Facile and rapid detection of SARS-CoV-2 antibody based on a noncompetitive fluorescence polarization immunoassay in human serum samples

Antibody detection methods for viral infections have received broad attention due to the COVID-19 pandemic. In addition, there remains an ever-increasing need to quantitatively evaluate the immune response to develop vaccines and treatments for COVID-19. Here, we report an analytical method for the rapid and quantitative detection of SARS-CoV-2 antibody in human serum by fluorescence polarization immunoassay (FPIA). A recombinant SARS-CoV-2 receptor binding domain (RBD) protein labeled with HiLyte Fluor 647 (F-RBD) was prepared and used for FPIA. When the anti-RBD antibody in human serum binds to F-RBD, the degree of polarization (P) increases by suppressing the rotational diffusion of F-RBD. The measurement procedure required only mixing a reagent containing F-RBD with serum sample and measuring the P value with a portable fluorescence polarization analyzer after 15 min incubation. We evaluated analytical performance of the developed FPIA system using 30 samples: 20 COVID-19 positive sera and 10 negative sera. The receiver operating characteristic curve drawn with the obtained results showed that this FPIA system had high accuracy for discriminating COVID-19 positive or negative serum (AUC = 0.965). The total measurement time was about 20 min, and the serum volume required for measurement was 0.25 μL. Therefore, we successfully developed the FPIA system that enables rapid and easy quantification of SARS-CoV-2 antibody. It is believed that our FPIA system will facilitate rapid on-site identification of infected persons and deepen understanding of the immune response to COVID-19.

Development and Application of Human Coronavirus Protein Microarray for Specificity Analysis

Coronavirus is an enveloped RNA virus that causes mild to severe respiratory diseases in humans, including HKU1-CoV, 229E-CoV, NL63-CoV, OC43-CoV, SARS-CoV, MERS-CoV, and SARS-CoV-2. Due to the outbreak of SARS-CoV-2, it is important to identify the patients and investigate their immune responses. Protein microarray is one of the best platforms to profile the antibodies in the blood because of its fast, multiplexed, and sensitive nature. To fully understand the immune responses and biological specificities, this study developed a human coronavirus (HCoV) protein microarray and included all seven human coronaviruses and three influenza viruses. Each protein was printed in triplicate and formed 14 identical blocks per array. The HCoV protein microarray showed high reproducibility and sensitivity to the monoclonal antibodies against spike and nucleocapsid protein with detection limits of 10-200 pg. The HCoV proteins that were immobilized on the array were properly folded and functional by showing interactions with a known human receptor, e.g., ACE2. By profiling the serum IgG and IgA from 32 COVID-19 patients and 36 healthy patients, the HCoV protein microarray demonstrated 97% sensitivity and 97% specificity with two biomarkers. The results also showed the cross-reactivity of IgG and IgA in COVID-19 patients to spike proteins from various coronaviruses, including that from SARS-CoV, HKU1-CoV, and OC43-CoV. Finally, an innate immune protein named surfactant protein D showed broad affinities to spike proteins in all human coronaviruses. Overall, the HCoV protein microarray is multiplexed, sensitive, and specific, which is useful in diagnosis, immune assessment, biological development, and drug screening.

Simultaneous detection of the spike and nucleocapsid proteins from SARS-CoV-2 based on ultrasensitive single molecule assays

Nucleic acid detection technology based on polymerase chain reaction (PCR) and antibody detection based on immunochromatography still have many problems such as false negatives for the diagnosis of coronavirus disease 2019 (COVID-19). Therefore, it is of great importance to develop new techniques to improve the diagnostic accuracy of COVID-19. We herein developed an ultrasensitive, rapid, and duplex digital enzyme-linked immunosorbent assay (dELISA) for simultaneous detection of spike (S-RBD) and nucleocapsid (N) proteins of SARS-CoV-2 based on a single molecule array. This assay effectively combines magnetic bead encoding technology and the ultrasensitive detection capability of a single molecule array. The detection strategies of S-RBD protein and N-protein exhibited wide response ranges of 0.34–1065 pg/mL and 0.183–338 pg/mL with detection limits of 20.6 fg/mL and 69.8 fg/mL, respectively. It is a highly specific method for the simultaneous detection of S-RBD protein and N-protein and has minimal interference from other blood proteins. Moreover, the spike assay showed a satisfactory and reproducible recovery rate for the detection of S-RBD protein and N-protein in serum samples. Overall, this work provides a highly sensitive method for the simultaneous detection of S-RBD protein and N-protein, which shows ultrasensitivity and high signal-to-noise ratio and contributes to improve the diagnosis accuracy of COVID-19.

A Ligation/Recombinase Polymerase Amplification Assay for Rapid Detection of SARS-CoV-2

The pandemic of COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to more than 117 million reported cases and 2.6 million deaths. Accurate diagnosis technologies are vital for controlling this pandemic. Reverse transcription (RT)-based nucleic acid detection assays have been developed, but the strict sample processing requirement of RT has posed obstacles on wider applications. This study established a ligation and recombinase polymerase amplification (L/RPA) combined assay for rapid detection of SARS-CoV-2 on genes N and ORF1ab targeting the specific biomarkers recommended by the China CDC. Ligase-based strategies usually have a low-efficiency problem on RNA templates. This study has addressed this problem by using a high concentration of the T4 DNA ligase and exploiting the high sensitivity of RPA. Through selection of the ligation probes and optimization of the RPA primers, the assay achieved a satisfactory sensitivity of 10¹ viral RNA copies per reaction, which was comparable to RT-quantitative polymerase chain reaction (RT-qPCR) and other nucleic acid detection assays for SARS-CoV-2. The assay could be finished in less than 30 min with a simple procedure, in which the requirement for sophisticated thermocycling equipment had been avoided. In addition, it avoided the RT procedure and could potentially ease the requirement for sample processing. Once validated with clinical samples, the L/RPA assay would increase the practical testing availability of SARS-CoV-2. Moreover, the principle of L/RPA has an application potential to the identification of concerned mutations of the virus.

CRISPR/Cas12a-Assisted Ligation-Initiated Loop-Mediated Isothermal Amplification (CAL-LAMP) for Highly Specific Detection of microRNAs

Loop-mediated isothermal amplification (LAMP) has been increasingly applied in nucleic acid detection for clinical diagnosis and monitoring pathogenic microorganisms due to its isothermal nature and high sensitivity. However, the false-positive signal resulting from the non-specific amplification and the complexity of primer design are still technically challenging for wide applications. In this paper, we developed the CRISPR/Cas12a-assisted sequence-specific detection of LAMP products to eliminate the effect of non-specific amplification from primer dimers and spurious amplicons. Moreover, by designing a pair of target-specific stem-loop DNA probes, we greatly simplified the primer design for LAMP. The DNA probes could be ligated to form a double-stem-loop DNA template by the detected target, which initiated LAMP reaction and achieved one-nucleotide resolution due to the highly specific ligase reaction. Using microRNAs (miRNAs) as the model targets, the CRISPR/Cas12a-assisted ligation-initiated loop-mediated isothermal amplification (CAL-LAMP) can sensitively detect as low as 0.1 fM miRNAs with high specificity.

Advances in Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)-Based Diagnostic Assays Assisted by Micro/Nanotechnologies

Clustered, regularly interspaced short palindromic repeats (CRISPR)-based diagnoses, derived from gene-editing technology, have been exploited for less than 5 years and are now reaching the stage of precommercial use. CRISPR tools have some notable features, such as recognition at physiological temperature, excellent specificity, and high-efficiency signal amplification capabilities. These characteristics are promising for the development of next-generation diagnostic technologies. In this Perspective, we present a detailed summary of which micro/nanotechnologies play roles in the advancement of CRISPR diagnosis and how they are involved. The use of nanoprobes, nanochips, and nanodevices, microfluidic technology, lateral flow strips, etc. in CRISPR detection systems has led to new opportunities for CRISPR-based diagnosis assay development, such as achieving equipment-free detection, providing more compact detection systems, and improving sensitivity and quantitative capabilities. Although tremendous progress has been made, CRISPR diagnosis has not yet reached its full potential. We discuss upcoming opportunities and improvements and how micro/nanotechnologies will continue to play key roles.

Performance characteristics of the Abbott Alinity m SARS-CoV-2 assay

Mass molecular diagnostic testing for the SARS-CoV-2 pandemic has drawn on laboratory developed tests, commercial assays, and fully-automated platforms to accommodate widespread demand. The Alinity m instrument by Abbott is capable of detecting several clinically relevant pathogens and has recently received FDA emergency use authorization for SARS-CoV-2 molecular testing. The Alinity m performs automatic sample preparation, RT-PCR assembly, amplification, detection, and result calculation in under two hours. Here, we validate the performance characteristics of the Alinity m SARS-CoV-2 assay in comparison with the Roche cobas 6800 and Hologic Panther Fusion platforms. Across 178 positive and 195 negative nasopharyngeal swab specimens (C_T range 14.30–38.84), the Alinity m detected one additional positive specimen that was found to be negative on the Roche cobas 6800 (PPA 100%, NPA 99.5%). Across a separate set of 30 positive and 174 negative nasopharyngeal swab specimens (C_T range 14.1–38.5), the Alinity m had 100% positive and negative agreement with the Hologic Panther Fusion. Using SeraCare SARS-CoV-2 RNA standards, the assay limit of detection was verified to be two-fold more sensitive than the parameters stated by the SARS-CoV-2 AMP kit package insert, at 50 virus copies/mL. Assay specificity was 100% over 20 specimens positive for other respiratory viruses and intraday precision was 100% concordant with <2% CV. These data illst u illustrate the Abbott Alinity m system's high concordance with reference assays and analyti high analytical for SARS-CoV-2 molecular detection.

Coinfections with Respiratory Pathogens among COVID-19 Patients in Korea

The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 (COVID-19) was investigated. Study subjects (N = 342) were retrospectively enrolled after being confirmed as SARS-CoV-2 positive, and their nasopharyngeal swab (NPS), oropharyngeal swab (OPS), and sputum specimens were restored for SARS-CoV-2 retesting and respiratory pathogen detection. The majority of the subjects (96.5%, N = 330) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens. Among the COVID-19 patients (N = 342), 7.9% (N = 27) and 0.9% (N = 3) were coinfected with respiratory viruses and Mycoplasma pneumoniae, respectively, yielding an 8.8% (N = 30) overall respiratory pathogen coinfection rate. Of the respiratory virus coinfection cases (N = 27), 92.6% (N = 25) were coinfected with a single respiratory virus and 7.4% (N = 2) with two viruses (metapneumovirus/adenovirus and rhinovirus/bocavirus). No triple coinfections of other respiratory viruses or bacteria with SARS-CoV-2 were detected. Respiratory viruses coinfected in the patients with COVID-19 were as follows: rhinovirus (N = 7, 2.1%), respiratory syncytial virus A and B (N = 6, 1.8%), non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.5%), metapneumovirus (N = 4, 1.2%), influenza A (N = 3, 0.9%), adenovirus (N = 3, 0.9%), and bocavirus (N = 1, 0.3%). In conclusion, the diagnostic value of utilizing NPS/OPS specimens is excellent, and, as the first report in Korea, coinfection with respiratory pathogens was detected at a rate of 8.8% in patients with COVID-19.

Mass spectrometry analytical responses to the SARS-CoV2 coronavirus in review

This article reviews the many and varied mass spectrometry based responses to the SARS-CoV2 coronavirus amidst a continuing global healthcare crisis. Although RT-PCR is the most prevalent molecular based surveillance approach, improvements in the detection sensitivities with mass spectrometry coupled to the rapid nature of analysis, the high molecular precision of measurements, opportunities for high sample throughput, and the potential for in-field testing, offer advantages for characterising the virus and studying the molecular pathways by which it infects host cells. The detection of biomarkers by MALDI-TOF mass spectrometry, studies of viral peptides using proteotyping strategies, targeted LC-MS analyses to identify abundant peptides in clinical specimens, the analysis of viral protein glycoforms, proteomics approaches to understand impacts of infection on host cells, and examinations of point-of-care breath analysis have all been explored. This review organises and illustrates these applications with reference to the many studies that have appeared in the literature since the outbreak. In this respect, those studies in which mass spectrometry has a major role are the focus, and only those which have peer-reviewed have been cited.

Rational Engineering of the DNA Walker Amplification Strategy by Using a Au@Ti3C2@PEI-Ru(dcbpy)32+ Nanocomposite Biosensor for Detection of the SARS-CoV-2 RdRp Gene

The detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for preventing and controlling infectious diseases and disease treatment. In this work, a Au@Ti3C2@PEI-Ru(dcbpy)32+ nanocomposite-based electrochemiluminescence (ECL) biosensor was rationally designed, which realized sensitive detection of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2. In addition, a DNA walker was also used to excise the hairpin DNAs under the action of Nb.BbvCI endonuclease. Furthermore, model DNA-Ag nanoclusters (model DNA-AgNCs) were used to quench the initial ECL signal. As a result, the ECL biosensor was used to sensitively detect the SARS-CoV-2 RdRp gene with a detection range of 1 fM to 100 pM and a limit of detection of 0.21 fM. It was indicated that the ECL biosensor had a great application potential for clinical medical detection. Furthermore, the DNA walker amplification also played a reliable candidate strategy for other detection methods.

Rapid One-Step Detection of Viral Particles Using an Aptamer-Based Thermophoretic Assay

Rapid and sensitive identification of viral pathogens such as SARS-CoV-2 is a critical step to control the pandemic disease. Viral antigen detection can compete with gold-standard PCR-based nucleic acid diagnostics in terms of better reflection of viral infectivity and reduced risk of contamination from enzymatic amplification. Here, we report the development of a one-step thermophoretic assay using an aptamer and polyethylene glycol (PEG) for direct quantitative detection of viral particles. The assay relies on aptamer binding to the spike protein of SARS-CoV-2 and simultaneous accumulation of aptamer-bound viral particles in laser-induced gradients of temperature and PEG concentration. Using a pseudotyped lentivirus model, a limit of detection of ∼170 particles μL^-1 (26 fM of the spike protein) is achieved in 15 min without the need of any pretreatment. As a proof of concept, the one-step thermophoretic assay is used to detect synthetic samples by spiking viral particles into oropharyngeal swabs with an accuracy of 100%. The simplicity, speed, and cost-effectiveness of this thermophoretic assay may expand the diagnostic tools for viral pathogens.

A CRISPR/Cas9 eraser strategy for contamination-free PCR end-point detection

Polymerase chain reaction (PCR), a central technology for molecular diagnostics, is highly sensitive but susceptible to the risk of false positives caused by aerosol contamination, especially when an end-point detection mode is applied. Here, we proposed a solution by designing a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 eraser strategy for eliminating potential contamination amplification. The CRISPR/Cas9 engineered eraser is firstly adopted into artpcr reverse-transcription PCR (RT-PCR) system to achieve contamination-free RNA detection. Subsequently, we extended this CRISPR/Cas9 eraser to the PCR system. We engineered conventional PCR primers to enable the amplified products to contain an implanted NGG (protospacer adjacent motif, PAM) site, which is used as a code for specific CRISPR/Cas9 recognition. Pre-incubation of Cas9/sgRNA with PCR mix leads to a selective cleavage of contamination amplicons, thus only the template DNA is amplified. The developed CRISPR/Cas9 eraser, adopted by both RT-PCR and PCR systems, showed high-fidelity detection of SARS-CoV-2 and African swine fever virus with a convenient strip test.

Development of multiplex real-time RT-PCR assay for the detection of SARS-CoV-2

The outbreak of the new human coronavirus SARS-CoV-2 (also known as 2019-nCoV) continues to increase globally. The real-time reverse transcription polymerase chain reaction (rRT-PCR) is the most used technique in virus detection. However, possible false-negative and false-positive results produce misleading consequences, making it necessary to improve existing methods. Here, we developed a multiplex rRT-PCR diagnostic method, which targets two viral genes (RdRP and E) and one human gene (RP) simultaneously. The reaction was tested by using pseudoviral RNA and human target mRNA sequences as a template. Also, the protocol was validated by using 14 clinical SARS-CoV-2 positive samples. The results are in good agreement with the CDC authorized Cepheid`s Xpert® Xpress SARS-CoV-2 diagnostic system (100%). Unlike single gene targeting strategies, the current method provides the amplification of two viral regions in the same PCR reaction. Therefore, an accurate SARS-CoV-2 diagnostic assay was provided, which allows testing of 91 samples in 96-well plates in per run. Thanks to this strategy, fast, reliable, and easy-to-use rRT-PCR method is obtained to diagnose SARS-CoV-2.

Nucleic acid analysis on paper substrates (NAAPs): an innovative tool for Point of Care (POC) infectious disease diagnosis

The cost-effective rapid diagnosis of infectious diseases is an essential and important factor for curing such diseases in the global public health care picture. Owing to poor infrastructure and lack of sanitation, these diseases have an extreme impact on remote and rural areas, especially in developing countries, and there are unresolved challenges. Molecular diagnosis, such as nucleic acid analysis, plays a key role in the significant treatment of numerous infectious diseases. Current molecular diagnostic assays require a sophisticated laboratory setup with expensive components. Molecular diagnosis on a microfluidic point-of-care (POC) platform is attractive to researchers for disease detection with proper prevention. Compared to various microfluidic substrate materials, paper-based POC technologies offer significant cost-effective solutions over high-cost clinical instruments to fill the gap between the needs of users and affordability. Low-cost paper-based microfluidic POC technologies provide portable and disposable diagnostic systems for multiple disease detection that may be extremely useful in remote areas. This article presents a critical review of paper-based microfluidic device technology which has become an imminent platform to adjust the current health scenario for the detection of diseases using different stages of nucleic acid analysis, such as extraction, amplification and detection of nucleic acid, with future perspectives for paper substrates.

Elliptical Pipette Generated Large Microdroplets for POC Visual ddPCR Quantification of Low Viral Load

Rapid point-of-care (POC) quantification of low virus RNA load would significantly reduce the turn-around time for the PCR test and help contain a fast-spreading epidemic. Herein, we report a droplet digital PCR (ddPCR) platform that can achieve this sensitivity and rapidity without bulky lab-bound equipment. The key technology is a flattened pipette tip with an elliptical cross-section, which extends a high aspect-ratio microfluidic chip design to pipette scale, for rapid (<5 min) generation of several thousand monodispersed droplets ∼150 to 350 μm in size with a CV of ∼2.3%. A block copolymer surfactant (polyoxyalkylene F127) is used to stabilize these large droplets in oil during thermal cycling. At this droplet size and number, positive droplets can be counted by eye or imaged by a smartphone with appropriate illumination/filtering to accurately quantify up to 100 target copies. We demonstrate with 2019 nCoV-PCR assay LODs of 3.8 copies per 20 μL of sample and a dynamic range of 4-100 copies. The ddPCR platform is shown to be inhibitor resistant with spiked saliva samples, suggesting RNA extraction may not be necessary. It represents a rapid 1.5-h POC quantitative PCR test that requires just a pipette equipped with elliptical pipette tip, a commercial portable thermal cycler, a smartphone, and a portable trans-illuminator, without bulky and expensive micropumps and optical detectors that prevent POC application.

Optical technologies for the detection of viruses like COVID-19: Progress and prospects

The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.

Entropy-driven amplified electrochemiluminescence biosensor for RdRp gene of SARS-CoV-2 detection with self-assembled DNA tetrahedron scaffolds

Dependable, specific and rapid diagnostic methods for severe acute respiratory syndrome β-coronavirus (SARS-CoV-2) detection are needed to promote public health interventions for coronavirus disease 2019 (COVID-19). Herein, we have established an entropy-driven amplified electrochemiluminescence (ECL) strategy to detect the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 known as RdRp-COVID which as the target for SARS-CoV-2 plays an essential role in the diagnosis of COVID-19. For the construction of the sensors, DNA tetrahedron (DT) is modified on the surface of the electrode to furnish robust and programmable scaffolds materials, upon which target DNA-participated entropy-driven amplified reaction is efficiently conducted to link the Ru (bpy)32+ modified S3 to the linear ssDNA at the vertex of the tetrahedron and eventually present an "ECL on" state. The rigid tetrahedral structure of the DT probe enhances the ECL intensity and avoids the cross-reactivity between single-stranded DNA, thus increasing the sensitivity of the assays. The enzyme-free entropy-driven reaction prevents the use of expensive enzyme reagents and facilitates the realization of large-scale screening of SARS-CoV-2 patients. Our DT-based ECL sensor has demonstrated significant specificity and high sensitivity for SARS-CoV-2 with a limit of detection (LOD) down to 2.67 fM. Additionally, our operational method has achieved the detection of RdRp-COVID in human serum samples, which supplies a reliable and feasible sensing platform for the clinical bioanalysis.

SARS-CoV-2 IgG Antibodies Seroprevalence and Sera Neutralizing Activity in MEXICO: A National Cross-Sectional Study during 2020

Until recently, the incidence of COVID-19 was primarily estimated using molecular diagnostic methods. However, the number of cases is vastly underreported using these methods. Seroprevalence studies estimate cumulative infection incidences and allow monitoring of transmission dynamics, and the presence of neutralizing antibodies in the population. In February 2020, the Mexican Social Security Institute began conducting anonymous unrelated sampling of residual sera from specimens across the country, excluding patients with fever within the previous two weeks and/or patients with an acute respiratory infection. Sampling was carried out weekly and began 17 days before Mexico's first officially confirmed case. The 24,273 sera obtained were analyzed by chemiluminescent-linked immunosorbent assay (CLIA) IgG S1/S2 and, later, positive cases using this technique were also analyzed to determine the rate of neutralization using the enzyme-linked immunosorbent assay (ELISA). We identified 40 CLIA IgG positive cases before the first official report of SARS-CoV-2 infection in Mexico. The national seroprevalence was 3.5% in February and 33.5% in December. Neutralizing activity among IgG positives patients during overall study period was 86.1%. The extent of the SARS-CoV-2 infection in Mexico is 21 times higher than that reported by molecular techniques. Although the general population is still far from achieving herd immunity, epidemiological indicators should be re-estimated based on serological studies of this type.