Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens

Antifibrotic effect of silymarin on arecoline-induced fibrosis in primary human buccal fibroblasts: an in silico and in vitro analysis

BACKGROUND

This study aimed to assess silymarin's anticancer and antifibrotic potential through in silico analysis and investigate its impact on in vitro arecoline-induced fibrosis in primary human buccal fibroblasts (HBF).

METHODS & RESULTS

The study utilized iGEMDOCK for molecular docking, evaluating nine bioflavonoids, and identified silymarin and baicalein as the top two compounds with the highest target affinity, followed by subsequent validation through a 100ns Molecular Dynamic Simulation demonstrating silymarin's stable behavior with Transforming Growth Factor Beta. HBF cell lines were developed from tissue samples obtained from patients undergoing third molar extraction. Arecoline, a known etiological factor in oral submucous fibrosis (OSMF), was employed to induce fibrogenesis in these HBFs. The inhibitory concentration (IC50) of arecoline was determined using the MTT assay, revealing dose-dependent cytotoxicity of HBFs to arecoline, with notable cytotoxicity observed at concentrations exceeding 50µM. Subsequently, the cytotoxicity of silymarin was assessed at 24 and 72 h, spanning concentrations from 5µM to 200µM, and an IC50 value of 143µM was determined. Real-time polymerase chain reaction (qPCR) was used to analyze the significant downregulation of key markers including collagen, epithelial-mesenchymal transition (EMT), stem cell, hypoxia, angiogenesis and stress markers in silymarin-treated arecoline-induced primary buccal fibroblast cells.

CONCLUSION

Silymarin effectively inhibited fibroblast proliferation and downregulated genes associated with cancer progression and EMT pathway, both of which are implicated in malignant transformation. To our knowledge, this study represents the first exploration of silymarin's potential as a novel therapeutic agent in an in vitro model of OSMF.

Novel Mutations in the Non-Structure Protein 2 of SARS-CoV-2

Introduction

Mutation in the genome of SARS-CoV-2 may play a role in immune evasion, pathogenicity, and speed of its transmission. Our investigation aimed to evaluate the mutations that exist in the NSP2.

Materials and Method

RNA was extracted from nasopharyngeal swabs from 100 COVID-19 patients. RT-PCR was performed on all samples using NSP2-specific primers. Following gel electrophoresis, the bands were cut, purified, and sequenced using the Sanger method. After sequencing, 90 sequences could be used for further analysis. Bioinformatics analysis was conducted to investigate the effect of mutations on protein structure, stability, prediction of homology models, and phylogeny tree.

Results

The patients' mean age was 51.08. The results revealed that 8 of the 17 NSP2 mutations (R207C, T224I, G262V, T265I, K337D, N348S, G392D, and I431M) were missense. One deletion was also found in NSP2. Among NSP2 missense mutations studied, K337D and G392D increased structural stability while the others decreased it. The homology-designed models demonstrated that the homologies were comparable to the sequences of the Wuhan-HU-1 virus.

Conclusion

Our study suggested that the mutations K337D and G392D modulate the stability of NSP2, and tracking viral evolution should be implemented and vaccine development updated.

Clinicopathological Significance of Cancer Stem Cell Markers (OCT-3/4 and SOX-2) in Oral Submucous Fibrosis and Oral Squamous Cell Carcinoma

Oral submucous fibrosis (OSMF) is highly prevalent in South East Asia with higher rates of malignant transformation in Indian subcontinent. Numerous biomarkers are now being studied to predict disease prognosis and detect malignant alterations at an early stage. Patients with clinically and biopsy-proven oral submucous fibrosis and oral squamous cell carcinoma were included in the study as the experimental group, while patients without a tobacco or betel nut habit who had their third molars surgically removed were included as the healthy control group. For the immunohistochemistry (IHC) investigation, 5-μm slices from formalin-fixed, paraffin-embedded tissue blocks (FFPE) were obtained. Fresh tissues (n = 45) from all three groups were collected and gene expression was studied using relative quantitation-based qPCR. The protein expression of octamer-binding transcription factor 3/4 (OCT 3/4) and sex-determining region Y-box 2 (SOX 2) was evaluated in the experimental group and compared with healthy controls. The IHC results showed a significant correlation with the expression of OCT 3/4 (p value = 0.000; χ2 = 20.244) and SOX 2 (p value = 0.006; χ2 = 10.101) among OSCC and OSMF patients in comparison to healthy controls. Both OCT 3/4 and SOX 2 showed overexpression of four-fold and three-fold in OSMF when compared to OSCC and healthy controls, respectively. This study shows the significant importance of cancer stem cell markers OCT 3/4 and SOX 2 to assess the disease prognosis in OSMF.

Development and Validation of a Novel COVID-19 nsp8 One-Tube RT-LAMP-CRISPR Assay for SARS-CoV-2 Diagnosis

Accurate and simple diagnostic tests for coronavirus disease 2019 (COVID-19) are essential components of the pandemic response. In this study, we evaluated a one-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay coupled with clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein-mediated endpoint detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in clinical samples. RT-LAMP-CRISPR is fast and affordable, does not require bulky thermocyclers, and minimizes carryover contamination risk. Results can be read either visually or with a fluorometer. RT-LAMP-CRISPR assays using primers targeting a highly expressed nsp8 gene and previously described nucleocapsid (N) gene primers were designed. The analytical characteristics and diagnostic performance of RT-LAMP-CRISPR assays were compared to those of a commercial real-time RT-PCR E gene assay. The limits of detection (LODs) of the nsp8 and N RT-LAMP-CRISPR assays were 750 and 2,000 copies/mL, which were higher than that of the commercial real-time RT-PCR assay (31.3 copies/mL). Despite the higher LOD, RT-LAMP-CRISPR assays showed diagnostic sensitivity and specificity of 98.6% and 100%, respectively, equivalent to those of the real-time RT-PCR assay (P = 0.5). The median fluorescence reading from the nsp8 assay (378.3 raw fluorescence unit [RFU] [range, 215.6 to 592.6]) was significantly higher than that of the N gene assay (342.0 RFU [range, 143.0 to 576.6]) (P < 0.0001). In conclusion, we demonstrate that RT-LAMP-CRISPR assays using primers rationally designed from highly expressed gene targets are highly sensitive, specific, and easy to perform. Such assays are a valuable asset in resource-limited settings. IMPORTANCE Accurate tests for the diagnosis of SARS-CoV-2, the virus causing coronavirus disease 2019 (COVID-19), are important for timely treatment and infection control decisions. Conventional tests such as real-time reverse transcription-PCR (RT-PCR) require specialized equipment and are expensive. On the other hand, rapid antigen tests suffer from a lack of sensitivity. In this study, we describe a novel assay format for the diagnosis of COVID-19 that is based on principles of loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas chemistry. A major advantage of this assay format is that it does not require expensive equipment to perform, and results can be read visually. This method proved to be fast, easy to perform, and inexpensive. The test compared well against an RT-PCR assay in terms of the ability to detect SARS-CoV-2 RNA in clinical samples. No false-positive test results were observed. The new assay format is ideal for SARS-CoV-2 diagnosis in resource-limited settings.

Advancements in Detection Approaches of Severe Acute Respiratory Syndrome Coronavirus 2

Diagnostic testing to identify individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in selecting appropriate treatments, saving people's lives and preventing the global pandemic of COVID-19. By testing on a massive scale, some countries could successfully contain the disease spread. Since early viral detection may provide the best approach to curb the disease outbreak, the rapid and reliable detection of coronavirus (CoV) is therefore becoming increasingly important. Nucleic acid detection methods, especially real-time reverse transcription polymerase chain reaction (RT-PCR)-based assays are considered the gold standard for COVID-19 diagnostics. Some non-PCR-based molecular methods without thermocycler operation, such as isothermal nucleic acid amplification have been proved promising. Serologic immunoassays are also available. A variety of novel and improved methods based on biosensors, Clustered-Regularly Interspaced Short Palindromic Repeats (CRISPR) technology, lateral flow assay (LFA), microarray, aptamer etc. have also been developed. Several integrated, random-access, point-of-care (POC) molecular devices are rapidly emerging for quick and accurate detection of SARS-CoV-2 that can be used in the local hospitals and clinics. This review intends to summarize the currently available detection approaches of SARS-CoV-2, highlight gaps in existing diagnostic capacity, and propose potential solutions and thus may assist clinicians and researchers develop better technologies for rapid and authentic diagnosis of CoV infection.

Identification of mutations in SARS-CoV-2 PCR primer regions

Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as "prone to misclassification" vs. "likely to be correctly detected" by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.

Identification of EGFR as a Biomarker in Saliva and Buccal Cells from Oral Submucous Fibrosis Patients—A Baseline Study

Oral Submucous Fibrosis (OSMF) is a chronic debilitating disease more frequently encountered in the South-East Asian population. This disease represents a public health priority as it is grouped within oral potentially malignant disorders, with malignant transformation rates of around 7–19%. Hence, early identification of high-risk OSMF patients is of the utmost importance to prevent malignant transformation. Among various biomarkers, EGFR overexpression has an unfavorable clinical outcome, poor prognosis, and low survival rates in Oral Squamous Cell Carcinoma (OSCC). The current study aimed to evaluate the expression of EGFR in saliva and exfoliated buccal cells of OSMF. Immunoexpression of EGFR was observed in healthy controls (n = 11), OSCC (n = 106), and OPMD with dysplasia (n = 56), which showed significant expression with increasing grades of dysplasia and OSCC. EGFR expression was evaluated in saliva and exfoliated buccal cells of healthy controls (n = 15), OSMF (n = 24), and OSCC (n = 10) patients using ELISA, which revealed significant expression in OSMF and OSCC. Validation studies were also performed using real-time PCR (RT-PCR) to compare gene expression in healthy controls (n = 9), OSMF (n = 9), and OSCC (n = 25), which showed significant 18-fold upregulation in OSCC and three-fold upregulation in OSMF when compared to healthy controls. Hence, saliva and exfoliated buccal cells could be considered as potential non-invasive diagnostic samples for the evaluation of high-risk patients of OSMF using EGFR as a biomarker.

Identification of conserved regions from 230,163 SARS-CoV-2 genomes and their use in diagnostic PCR primer design

BACKGROUND

As the rapidly evolving characteristic of SARS-CoV-2 could result in false negative diagnosis, the use of as much sequence data as possible is key to the identification of conserved viral sequences. However, multiple alignment of massive genome sequences is computationally intensive.

OBJECTIVE

To extract conserved sequences from SARS-CoV-2 genomes for the design of diagnostic PCR primers using a bioinformatics approach that can handle massive genomic sequences efficiently.

METHODS

A total of 230,163 full-length viral genomes were retrieved from the NCBI SARS-CoV-2 Resources and GISAID EpiCoV database. This number was reduced to 14.11% following removal of 5'-/3'-untranslated regions and sequence dereplication. Fast, reference-based, multiple sequence alignments identified conserved sequences and specific primer sets were designed against these regions using a conventional tool. Primer sets chosen among the candidates were evaluated by in silico PCR and RT-qPCR.

RESULTS

Out of 17 conserved sequences (totaling 4.3 kb), two primer sets targeting the nsp2 and ORF3a genes were picked that exhibited > 99.9% in silico amplification coverage against the original dataset (230,163 genomes) when a 5% mismatch between the primers and target was allowed. In addition, the primer sets successfully detected nine SARS-CoV-2 variant RNA samples (Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Iota, and Kappa) in experimental RT-qPCR validations.

CONCLUSION

In addition to the RdRp, E, N, and S genes that are targeted commonly, our approach can be used to identify novel primer targets in SARS-CoV-2 and should be a priority strategy in the event of novel SARS-CoV-2 variants or other pandemic outbreaks.

Impact of SARS-CoV-2 Mutations on PCR Assay Sequence Alignment

Real-time reverse transcription polymerase chain reaction (RT-PCR) assays are the most widely used molecular tests for the detection of SARS-CoV-2 and diagnosis of COVID-19 in clinical samples. PCR assays target unique genomic RNA regions to identify SARS-CoV-2 with high sensitivity and specificity. In general, assay development incorporates the whole genome sequences available at design time to be inclusive of all target species and exclusive of near neighbors. However, rapid accumulation of mutations in viral genomes during sustained growth in the population can result in signature erosion and assay failures, creating situational blind spots during a pandemic. In this study, we analyzed the signatures of 43 PCR assays distributed across the genome against over 1.6 million SARS-CoV-2 sequences. We present evidence of significant signature erosion emerging in just two assays due to mutations, while adequate sequence identity was preserved in the other 41 assays. Failure of more than one assay against a given variant sequence was rare and mostly occurred in the two assays noted to have signature erosion. Assays tended to be designed in regions with statistically higher mutations rates. in silico analyses over time can provide insights into mutation trends and alert users to the emergence of novel variants that are present in the population at low proportions before they become dominant. Such routine assessment can also potentially highlight false negatives in test samples that may be indicative of mutations having functional consequences in the form of vaccine and therapeutic failures. This study highlights the importance of whole genome sequencing and expanded real-time monitoring of diagnostic PCR assays during a pandemic.

CovDif, a Tool to Visualize the Conservation between SARS-CoV-2 Genomes and Variants

The spread of the newly emerged severe acute respiratory syndrome (SARS-CoV-2) virus has led to more than 430 million confirmed cases, including more than 5.9 million deaths, reported worldwide as of 24 February 2022. Conservation of viral genomes is important for pathogen identification and diagnosis, therapeutics development and epidemiological surveillance to detect the emergence of new viral variants. An intense surveillance of virus variants has led to the identification of Variants of Interest and Variants of Concern. Although these classifications dynamically change as the pandemic evolves, they have been useful to guide public health efforts on containment and mitigation. In this work, we present CovDif, a tool to detect conserved regions between groups of viral genomes. CovDif creates a conservation landscape for each group of genomes of interest and a differential landscape able to highlight differences in the conservation level between groups. CovDif is able to identify loss in conservation due to point mutations, deletions, inversions and chromosomal rearrangements. In this work, we applied CovDif to SARS-CoV-2 clades (G, GH, GR, GV, L, O, S and G) and variants. We identified all regions for any defining SNPs. We also applied CovDif to a group of population genomes and evaluated the conservation of primer regions for current SARS-CoV-2 detection and diagnostic protocols. We found that some of these protocols should be applied with caution as few of the primer-template regions are no longer conserved in some SARS-CoV-2 variants. We conclude that CovDif is a tool that could be widely applied to study the conservation of any group of viral genomes as long as whole genomes exist.

Insight into prognostics, diagnostics, and management strategies for SARS CoV-2

The foremost challenge in countering infectious diseases is the shortage of effective therapeutics. The emergence of coronavirus disease (COVID-19) outbreak has posed a great menace to the public health system globally, prompting unprecedented endeavors to contain the virus. Many countries have organized research programs for therapeutics and management development. However, the longstanding process has forced authorities to implement widespread infrastructures for detailed prognostic and diagnostics study of severe acute respiratory syndrome (SARS CoV-2). This review discussed nearly all the globally developed diagnostic methodologies reported for SARS CoV-2 detection. We have highlighted in detail the approaches for evaluating COVID-19 biomarkers along with the most employed nucleic acid- and protein-based detection methodologies and the causes of their severe downfall and rejection. As the variable variants of SARS CoV-2 came into the picture, we captured the breadth of newly integrated digital sensing prototypes comprised of plasmonic and field-effect transistor-based sensors along with commercially available food and drug administration (FDA) approved detection kits. However, more efforts are required to exploit the available resources to manufacture cheap and robust diagnostic methodologies. Likewise, the visualization and characterization tools along with the current challenges associated with waste-water surveillance, food security, contact tracing, and their role during this intense period of the pandemic have also been discussed. We expect that the integrated data will be supportive and aid in the evaluation of sensing technologies not only in current but also future pandemics.

Diagnostic performance and clinical feasibility of a novel one-step RT-qPCR assay for simultaneous detection of multiple severe acute respiratory syndrome coronaviruses

Coronavirus disease 2019 (COVID-19) is an acute respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Other coronaviruses (CoVs) can also infect humans, although the majority cause only mild respiratory symptoms. Because early diagnosis of SARS-CoV-2 is critical for preventing further transmission events and improving clinical outcomes, it is important to be able to distinguish SARS-CoV-2 from other SARS-related CoVs in respiratory samples. Therefore, we developed and evaluated a novel reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the genes encoding the spike (S) and membrane (M) proteins to enable the rapid identification of SARS-CoV-2, including several new circulating variants and other emerging SARS-like CoVs. By analysis of in vitro-transcribed mRNA, we established multiplex RT-qPCR assays capable of detecting 5 × 10° copies/reaction. Using RNA extracted from cell culture supernatants, our multiple simultaneous SARS-CoV-2 assays had a limit of detection of 1 × 10° TCID₅₀/mL and showed no cross-reaction with human CoVs or other respiratory viruses. We also validated our method using human clinical samples from patients with COVID-19 and healthy individuals, including nasal swab and sputum samples. This novel one-step multiplex RT-qPCR assay can be used to improve the laboratory diagnosis of human-pathogenic CoVs, including SARS-CoV-2, and may be useful for the identification of other SARS-like CoVs of zoonotic origin.

Novel approaches for rapid detection of COVID-19 during the pandemic: A review

The rapid spread of the SARS-CoV-2 virus that caused the COVID-19 disease, has highlighted our urgent need for sensitive, fast and accurate diagnostic technologies. In fact, one of the main challenges for flatting COVID-19 spread charts is the ability to accurately and rapidly identify asymptomatic cases that result in spreading the virus to close contacts. SARS-CoV-2 virus mutation is also relatively rapid, which makes the detection of COVID-19 diseases still crucial even after the vaccination. Conventional techniques, which are commercially available have focused on clinical manifestation, along with molecular and serological detection tools that can identify the SARS-CoV-2 virus however, owing to various disadvantages including low specificity and sensitivity, a quick, low cost and easy approach is needed for diagnosis of COVID-19. Scientists are now showing extensive interest in an effective portable and simple detection method to diagnose COVID-19. There are several novel methods and approaches that are considered viable advanced systems that can meet the demands. This study reviews the new approaches and sensing technologies that work on COVID-19 diagnosis for easy and successful detection of SARS-CoV-2 virus.

An outlook on coronavirus disease 2019 detection methods

Diagnostic testing plays a fundamental role in the mitigation and containment of coronavirus disease 2019 (COVID-19), as it enables immediate quarantine of those who are infected and contagious and is essential for the epidemiological characterization of the virus and estimating the number of infected cases worldwide. Confirmation of viral infections, such as COVID-19, can be achieved through two general approaches: nucleic acid amplification tests (NAATs) or molecular tests, and serological or antibody-based tests. The genetic material of the pathogen is detected in NAAT, and in serological tests, host antibodies produced in response to the pathogen are identified. Other methods of diagnosing COVID-19 include radiological imaging of the lungs and in vitro detection of viral antigens. This review covers different approaches available to diagnosing COVID-19 by outlining their advantages and shortcomings, as well as appropriate indications for more accurate testing.

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Diagnostic tests to detect coronavirus disease 2019 (COVID-19).

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Advantages and disadvantages associated with each detection method.

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Implications for a more accurate and rapid testing of COVID-19 or other similar future emergent viruses.

Diagnosis of COVID-19, vitality of emerging technologies and preventive measures

Coronavirus diseases-2019 (COVID-19) is becoming increasing serious and major threat to public health concerns. As a matter of fact, timely testing enhances the life-saving judgments on treatment and isolation of COVID-19 infected individuals at possible earliest stage which ultimately suppresses spread of infectious diseases. Many government and private research institutes and manufacturing companies are striving to develop reliable tests for prompt quantification of SARS-CoV-2. In this review, we summarize existing diagnostic methods as manual laboratory-based nucleic acid assays for COVID-19 and their limitations. Moreover, vitality of rapid and point of care serological tests together with emerging biosensing technologies has been discussed in details. Point of care tests with characteristics of rapidity, accurateness, portability, low cost and requiring non-specific devices possess great suitability in COVID-19 diagnosis and detection. Besides, this review also sheds light on several preventive measures to track and manage disease spread in current and future outbreaks of diseases.

CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers

As mutations in SARS-CoV-2 virus accumulate rapidly, novel primers that amplify this virus sensitively and specifically are in demand. We have developed a webserver named CoVrimer by which users can search for and align existing or newly designed conserved/degenerate primer pair sequences against the viral genome and assess the mutation load of both primers and amplicons. CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations, from which potential primer pairs are designed and provided to the user for filtering based on generalized and SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation. Consequently, CoVrimer is likely to help researchers with the challenges posed by viral evolution and is freely available at http://konulabapps.bilkent.edu.tr:3838/CoVrimer/.

Nsp2 has the potential to be a drug target revealed by global identification of SARS-CoV-2 Nsp2-interacting proteins

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global health threat since December 2019, and there is still no highly effective drug to control the pandemic. To facilitate drug target identification for drug development, studies on molecular mechanisms, such as SARS-CoV-2 protein interactions, are urgently needed. In this study, we focused on Nsp2, a non-structural protein with largely unknown function and mechanism. The interactome of Nsp2 was revealed through the combination of affinity purification mass spectrometry (AP-MS) and stable isotope labeling by amino acids in cell culture (SILAC), and 84 proteins of high-confidence were identified. Gene ontology analysis demonstrated that Nsp2-interacting proteins are involved in several biological processes such as endosome transport and translation. Network analysis generated two clusters, including ribosome assembly and vesicular transport. Bio-layer interferometry (BLI) assay confirmed the bindings between Nsp2- and 4-interacting proteins, i.e. STAU2 (Staufen2), HNRNPLL, ATP6V1B2, and RAP1GDS1 (SmgGDS), which were randomly selected from the list of 84 proteins. Our findings provide insights into the Nsp2-host interplay and indicate that Nsp2 may play important roles in SARS-CoV-2 infection and serve as a potential drug target for anti-SARS-CoV-2 drug development.

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

SARS-CoV-2 has become a global pandemic threatening human health and safety. It is urgent to find effective therapeutic agents and targets with the continuous emergence of novel mutant strains. The knowledge of the molecular basis and pathogenesis of SARS-CoV-2 in host cells requires to be understood comprehensively. The unknown structure and function of nsp2 have hindered our understanding of its role in SARS-CoV-2 infection. Here, we report the crystal structure of the N-terminal of SARS-CoV-2 nsp2 to a high resolution of 1.96 Å. This novel structure contains three zinc fingers, belonging to the C2H2, C4, and C2HC types, respectively. Structure analysis suggests that nsp2 may be involved in binding nucleic acids and regulating intracellular signaling pathways. The binding to single or double-stranded nucleic acids was mainly through the large positively charged region on the surface of nsp2, and K111, K112, K113 were key residues. Our findings lay the foundation for a better understanding of the relationship between structure and function for nsp2. It is helpful to make full use of nsp2 as further research and development of antiviral targets and drug design.

Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations

The ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a severe threat to human health and the global economy and has resulted in overwhelming stress on health care systems worldwide. Despite the global health catastrophe, especially in the number of infections and fatalities, the COVID-19 pandemic has also revolutionized research and discovery with remarkable success in diagnostics, treatments, and vaccine development. The use of many diagnostic methods has helped establish public health guidelines to mitigate the spread of COVID-19. However, limited information has been shared about these methods, and there is a need for the scientific community to learn about these technologies, in addition to their sensitivity, specificity, and limitations. This review article is focused on providing insights into the major methods used for SARS-CoV-2 detection. We describe in detail the core principle of each method, including molecular and serological approaches, along with reported claims about the rates of false negatives and false positives, the types of specimens needed, and the level of technology and the time required to perform each test. Although this study will not rank or prioritize these methods, the information will help in the development of guidelines and diagnostic protocols in clinical settings and reference laboratories.

Road toward universal COVID-19 testing method - A review

Patients infected with novel coronavirus exhibit a wide range of symptoms from common cold to pneumonia. Furthermore, several cases have been reported as asymptomatic across the globe. Since there are no conclusive clinical manifestations, clinicians have to rely more on laboratory diagnostic methods for confirmation of coronavirus disease. Hematological and biochemical tests are found to be of more prognostic value. Genetic assays by means of rRT-PCR technique is time-consuming but seems to be a more sensitive and specific test among the available testing methods for diagnosis of the coronavirus disease. Radiological imaging of the CT chest of the confirmed positive patients taken during the initial few days doesn't show any significant changes. However, from the second week onward a ground glass lesion pattern is observed. The immunological tests which are being used as a rapid testing method are found to be more false test negative. Hence, based on the effectiveness of various testing methods, it can be concluded that either rRT-PCR or mass antibody testing has to be done, and it has to be compared with CT chest in order to avoid false negatives across the globe which may help in the prevention of community spread of the disease.

Comparative evaluation of a dual-target real-time RT-PCR assay for COVID-19 diagnosis and assessment of performance in pooled saliva and nasopharyngeal swab samples

OBJECTIVES

Sensitive molecular diagnostic assays are essential for COVID-19 diagnosis. We evaluated the Hecin Scientific SARS-CoV-2 nucleic acid test kit, a dual-target real-time RT-PCR assay targeting the SARS-CoV-2 N and ORF1ab genes.

METHODS

The Hecin test kit's diagnostic performance in detecting SARS-CoV-2 RNA was compared to the LightMix Modular SARS and Wuhan CoV E-gene kit (TIB Molbiol) and an in-house single-tube nested real-time RT-PCR using 296 clinical specimens, 11 proficiency testing samples, and 30 low-positive deep throat saliva and nasopharyngeal swab (NPS) samples pooled into negative samples in ratios of 1:5, 1:10, and 1:30.

RESULTS

The limit-of-detection of the Hecin test kit was around 500 dC/mL for the N and ORF1ab targets. Sensitivity and specificity of the Hecin test kit were 98.1% (95% CI: 93.4-99.8%) and 100% (98.1-100%), respectively, when measured against the reference method. The Hecin test kit showed fair sensitivity (80%) in low-positive NPS samples pooled in ratios of 1:5 and 1:10. Its performance in pooled samples could be dramatically improved by adjusting the assay Ct cutoff.

CONCLUSION

The Hecin test kit enables sensitive and specific detection of SARS-CoV-2 in clinical samples and pooled samples.

Development and validation of a new triplex real-time quantitative reverse Transcriptase-PCR assay for the clinical detection of SARS-CoV-2

To increase the repertoire of PCR based laboratory developed tests (LDTs) for the detection of SARS-CoV-2, we describe a new multiplex assay (SORP), targeting the SARS-CoV-2's, Spike and ORF8 genes. The widely used human RNaseP internal control was modified to specifically co-amplify the RNaseP mRNA. The SORP triplex assay was tested on a cohort (n = 372; POS = 144/NEG = 228) of nasopharyngeal flocked swab (NPFS) specimens, previously tested for the presence of SARS-CoV-2 using a PCR assay targeting E and RdRp genes. The overall sensitivity and specificity of the SORP assay was: 99.31% (95% CI: 96.22–99.98%), 100.0% (95% CI: 98.4–100%) respectively. The SORP assay could also detect a panel of variants of concern (VOC) from the B1.1.7 (UK) and B1.351 (SA) lineage. In summary, access to a repertoire of new SARS-CoV-2 LDT's would assist diagnostic laboratories in developing strategies to overcome some of the testing issues encountered during high-throughput SARS-CoV-2 testing.

Review of the Microbiological Diagnostic Approaches of COVID-19

On March 12, the World Health Organization declared a pandemic following the exponential increase of SARS-CoV-2 cases. The rapid spread of the virus is due to both its high infectivity and the free circulation of unrecognized infectious cases. Thus, diagnostic testing is a key element to prevent further dissemination of the virus. Urged by WHO's call, laboratories worldwide have been working on nucleic acid tests protocols and immunoassays that became available, albeit poorly validated, within a comparatively short time. Since then, external studies evaluating these diagnostic tests have been published. The present study is a review of the COVID-19 diagnostic approaches, discussing both direct and indirect microbiological diagnoses. A compendium of the literature on commercial assays kits available to date is provided together with the conclusions drawn as well as RT-PCR protocols published by the WHO. Briefly, diagnostic accuracy varies according to time elapsed since symptom onset and evolves together with understanding of the COVID-19 disease. Taking into account all these variables will allow determining the most adequate diagnostic test to use and how to optimize diagnostic testing for COVID-19.

Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFY™) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS^® easyMAG^®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs. 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

COVID-19 Antibody Tests and Their Limitations

COVID-19, caused by the SARS-CoV-2 virus, has developed into a global health crisis, causing over 2 million deaths and changing people's daily life the world over. Current main-stream diagnostic methods in the laboratory include nucleic acid PCR tests and direct viral antigen tests for detecting active infections, and indirect human antibody tests specific to SARS-CoV-2 to detect prior exposure. In this Perspective, we briefly describe the PCR and antigen tests and then focus mainly on existing antibody tests and their limitations including inaccuracies and possible causes of unreliability. False negatives in antibody immunoassays can arise from assay formats, selection of viral antigens and antibody types, diagnostic testing windows, individual variance, and fluctuation in antibody levels. Reasons for false positives in antibody immunoassays mainly involve antibody cross-reactivity from other viruses, as well as autoimmune disease. The spectrum bias has an effect on both the false negatives and false positives. For assay developers, not only improvement of assay formats but also selection of viral antigens and isotopes of human antibodies need to be carefully considered to improve sensitivity and specificity. For clinicians, the factors influencing the accuracy of assays must be kept in mind to test patients using currently imperfect but available tests with smart tactics and realistic interpretation of the test results.

Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays

Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.

COVID-19 Pandemic: Review of Contemporary and Forthcoming Detection Tools

Recent severe acute respiratory syndrome 2 (SARS-CoV-2) known as COVID-19, presents a deadly challenge to the global healthcare system of developing and developed countries, exposing the limitations of health facilities preparedness for emerging infectious disease pandemic. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. In this review, we elaborate on various COVID-19 diagnostic tools that are available or under investigation. Consequently, cell culture, followed by an indirect fluorescent antibody, is one of the most accurate methods for detecting SARS-CoV-2 infection. However, restrictions imposed by the regulatory authorities prevented its general use and implementation. Diagnosis via radiologic imaging and reverse transcriptase PCR assay is frequently employed, considered as standard procedures, whereas isothermal amplification methods are currently on the verge of clinical introduction. Notably, techniques such as CRISPR-Cas and microfluidics have added new dimensions to the SARS-CoV-2 diagnosis. Furthermore, commonly used immunoassays such as enzyme-linked immunosorbent assay (ELISA), lateral flow immunoassay (LFIA), neutralization assay, and the chemiluminescent assay can also be used for early detection and surveillance of SARS-CoV-2 infection. Finally, advancement in the next generation sequencing (NGS) and metagenomic analysis are smoothing the viral detection further in this global challenge.

Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes

Background

DNA mismatches can affect the efficiency of PCR techniques if the intended target has mismatches in primer or probe regions. The accepted rule is that mismatches are detrimental as they reduce the hybridization temperatures, yet a more quantitative assessment is rarely performed.

Methods

We calculate the hybridization temperatures of primer/probe sets after aligning to SARS-CoV-2, SARS-CoV-1 and non-SARS genomes, considering all possible combinations of single, double and triple consecutive mismatches. We consider the mismatched hybridization temperature within a range of 5 ^∘C to the fully matched reference temperature.

Results

We obtained the alignments of 19 PCR primers sets that were recently reported for the detection of SARS-CoV-2 and to 21665 SARS-CoV-2 genomes as well as 323 genomes of other viruses of the coronavirus family of which 10 are SARS-CoV-1. We find that many incompletely aligned primers become fully aligned to most of the SARS-CoV-2 when mismatches are considered. However, we also found that many cross-align to SARS-CoV-1 and non-SARS genomes.

Conclusions

Some primer/probe sets only align substantially to most SARS-CoV-2 genomes if mismatches are taken into account. Unfortunately, by the same mechanism, almost 75% of these sets also align to some SARS-CoV-1 and non-SARS viruses. It is therefore recommended to consider mismatch hybridization for the design of primers whenever possible, especially to avoid undesired cross-reactivity.

Conventional and Nanotechnology-Based Sensing Methods for SARS Coronavirus (2019-nCoV)

Ongoing pandemic coronavirus (COVID-19) has affected over 218 countries and infected 88,512,243 and 1,906,853 deaths reported by Jan. 8, 2021. At present, vaccines are being developed in Europe, Russia, USA, and China, although some of these are in phase III of trials, which are waiting to be available for the general public. The only option available now is by vigorous testing, isolation of the infected cases, and maintaining physical and social distances. Numerous methods are now available or being developed for testing the suspected cases, which may act as carriers of the virus. In this review, efforts have been made to discuss the conventional as well as fast, rapid, and efficient testing methods developed for the diagnosis of 2019-nCoV.Testing methods can be based on the sensing of targets, which include RNA, spike proteins and antibodies such as IgG and IgM. Apart from the development of RNA targeted PCR, antibody and VSV pseudovirus neutralization assay along with several other diagnostic techniques have been developed. Additionally, nanotechnology-based sensors are being developed for the diagnosis of the virus, and these are also discussed.

Narrative review of the novel coronavirus SARS-CoV-2: update on genomic characteristics, transmissions and animal model

Two outbreaks of severe respiratory infection caused by severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) caused global pandemics and highlighted the importance of preparedness for respiratory CoVs. Recently, a third highly pathogenic CoV, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, Hubei, China and posed a public health crisis worldwide. Here, we focus on the recent advances of the novel CoV, and discuss its genomic similarity with other CoVs, transmission, animal model and clinical treatment of coronavirus disease 2019 (COVID-19) induced by SARS-CoV-2, which help epidemic prevention and control, and guide treatment strategies.

Current advances in the detection of COVID-19 and evaluation of the humoral response

The new outbreak caused by coronavirus SARS-CoV-2 started at the end of 2019 and was declared a pandemic in March 2020. Since then, several diagnostic approaches have been re-adapted, and also improved from the previous detections of SARS and MERS coronavirus. The best strategy to handle this situation seems to rely on a triad of detection methods: (i) highly sensitive and specific techniques as the gold standard method, (ii) easier and faster point of care tests accessible for large population screening, and (iii) serology assays to complement the direct detection and to use for surveillance. In this study, we assessed the techniques and tests described in the literature, their advantages and disadvantages, and the interpretation of the results. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) is undoubtedly the gold standard technique utilized not only for diagnostics, but also as a standard for comparison and validation of newer approaches. Other nucleic acid amplification methods have been shown to be adequate as point of care (POC) diagnostic tests with similar performance as RT-qPCR. The analysis of seroconversion with immunotests shows the complexity of the immune response to COVID-19. The detection of anti-SARS-CoV-2 antibodies can also help to detect previously infected asymptomatic individuals with negative RT-qPCR tests. Nevertheless, more controlled serology cohort studies should be performed as soon as possible to understand the immune response to SARS-CoV-2.

Approaches towards fighting the COVID‑19 pandemic (Review)

The coronavirus disease 2019 (COVID‑19) outbreak, which has caused >46 millions confirmed infections and >1.2 million coronavirus related deaths, is one of the most devastating worldwide crises in recent years. Infection with COVID‑19 results in a fever, dry cough, general fatigue, respiratory symptoms, diarrhoea and a sore throat, similar to those of acute respiratory distress syndrome. The causative agent of COVID‑19, SARS‑CoV‑2, is a novel coronavirus strain. To date, remdesivir has been granted emergency use authorization for use in the management of infection. Additionally, several efficient diagnostic tools are being actively developed, and novel drugs and vaccines are being evaluated for their efficacy as therapeutic agents against COVID‑19, or in the prevention of infection. The present review highlights the prevalent clinical manifestations of COVID‑19, characterizes the SARS‑CoV‑2 viral genome sequence and life cycle, highlights the optimal methods for preventing viral transmission, and discusses possible molecular pharmacological mechanisms and approaches in the development of anti‑SARS‑CoV‑2 therapeutic agents. In addition, the use of traditional Chinese medicines for management of COVID‑19 is discussed. It is expected that novel anti‑viral agents, vaccines or an effective combination therapy for treatment/management of SARS‑CoV‑2 infection and spread therapy will be developed and implemented in 2021, and we would like to extend our best regards to the frontline health workers across the world in their fight against COVID‑19.

COVID-19 diagnostic laboratory strategies: modern technologies and development trends (review of literature)

The COVID-19 pandemic, associated with the new coronavirus SARS-CoV-2, has caused a surge in incidence worldwide, as well as a severe crisis in global health and economy. Therefore, fast and accurate diagnosis of infection is key to timely treatment and elimination of the spread of the virus. Currently, the standard method for detecting coronavirus is reverse transcription polymerase chain reaction (RT-PCR). However, this method requires expensive equipment and trained personnel, which limits the conduct of mass testing and lengthens the time to obtain a research result. Serological tests for antibodies against SARS-CoV-2 and the determination of protective immunity in various populations are used to retrospectively identify patients with asymptomatic and mild forms of infection, monitor the course of infection in hospitalized patients, and also track contacts and epidemiological surveillance. The use of standard methods for diagnosing COVID-19 in conditions of mass morbidity, especially in conditions of insufficient resources and lack of appropriate infrastructure, is associated with a number of limitations. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. Therefore, the search and development of new, fast, inexpensive, simple, device-free and no less sensitive and specific tests is an urgent task. The review examines new laboratory technologies for diagnosing a new infection - loop isothermal amplification (LAMP) and immunochromatographic analysis (ICA), which can become a real alternative to the used molecular and enzyme immunoassay methods. The dynamic development of these methods in recent years expands the prospects for their use both for diagnosing COVID-19 and monitoring a pandemic.

On the Challenges for the Diagnosis of SARS-CoV-2 Based on a Review of Current Methodologies

Diagnosis of COVID-19 has been challenging owing to the need for mass testing and for combining distinct types of detection to cover the different stages of the infection. In this review, we have surveyed the most used methodologies for diagnosis of COVID-19, which can be basically categorized into genetic-material detection and immunoassays. Detection of genetic material with real-time polymerase chain reaction (RT-PCR) and similar techniques has been achieved with high accuracy, but these methods are expensive and require time-consuming protocols which are not widely available, especially in less developed countries. Immunoassays for detecting a few antibodies, on the other hand, have been used for rapid, less expensive tests, but their accuracy in diagnosing infected individuals has been limited. We have therefore discussed the strengths and limitations of all of these methodologies, particularly in light of the required combination of tests owing to the long incubation periods. We identified the bottlenecks that prevented mass testing in many countries, and proposed strategies for further action, which are mostly associated with materials science and chemistry. Of special relevance are the methodologies which can be integrated into point-of-care (POC) devices and the use of artificial intelligence that do not require products from a well-developed biotech industry.

Perceived Effectiveness, Safety, and Attitudes Toward the Use of Nucleic Tests of SARS-CoV-2 Among Clinicians and General Public in China

Objective: To assess whether there is a knowledge gap about the use of test kits for residents and to explore the knowledge, attitudes, and practices of using test kits in China during the coronavirus disease 2019 (COVID-19) epidemic. Method: An online-based, nationwide, and cross-sectional study was conducted. A total of 1,167 respondents were recruited from June 19 to July 2, 2020. All participants completed a validated questionnaire written in Chinese. Electronic consent was obtained from all participants upon their agreement to commence the questionnaire. Perceived efficacy, safety, and their attitudes toward the use of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing kits were measured. Result: The majority of the study respondents were female [749 (64.2%)], aged 31-40 years old [372 (31.9%)], and located in mainland China [1,137 (97.4%)]. The majority of the respondents held a positive view toward the introduction of the fast-track approval policy for novel coronavirus testing products (6.16 ± 1.30) as well as toward putting more investment in scientific research and biomedicine to improve the detection accuracy of detection kits (5.94 ± 1.55) in China. The respondents valued the detection accuracy more as opposed to the detection time of the testing kits (4.66 ± 2.00), whereas few participants agreed that in the research and development process, detection accuracy could be sacrificed to speed up production and coverage capacity (3.02 ± 2.04). Conclusion: The majority of the participants have a basic knowledge of the detection methods of the SARS-CoV-2 virus and the types of test kits, as well as great confidence in China's domestic production of test kits and decisions. However, how basic knowledge, high compliance, and positive attitudes play a role in easing the tension of the pandemic still remains unknown.

SARS-CoV-2 RapidPlex: A Graphene-Based Multiplexed Telemedicine Platform for Rapid and Low-Cost COVID-19 Diagnosis and Monitoring

The COVID-19 pandemic is an ongoing global challenge for public health systems. Ultrasensitive and early identification of infection is critical in preventing widespread COVID-19 infection by presymptomatic and asymptomatic individuals, especially in the community and in-home settings. We demonstrate a multiplexed, portable, wireless electrochemical platform for ultra-rapid detection of COVID-19: the SARS-CoV-2 RapidPlex. It detects viral antigen nucleocapsid protein, IgM and IgG antibodies, as well as the inflammatory biomarker C-reactive protein, based on our mass-producible laser-engraved graphene electrodes. We demonstrate ultrasensitive, highly selective, and rapid electrochemical detection in the physiologically relevant ranges. We successfully evaluated the applicability of our SARS-CoV-2 RapidPlex platform with COVID-19-positive and COVID-19-negative blood and saliva samples. Based on this pilot study, our multiplexed immunosensor platform may allow for high-frequency at-home testing for COVID-19 telemedicine diagnosis and monitoring.

Reliability of real-time RT-PCR tests to detect SARS-Cov-2: A literature review

In the face of the COVID-19 (Coronavirus Disease 2019) pandemic, the World Health Organization (WHO) has urged countries to test the population more widely. Clinical laboratories have been confronted with a huge demand for testing and have had to make urgent preparations for staff training, to establish new analytical processes, reorganize the workspace, and stock up on specific equipment and diagnostic test kits. The reliability of SARS-Cov-2 test results is of critical importance, given the impact it has on patient care and the management of the health crisis. A review of the literature available for the period leading up to and including June 2020 on the reliability of SARS-Cov-2 (Severe Acute Respiratory Syndrome Coronavirus) detection methods using real-time RT PCR (Reverse Transcription - Polymerase Chain Reaction) brings together the primary factors teams of scientists claim or demonstrate to affect the reliability of results. A description is given of the RT-PCR testing method, followed by a presentation of the characteristics and validation techniques used. A summary of data from the literature on the reliability of tests and commercial kits for SARS-Cov-2 detection, including current uncertainties with regard to the molecular targets selected and genetic diversity of SARS-Cov-2 is provided. The limitations and perspectives are then discussed in detail in the light of the bibliographic data available. Many questions have been asked that still remain unanswered. The lack of knowledge about this novel virus, which appeared at the end of 2019, has a significant impact on the technical capacity to develop reliable, rapid and practical tools for its detection.

Contribution of CT Features in the Diagnosis of COVID-19

The outbreak of novel coronavirus disease 2019 (COVID-19) first occurred in Wuhan, Hubei Province, China, and spread across the country and worldwide quickly. It has been defined as a major global health emergency by the World Health Organization (WHO). As this is a novel virus, its diagnosis is crucial to clinical treatment and management. To date, real-time reverse transcription-polymerase chain reaction (RT-PCR) has been recognized as the diagnostic criterion for COVID-19. However, the results of RT-PCR can be complemented by the features obtained in chest computed tomography (CT). In this review, we aim to discuss the diagnosis and main CT features of patients with COVID-19 based on the results of the published literature, in order to enhance the understanding of COVID-19 and provide more detailed information regarding treatment.

Combinations of PCR and Isothermal Amplification Techniques Are Suitable for Fast and Sensitive Detection of SARS-CoV-2 Viral RNA

The newly identified coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes coronavirus disease 2019 (COVID-19) and has affected over 25 million people worldwide as of August 31, 2020. To aid in the development of diagnostic kits for rapid and sensitive detection of the virus, we evaluated a combination of polymerase chain reaction (PCR) and isothermal nucleic acid amplification techniques. Here, we compared conventional PCR and loop-mediated isothermal amplification (LAMP) methods with hybrid techniques such as polymerase chain displacement reaction (PCDR) and a newly developed PCR-LAMP method. We found that the hybrid methods demonstrated higher sensitivity and assay reaction rates than those of the classic LAMP and PCR techniques and can be used to for SARS-CoV-2 detection. The proposed methods based on the modern hybrid amplification techniques markedly improve virus detection and, therefore, can be extremely useful in the development of new diagnostic kits.

Gene signatures of SARS-CoV/SARS-CoV-2-infected ferret lungs in short- and long-term models

Coronaviruses (CoVs) consist of six strains, and the severe acute respiratory syndrome coronavirus (SARS-CoV), newly found coronavirus (SARS-CoV-2) has rapidly spread leading to a global outbreak. The ferret (Mustela putorius furo) serves as a useful animal model for studying SARS-CoV/SARS-CoV-2 infection and developing therapeutic strategies. A holistic approach for distinguishing differences in gene signatures during disease progression is lacking. The present study discovered gene expression profiles of short-term (3 days) and long-term (14 days) ferret models after SARS-CoV/SARS-CoV-2 infection using a bioinformatics approach. Through Gene Ontology (GO) and MetaCore analyses, we found that the development of stemness signaling was related to short-term SARS-CoV/SARS-CoV-2 infection. In contrast, pathways involving extracellular matrix and immune responses were associated with long-term SARS-CoV/SARS-CoV-2 infection. Some highly expressed genes in both short- and long-term models played a crucial role in the progression of SARS-CoV/SARS-CoV-2 infection, including DPP4, BMP2, NFIA, AXIN2, DAAM1, ZNF608, ME1, MGLL, LGR4, ABHD6, and ACADM. Meanwhile, we revealed that metabolic, glucocorticoid, and reactive oxygen species-associated networks were enriched in both short- and long-term infection models. The present study showed alterations in gene expressions from short-term to long-term SARS-CoV/SARS-CoV-2 infection. The current result provides an explanation of the pathophysiology for post-infectious sequelae and potential targets for treatment.

Coronavirus (SARS-CoV-2) Pandemic: Future Challenges for Dental Practitioners

In the context of the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) pandemic, the medical system has been subjected to many changes. Face-to-face treatments have been suspended for a period of time. After the lockdown, dentists have to be aware of the modalities to protect themselves and their patients in order not to get infected. Dental practitioners are potentially exposed to a high degree of contamination with SARS-CoV-2 while performing dental procedures that produce aerosols. It should also be noted that the airways, namely the oral cavity and nostrils, are the access pathways for SARS-CoV-2. In order to protect themselves and their patients, they have to use full personal protective equipment. Relevant data regarding this pandemic are under evaluation and are still under test. In this article, we made a synthesis about the way in which SARS-CoV-2 spreads, how to diagnose a novel corona virus infection, what the possible treatments are, and which protective personal equipment we can use to stop its spreading.

A Body Tracking-Based Low-Cost Solution for Monitoring Workers' Hygiene Best Practices during Pandemics

Since its beginning at the end of 2019, the pandemic spread of the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) caused more than one million deaths in only nine months. The threat of emerging and re-emerging infectious diseases exists as an imminent threat to human health. It is essential to implement adequate hygiene best practices to break the contagion chain and enhance society preparedness for such critical scenarios and understand the relevance of each disease transmission route. As the unconscious hand-face contact gesture constitutes a potential pathway of contagion, in this paper, the authors present a prototype system based on low-cost depth sensors able to monitor in real-time the attitude towards such a habit. The system records people's behavior to enhance their awareness by providing real-time warnings, providing for statistical reports for designing proper hygiene solutions, and better understanding the role of such route of contagion. A preliminary validation study measured an overall accuracy of 91%. A Cohen's Kappa equal to 0.876 supports rejecting the hypothesis that such accuracy is accidental. Low-cost body tracking technologies can effectively support monitoring compliance with hygiene best practices and training people in real-time. By collecting data and analyzing them with respect to people categories and contagion statistics, it could be possible to understand the importance of this contagion pathway and identify for which people category such a behavioral attitude constitutes a significant risk.

Detection of COVID-19: A review of the current literature and future perspectives

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) worldwide pandemic. This unprecedented situation has garnered worldwide attention. An effective strategy for controlling the COVID-19 pandemic is to develop highly accurate methods for the rapid identification and isolation of SARS-CoV-2 infected patients. Many companies and institutes are therefore striving to develop effective methods for the rapid detection of SARS-CoV-2 ribonucleic acid (RNA), antibodies, antigens, and the virus. In this review, we summarize the structure of the SARS-CoV-2 virus, its genome and gene expression characteristics, and the current progression of SARS-CoV-2 RNA, antibodies, antigens, and virus detection. Further, we discuss the reasons for the observed false-negative and false-positive RNA and antibody detection results in practical clinical applications. Finally, we provide a review of the biosensors which hold promising potential for point-of-care detection of COVID-19 patients. This review thereby provides general guidelines for both scientists in the biosensing research community and for those in the biosensor industry to develop a highly sensitive and accurate point-of-care COVID-19 detection system, which would be of enormous benefit for controlling the current COVID-19 pandemic.

Molecular diagnosis of COVID-19 in different biologic matrix, their diagnostic validity and clinical relevance: A systematic review

Due to COVID 19 outbreak many studies are being conducted for therapeutic strategies and vaccines but detection methods play an important role in the containment of the disease. Hence, this systematic review aims to evaluate the effectiveness of the molecular detection techniques in COVID-19. For framing the systematic review 6 literature databases (PubMed, EMBASE, OVID, Web of Science, Scopus and Google Scholar) were searched for relevant studies and articles were screened for relevant content till 25th April 2020. Observations from this systematic review reveal the utility of RT-PCR with serological testing as one such method cannot correlate with accurate results. Availability of point of care devices do not conform to sensitivity and specificity in comparison to the conventional methods due to lack of clinical investigations. Pivotal aim of molecular and serological research is the development of detection methods that can support the clinical decision making of patients suspected with SARS-CoV-2. However, none of the methods were 100% sensitive and specific; hence additional studies are required to overcome the challenges addressed here. We hope that the present article with its observations and suggestions will assist the researchers to realize this vision in future.

Biosafety Concerns During the Collection, Transportation, and Processing of COVID-19 Samples for Diagnosis

The coronavirus disease 2019 (COVID-19) pandemic, which started in China, has created a panic among the general public and health care/laboratory workers. Thus far, there is no medication or vaccine to prevent and control the spread of COVID-19. As the virus is airborne and transmitted through droplets, there has been significant demand for face masks and other personal protective equipment to prevent the spread of infection. Health care and laboratory workers who come in close contact with infected people or material are at a high risk of infection. Therefore, robust biosafety measures are required at hospitals and laboratories to prevent the spread of COVID-19. Various diagnostic platforms including of serological, molecular and other advanced tools and techniques have been designed and developed for rapid detection of SARS-CoV-2 and each has its own merits and demerits. Molecular assays such as real-time reverse transcriptase polymerase chain reaction (rRT-PCR) has been used worldwide for diagnosis of COVID-19. Samples such as nasal swabs or oropharyngeal swabs are used for rRT-PCR. Laboratory acquired infection has been a significant problem worldwide, which has gained importance during the current pandemic as the samples for rRT-PCR may contain intact virus with serious threat. COVID-19 can spread to workers during the sampling, transportation, processing, and disposal of tested samples. Here, we present an overview on advances in diagnosis of COVID-19 and details the issues associated with biosafety procedures and potential safety precautions to be followed during collection, transportation, and processing of COVID-19 samples for laboratory diagnosis so as to avoid virus infection.

The diagnostic methods in the COVID-19 pandemic, today and in the future

INTRODUCTION

The emergence of anovel coronavirus identified in patients with unknown cause of acute respiratory disease in Wuhan, China at the end of 2019 has caused aglobal outbreak. The causative coronavirus was later named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease caused by SARS-CoV-2 was named as Coronavirus Disease-2019 (COVID-19). As of 10 August 2020, more than 19,718,030 confirmed cases and 728,013 deaths have been reported. COVID-19 is spread via respiratory droplets which are inhaled into the lungs.

AREAS COVERED

In this article, we summarized the knowledge about the causative pathogen of COVID-19 and various diagnostic methods in this pandemic for better understanding of the limitations and the nuances of virus testing for COVID-19.

EXPERT OPINION

In this pandemic, rapid and accurate identification of COVID-19 patients are critical to break the chain of infection in the community. RT-PCR provides a rapid and reliable identification of SARS-CoV-2 infection. In the future, molecular diagnostics will still be the gold standard and next-generation sequencing can help us to understand more on the pathogenesis and detect novel mutations. It is believed that more sophisticated detection methods will be introduced to detect SARS-CoV-2 as earliest as possible.

Heat inactivation decreases the qualitative real-time RT-PCR detection rates of clinical samples with high cycle threshold values in COVID-19

SARS-CoV-2 has caused COVID-19 pandemic globally in the beginning of 2020, and qualitative real-time RT-PCR has become the gold standard in diagnosis. As SARSCoV-2 with strong transmissibility and pathogenicity, it has become a professional consensus that clinical samples from suspected patients should be heat inactivated at 56°C for 30 min before further processing. However, previous studies on the effect of inactivation on qualitative real-time RT-PCR were conducted with diluted samples rather than clinical samples. The aim of this study was to investigate whether heat inactivation on clinical samples before detection will affect the accuracy of qualitative real-time RT-PCR detection. All 46 throat swab samples from 46 confirmed inpatients were detected by qualitative real-time RT-PCR directly, as well as after heat inactivation. Heat-Inactivation has significantly influenced the qualitative detection results on clinical samples, especially weakly positive samples. The results indicate the urgency to establish a more suitable protocol for COVID-19 clinical sample's inactivation.

Six decades of lateral flow immunoassay: from determining metabolic markers to diagnosing COVID-19

Technologies based on lateral flow immunoassay (LFIA), known in some countries of the world as immunochromatographic tests, have been successfully used for the last six decades in diagnostics of many diseases and conditions as they allow rapid detection of molecular ligands in biosubstrates. The popularity of these diagnostic platforms is constantly increasing in healthcare facilities, particularly those facing limited budgets and time, as well as in household use for individual health monitoring. The advantages of these low-cost devices over modern laboratory-based analyzers come from their availability, opportunity of rapid detection, and ease of use. The attractiveness of these portable diagnostic tools is associated primarily with their high analytical sensitivity and specificity, as well as with the easy visual readout of results. These qualities explain the growing popularity of LFIA in developing countries, when applied at small hospitals, in emergency situations where screening and monitoring health condition is crucially important, and as well as for self-testing of patients. These tools have passed the test of time, and now LFIA test systems are fully consistent with the world's modern concept of ‘point-of-care testing’, finding a wide range of applications not only in human medicine, but also in ecology, veterinary medicine, and agriculture. The extensive opportunities provided by LFIA contribute to the continuous development and improvement of this technology and to the creation of new-generation formats. This review will highlight the modern principles of design of the most widely used formats of test-systems for clinical laboratory diagnostics, summarize the main advantages and disadvantages of the method, as well as the current achievements and prospects of the LFIA technology. The latest innovations are aimed at improving the analytical performance of LFIA platforms for the diagnosis of bacterial and viral infections, including COVID-19.

Development and Evaluation of Novel and Highly Sensitive Single-Tube Nested Real-Time RT-PCR Assays for SARS-CoV-2 Detection

Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.