Laboratory verification of an RT-PCR assay for SARS-CoV-2

Rapid and sensitive detection of SARS-CoV-2 IgM through luciferase luminescence on an automatic platform

SARS-CoV-2 has brought a global health crisis worldwide. IgM is an early marker in sera after the infections, and the detection of IgM is crucial to assist diagnosis and evaluate the vaccination clinically. Herein, we developed an automated platform to identify IgM against SARS-CoV-2 in sera. Streptavidin-magnetic beads were utilized to bind to a biotinylated anti-IgM antibody, which was employed to capture IgM in sera. RBD fused luciferase hGluc was employed to label the trapped IgM against RBD and the signal of luminescence of hGluc with the substrate of coelenterazine corresponded to the amount of SARS-CoV-2 IgM conjugated to the magnetic beads. An appropriate cut-off value of the designed method was defined by a set of negative samples and positive samples with 100 % sensitivity and 100 % specificity. Through serial dilution of a positive sample, it was found that the method has a better sensitivity than ELISA. The application to determine IgM against SARS-CoV-2 demonstrated a good performance of the method. The developed system can complete the analysis of SARS-CoV-2 IgM within 25 min. Through the substitution of RBD antigen with antigens of other pathogens in this platform, the automated detection of IgM against the corresponding pathogens can be realized.

M gene targeted qRT-PCR approach for SARS-CoV-2 virus detection

Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection, and several qRT-PCR kits have been established targeting different genes of the virus. Due to the high mutation rate of these genes, false negative results arise thus complicating the interpretation of the diagnosis and increasing the need of alternative targets. In this study, an alternative approach for the detection of SARS-CoV-2 viral RNA targeting the membrane (M) gene of the virus using qRT-PCR was described. Performance evaluation of this newly developed in-house assay against commercial qRT-PCR kits was done using clinical oropharyngeal specimens of COVID-19 positive patients. The limit of detection was determined using successive dilutions of known copies of SARS-CoV-2 pseudovirus. The M gene based assay was able to detect a minimum of 100 copies of virus/mL indicating its capacity to detect low viral load. The assay showed comparable accuracy, sensitivity and specificity with commercially available kits while detecting all the variants efficiently. The study concluded that the in-house M gene based assay might be an effective alternative for the currently available commercial qRT-PCR kits.

Portable high-throughput multimodal immunoassay platform for rapid on-site COVID-19 diagnostics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a causal agent of Coronavirus Disease 2019 (COVID-19) has led to the global pandemic. Though the real-time reverse transcription polymerase chain reaction (RT-PCR) acting as a gold-standard method has been widely used for COVID-19 diagnostics, it can hardly support rapid on-site applications or monitor the stage of disease development as well as to identify the infection and immune status of rehabilitation patients. To suit rapid on-site COVID-19 diagnostics under various application scenarios with an all-in-one device and simple detection reagents, we propose a high-throughput multimodal immunoassay platform with fluorescent, colorimetric, and chemiluminescent immunoassays on the same portable device and a multimodal reporter probe using quantum dot (QD) microspheres modified with horseradish peroxidase (HRP) coupled with goat anti-human IgG. The recombinant nucleocapsid protein fixed on a 96-well plate works as the capture probe. In the condition with the target under detection, both reporter and capture probes can be bound by such target. When illuminated by excitation light, fluorescence signals from QD microspheres can be collected for target quantification often at a fast speed. Additionally, when pursuing simple detection without using any sensing devices, HRP-catalyzed TMB colorimetric immunoassay is employed; and when pursuing highly sensitive detection, HRP-catalyzed luminol chemiluminescent immunoassay is established. Verified by the anti-SARS-CoV-2 N humanized antibody, the sensitivities of colorimetric, fluorescent, and chemiluminescent immunoassays are respectively 20, 80, and 640 times more sensitive than that of the lateral flow colloidal gold immunoassay strip. Additionally, such a platform can simultaneously detect multiple samples at the same time thus supporting high-throughput sensing; and all these detecting operations can be implemented on-site within 50 min relying on field-operable processing and field-portable devices. Such a high-throughput multimodal immunoassay platform can provide a new all-in-one solution for rapid on-site diagnostics of COVID-19 for different detecting purposes.

A loop-mediated isothermal amplification-enabled analytical assay for the detection of SARS-CoV-2: A review

The number of words: 4645, the number of figures: 4, the number of tables: 1The outbreak of COVID-19 in December 2019 caused a global pandemic of acute respiratory disease, and with the increasing virulence of mutant strains and the number of confirmed cases, this has resulted in a tremendous threat to global public health. Therefore, an accurate diagnosis of COVID-19 is urgently needed for rapid control of SARS-CoV-2 transmission. As a new molecular biology technology, loop-mediated isothermal amplification (LAMP) has the advantages of convenient operation, speed, low cost and high sensitivity and specificity. In the past two years, rampant COVID-19 and the continuous variation in the virus strains have demanded higher requirements for the rapid detection of pathogens. Compared with conventional RT-PCR and real-time RT-PCR methods, genotyping RT-LAMP method and LAMP plus peptide nucleic acid (PNA) probe detection methods have been developed to correctly identified SARS-CoV-2 variants, which is also why LAMP technology has attracted much attention. LAMP detection technology combined with lateral flow assay, microfluidic technology and other sensing technologies can effectively enhance signals by nucleic acid amplification and help to give the resulting output in a faster, more convenient and user-friendly way. At present, LAMP plays an important role in the detection of SARS-CoV-2.

Evaluation of Alternative Transport Media for RT-qPCR-Based SARS-CoV-2 Testing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is still rapidly spreading as of March 2022. An accurate and rapid molecular diagnosis is essential to determine the exact number of confirmed cases. Currently, the viral transport medium (VTM) required for testing is in short supply due to a sharp increase in the laboratory tests performed, and alternative VTMs are needed to alleviate the shortage. Guanidine thiocyanate-based media reportedly inactivate SARS-CoV-2 and are compatible with quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays, but the compatibility and the viral detection capacity have not been fully validated. To evaluate the guanidine thiocyanate-based Gene Transport Medium (GeneTM) as an alternative VTM, we prepared 39 SARS-CoV-2-positive and 7 SARS-CoV-2-negative samples in GeneTM, eNAT™, and phosphate-buffered saline (PBS). The cycle threshold (Ct) values of three SARS-CoV-2 targets (the S, RdRP, and N genes) were analyzed using RT-qPCR testing. The comparison of Ct values from the positive samples showed a high correlation (R2= 0.95–0.96) between GeneTM and eNAT™, indicating a comparable viral detection capacity. The delta Ct values of the SARS-CoV-2 genes in each transport medium were maintained for 14 days at cold (4°C) or room (25°C) temperatures, suggesting viral samples were stably preserved in the transport media for 14 days. Together, GeneTM is a potential alternative VTM with comparable RT-qPCR performance and stability to those of standard media.

The immunomodulatory effects of Qushi Jianpi Hewei Decoction (QJHD) for patients with COVID-19 by metagenomics and transcriptomic sequencing

Ethnopharmacological relevance

Several studies have confirmed that intestinal microflora dysbiosis correlates with the severity of COVID-19 patients. Clinical meta-analysis and our data show that the circulating miRNAs like miRNA-146 and the levels of serum cytokines in the peripheral blood are closely related to mild to moderate COVID-19 patients. Despite the widespread use of traditional herbal medicine for COVID-19 in China, the mechanisms remain largely uncovered.

Aim of the study

We conducted an observational case-control study to verify the efficacy and safety of traditional Chinese herbal medicine Qushi Jianpi Hewei Decoction (QJHD) for mild to moderate COVID-19 patients, and investigated the potential biomolecular mechanisms through metagenomics and transcriptomic sequencing methods.

Materials and methods

QJHD was given orally twice a day individually for 14 to 28 days. A total of 10 patients were enrolled in the study and given QJHD. We observed advantages in clinical cure time rate, and the relief of gastrointestinal symptoms as compared with reports in the literature. The metagenomics sequencing data of fecal microflora and transcriptomic sequencing data of blood cell in patients with SARS-Cov-2 infection patients were selected compared to the healthy control donors.

Results

No serious adverse events were reported. Meanwhile, the transcriptome analysis showed a decrease of the hsa-miR-21-5p expression in peripheral blood without QJHD. The species composition analysis showed an increase in the expression of Faecalibacterium prausnitzii in the intestinal tract; The interleukin-10 (IL-10) expression also in COVID-19 patient decreased in peripheral blood compared with healthy control donors. And we found an improvement in these parameters in patients taking QJHD.

Conclusions

Our findings show that QJHD could improve clinical outcomes of mild to moderate COVID-19 patients, probably through beneficial immunomodulatory effects by regulating Faecalibacterium prausnitzii in the intestinal tract and hsa-miR-21 and IL-10 expression in peripheral blood. (chictr.org.cn, ChiCTR2000030305)

Current molecular diagnostics assays for SARS-CoV-2 and emerging variants

Since the SARS-CoV-2 virus triggered the beginning of the COVID-19 pandemic, scientists, government officials, and healthcare professionals around the world recognized the need for accessible, affordable, and accurate testing to predict and contain the spread of COVID-19. In the months that followed, research teams designed, tested, and rolled out hundreds of diagnostic assays, each with different sampling methods, diagnostic technologies, and sensitivity levels. However, the contagious virus continued to spread; SARS-CoV-2 travelled through airborne particles and spread rapidly, despite the widening use of diagnostic assays. As the pandemic continued, hundreds of millions of people contracted COVID-19 and millions died worldwide. With so many infections, SARS-CoV-2 received many opportunities to replicate and mutate, and from these mutations emerged more contagious, deadly, and difficult-to-diagnose viral mutants. Each change to the viral genome presented potential added challenges to containing the virus, and as such, researchers have continued developing and improving testing methods to keep up with COVID-19. In this chapter, we examine several SARS-CoV-2 variants that have emerged during the pandemic. Additionally, we discuss a few major COVID-19 diagnostic technique categories, including those involving real-time PCR, serology, CRISPR, and electronic biosensors. Finally, we address SARS-CoV-2 variants and diagnostic assays in the age of COVID-19 vaccines.

Rapid and Convenient Quantitative Analysis of SARS-CoV-2 RNA in Serous Saliva with a Direct PCR Method

Sensitive and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), frequently performed using direct polymerase chain reaction (PCR), is essential for restricting the spread of coronavirus disease 2019 (COVID-19). However, studies evaluating accurate detection are still required. This study evaluated the quantitativeness and sensitivity of the Ampdirect™ 2019-nCoV detection kit, a direct PCR method. Using saliva with or without Tris-buffered saline (TBS) dilution, linearity, and limits of the N1 and N2 regions of SARS-CoV-2 genomic RNA were assessed using EDX SARS-CoV-2 RNA standard dissolved in RNase-free water (RFW). Fluorescence intensities in non-diluted saliva were higher than those in TBS-diluted samples. Linear regression analysis of detected quantification cycle values and spiked standard RNA concentrations showed that the coefficient of determination of the N1 and N2 genes was 0.972 and 0.615 in RFW and 0.947 and 0.660 in saliva, respectively. N1- and N2-positive detection rates in saliva were 46% (6/13 tests) and 0% (0/12 tests) at one copy/reaction, respectively. These results indicate good quantitativeness and sensitivity for N1 but not for N2. Therefore, our findings reveal that the Ampdirect™ 2019-nCoV system, especially targeting the N1 gene, enables rapid and convenient quantification of SARS-CoV-2 RNA in saliva at one copy/reaction.

Comparison of four commercial RT-PCR diagnostic kits for COVID-19 in China

We compared the sensitivity and specificity of four commercial coronavirus disease (COVID-19) diagnostic kits using real-time reverse transcription-polymerase chain reaction (RT-PCR). Kits I-IV approved by the State Drug Administration of China were selected, and the detection targets were ORF1ab gene and N gene. Specificity was evaluated by detecting other respiratory viruses. The sensitivity and batch effect of each kit were evaluated by testing 10-fold dilutions of RNA. Clinical application was verified by testing nasopharyngeal swab and sputum specimens from COVID-19 patients. Among the 78 cases infected by other respiratory viruses, no amplification curve was observed using these four COVID-19 RT-PCR kits. The minimum detection limits of kits I-IV were 10-6 , 10-5 , 10-5 , and 10-6 dilutions, respectively, and concentrations were 10 copies/mL (10-5 dilution) and 1 copies/mL (10-6 dilution). The sensitivities of kits I-IV detected using 142 nasopharyngeal swab specimens from COVID-19 patients were 91.55%, 81.69%, 80.28%, and 90.85%, respectively, while they were 92.68%, 85.37%, 82.93%, and 93.90%, respectively, for the 82 sputum samples. The specificity of each kit was 100.00% (77/77). The total expected detection rate using sputum samples was 88.59% (691/780) higher than 86.15% (672/780) of nasopharyngeal swabs. Comparison of nasopharyngeal swab and sputum samples from the same COVID-19 patient led to the detection of ORF1ab and N genes in 16 (100%) sputum samples; only ORF1ab and N genes were detected in 12 (75%) and 14 (87.5%) nasopharyngeal swab specimens, respectively. In conclusion, comparison of commercial COVID-19 RT-PCR kits should be performed before using a new batch of such kits in routine diagnostics.

Laboratory verification of an RT-PCR assay for SARS-CoV-2

BACKGROUND

Reverse transcription-polymerase chain reaction (RT-PCR) is an extremely common clinical method for detecting pathogens, particularly for emerging infectious diseases such as the new coronavirus disease (COVID-19). Currently, detection of the RNA from the novel coronavirus SARS-CoV-2 is the gold standard for establishing a COVID-19 diagnosis. This study evaluates the characteristic performance of the analytical system in a clinical laboratory.

METHODS

A commercial SARS-CoV-2 RNA RT-PCR Kit used in a clinical laboratory is assessed based on ISO 15189 verification requirements. A multiple real-time RT-PCR assay for the RdRP, N, and E genes in SARS-CoV-2 is verified.

RESULTS

The analytical system exhibits good analytical sensitivity (1000 copies/mL) and specificity (100%); however, the values of 86.7% and 100% for analytical accuracy deserved attention, compared with two other types of methods. Overall, the kit is potentially useful for SARS-CoV-2 diagnostic testing and meets the verification requirements.

CONCLUSION

Compliance with international standards, such as ISO 15189, is valuable for clinical laboratories and for improving laboratory medicine quality and safety. Normalization is essential for obtaining reliable results from the SARS-CoV-2 RNA RT-PCR assay. This study aims to develop an improved SARS-CoV-2 verification framework compared with traditional molecular diagnostic methods, given the urgency of implementing new assays in clinical laboratories.