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1.
Chemosphere ; 333: 138682, 2023 Aug.
Article in English | MEDLINE | ID: covidwho-2317833

ABSTRACT

Wastewater monitoring and epidemiology have seen renewed interest during the recent COVID-19 pandemic. As a result, there is an increasing need to normalize wastewater-derived viral loads in local populations. Chemical tracers, both exogenous and endogenous compounds, have proven to be more stable and reliable for normalization than biological indicators. However, differing instrumentation and extraction methods can make it difficult to compare results. This review examines current extraction and quantification methods for ten common population indicators: creatinine, coprostanol, nicotine, cotinine, sucralose, acesulfame, androstenedione 5-hydroindoleacetic acid (5-HIAA), caffeine, and 1,7-dimethyluric acid. Some wastewater parameters such as ammonia, total nitrogen, total phosphorus, and daily flowrate were also evaluated. The analytical methods included direct injection, dilute and shoot, liquid/liquid, and solid phase extraction (SPE). Creatine, acesulfame, nicotine, 5-HIAA and androstenedione have been analysed by direct injection into LC-MS; however, most authors prefer to include SPE steps to avoid matrix effects. Both LC-MS and GC-MS have been successfully used to quantify coprostanol in wastewater, and the other selected indicators have been quantified successfully with LC-MS. Acidification to stabilize the sample before freezing to maintain the integrity of samples has been reported to be beneficial. However, there are arguments both for and against working at acidic pHs. Wastewater parameters mentioned earlier are quick and easy to quantify, but the data does not always represent the human population effectively. A preference for population indicators originating solely from humans is apparent. This review summarises methods employed for chemical indicators in wastewater, provides a basis for choosing an appropriate extraction and analysis method, and highlights the utility of accurate chemical tracer data for wastewater-based epidemiology.


Subject(s)
COVID-19 , Water Pollutants, Chemical , Humans , Wastewater , Nicotine/analysis , RNA, Viral , SARS-CoV-2 , Hydroxyindoleacetic Acid/analysis , Androstenedione/analysis , Cholestanol/analysis , Pandemics , Water Pollutants, Chemical/analysis , COVID-19/epidemiology , Solid Phase Extraction/methods , Indicators and Reagents
2.
Microbiol Spectr ; 11(3): e0373122, 2023 Jun 15.
Article in English | MEDLINE | ID: covidwho-2314896

ABSTRACT

Rapid diagnostic tests (RDTs) that detect antigen indicative of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection can help in making quick health care decisions and regularly monitoring groups at risk of infection. With many RDT products entering the market, it is important to rapidly evaluate their relative performance. Comparison of clinical evaluation study results is challenged by protocol design variations and study populations. Laboratory assays were developed to quantify nucleocapsid (N) and spike (S) SARS-CoV-2 antigens. Quantification of the two antigens in nasal eluates confirmed higher abundance of N than S antigen. The median concentration of N antigen was 10 times greater than S per genome equivalent. The N antigen assay was used in combination with quantitative reverse transcription (RT)-PCR to qualify a panel composed of recombinant antigens, inactivated virus, and clinical specimen pools. This benchmarking panel was applied to evaluate the analytical performance of the SD Biosensor Standard Q COVID-19 antigen (Ag) test, Abbott Panbio COVID-19 Ag rapid test, Abbott BinaxNOW COVID-19 Ag test, and the LumiraDx SARS-CoV-2 Ag test. The four tests displayed different sensitivities toward the different panel members, but all performed best with the clinical specimen pool. The concentration for a 90% probability of detection across the four tests ranged from 21 to 102 pg/mL of N antigen in the extracted sample. Benchmarking panels provide a quick way to verify the baseline performance of a diagnostic and enable direct comparisons between diagnostic tests. IMPORTANCE This study reports the results for severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) nucleocapsid (N) and spike (S) antigen quantification assays and their performance against clinical reverse transcription (RT)-PCR results, thus describing an open-access quantification method for two important SARS-CoV-2 protein analytes. Characterized N antigen panels were used to evaluate the limits of detection of four different rapid tests for SARS-CoV-2 against multiple sources of nucleocapsid antigen, demonstrating proof-of-concept materials and methodology to evaluate SARS-CoV-2 rapid antigen detection tests. Quantification of N antigen was used to characterize the relationship between viral count and antigen concentration among clinical samples and panel members of both clinical sample and viral culture origin. This contributes to a deeper understanding of protein antigen and molecular analytes and presents analytical methods complementary to clinical evaluation for characterizing the performance of both laboratory-based and point-of-care rapid diagnostics for SARS-CoV-2.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2 , Indicators and Reagents , Benchmarking , Diagnostic Tests, Routine , COVID-19 Testing
3.
Am J Clin Pathol ; 158(3): 401-408, 2022 09 02.
Article in English | MEDLINE | ID: covidwho-2287109

ABSTRACT

OBJECTIVES: In the fall of 2020, US medical centers were running out of rapid coronavirus disease 2019 (COVID-19) tests. The aim of this study is to evaluate the impact of an intervention to eliminate rapid test misutilization and to quantify the effect of the countermeasures to control rapid test ordering using a test utilization dashboard. METHODS: Interventions were made to preserve a severely limited supply of rapid diagnostic tests based on real-time analysis of a COVID-19 test utilization dashboard. This study is a retrospective observational study evaluating pre- and postintervention rates of appropriate rapid test use, reporting times, and cost/savings of resources used. RESULTS: This study included 14,462 severe acute respiratory syndrome coronavirus 2 reverse transcriptase polymerase chain reaction tests ordered during the study period. After the intervention, there was a 27.3% decrease in nonconforming rapid tests. Rapid test reporting time from laboratory receipt decreased by 1.47 hours. The number of days of rapid test inventory on hand increased by 39 days. CONCLUSIONS: Performing diagnostic test stewardship, informed by real-time review of a test utilization dashboard, was associated with significantly improved appropriate utilization of rapid diagnostic COVID-19 tests, improved reporting times, implied cost savings, and improved reagent inventory on hand, which facilitated the management of scarce resources during a pandemic.


Subject(s)
COVID-19 , COVID-19/diagnosis , COVID-19 Testing , Humans , Indicators and Reagents , Pandemics , SARS-CoV-2
4.
Diagn Microbiol Infect Dis ; 105(2): 115861, 2023 Feb.
Article in English | MEDLINE | ID: covidwho-2246547

ABSTRACT

Transmission by asymptomatic individuals is a persistent hurdle in the effort to control the spread of SARS-CoV-2. Therefore, it is essential to continue developing assays and evaluate their performance for detection of SARS-CoV-2 in individuals without COVID-19 symptoms. In this study, 223 nasopharyngeal swab specimens collected from COVID-19 asymptomatic individuals were tested using the BD SARS-CoV-2 (RT-PCR-based) reagents for the BD MAX™ System and compared with results obtained with the Biomerieux BioFire® Respiratory RT-PCR Panel. Positive and negative percent agreements of 100% (95% CI, 84.5%-100%) and 99.0% (95% CI, 96.5%-99.7%), respectively, were observed for the BD SARS-CoV-2 assay. These results demonstrate the effectiveness of the BD SARS-CoV-2 assay for detecting SARS-CoV-2 in asymptomatic individuals and suggest that this assay can facilitate optimized case surveillance and infection control efforts. Investigations using larger sample sizes of asymptomatic individuals would be beneficial to support the findings in this study.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19 Testing , Indicators and Reagents , Sensitivity and Specificity , Nasopharynx
5.
Molecules ; 28(1)2022 Dec 21.
Article in English | MEDLINE | ID: covidwho-2243502

ABSTRACT

Sulfonamides are the basic motifs for a whole generation of drugs from a large group of antibiotics. Currently, research in the field of the new sulfonamide synthesis has received a "second wind", due to the increase in the synthetic capabilities of organic chemistry and the study of their medical and biological properties of a wide spectrum of biological activity. New reagents and new reactions make it possible to significantly increase the number of compounds with a sulfonamide fragment in combination with other important pharmacophore groups, such as, for example, a wide class of N-containing heterocycles. The result of these synthetic possibilities is the extension of the activity spectrum-along with antibacterial activity, many of them exhibit other types of biological activity. Antiviral activity is also observed in a wide range of sulfonamide derivatives. This review provides examples of the synthesis of sulfonamide compounds with antiviral properties that can be used to develop drugs against coxsackievirus B, enteroviruses, encephalomyocarditis viruses, adenoviruses, human parainfluenza viruses, Ebola virus, Marburg virus, SARS-CoV-2, HIV and others. Since over the past three years, viral infections have become a special problem for public health throughout the world, the development of new broad-spectrum antiviral drugs is an extremely important task for synthetic organic and medicinal chemistry. Sulfonamides can be both sources of nitrogen for building a nitrogen-containing heterocyclic core and the side chain substituents of a biologically active substance. The formation of the sulfonamide group is often achieved by the reaction of the N-nucleophilic center in the substrate molecule with the corresponding sulfonylchloride. Another approach involves the use of sulfonamides as the reagents for building a nitrogen-containing framework.


Subject(s)
Antiviral Agents , COVID-19 , Humans , Antiviral Agents/pharmacology , Sulfonamides/pharmacology , Sulfonamides/chemistry , SARS-CoV-2 , Sulfanilamide , Anti-Bacterial Agents , Indicators and Reagents , Nitrogen
6.
Anal Chem ; 95(2): 1366-1375, 2023 01 17.
Article in English | MEDLINE | ID: covidwho-2185431

ABSTRACT

mRNA-based medicines are a promising modality for preventing virus-caused illnesses, including COVID-19, and treating various types of cancer and genetic diseases. To develop such medicines, methods to characterize long mRNA molecules are needed for quality control and metabolic analysis. Here, we developed an analytical platform based on isotope-dilution liquid chromatography-mass spectrometry (LC-MS) that quantitatively characterizes long, modified mRNAs by comparing them to a stable isotope-labeled reference with an identical sequence to that of the target medicine. This platform also includes database searching using the mass spectra as a query, which allowed us to confirm the primary structures of 200 to 4300 nt mRNAs including chemical modifications, with sequence coverage at 100%, to detect/identify defects in the sequences, and to define the efficiencies of the 5'-capping and integrity of the polyadenylated tail. Our findings indicated that this platform should be valuable for quantitatively characterizing mRNA vaccines and other mRNA medicines.


Subject(s)
COVID-19 , Humans , Indicators and Reagents , Mass Spectrometry/methods , Chromatography, Liquid/methods , Reference Standards , Isotopes , Isotope Labeling/methods
7.
Nature ; 611(7936): 570-577, 2022 11.
Article in English | MEDLINE | ID: covidwho-2106425

ABSTRACT

Expanding our global testing capacity is critical to preventing and containing pandemics1-9. Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required10-14. Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence15-20; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies21-29. Here we use a swarm of millimetre-sized magnets as mobile robotic agents ('ferrobots') for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations. Within a palm-sized printed circuit board-based programmable platform, we demonstrated the myriad of laboratory-equivalent operations involved in pooled testing. These operations were guided by an introduced square matrix pooled testing algorithm to identify the samples from infected patients, while maximizing the testing efficiency. We applied this automated technology for the loop-mediated isothermal amplification and detection of the SARS-CoV-2 virus in clinical samples, in which the test results completely matched those obtained off-chip. This technology is easily manufacturable and distributable, and its adoption for viral testing could lead to a 10-300-fold reduction in reagent costs (depending on the viral prevalence) and three orders of magnitude reduction in instrumentation cost. Therefore, it is a promising solution to expand our testing capacity for pandemic preparedness and to reimagine the automated clinical laboratory of the future.


Subject(s)
Automation , COVID-19 Testing , Magnets , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Robotics , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing/methods , Molecular Diagnostic Techniques/economics , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/economics , Nucleic Acid Amplification Techniques/methods , Pandemics/prevention & control , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Algorithms , Automation/economics , Automation/methods , Robotics/methods , Indicators and Reagents/economics
8.
Anal Chem ; 94(43): 14835-14845, 2022 11 01.
Article in English | MEDLINE | ID: covidwho-2087110

ABSTRACT

AZD7442 (tixagevimab [AZD8895]/cilgavimab [AZD1061]) is a monoclonal antibody (mAb) combination in development for the prevention and treatment of coronavirus disease 2019. Traditionally, bioanalysis of mAbs is performed using ligand binding assays (LBAs), which offer sensitivity, robustness, and ease of implementation. However, LBAs frequently require generation of critical reagents that typically take several months. Instead, we developed a highly sensitive (5 ng/mL limit of quantification) method using a hybrid LBA-liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) approach for quantification of the two codosed antibodies in serum and nasal lining fluid (NLF), a rare matrix. The method was optimized by careful selection of multiple reaction monitoring, capture reagents, magnetic beads, chromatographic conditions, evaluations of selectivity, and matrix effect. The final assay used viral spike protein receptor-binding domain as capture reagent and signature proteotypic peptides from the complementarity-determining region of each mAb for detection. In contrast to other methods of similar/superior sensitivity, our approach did not require multidimensional separations and can be operated in an analytical flow regime, ensuring high throughput and robustness required for clinical analysis at scale. The sensitivity of this method significantly exceeds typical sensitivity of ∼100 ng/mL for analytical flow 1D LBA-LC-MS/MS methods for large macromolecules, such as antibodies. Furthermore, infection and vaccination status did not impact method performance, ensuring method robustness and applicability to a broad patient population. This report demonstrated the general applicability of the hybrid LBA-LC-MS/MS approach to platform quantification of antibodies with high sensitivity and reproducibility, with specialized extension to matrices of increasing interest, such as NLF.


Subject(s)
COVID-19 , Tandem Mass Spectrometry , Humans , Chromatography, Liquid/methods , Tandem Mass Spectrometry/methods , SARS-CoV-2 , Reproducibility of Results , Antibodies, Monoclonal/analysis , Indicators and Reagents , Antibodies, Viral
9.
Clin Chim Acta ; 532: 89-94, 2022 Jul 01.
Article in English | MEDLINE | ID: covidwho-1966415

ABSTRACT

BACKGROUND: Determining what quarantine period and detection strategy are more effective and sustainable remains a challenge for further prevention and social stability. METHODS: From October 2020 to December 2021, 290,547 inbound overseas travelers were subject to government quarantine in Xiamen, China. The detection rate of COVID-19 during different quarantine periods using dual or single nucleic acid testing reagents. RESULTS: The COVID-19 positive rate was 1.79% (519/290,547). The detection rates during the 7-day, 14-day and 14+7-day quarantine periods using the dual reagents were 78.4%, 91.7%, and 100%, respectively. The detection rate of the 7-day, 14-day and 14+7-day quarantine periods were 73.99%, 86.51%, and 94.22%, respectively, using the Liferiver reagent and 72.25%, 84.59%, and 91.91%, respectively, using the Daan reagent. Based on the 14+7 day strategy, dual nucleic acid testing reagent strategy detected all imported cases, but 30 cases (5.78%) were not detected via Liferiver reagent and 42 (8.09%) cases not detected via Daan reagent. CONCLUSION: A 14+7-day quarantine period and dual nucleic acid testing reagent strategy are effective screening methods for COVID-19 among inbound overseas travelers. The superior detection rate of these strategies reduce the risk of secondary transmission of the SARS-CoV-2 virus.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , China , Humans , Indicators and Reagents , Quarantine , SARS-CoV-2
10.
11.
J Infect Chemother ; 28(9): 1295-1303, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1867379

ABSTRACT

BACKGROUND: To evaluate the performance of various reagents in automated analyzers for antibody detection against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: Using 100 serum samples from 100 individual patients diagnosed with SARS-CoV-2 infection, the precision, linearity, determination agreement, and correlation of five qualitative reagents (Elecsys Anti-SARS-CoV-2, ARCHITECT SARS-CoV-2 IgG, ARCHITECT SARS-CoV-2 IgM, Access SARS-CoV-2 IgM, and SARS-CoV-2 IgM) and four quantitative reagents (Elecsys Anti-SARS-CoV-2 S, ARCHITECT SARS-CoV-2 IgG II, Access SARS-CoV-2 IgG 1st IS, and SARS-COV-2 IgG S) were analyzed. A surrogate virus-neutralizing test (sVNT) kit was used to evaluate the measurement value of each quantitative reagent corresponding to the amount of neutralizing antibody, similar to that of patients in the late stage of infection. RESULTS: Precision and linearity were found to be sufficient for clinical use. Five discrepant samples were observed in the positive and negative judgments of the qualitative reagents for IgG, and one discrepant sample was observed in the qualitative reagent for IgM. Although the measurement values of the quantitative reagents were different, they were correlated with each reagent. The reference values inferred from the sVNT were Elecsys Anti-SARS-CoV-2: 71.8 U/L, ARCHITECT SARS-CoV-2 IgGⅡ: 2976.3 AU/mL, Access SARS-CoV-2 IgG 1st IS: 689.6 IU/mL, and SARS-CoV-2 IgG S: 19.3 U/L. CONCLUSIONS: The performance observed for each anti-SARS-CoV-2 antibody detection reagent was sufficient. The reference values based on the inhibition rate of sVNT have potential as indicators of the correlation of protection and are expected to be leveraged in automated antibody tests.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , COVID-19/diagnosis , Humans , Immunoglobulin G , Immunoglobulin M , Indicators and Reagents , Sensitivity and Specificity , Serologic Tests
12.
Lab Chip ; 22(12): 2307-2314, 2022 06 14.
Article in English | MEDLINE | ID: covidwho-1805674

ABSTRACT

The global COVID-19 pandemic caused by SARS-CoV-2 has resulted in an unprecedented economic and societal impact. Developing simple and accurate testing methods for point-of-care (POC) diagnosis is crucial not only for the control of COVID-19, but also for better response to similar outbreaks in the future. In this work, we present a novel proof-of-concept of a microfluidic microwave sensing method for POC diagnosis of the SARS-CoV-2 virus. This method relies on the antibody immobilized on the microwave sensor to selectively capture and concentrate the SARS-CoV-2 antigen or virus present in a buffer solution flowing through the sensor region in a microchannel. The capturing of the SARS-CoV-2 antigen or virus results in a change in the permittivity of the medium near the sensor region reflected by the resonance frequency shift which is used for detection. The use of microchannels offers precise control of the sample volume and the continuous flow nature also offers the potential to monitor the dynamic capturing process. The microwave-microfluidic device shows a good sensitivity of 0.1 ng ml-1 for the SARS-CoV-2 antigen and 4000 copies per ml for the SARS-CoV-2 virus. The resonance frequency shift presents a linear relationship with the logarithm of antigen or virus concentration, respectively. This detection method is able to distinguish SARS-CoV-2 from the antigen of human CD4 and two human coronaviruses (MERS and HKU1), which presents a new pathway towards POC diagnosis of the COVID-19 at the community level. It presents the potential to detect other viruses by functionalizing the microwave sensor with respective antibodies.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Indicators and Reagents , Microfluidics , Microwaves , Pandemics
13.
Spectrochim Acta A Mol Biomol Spectrosc ; 276: 121188, 2022 Aug 05.
Article in English | MEDLINE | ID: covidwho-1768515

ABSTRACT

Remdesivir was approved by the Food and Drug Administration for the treatment of COVID -19 in hospitalized adult and pediatric patients. Application of computational calculations for choosing the sensitive reagent in spectrophotometric quantitative analysis is very limited. Computational and theoretical studies were used for choosing the best acid dye for selective visible spectrophotometric quantitative analysis of remdesivir. The calculations were performed using Gaussian 03 software with the density functional theory method using B3LYP/6-31G(d) basis set. The theoretical studies revealed that bromophenol blue is a better match for remdesivir than other acid dyes due to the higher calculated interaction energy. The proposed method was based on the reaction of remdesivir with the computationally selected acid dye bromophenol blue to form a yellow ion-pair complex. The spectra showed absorption peaks at 418 nm. Various factors affecting the reaction were optimized. The method was successfully applied for the determination of remdesivir in the pharmaceutical preparation with good accuracy and precision. Beer's law was observed in the concentration range of 2-12 µg/mL of remdesivir. The proposed reaction was used as a basis for the spectrophotometric determination of remdesivir in pure form and in the pharmaceutical preparation.


Subject(s)
COVID-19 Drug Treatment , Coloring Agents , Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Bromphenol Blue/analysis , Child , Humans , Indicators and Reagents , Pharmaceutical Preparations/analysis , United States
14.
Bioanalysis ; 14(6): 317-324, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1704052

ABSTRACT

The COVID-19 pandemic continues to spread all over the world. In the process of emergency use authorization, the Center for Medical Device Evaluation of the China National Medical Products Administration issued 'Key Points of Technical Review for the Registration of SARS-CoV-2 Antigen/Antibody Detection Reagents' as the guidance of registration of antigen and antibody test reagents for the industry. In this document, clinical evaluation requirements of antigen detection reagents are elaborated. Based on the Key Points document and the authors' review practice, this article explains the evaluation methods and requirements of clinical performance of SARS-CoV-2 antigen-detecting rapid diagnostic tests, then analyzes the application scenarios and intended use of antigen detection reagents.


Subject(s)
COVID-19 Serological Testing/methods , Specimen Handling/methods , Antigens, Viral , COVID-19 Nucleic Acid Testing , China , Clinical Trials as Topic , Humans , Indicators and Reagents , Reagent Kits, Diagnostic , SARS-CoV-2/immunology
15.
Front Public Health ; 9: 808751, 2021.
Article in English | MEDLINE | ID: covidwho-1686574

ABSTRACT

The rapid global rise of COVID-19 from late 2019 caught major manufacturers of RT-qPCR reagents by surprise and threw into sharp focus the heavy reliance of molecular diagnostic providers on a handful of reagent suppliers. In addition, lockdown and transport bans, necessarily imposed to contain disease spread, put pressure on global supply lines with freight volumes severely restricted. These issues were acutely felt in New Zealand, an island nation located at the end of most supply lines. This led New Zealand scientists to pose the hypothetical question: in a doomsday scenario where access to COVID-19 RT-qPCR reagents became unavailable, would New Zealand possess the expertise and infrastructure to make its own reagents onshore? In this work we describe a review of New Zealand's COVID-19 test requirements, bring together local experts and resources to make all reagents for the RT-qPCR process, and create a COVID-19 diagnostic assay referred to as HomeBrew (HB) RT-qPCR from onshore synthesized components. This one-step RT-qPCR assay was evaluated using clinical samples and shown to be comparable to a commercial COVID-19 assay. Through this work we show New Zealand has both the expertise and, with sufficient lead time and forward planning, infrastructure capacity to meet reagent supply challenges if they were ever to emerge.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19 , Humans , Indicators and Reagents/supply & distribution , SARS-CoV-2
16.
J Biomed Opt ; 27(2)2022 02.
Article in English | MEDLINE | ID: covidwho-1677373

ABSTRACT

SIGNIFICANCE: The primary method of COVID-19 detection is reverse transcription polymerase chain reaction (RT-PCR) testing. PCR test sensitivity may decrease as more variants of concern arise and reagents may become less specific to the virus. AIM: We aimed to develop a reagent-free way to detect COVID-19 in a real-world setting with minimal constraints on sample acquisition. The machine learning (ML) models involved could be frequently updated to include spectral information about variants without needing to develop new reagents. APPROACH: We present a workflow for collecting, preparing, and imaging dried saliva supernatant droplets using a non-invasive, label-free technique-Raman spectroscopy-to detect changes in the molecular profile of saliva associated with COVID-19 infection. RESULTS: We used an innovative multiple instance learning-based ML approach and droplet segmentation to analyze droplets. Amongst all confounding factors, we discriminated between COVID-positive and COVID-negative individuals yielding receiver operating coefficient curves with an area under curve (AUC) of 0.8 in both males (79% sensitivity and 75% specificity) and females (84% sensitivity and 64% specificity). Taking the sex of the saliva donor into account increased the AUC by 5%. CONCLUSION: These findings may pave the way for new rapid Raman spectroscopic screening tools for COVID-19 and other infectious diseases.


Subject(s)
COVID-19 , Saliva , Female , Humans , Indicators and Reagents , Machine Learning , Male , SARS-CoV-2 , Sensitivity and Specificity , Spectrum Analysis, Raman
17.
J Virol Methods ; 300: 114372, 2022 02.
Article in English | MEDLINE | ID: covidwho-1654861

ABSTRACT

The current gold standard technique for SARS-CoV-2 diagnostics is hydrolysis probe-based RT-qPCR. Reliable testing requires reliable control reagents to monitor the efficiency of RNA extraction, reverse transcription and PCR amplification. Here we describe a custom RNA packaging system from the plant virus cowpea mosaic virus to produce virus-like particles that encapsidate specifically designed portions of the genome of SARS-CoV-2, the causative agent of COVID-19. These encapsidated mimics are highly stable particles which can be used either to spike patient swab samples for use as an in-tube extraction and reaction positive control in multiplex RT-qPCR, or alone as a side-by-side mock-positive control reagent. The selection of sequences in the packaged pseudogenomes ensures that these mimics are compatible with the most commonly used primer/probe combinations for SARS-CoV-2 diagnostics (including German Berlin Charité Hospital, American CDC, and Chinese CDC protocols). The plant transient expression system used to produce these encapsidated mimics is inherently low-cost, and sufficiently high-yielding that a single laboratory-scale preparation can provide enough positive control reagent for millions of tests.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Indicators and Reagents , RNA, Viral/genetics , Sensitivity and Specificity
18.
19.
J Virol Methods ; 299: 114339, 2022 01.
Article in English | MEDLINE | ID: covidwho-1472084

ABSTRACT

The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19 Testing , Humans , Indicators and Reagents , Magnetic Phenomena , Pandemics , RNA, Viral/genetics , SARS-CoV-2 , Sensitivity and Specificity
20.
J Clin Microbiol ; 59(12): e0101921, 2021 11 18.
Article in English | MEDLINE | ID: covidwho-1443351

ABSTRACT

Nucleic acid amplification testing (NAAT) for SARS-CoV-2 is the standard approach for confirming COVID-19 cases. This study compared results between two emergency use authorization (EUA) NAATs, with two additional EUA NAATs utilized for discrepant testing. The limits of detection (LOD) for the BD SARS-CoV-2 reagents for the BD MAX system (MAX SARS-CoV-2 assay), the bioMérieux BioFire respiratory panel 2.1 (BioFire SARS-CoV-2 assay), the Roche cobas SARS-CoV-2 assay (cobas SARS-CoV-2 assay), and the Hologic Aptima SARS-CoV-2 assay Panther (Aptima SARS-CoV-2 assay) NAAT systems were determined using a total of 84 contrived nasopharyngeal specimens with 7 target levels for each comparator. The positive and negative percent agreement (PPA and NPA, respectively) of the MAX SARS-CoV-2 assay, compared to the Aptima SARS-CoV-2 assay, was evaluated in a postmarket clinical study utilizing 708 nasopharyngeal specimens collected from suspected COVID-19 cases. Discordant testing was achieved using the cobas and BioFire SARS-CoV-2 NAATs. In this study, the measured LOD for the MAX SARS-CoV-2 assay (251 copies/ml; 95% confidence interval [CI], 186 to 427) was comparable to the cobas SARS-CoV-2 assay (298 copies/ml; 95% CI, 225 to 509) and the BioFire SARS-CoV-2 assay (302 copies/ml; 95% CI, 219 to 565); the Aptima SARS-CoV-2 assay had an LOD of 612 copies/ml (95% CI, 474 to 918). The MAX SARS-CoV-2 assay had a PPA of 100% (95% CI, 97.3% to 100.0%) and an NPA of 96.7% (95% CI, 94.9% to 97.9%) compared to the Aptima SARS-CoV-2 assay. The clinical performance of the MAX SARS-CoV-2 assay agreed with another sensitive EUA assay.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Indicators and Reagents , Molecular Diagnostic Techniques , Nasopharynx , Sensitivity and Specificity
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