Performance Analysis of VGG-16 Deep Learning Model for COVID-19 Detection using Chest X-Ray Images

COVID-19 is an infectious disease caused by newly discovered coronavirus. Currently, RT-PCR and Rapid Testing are used to test a person against COVID-19. These methods do not produce immediate results. Hence, we propose a solution to detect COVID-19 from chest X-ray images for immediate results. The solution is developed using a convolutional neural network architecture (VGG-16) model to extract features by transfer learning and a classification model to classify an input chest X-ray image as COVID-19 positive or negative. We introduced various parameters and computed the impact on the performance of the model to identify the parameters with high impact on the model's performance. The proposed solution is observed to provide best results compared to the existing ones. © 2023 Bharati Vidyapeeth, New Delhi.

The Implementation and Role of Antigen Rapid Test for COVID-19 in Hemodialysis Units.

As we move into the third year with COVID-19, many countries have attempted to manage the disease as an endemic. However, this is limited by the disease's morbidity and mortality, the emergence of new strains, and the effectiveness of the vaccine. This brief report describes, evaluates, and discusses the implementation of regular antigen rapid tests (ARTs) for COVID-19 in hemodialysis units. We introduced ARTs during the surge in our hemodialysis units. As compliance with the test was mandatory by regulatory requirements, we surveyed patients and caregivers to measure their acceptability, appropriateness, and feasibility of the ART's implementation. Acceptability measured confidence and level of comfort when performing ART tests, while appropriateness measured the perception of the necessity of ARTs, safety in the dialysis unit with the implementation of ARTs, and understanding using a Likert scale. Feasibility measured the perception of the timely start of dialysis treatment and the convenience of the test. Our survey found that ARTs were acceptable to 98% of patients and caregivers, with the majority reporting no discomfort. The majority of the patients agreed that ARTs were appropriate and feasible. We reported successful ART implementation in a healthcare setting with no false-positive or transmission within the unit during this period. Nevertheless, the long-term implementation outcome will require further evaluation.

Development of a rapid, simple, and sensitive point-of-care technology platform utilizing ternary NanoLuc.

Point-of-care tests are highly valuable in providing fast results for medical decisions for greater flexibility in patient care. Many diagnostic tests, such as ELISAs, that are commonly used within clinical laboratory settings require trained technicians, laborious workflows, and complex instrumentation hindering their translation into point-of-care applications. Herein, we demonstrate the use of a homogeneous, bioluminescent-based, split reporter platform that enables a simple, sensitive, and rapid method for analyte detection in clinical samples. We developed this point-of-care application using an optimized ternary, split-NanoLuc luciferase reporter system that consists of two small reporter peptides added as appendages to analyte-specific affinity reagents. A bright, stable bioluminescent signal is generated as the affinity reagents bind to the analyte, allowing for proximity-induced complementation between the two reporter peptides and the polypeptide protein, in addition to the furimazine substrate. Through lyophilization of the stabilized reporter system with the formulated substrate, we demonstrate a shelf-stable, all-in-one, add-and-read analyte-detection system for use in complex sample matrices at the point-of-care. We highlight the modularity of this platform using two distinct SARS-CoV-2 model systems: SARS-CoV-2 N-antigen detection for active infections and anti-SARS-CoV-2 antibodies for immunity status detection using chemically conjugated or genetically fused affinity reagents, respectively. This technology provides a simple and standardized method to develop rapid, robust, and sensitive analyte-detection assays with flexible assay formatting making this an ideal platform for research, clinical laboratory, as well as point-of-care applications utilizing a simple handheld luminometer.

Dataset from the comparative evaluation of the STANDARD M10 point-of-care analyzer versus the NeuMoDx assay for the molecular diagnosis of SARS-CoV-2.

The STANDARD M10 is a novel cartridge-based real time RT-PCR point of care platform that provides significant advantages regarding SARS-CoV-2 detection including fast turnaround times and no need for specialized personnel and facilities. This assay was recently evaluated in our hospital as a rapid alternative to the already present NeuMoDx assay that is used in everyday practice. For this purpose, 30 nasopharyngeal samples by patients admitted to our hospital were used, regardless of clinical suspicion of COVID-19. In our evaluation, the sensitivity of STANDARD M10 was 95%, the specificity was 100%, the positive predictive value was 100%, the negative predictive value was 90% and the kappa coefficient of agreement was 0.927 (p < 0.001).

Validation of the COVID-19 IgG/IgM Rapid Test Cassette (BNCP - 402 and BNCP402) in a South African setting.

Background: Different diagnostic tools could improve early detection of coronavirus disease 2019 (COVID-19). A number of antibody-based serological point-of-care tests have been developed to supplement real-time reverse transcriptase polymerase chain reaction (RT-PCR)-based diagnosis. This study describes the validity of an antibody test, namely the immunoglobulin G (IgG)/immunoglobulin M (IgM) Rapid Test Cassette® (BNCP - 402 and BNCP402), manufactured by Spring Healthcare Services. Methods: A prospective cohort validation study was undertaken at Chris Hani Baragwanath Academic Hospital between 16 July 2020 and 12 August 2020. A total of 101 patients admitted as COVID-19 cases under investigation were included in the study. They were divided into two categories depending on time since symptom onset: testing performed within seven days (early cohort) and after seven days (late cohort). The rapid antibody test was compared to the RT-PCR. Results: Overall, the test has a sensitivity and specificity of 85.2% and 80.0%, respectively, for a combination of IgG and IgM. Sensitivity and specificity of IgG testing alone were 81.5% and 85%. Sensitivity improved for testing with increasing time from symptom onset; however, specifity was not significantly different. Conclusion: The study data adds to the body of evidence that because of relatively low sensitivity and specificity, there is a limited role for antibody-based point-of-care testing in the acute phase of COVID-19 infection, as was the case with this IgG/IgM Rapid Test Cassette (BNCP - 402 and BNCP402). There may exist a role for such testing in patients recovered from prior COVID-19 infection or in seroprevalence studies; however, additional evaluations at later timepoints from symptom onset are required.

A functionalized microwave sensor in a microfluidic platform for rapid detection of SARS-CoV-2

The global COVID-19 pandemic caused by the SARS-CoV-2 has claimed >3.5 million lives and resulted in detrimental social-economic impact. If reliable and rapid test systems were available at home or community level such as drive-by stations, the scope and impact of this tragedy could be largely reduced. Although the vaccine roll out has helped control the pandemic, it is important to develop rapid and accurate testing methods for detection of the SARS-CoV-2 which can be tuned to respond to its variants or similar corona viruses in response to potential outbreaks. In this work, we present a novel method for detection of the SARS-CoV-2 virus based on an antibody functionalized microwave sensor integrated with a microfluidic platform. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

Caregiver perceptions of in-home COVID-19 testing for children with medical complexity: a qualitative study.

BACKGROUND: In-home direct antigen rapid testing (DART) plays a major role in COVID-19 mitigation and policy. However, perceptions of DART within high-risk, intellectually impaired child populations are unknown. This lack of research could negatively influence DART uptake and utility among those who stand to benefit most from DART. The purpose of this study was to describe caregivers' perceptions of an in-home COVID-19 DART regimen in children with medical complexity, including the benefits and limitations of DART use. METHODS: This qualitative study was a subproject of the NIH Rapid Acceleration of Diagnostics Underserved Populations research program at the University of Wisconsin. We combined survey data and the thematic analysis of semi-structured interview data to understand caregivers' perceptions of in-home COVID-19 testing and motivators to perform testing. Caregivers of children with medical complexity were recruited from the Pediatric Complex Care Program at the University of Wisconsin (PCCP). Data were collected between May and August 2021. RESULTS: Among n = 20 caregivers, 16/20 (80%) of their children had neurologic conditions and 12/20 (60%) used home oxygen. Survey data revealed that the largest caregiver motivators to test their child were to get early treatment if positive (18/20 [90%] of respondents agreed) and to let the child's school know if the child was safe to attend (17/20 [85%] agreed). Demotivators to testing included that the child could still get COVID-19 later (7/20 [35%] agreed), and the need for officials to reach out to close contacts (6/20 [30%] agreed). From interview data, four overarching themes described perceptions of in-home COVID-19 testing: Caregivers perceived DART on a spectrum of 1) benign to traumatic and 2) simple to complex. Caregivers varied in the 3) extent to which DART contributed to their peace of mind and 4) implications of test results for their child. CONCLUSIONS: Although participants often described DART as easy to administer and contributing to peace of mind, they also faced critical challenges and limitations using DART. Future research should investigate how to minimize the complexity of DART within high-risk populations, while leveraging DART to facilitate safe school attendance for children with medical complexity and reduce caregiver burden.

Validation of the NeuMoDx™ SARS-CoV-2 assay with COPAN eNAT® and E&O Viral PCR Sample Solution collection media types in comparison with other validated SARS-CoV-2 RNA assays.

OBJECTIVES: This study aimed to confirm NeuMoDx™ SARS-CoV-2 assay (NeuMoDx assay) functionality using off-label collection media, determine assay performance versus other SARS-CoV-2 RNA assays, and assess any cross-reactivity with other respiratory viruses (human coronavirus NL63, influenza, and respiratory syncytial virus). METHODS: Nasopharyngeal swab samples in off-label collection media and external quality assessment (EQA) samples were dual-tested, first using either the RealStar® SARS-CoV-2 reverse transcriptase polymerase chain reaction assay or the QIAstat-Dx® Respiratory SARS-CoV-2 Panel and then using the NeuMoDx assay. Samples found to be positive for respiratory viruses and negative for SARS-CoV-2 were then tested using the NeuMoDx assay to assess cross-reactivity. RESULTS: Overall, 274 samples (244 patient and 30 EQA samples) were dual-tested; 154 were SARS-CoV-2 positive and 120 were negative. No false-positive or false-negative results were identified, regardless of collection medium used. The NeuMoDx assay sensitivity was 100% (95% confidence interval [CI] 97.63-100.00) and the specificity was 100% (95% CI 96.97-100.00). The assay did not exhibit any cross-reactivity with other respiratory viruses. CONCLUSION: The NeuMoDx assay demonstrated high sensitivity and specificity on a platform well-suited for fully automated SARS-CoV-2 testing.

Rapid Detection of the Omicron (B.1.1.529) SARS-CoV-2 Variant Using a COVID-19 Diagnostic PCR Assay.

The Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the last variant of concern (VOC) identified to date. Compared to whole-genome or gene-specific sequencing methods, reverse-transcription PCR assays may be a simpler approach to study VOCs. We used a point-of-care COVID-19 diagnostic PCR assay to detect the Omicron SARS-CoV-2 variant in the respiratory tract samples of COVID-19 patients who had tested positive for SARS-CoV-2 RNA between April 2021 and January 2022. Sequencing analyses had shown that 87 samples were positive for the Omicron variant and 43 samples were positive for a non-Omicron variant (Delta, 18 samples; Alpha, 13 samples; Gamma, 10 samples; Beta, 1 sample; or Epsilon, 1 sample). According to results by the PCR assay, whose primers anneal a nucleocapsid (N) gene region that comprises the E31/R32/S33 deletion (also termed the del31/33 mutation), we found that N gene target failure/dropout (i.e., a negative/low result) occurred in 86 (98.8%) of 87 Omicron variant-positive samples tested. These results were assessed in relation to those of the spike (S) gene, which expectedly, was detected in all (100%) 130 samples. A total of 43 (100%) of 43 Delta, Alpha, Gamma, Beta, or Epsilon variant-positive samples had a positive result with the N gene. Importantly, in 86 of 87 Omicron variant-positive samples, the del31/33 mutation was detected together with a P13L mutation, which was, instead, detected alone in the Omicron variant-positive sample that had a positive N-gene result. IMPORTANCE Rapid detection of the Omicron SARS-CoV-2 variant in patients' respiratory tract samples may influence therapeutic choices, because this variant is known to escape from certain monoclonal antibodies. Our findings strengthen the importance of manufacturers' efforts to improve the existing COVID-19 diagnostic PCR assays and/or to develop novel variant-specific PCR assays. Furthermore, our findings show that only a small fraction of SARS-CoV-2-positive samples may require whole-genome sequencing analysis, which is still crucial to validate PCR assay results. We acknowledge that the emergence of novel variants containing mutations outside the PCR assay target region could, however, allow an assay to work as per specifications without being able to identify a SARS-CoV-2-positive sample as a variant. Future work and more experience in this topic will help to reduce the risk of misidentification of SARS-CoV-2 variants that is unavoidable when using the current PCR assays.

Understanding Healthcare Professionals' Perspectives on Point-of-Care Testing.

Point-of-care testing (POCT) is an emerging technology that provides crucial assistance in delivering healthcare. The COVID-19 pandemic led to the accelerated importance of POCT technology due to its in-home accessibility. While POCT use and implementation has increased, little research has been published about how healthcare professionals perceive these technologies. The objective of our study was to examine the current perspectives of healthcare professionals towards POCT. We surveyed healthcare professionals to quantify perceptions of POCT usage, adoption, benefits, and concerns between October 2020 and November 2020. Questions regarding POCT perception were assessed on a 5-point Likert Scale. We received a total of 287 survey responses. Of the respondents, 53.7% were male, 66.6% were white, and 30.7% have been in practice for over 20 years. We found that the most supported benefit was POCTs ability to improve patient management (92%) and that the most supported concern was that POCTs lead to over-testing (30%). This study provides a better understanding of healthcare workers' perspectives on POCT. To improve patient outcomes through the usage of POCT, greater research is needed to assess the needs and concerns of industry and healthcare stakeholders.

Evaluating the Ability to ID (COVID-19) NOW: a Large Real-World Prospective Evaluation of the Abbott ID NOW COVID-19 Assay.

The Abbott ID NOW COVID-19 assay is a rapid point-of-care molecular test for SARS-CoV-2 detection. In theory, it has the potential to decrease turnaround times (TATs) and rapidly facilitate patient flow and triage. Reports for its performance have been mixed, likely due to variations in patient cohorts, preanalytical considerations, and study design. We prospectively evaluated the ID NOW performance against reference reverse transcriptase PCR (RT-PCR) tests, using dual swabs. Patients presented at a large multisite academic hospital with the highest volumes of COVID-19 admissions in Canada. From 1,968 valid swabs, 186 were true positive, 1,760 were true negative, 21 were false negatives, and 1 was false positive. At 10.5% positivity rate, the positive and negative predictive values were 99.5% and 98.8%, respectively. This led to a modest increase in the pretest probability in this cohort of individuals presenting <7 days of symptom onset. The mean times from collection to laboratory receipt and receipt to reporting were 31 and 23 min, respectively. This reduced TAT observed in our study may assist with triage of admitted patients and breaking the chain of transmission through immediate notification of status. We also observed how test performance changed with prevalence, and thus, how the test is used to "rule in" or "rule out" disease must be considered. Although the ID NOW is regarded as a rapid test, it is not high throughput and requires rapid transportation times (<1 h) that may not be plausible in large centers. The utility of this test should be considered with the observed TAT and interpreted in the context of limitations discussed. IMPORTANCE Rapid testing for COVID-19 has been recognized as one potentially important measure in managing the pandemic. However, these rapid tests vary grossly in their performance and their applicability. There have been many studies evaluating the performance of rapid tests for SARS-CoV-2 detection. However, they are frequently not prospective, and patients are not simultaneously swabbed to compare the reference standard RT-PCR. Previous ID NOW study findings are mixed, which may be due to various factors, including patient, epidemiological, and preanalytical considerations. It is critical to consider how the pretest and posttest probabilities and epidemiological factors may affect the performance as the community prevalence of disease fluctuates during this highly dynamic pandemic. We consider how the ID NOW may be utilized in different settings, with considerations of public health and infection control and prevention risk tolerance.

`Development of a rapid neutralizing antibody test for SARS-CoV-2 and its application for neutralizing antibody screening and vaccinated serum testing

Background : Since the outbreak of coronavirus disease (COVID-19), the high infection rate and mutation frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent, have contributed to the ongoing global pandemic. Vaccination has become the most effective means of controlling COVID-19. Traditional neutralizing tests of sera are complex and labor-intensive, therefore, a rapid test for detecting neutralizing antibodies and antibody status post-immunization is needed. Methods : Based on the fact that antibodies exhibit neutralizing activity by blocking the binding of the S protein receptor-binding domain (S-RBD) to ACE2, we developed a rapid neutralizing antibody test, ACE2-Block-ELISA. To evaluate the sensitivity and specificity, we used 54 positive and 84 negative serum samples. We also tested the neutralizing activities of monoclonal antibodies (mAbs) and 214 sera samples from healthy individuals immunized with the inactivated SARS-CoV-2 vaccine. Results : The sensitivity and specificity of the ACE2-Block ELISA were 96.3% and 100%, respectively. For neutralizing mAb screening, ch-2C5 was selected for its ability to block the ACE2–S-RBD interaction. A plaque assay confirmed that ch-2C5 neutralized SARS-CoV-2, with NT50 values of 4.19, 10.63, and 1.074 μg/mL against the SARS-CoV-2 original strain, and the Beta and Delta variants, respectively. For the immunized sera samples, the neutralizing positive rate dropped from 82.14% to 32.16% within 4 months post-vaccination. Conclusions : This study developed and validated an ACE2-Block-ELISA to test the neutralizing activities of antibodies. As a rapid, inexpensive and easy-to-perform method, this ACE2-Block-ELISA has potential applications in rapid neutralizing mAb screening and SARS-CoV-2 vaccine evaluation.

Lab-in-a-van: Rapid SARS-CoV-2 testing response with a mobile laboratory.

BACKGROUND: High testing rates and rapid contact tracing have been key interventions to control COVID-19 in Victoria, Australia. A mobile laboratory (LabVan), for rapid SARS-CoV-2 diagnostics, was deployed at sites deemed critical by the Victorian State Department of Health as part of the response. We describe the process of design, implementation, and performance benchmarked against a central reference laboratory. METHODS: A BSL2 compliant laboratory, complete with a class II biological safety cabinet, was built within a Mercedes-Benz Sprinter Panel Van. Swabs were collected by on-site collection teams, registered using mobile internet-enabled tablets and tested using the Xpert® Xpress SARS-CoV-2 assay. Results were reported remotely via HL7 messaging to Public Health Units. Patients with negative results were automatically notified by mobile telephone text messaging (SMS). FINDINGS: A pilot trial of the LabVan identified a median turnaround time (TAT) from collection to reporting of 1:19 h:mm (IQR 0:18, Range 1:03-18:32) compared to 9:40 h:mm (IQR 8:46, Range 6:51-19:30) for standard processing within the central laboratory. During deployment in nine rural and urban COVID-19 outbreaks the median TAT was 2:18 h:mm (IQR 1:18, Range 0:50-16:52) compared to 19:08 h:mm (IQR 5:49, Range 1:36-58:52) for samples submitted to the central laboratory. No quality control issues were identified in the LabVan. INTERPRETATION: The LabVan is an ISO15189 compliant testing facility fully operationalized for mobile point-of-care testing that significantly reduces TAT for result reporting, facilitating rapid public health actions. FUNDING: This work was supported by the Department of Health, Victoria State Government, Australia.

Effectiveness of rapid antigen testing for screening of asymptomatic individuals to limit the transmission of SARS-CoV-2: A rapid review.

Rapid antigen detection tests (RADTs) offer advantages over gold-standard reverse transcription polymerase chain reaction (RT-PCR) tests in that they are cheaper and provide faster results, thus enabling prompt isolation of positive SARS-CoV-2 cases and quarantine of close contacts. The aim of this study was to collate and synthesise empirical evidence on the effectiveness of rapid antigen testing for the screening (including serial testing) and surveillance of asymptomatic individuals to limit the transmission of SARS-CoV-2. A rapid review was undertaken in MEDLINE (EBSCO), EMBASE (OVID), Cochrane Library, Europe PMC and Google Scholar up until 19 July 2021, supplemented by a grey literature search. Of the identified 1222 records, 19 reports referring to 16 studies were included. Eight included studies examined the effectiveness of RADTs for population-level screening, four for pre-event screening and four for serial testing (schools, a prison, a university sports programme and in care homes). Overall, there is uncertainty regarding the effectiveness of rapid antigen testing for the screening of asymptomatic individuals to limit the transmission of SARS-CoV-2. This uncertainty is due to the inconsistent results, the relatively low number of studies identified, the predominantly observational and/or uncontrolled nature of the study designs used, and concerns regarding methodological quality. Given this uncertainty, more real-world research evidence in relevant settings, which is of good quality and timely, as well as economic evaluation, is required to inform public policy on the widespread use of RADTs in asymptomatic individuals.

Who is accessing community lateral flow device testing and why? Characteristics and motivations of individuals participating in COVID-19 community testing in two English local authority areas.

BACKGROUND: Antigen testing using lateral flow devices (LFDs) plays an important role in the management of the novel coronavirus pandemic of 2019 (COVID-19) by rapidly identifying individuals who are asymptomatically carrying high levels of the virus. By January 2021, LFD community testing sites were set up across English local authority areas to support the management and containment of regional COVID-19 cases, initially targeting essential workers unable to work from home during the national lockdown. This study aimed to examine the characteristics and motivations of individuals accessing community LFD testing across two local authority areas (LAAs) in the South West of England. METHODS: Data were collected as part of a service evaluation from December 22nd 2020 until March 15th 2021 for two LAAs. Demographic and postcode data were collected from an online test appointment booking platform and the National Health Service testing service online system, with data accessed from Public Health England. An online survey was sent to individuals who made a testing appointment at an LAA1 site using the online booking platform, consisting of 12 questions to collect data on individual's motivations for and experiences of testing. RESULTS: Data were available for individuals who completed 12,516 tests in LAA1 and 12,327 tests in LAA2. Most individuals who engaged with testing were female, working age, white, and worked as early years or education staff, health and social care staff, and supermarket or food production staff. 1249 individuals completed the survey with 60% of respondents reported getting tested for work-related reasons. Individuals first heard about LFD testing through various channels including work, media, and word of mouth, and decided to get tested based on the ease and convenience of testing, workplace communications, and to identify asymptomatic cases to help stop the spread. Most tests were completed by individuals living in less deprived areas based on national deciles of deprivation. CONCLUSIONS: While national and local COVID-19 testing strategies have evolved, community and personal LFD testing remains a crucial pillar of the testing strategy. Future studies should collect quantitative and qualitative data from residents to most effectively shape testing offers based on the needs and preferences of their population.

A method comparison study of the high throughput automated HISCL® SARS-CoV-2 antigen assay using nasopharyngeal swab samples from symptomatic and asymptomatic subjects against conventional RT-PCR.

Our study aim was to evaluate the performance of the automated Sysmex HISCL® severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen assay against reverse-transcription polymerase chain reaction (RT-PCR). We tested 277 remnant frozen nasopharyngeal swab samples, stored in universal transport medium (UTM), yielding a sensitivity of 94.9% against historical RT-PCR results with cycle threshold (Ct ) < 30, and a sensitivity of 76.7% for Ct < 35, and specificity of 100% (all Ct values) confirming compatibility of UTM-diluted samples with the assay system. Thereafter, we prospectively collected 141 nasopharyngeal swab samples in UTM from healthcare workers and 1369 paired swabs (400 UTM; 969 dry) from individuals at a public health testing center, with the first swab (UTM) reserved for RT-PCR, yielding a positivity rate of 4.6%. HISCL assay performance using UTM swabs was superior to dry swabs, with a sensitivity of 100% (95% confidence interval [CI] 71.5%-100%) at Ct < 30 versus 92.3% (95%CI 81.5%-97.9%), and a specificity of 99.3% (95% CI 98.1-99.89) against 83.3% (95%CI 80.7%-85.6%). We conclude that this antigen assay is suitable for high throughput facilities where the primary indication for testing is to rule out infection with low RT-PCR Ct values (proxy for high viral loads) to curb viral spread.

Application of Deep Learning Techniques for Detection of COVID-19 Using Lung CT Scans: Model Development and Validation

Due to the worldwide spread of the COVID-19, efforts to combat the disease have intensified. Among these efforts, the only effective way to prevent further spread to communities and disease progression is to control the spread of the disease, which is done using public vaccination as well as repeated and rapid testing to diagnose and isolate sick people. In this regard, computer systems with the help of medical science can speed up the diagnosis of COVID-19 disease. This paper, proposed a review of the methods used in rapid and automatic detection of COVID-19 using CT scan images. Finally, by presenting a new method based on deep learning, the obtained results compared with the results of widely used algorithms such as VGG-16 and MobileNet. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Comparison of the clinical sensitivity and specificity of two commercial RNA SARS-CoV-2 assays.

OBJECTIVES: This study aimed to compare the performance of the NeuMoDx™ SARS-CoV-2 Assay, implemented on the NeuMoDx 96 Molecular System, with that of the ThermoFisher TaqPath™ COVID-19 CE-IVD RT-PCR Kit (reference method). METHODS: Overall, 450 nasopharyngeal swab samples, previously tested using the reference method, were tested by the NeuMoDx Assay, and the clinical sensitivity and specificity of the assay were analyzed. RESULTS: By retrospective statistical analysis of all valid results, the NeuMoDx Assay had a clinical specificity of 100% (95% confidence interval [CI]: 98.65-100.00) and a clinical sensitivity of 98.73% (95% CI: 95.47-99.85). CONCLUSIONS: The NeuMoDx SARS-CoV-2 Assay demonstrated comparable analytical and clinical performance to the ThermoFisher TaqPath COVID-19 CE-IVD RT-PCR Kit. The NeuMoDx 96 Molecular System is well suited for automating medium-throughput routine SARS-CoV-2 testing or as an addition to high-throughput systems to allow fast-tracking for highly urgent clinical samples.

A point-of-care SARS-CoV-2 test based on reverse transcription loop-mediated isothermal amplification without RNA extraction with diagnostic performance same as RT-PCR.

The global public health crisis and economic losses resulting from the current novel coronavirus disease (COVID-19) pandemic have been dire. The most used real-time reverse transcription polymerase chain reaction (RT-PCR) method needs expensive equipment, technical expertise, and a long turnaround time. Therefore, there is a need for a rapid, accurate, and alternative technique of diagnosis that is deployable at resource-poor settings like point-of-care. This study combines heat deactivation and a novel mechanical lysis method by bead beating for quick and simple sample preparation. Then, using an optimized reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to target genes encoding the open reading frame 8 (ORF8), spike and nucleocapsid proteins of the novel coronavirus, SARS-CoV-2. The test results can be read simultaneously in fluorometric and colorimetric readouts within 40 min from sample collection. We also calibrated a template transfer tool to simplify sample addition into LAMP reactions when pipetting skills are needed. Most importantly, validation of the direct RT-LAMP system based on multiplexing primers S1:ORF8 in a ratio (1:0.8) using 143 patients' nasopharyngeal swab samples showed a diagnostic performance of 99.30% accuracy, with 98.81% sensitivity and 100% selectivity, compared to commercial RT-PCR kits. Since our workflow does not rely on RNA extraction and purification, the time-to-result is two times faster than other workflows with FDA emergency use authorization. Considering all its strengths: speed, simplicity, accuracy and extraction-free, the system can be useful for optimal point-of-care testing of COVID-19.