Performance and cost-effectiveness of a pooled testing strategy for SARS-CoV-2 using real-time polymerase chain reaction in Uganda

Development and Clinical Evaluation of a CRISPR/Cas12a-Based Nucleic Acid Detection Platform for the Diagnosis of Keratomycoses

Objective

The objective of this study was to develop a rapid and accurate clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-based molecular diagnostic assay (Rapid Identification of Mycoses using CRISPR, RID-MyC assay) to detect fungal nucleic acids and to compare it with existing conventional mycologic methods for the diagnosis of fungal keratitis (FK).

Design

This study was structured as a development and validation study focusing on the creation and assessment of the RID-MyC assay as a novel diagnostic modality for FK.

Subjects

Participants comprised 142 individuals presenting with suspected microbial keratitis at 3 tertiary care institutions in South India.

Methods

The RID-MyC assay utilized recombinase polymerase amplification targeting the 18S ribosomal RNA gene for isothermal amplification, followed by a CRISPR/Cas12a reaction. This was benchmarked against microscopy, culture, and polymerase chain reaction for the diagnosis of FK.

Main Outcome Measures

The primary outcome measures focused on the analytical sensitivity and specificity of the RID-MyC assay in detecting fungal nucleic acids. Secondary outcomes measured the assay's diagnostic sensitivity and specificity for FK, including its concordance with conventional diagnostic methods.

Results

The RID-MyC assay exhibited a detection limit ranging from 13.3 to 16.6 genomic copies across 4 common fungal species. In patients with microbial keratitis, the RID-MyC assay showed substantial agreement with microscopy (kappa = 0.714) and fair agreement with culture (kappa = 0.399). The assay demonstrated a sensitivity of 93.27% (95% confidence interval [CI], 86.62%-97.25%) and a specificity of 89.47% (95% CI, 66.86%-98.70%) for FK diagnosis, with a median diagnostic time of 50 minutes (range, 35-124 minutes).

Conclusions

The RID-MyC assay, utilizing CRISPR-Cas12a technology, offers high diagnostic accuracy for FK. Its potential for point-of-care use could expedite and enhance the precision of fungal diagnostics, presenting a promising solution to current diagnostic challenges.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Comparison of RT-PCR cycle threshold values between individual and pooled SARS-CoV-2 infected nasopharyngeal swab specimens

The molecular reverse transcription-polymerase chain reaction (RT-PCR) testing of respiratory tract swabs has become mandatory to confirm the diagnosis of coronavirus disease 2019 (COVID-19). However, RT-PCR tests are expensive, require standardized equipment, and relatively long testing times, and the sample pooling method has been introduced to solve this issue. The aim of this study was to compare the cycle threshold (Ct) values of the individual sample and pooled sample methods to assess how accurate the pooling method was. Repeat RT-PCR examinations were initially performed to confirm the Ct values for each sample before running the pooled test procedure. Sample extraction and amplification were performed in both assays to detect ORF1ab, N, and E genes with a cut-off point value of Ct <38. Overall, there was no difference in Ct values between individual sample and pooled sample groups at all concentrations (p=0.259) and for all pooled sizes. Only pooled size of five could detect the Ct value in the pooled samples for all concentration samples, including low-concentration sample (Ct values 36 to 38). This study highlighted that pooled RT-PCR testing strategy did not reduce the quality of individually measured RT-PCR Ct values. A pool size of five could provide a practical technique to expand the screening capacity of RT-PCR.

High capacity clinical SARS-CoV-2 molecular testing using combinatorial pooling

BACKGROUND

The SARS-CoV-2 pandemic led to unprecedented testing demands, causing major testing delays globally. One strategy used for increasing testing capacity was pooled-testing, using a two-stage technique first introduced during WWII. However, such traditional pooled testing was used in practice only when positivity rates were below 2%.

METHODS

Here we report the development, validation and clinical application of P-BEST - a single-stage pooled-testing strategy that was approved for clinical use in Israel.

RESULTS

P-BEST is clinically validated using 3636 side-by-side tests and is able to correctly detect all positive samples and accurately estimate their Ct value. Following regulatory approval by the Israeli Ministry of Health, P-BEST was used in 2021 to clinically test 837,138 samples using 270,095 PCR tests - a 3.1fold reduction in the number of tests. This period includes the Alpha and Delta waves, when positivity rates exceeded 10%, rendering traditional pooling non-practical. We also describe a tablet-based solution that allows performing manual single-stage pooling in settings where liquid dispensing robots are not available.

CONCLUSIONS

Our data provides a proof-of-concept for large-scale clinical implementation of single-stage pooled-testing for continuous surveillance of multiple pathogens with reduced test costs, and as an important tool for increasing testing efficiency during pandemic outbreaks.

Organic Fluorophores with Large Stokes Shift for the Visualization of Rapid Protein and Nucleic Acid Assays

Organic small-molecule fluorophores, characterized by flexible chemical structure and adjustable optical performance, have shown tremendous potential in biosensing. However, classical organic fluorophore motifs feature large overlap between excitation and emission spectra, leading to the requirement of advanced optical set up to filter desired signal, which limits their application in scenarios with simple settings. Here, a series of wavelength-tunable small-molecule fluorescent dyes (PTs) bearing simple organic moieties have been developed, which exhibit Stokes shift up to 262 nm, molar extinction coefficients ranged 30,000-100,000 M-1 cm-1, with quantum yields up to 54.8 %. Furthermore, these dyes were formulated into fluorescent nanoparticles (PT-NPs), and applied in lateral flow assay (LFA). Consequently, limit of detection for SARS-CoV-2 nucleocapsid protein reached 20 fM with naked eye, a 100-fold improvement in sensitivity compared to the pM detection level for colloidal gold-based LFA. Besides, combined with loop-mediated isothermal amplification (LAMP), the LFA system achieved the visualization of single copy level nucleic acid detection for monkeypox (Mpox).

SARS-CoV-2 Testing Strategies in the Diagnosis and Management of COVID-19 Patients in Low-Income Countries: A Scoping Review

The accuracy of diagnostic laboratory tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can impact downstream clinical procedures in managing and controlling the outbreak of coronavirus disease 2019 (COVID-19). To assess the effectiveness of laboratory tools for managing COVID-19 patients in low-income countries (LICs), we systematically searched the PubMed, Embase, Scopus and CINHAL databases for reports published between January 2020 and June 2022. We found that 22 of 1303 articles reported the performance of various SARS-CoV-2 detection tools across 10 LICs. These tools were (1) real-time reverse transcriptase polymerase chain reaction (RT-PCR); (2) reverse transcription loop-mediated isothermal amplification (RT-LAMP); (3) rapid diagnostic tests (RDTs); (4) enzyme-linked immunosorbent assay (ELISA); and (5) dot-blot immunoassay. The detection of COVID-19 is largely divided into two main streams-direct virus (antigen) detection and serology (immunoglobulin)-based detection. Point-of-care testing using antigen-based RDTs is preferred in LICs because of cost effectiveness and simplicity in the test procedures. The nucleic acid amplification technology (RT-PCR and RT-LAMP) has the highest diagnostic performance among the available tests, but it is not broadly used in this context due to costs and shortage of facilities/trained staff. The serology-based test method is affected by antibody interferences and varying amounts of SARS-CoV-2 immunoglobulins expressed at different stages of disease onset. We further discuss the effectiveness and shortcomings of each of these tools in the diagnosis and management of COVID-19. Using the LICs as the study model, our findings highlight ways to improve the quality and turnaround time of COVID-19 testing in resource-constrained settings, notably through local/international collaborative efforts to refine the molecular-based or immunoassay-based testing technologies.

Economic evaluation of laboratory diagnostic test types in Covid-19 epidemic: A systematic review

BACKGROUND

Corona 2 virus (SARS-CoV-2) is known as the causative agent of COVID-19 disease; the World Health Organization (WHO) declared it an epidemic on March 11, 2020. The Joint Guidelines of the Centers for Disease Control and Prevention (CDC) and the WHO including social distancing, the use of face masks, emphasis on hand washing, quarantine, and using diagnosis tests have been used widely, but the value of diagnostic interventions to prevent the transmission of SARS-CoV-2 is unclear. We compared the economic evaluation of different laboratory diagnostic interventions with each other and also with implementing the conservative CDC & WHO guidelines.

MATERIAL AND METHODS

Electronic searches were conducted on PubMed, Embase, Science Direct, Scopus, Cochrane Library, Web of Knowledge, NHSEED, NHS Health Technology assessment (CRD), and Cost-Effectiveness Analysis Registry databases. Related articles were reviewed from January 2020 to the end of November 2021.

RESULTS

Out of 1791 initial studies, 13 articles had the inclusion criteria. According to the Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist, ten studies were of excellent quality, and the remaining two studies were of very good quality. Most studies were cost-effectiveness analysis studies. The entered studies had different time horizons. Diagnostic tests reviewed in the studies included real-time polymerase chain reaction (RT-PCR) test, immunoglobulin G (IgG) & Antigen, point of care tests. Although polymerase chain reaction (PCR) testing improves the quality of life and survival for patients with infected Covid-19 based on its greater effectiveness compared to standard protection protocols, due to the high cost of this intervention, it has been considered a cost-effective method in some countries.

CONCLUSION

Since most studies have been conducted in developed countries, it unquestionably does not make sense to extend these results to low-income and developing countries. Therefore further studies are required in low-income and developing countries to evaluate the cost-effectiveness of laboratory-based diagnostic methods (RT-PCR) of covid-19 in variable prevalence of infectious cases.

Approaches to Deployment of Molecular Testing for SARS-CoV-2 in Resource-Limited Settings

Deployment of molecular testing for SARS-CoV-2 in resource-limited settings is challenging. Scale-up of molecular had to be conducted with a laboratory system strengthening approach that emphasize laboratory integration. National reference laboratories play a central role. In Malawi the molecular testing was underpinned by existing pathogen control programs for human immunodeficiency virus and tuberculosis that use Abbott and GeneXpert machines and reagents. Despite this, the impact on these programs was well managed. Antigen testing increased access to testing. Pooled testing and direct-to-polymerase chain reaction methods have the potential to save costs and further increase access to molecular tests.

Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a

As SARS-CoV-2 variants continue to evolve, identifying variants with adaptive diagnostic tool is critical to containing the ongoing COVID-19 pandemic. Herein, we establish a highly sensitive and portable on-site detection method for the HV69-70del which exist in SARS-CoV-2 Alpha and Omicron variants using a PCR-based CRISPR/Cas13a detection system (PCR-CRISPR). The specific crRNA (CRISPR RNA) targeting the HV69-70del is screened using the fluorescence-based CRISPR assay, and the sensitivity and specificity of this method are evaluated using diluted nucleic acids of SARS-CoV-2 variants and other pathogens. The results show that the PCR-CRISPR detection method can detect 1 copies/μL SARS-CoV-2 HV69-70del mutant RNA and identify 0.1% of mutant RNA in mixed samples, which is more sensitive than the RT-qPCR based commercial SARS-CoV-2 variants detection kits and sanger sequencing. And it has no cross reactivity with ten other pathogens nucleic acids. Additionally, by combined with our previously developed ERASE (Easy-Readout and Sensitive Enhanced) lateral flow strip suitable for CRISPR detection, we provide a novel diagnosis tool to identify SARS-CoV-2 variants in primary and resource-limited medical institutions without professional and expensive fluorescent detector.

Gauging the Impact of Artificial Intelligence and Mathematical Modeling in Response to the COVID-19 Pandemic: A Systematic Review

While the world continues to grapple with the devastating effects of the SARS-nCoV-2 virus, different scientific groups, including researchers from different parts of the world, are trying to collaborate to discover solutions to prevent the spread of the COVID-19 virus permanently. Henceforth, the current study envisions the analysis of predictive models that employ machine learning techniques and mathematical modeling to mitigate the spread of COVID-19. A systematic literature review (SLR) has been conducted, wherein a search into different databases, viz., PubMed and IEEE Explore, fetched 1178 records initially. From an initial of 1178 records, only 50 articles were analyzed completely. Around (64%) of the studies employed data-driven mathematical models, whereas only (26%) used machine learning models. Hybrid and ARIMA models constituted about (5%) and (3%) of the selected articles. Various Quality Evaluation Metrics (QEM), including accuracy, precision, specificity, sensitivity, Brier-score, F1-score, RMSE, AUC, and prediction and validation cohort, were used to gauge the effectiveness of the studied models. The study also considered the impact of Pfizer-BioNTech (BNT162b2), AstraZeneca (ChAd0x1), and Moderna (mRNA-1273) on Beta (B.1.1.7) and Delta (B.1.617.2) viral variants and the impact of administering booster doses given the evolution of viral variants of the virus.

On an optimal testing strategy for workplace settings operating during the COVID-19 pandemic

High quality daily testing for the presence of the SARS-CoV-2 in workplace settings has become part of the standard and mandatory protection measures implemented widely in response to the current pandemic. Such tests are often limited to a small fraction of the attending personnel due to cost considerations, limited availability and processing capabilities and the often cumbersome requirements of the test itself. A maximally efficient use of such an important and frequently scarce resource is clearly required. We here present an optimal testing strategy which minimises the presence of pre-symptomatic and asymptomatic infected members of the population in a workplace setting, derived under a series of simplifying statistical assumptions. These assumptions however, retain many of the generalities of the problem and yield robust results, as verified through a number of numerical simulations. We show that reduction in overall infected-person-days, IPD, by significant percentages can be achieved, for fixed numbers of tests per day of 5% and 10% of the population, of 30% and 50% in the IPD numbers, respectively.

Pooling for SARS-CoV2 Surveillance: Validation and Strategy for Implementation in K-12 Schools

Repeated testing of a population is critical for limiting the spread of the SARS-CoV-2 virus and for the safe reopening of educational institutions such as kindergarten-grade 12 (K-12) schools and colleges. Many screening efforts utilize the CDC RT-PCR based assay which targets two regions of the novel Coronavirus nucleocapsid gene. The standard approach of testing each person individually, however, poses a financial burden to these institutions and is therefore a barrier to using testing for re-opening. Pooling samples from multiple individuals into a single test is an attractive alternate approach that promises significant cost savings-however the specificity and sensitivity of such approaches needs to be assessed prior to deployment. To this end, we conducted a pilot study to evaluate the feasibility of analyzing samples in pools of eight by the established RT-PCR assay. Participants (1,576) were recruited from amongst the Tufts University community undergoing regular screening. Each volunteer provided two swabs, one analyzed separately and the other in a pool of eight. Because the positivity rate was very low, we spiked approximately half of the pools with laboratory-generated swabs produced from known positive cases outside the Tufts testing program. The results of pooled tests had 100% correspondence with those of their respective individual tests. We conclude that pooling eight samples does not negatively impact the specificity or sensitivity of the RT-PCR assay and suggest that this approach can be utilized by institutions seeking to reduce surveillance costs.