scholarly journals Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond

2021 ◽  
Author(s):  
Kody A. Waldstein ◽  
Jirong Yi ◽  
Michael Myung Cho ◽  
Raghuraman Mudumbai ◽  
Xiaodong Wu ◽  
...  
Keyword(s):  
Compressed Sensing ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Extraction Process ◽  
Prevalence Rates ◽  
High Prevalence ◽  
Rapid Spread ◽  
Significant Burden ◽  
Sample Pooling ◽  
Sample Dilution

The rapid spread of SARS-CoV-2 has placed a significant burden on public health systems to provide rapid and accurate diagnostic testing highlighting the critical need for innovative testing approaches for future pandemics. In this study, we present a novel sample pooling procedure based on compressed sensing theory to accurately identify virally infected patients at high prevalence rates utilizing an innovative viral RNA extraction process to minimize sample dilution. At prevalence rates ranging from 0-14.3%, the number of tests required to identify the infection status of all patients was reduced by 75.6% as compared to conventional testing in primary human SARS-CoV-2 nasopharyngeal swabs and a coronavirus model system. Additionally, our modified pooling and RNA extraction process minimized sample dilution which remained constant as pool sizes increased. Our use of compressed sensing can be adapted to a wide variety of diagnostic testing applications to increase throughput for routine laboratory testing as well as a means to increase testing throughput to combat future pandemics.

scholarly journals A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 within nasopharyngeal and oropharyngeal swabs at Hampshire Hospitals NHS Foundation Trust

2020 ◽  
Author(s):  
Veronica L. Fowler ◽  
Bryony Armson ◽  
Jose L. Gonzales ◽  
Emma L. Wise ◽  
Emma L. A. Howson ◽  
...  
Keyword(s):  
Diagnostic Testing ◽  
Rna Extraction ◽  
Lamp Assay ◽  
Standard Of Care ◽  
Positive Sample ◽  
Diagnostic Sensitivity ◽  
Nucleic Acid Amplification ◽  
Analytical Sensitivity ◽  
Synthetic Dna ◽  
High Prevalence

AbstractThe COVID-19 pandemic has illustrated the importance of rapid, accurate diagnostic testing for the effective triaging and cohorting of patients and timely tracking and tracing of cases. However, a surge in diagnostic testing quickly resulted in worldwide competition for the same sample preparation and real-time RT-PCR diagnostic reagents (rRT-PCR). Consequently, Hampshire Hospitals NHS Foundation Trust, UK sought to diversify their diagnostic portfolio by exploring alternative amplification chemistries including those that permit direct testing without RNA extraction. This study describes the validation of a SARS-CoV-2 RT-LAMP assay, which is an isothermal, autocycling, strand-displacement nucleic acid amplification technique which can be performed on extracted RNA, “RNA RT-LAMP” or directly from swab “Direct RT-LAMP”. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1×101 and 1×102 copies when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care (SoC) rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly, evidence suggests there is a very low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct-RT-LAMP was 67% and 97%, respectively. When setting CT cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively. Time from swab-to-result for a strong positive sample (CT < 25) was < 15 minutes. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increase in throughput, whereas Direct RT-LAMP could be used as a screening tool for triaging patients into appropriate hospitals wards, at GP surgeries and in care homes, or for population screening to identify highly contagious individuals (“super shedders”). Direct RT-LAMP could also be used during times of high prevalence to save critical extraction and rRT-PCR reagents by “screening” out those strong positives from diagnostic pipelines.

scholarly journals SalivaSTAT: Direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance

2020 ◽  
Author(s):  
Nikhil S Sahajpal ◽  
Ashis K Mondal ◽  
Sudha Ananth ◽  
Allan Njau ◽  
Pankaj Ahluwali ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Community Setting ◽  
Absolute Quantification ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Direct Pcr ◽  
Sample Pooling ◽  
Saliva Collection

BackgroundThe limitations of widespread current COVID-19 diagnostic testing lie at both pre-analytical and analytical stages. Collection of nasopharyngeal swabs is invasive and is associated with exposure risk, high cost, and supply-chain constraints. Additionally, the RNA extraction in the analytical stage is the most significant rate-limiting step in the entire testing process. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction free RT-PCR test using any of the commercially available RT-PCR kits.MethodsWe optimized saliva collection devices, heat-shock treatment and homogenization. The effect of homogenization on saliva samples for extraction-free RT-PCR assay was determined by evaluating samples with and without homogenization and preforming viscosity measurements. Saliva samples (872) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. Further, a five-sample pooling strategy was evaluated as per FDA guidelines using the SalivaSTAT protocol.ResultsThe saliva collection (done without any media) performed comparable to the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95°C for 30-minutes and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreement (NPA) of 95.8% and 100%, respectively. The LoD was established as ∼20-60 copies/ml by absolute quantification. Further, a five-sample pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively.ConclusionWe have optimized an extraction-free direct RT-PCR assay for saliva samples that demonstrated comparable performance to FDA-EUA assay (Extraction and RT-PCR). The SalivaSTAT protocol is a rapid, sensitive, and cost-effective method that can be adopted globally, and has the potential to meet testing needs and may play a significant role in management of the current pandemic.

Comparing the Impact of Religious Discourse on HIV/AIDS in Islam and Christianity in Africa

2012 ◽  
Vol 8 ◽  
Author(s):  
Sloane Speakman
Keyword(s):  
Social Factors ◽  
Negative Relationship ◽  
Hiv Prevalence ◽  
Religious Discourse ◽  
Prevalence Rates ◽  
The Social ◽  
High Prevalence ◽  
Islam And Christianity ◽  
Sub Saharan ◽  
The Impact

In examining the strikingly high prevalence rates of HIV in many parts of Africa, reaching as high as 5% in some areas, how does the discourse promoted by the predominant religions across the continent, Islam and Christianity, affect the outlook of their followers on the epidemic? This question becomes even more intriguing after discovering the dramatic difference in rate of HIV prevalence between Muslims and Christians in Africa, confirmed by studies that have found a negative relationship to exist between HIV prevalence and being Muslim in Africa, even in Sub-Saharan African nations. Why does this gap in prevalence rates exist? Does Islam advocate participating in less risky behavior more so than Christianity? By comparing the social construction, epidemiological understanding and public responses among Muslim populations in Africa with Christian ones, it becomes apparent that many similarities exist between the two regarding discourse and that, rather than religious discourse itself, other social factors, such as circumcision practices, contribute more to the disparity in HIV prevalence than originally thought.

scholarly journals Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Wei ◽  
Esther Kohl ◽  
Alexandre Djandji ◽  
Stephanie Morgan ◽  
Susan Whittier ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Cost Effective ◽  
Clinical Samples ◽  
Nasopharyngeal Swab ◽  
Percentage Agreement ◽  
Testing Method ◽  
Viral Transport

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.

scholarly journals Integrated Metabolomics and Transcriptomics Using an Optimised Dual Extraction Process to Study Human Brain Cancer Cells and Tissues

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 240
Author(s):  
Alison Woodward ◽  
Alina Pandele ◽  
Salah Abdelrazig ◽  
Catherine A. Ortori ◽  
Iqbal Khan ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Extraction Method ◽  
Limit Of Detection ◽  
Rna Extraction ◽  
Extraction Process ◽  
Extraction Methods ◽  
Serum Starvation ◽  
Extraction Techniques ◽  
Metabolic Genes ◽  
Dual Extraction

The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.

HIV epidemic in central african republic: High prevalence rates in both rural and urban areas

2004 ◽  
Vol 72 (3) ◽  
pp. 358-362 ◽  
Author(s):  
Marcelle Diane Matsika-Claquin ◽  
Marcel Massanga ◽  
Didier Ménard ◽  
Jean Mazi-Nzapako ◽  
Jean-Pierre Ténegbia ◽  
...  
Keyword(s):  
Urban Areas ◽  
Central African Republic ◽  
Prevalence Rates ◽  
Rural And Urban Areas ◽  
Hiv Epidemic ◽  
Rural And Urban ◽  
High Prevalence

scholarly journals Low Levels of Pyrethroid Resistance in Hybrid Offspring of a Highly Resistant and a More Susceptible Mosquito Strain

2020 ◽  
Vol 20 (4) ◽  
Author(s):  
Matthew Pinch ◽  
Stacy D Rodriguez ◽  
Soumi Mitra ◽  
Yashoda Kandel ◽  
Emily Moore ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Pyrethroid Resistance ◽  
Resistance Mutations ◽  
Human Host ◽  
High Prevalence ◽  
Rapid Spread ◽  
Choice Assay ◽  
Low Levels ◽  
Control Disease ◽  
Different Strains

Abstract The use of insecticides has been a central approach to control disease-transmitting mosquitoes for the last century. The high prevalence of pyrethroid use as public health insecticides has resulted in the evolution of pyrethroid resistance in many populations of Aedes aegypti (Linnaeus) (Diptera: Culicidae), throughout its global distribution range. Insecticide resistance is often correlated with an associated fitness cost. In this project, we studied the phenotypes of hybrid mosquitoes derived from crossing a pyrethroid-resistant strain of Ae. aegypti (Puerto Rico [PR]) with a more susceptible one (Rockefeller [ROCK]). We first sequenced and compared the para gene of both original strains. We then crossed males from one strain with females of the other, creating two hybrids (Puertofeller, Rockorico). We used a Y-tube choice assay to measure the attraction of these strains towards a human host. We then compared the levels of pyrethroid resistance in the different strains. We found three known resistance mutations in the para gene sequence of the PR strain. In our attraction assays, PR females showed lower attraction to humans, than the ROCK females. Both hybrid strains showed strong attraction to a human host. In the insecticide resistance bottle assays, both hybrid strains showed marginal increases in resistance to permethrin compared to the more susceptible ROCK strain. These results suggest that hybrids of sensitive and permethrin-resistant mosquitoes have an incremental advantage compared to more susceptible mosquitoes when challenged with permethrin. This explains the rapid spread of permethrin resistance that was observed many times in the field.

scholarly journals A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael A. Crone ◽  
Miles Priestman ◽  
Marta Ciechonska ◽  
Kirsten Jensen ◽  
David J. Sharp ◽  
...  
Keyword(s):  
Rapid Development ◽  
Community Sample ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Clinical Diagnostics ◽  
Virus Like Particle ◽  
Qpcr Platform ◽  
Sample Testing ◽  
Alternative Testing ◽  
Development And Validation

Abstract The SARS-CoV-2 pandemic has shown how a rapid rise in demand for patient and community sample testing can quickly overwhelm testing capability globally. With most diagnostic infrastructure dependent on specialized instruments, their exclusive reagent supplies quickly become bottlenecks, creating an urgent need for approaches to boost testing capacity. We address this challenge by refocusing the London Biofoundry onto the development of alternative testing pipelines. Here, we present a reagent-agnostic automated SARS-CoV-2 testing platform that can be quickly deployed and scaled. Using an in-house-generated, open-source, MS2-virus-like particle (VLP) SARS-CoV-2 standard, we validate RNA extraction and RT-qPCR workflows as well as two detection assays based on CRISPR-Cas13a and RT-loop-mediated isothermal amplification (RT-LAMP). In collaboration with an NHS diagnostic testing lab, we report the performance of the overall workflow and detection of SARS-CoV-2 in patient samples using RT-qPCR, CRISPR-Cas13a, and RT-LAMP. The validated RNA extraction and RT-qPCR platform has been installed in NHS diagnostic labs, increasing testing capacity by 1000 samples per day.

scholarly journals Heart failure in practice: enhancing knowledge for nursing and residential care

2020 ◽  
Vol 22 (4) ◽  
pp. 1-7
Author(s):  
Catherine Hayes ◽  
Christopher Cox ◽  
Lindsay Parkin ◽  
Jeanette Scott-Thomas ◽  
Yitka Graham
Keyword(s):  
Heart Failure ◽  
Older Adults ◽  
Residential Care ◽  
Prevalence Rates ◽  
High Prevalence ◽  
The University

The high prevalence rates of heart failure in older adults means that those who have been diagnosed require their specific needs to be recognised and addressed effectively by care professionals. Researchers at the University of Sunderland provide guidance on how to implement this in nursing and residential care settings

scholarly journals Zika among international travellers presenting to GeoSentinel sites, 2012–2019: implications for clinical practice

2020 ◽  
Vol 27 (4) ◽  
Author(s):  
Kristina M Angelo ◽  
Rhett J Stoney ◽  
Gaelle Brun-Cottan ◽  
Karin Leder ◽  
Martin P Grobusch ◽  
...  
Keyword(s):  
Descriptive Analysis ◽  
Diagnostic Testing ◽  
Healthcare Providers ◽  
International Travel ◽  
Onset Date ◽  
Prevention Measures ◽  
Illness Onset ◽  
Rapid Spread ◽  
The Caribbean ◽  
Large Decline

Abstract Introduction International travellers contribute to the rapid spread of Zika virus (ZIKV) and its sentinel identification globally. We describe ZIKV infections among international travellers seen at GeoSentinel sites with a focus on ZIKV acquired in the Americas and the Caribbean, describe countries of exposure and traveller characteristics, and assess ZIKV diagnostic testing by site. Methods Records with an international travel-related diagnosis of confirmed or probable ZIKV from January 2012 through December 2019 reported to GeoSentinel with a recorded illness onset date were included to show reported cases over time. Records from March 2016 through December 2019 with an exposure region of the Americas or the Caribbean were included in the descriptive analysis. A survey was conducted to assess the availability, accessibility and utilization of ZIKV diagnostic tests at GeoSentinel sites. Results GeoSentinel sites reported 525 ZIKV cases from 2012 through 2019. Between 2012 and 2014, eight cases were reported, and all were acquired in Asia or Oceania. After 2014, most cases were acquired in the Americas or the Caribbean, a large decline in ZIKV cases occurred in 2018–19. Between March 2016 and December 2019, 423 patients acquired ZIKV in the Americas or the Caribbean, peak reporting to these regions occurred in 2016 [330 cases (78%)]. The median age was 36 years (range: 3–92); 63% were female. The most frequent region of exposure was the Caribbean (60%). Thirteen travellers were pregnant during or after travel; one had a sexually acquired ZIKV infection. There was one case of fetal anomaly and two travellers with Guillain-Barré syndrome. GeoSentinel sites reported various challenges to diagnose ZIKV effectively. Conclusion ZIKV should remain a consideration for travellers returning from areas with risk of ZIKV transmission. Travellers should discuss their travel plans with their healthcare providers to ensure ZIKV prevention measures are taken.

Sign in / Sign up

Export Citation Format

Share Document