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New Testing Methods, Analysis of Sampling Techniques: COVID-19 Updates

July 31, 2020 | Diagnostic methods for SARS-CoV-2 are being refined with researchers studying sampling techniques, identifying early biomarkers of severe disease, and more. The diagnostics industry continues to rise to the need, releasing new tests and sharing resources to speed diagnosis and patient stratification. 

Literature Updates

A German team proposes reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a simple, scalable, and broadly applicable testing method for SARS-CoV-2. The team tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. They determined that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. Their work is published in Science Translational MedicineDOI: 10.1126/scitranslmed.abc7075

In a paper to be published in eBioMedicine, investigators from Brigham and Women's Hospital conducted a systematic review and meta-analysis of COVID-19 sampling techniques, analyzing data from more than 3,000 specimens to compare nasopharyngeal swabs, oropharyngeal swabs, and sputum sampling. They found that sputum sampling is a valuable method of COVID-19 diagnosis and monitoring, and they highlight the importance of early testing after symptom onset to increase the rates of COVID-19 diagnosis. The rate of viral detection was significantly higher in sputum than either oropharyngeal swabs or nasopharyngeal swabs. Detection rates were highest within one week of symptom onset for all three tests. DOI: 10.1016/j.ebiom.2020.102903

Researchers in Korea have identified acetylated K676 TGFBIp as a blood biomarker of severity of COVID-19. “The TGFBIp K676Ac was consistently elevated in the blood of SARS-CoV-2 pneumonia patients (n=113); especially in patients of intensive care unit,” they write. Previous reports have demonstrated that TGFBIp can induce signaling activation and up-regulation of NF-κB, they note. “Although NF-κB is vital for normal immune responses against infections, nuclear accumulation of activated NF-κB can lead to increase in endothelial cell apoptosis, vascular permeability and secretion of endotoxins.” Their work is published in Science Advances. DOI: 10.1126/sciadv.abc1564 

DXX Industry Updates

Veracyte and MAVIDx have announced an agreement for MAVIDx to develop ultra-high throughput genomic testing for SARS-CoV-2, the virus that causes COVID-19, on the nCounter Analysis System, Veracyte’s diagnostics platform. The agreement is intended to enable diagnostic testing and population screening for COVID-19 at an unprecedented scale – up to 40,000 samples per day performed on the easy-to-use nCounter instrument – through technology that attaches molecular barcodes to individual RNA molecules of the virus. Press release.

The University of Arizona College of Medicine - Phoenix has entered into an Other Transaction Agreement (OTA) with the Defense Threat Reduction Agency (DTRA), an agency within the U.S. Department of Defense. The agreement is a $9.5 million ceiling contract for three years, to provide about 3,000 devices that could easily, quickly and accurately detect pathogens and biological threats including COVID-19. The team is developing a vertical flow immunoassay diagnostic test that interfaces with a smartphone. Users would take a small finger prick of blood or a syringe of urine and then push the liquid onto a test strip. Essentially, the device would take a picture of that paper membrane, which would be analyzed and sent back to the users, telling them if they have been exposed to pathogens like anthrax, the plague-causing bacterium Yersinia pestis, or other bacteria and viruses. Press release.

Thermo Fisher Scientific is expanding its GlobalAccess Sequencing Program to include laboratories working in oncology. Originally introduced to accelerate multi-institutional-led studies focused on SARS-CoV-2, the expanded program now provides support to labs facing significant constraints as a result of the global pandemic by offering faster access to comprehensive, single-day molecular profiling of tumor tissue on Thermo Fisher’s Ion Torrent Genexus System. Under the GlobalAccess Sequencing Program, Thermo Fisher will subsidize a limited number of Genexus Systems for a short time in alignment with the company’s commitment to serve its customers and their important work during the global pandemic. The program, which is open to pathology laboratories that currently run or wish to begin sequencing samples with oncology assays, is available immediately and will continue through the end of this year. Press release

Two research teams—one from the Institut Pasteur, supported by the Fonds IMMUNOV and the Institut National de la Santé et de la Recherche Médicale (Inserm), and another on behalf of the International Center for Research in Infectious Diseases (CIRI) in Lyon, France—have deployed Quanterix’ highly sensitive Simoa technology to quantify and profile telltale markers, including inflammatory cytokines, in COVID-19 patients with a range of disease severity. Findings in both studies suggest a correlation between disease severity and low interferon production, suggesting that quantification of IFN production could be a promising strategy for identifying high-risk individuals and informing therapeutic response. Press release.

The COVID-collab research team at King's College London have launched a free mobile app which will allow scientists to investigate the use of wearable devices and smartphones for digital detection of COVID-19. The Mass Science app allows COVID-Collab study participants to connect wearables, such as Fitbit devices, and share data including heart rate, activity and sleep. Participants can also use the app to provide information on geographic location, mood, and mental health in addition to COVID-19 symptoms and a diagnosis if they have tested positive for the disease. The researchers hope to discovery how accurate wearable devices are as digital tests for COVID-19 and other respiratory illnesses? Could automated monitoring of disease symptoms help track the disease nationally or in local hotspots? And what symptoms are important and which are reliable, early predictors of infection? Press release.

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