September 25, 2020 | New CRISPR COVID-19 diagnostics from the University of Connecticut and MIT/Broad, Mass General compares testing strategies and recommends wide screening, and King’s College London doctors recommend CT scans to flag COVID-19 lung issues. Plus, Singapore invents the SwabBot—a robot swabber, DetectaChem releases portable test pouches, and Pacific Northwest National Lab validates diagnostic kits.
Research Updates
Researchers at Karolinska Institute have developed a method for fast, cheap, yet accurate testing for COVID-19 infection. The method, published in Nature Communications, circumvents the RNA-extraction procedure, so that once the patient sample has been inactivated by means of heating, rendering the virus particles no longer infectious, it can pass straight to the diagnostic reaction that detects the presence of the virus. The data from 85 clinically diagnosed nasopharyngeal frozen samples showed that the method, hid-RT-PCR, could be a working option to extraction-based SARS-CoV-2 diagnostics, and that efforts to optimize the hid-RT-PCR protocol for maximum performance would be worthwhile. DOI: 10.1038/s41467-020-18611-5
A retrospective cohort study using routinely collected primary care data from the UK between Jan 1, 2010, and May 31, 2020 modeled the changes in diagnoses between March 1 and May 31, 2020 and previous years. The researchers found a 50% reduction in diagnosis of common mental health problems, 43% reduction in diagnoses of circulatory system disease, and 49% reduction of diagnoses of type 2 diabetes. The number of first prescriptions of associated medications was also lower than expected for the same time period. The study is published in The Lancet Public Health. DOI: 10.1016/S2468-2667(20)30201-2
Researchers at Massachusetts General Hospital (MGH) compared four COVID-19 testing strategies to predict clinical impact: 1) Hospitalized: PCR testing only patients with severe/critical symptoms warranting hospitalization; 2) Symptomatic: PCR for any COVID-19-consistent symptoms, with self-isolation if positive; 3) Symptomatic+asymptomatic-once: Symptomatic and one-time PCR for the entire population; and, 4) Symptomatic+asymptomatic-monthly: Symptomatic with monthly re-testing for the entire population. We examined effective reproduction numbers (Re, 0.9-2.0) at which policy conclusions would change. Their findings suggest when the COVID-19 pandemic is slowing, low-cost, recurring screening of asymptomatic people—at an expense of approximately $3 or less per test every two weeks—could decrease COVID-19 infections and deaths and be cost-effective. When the pandemic is surging, screening can be cost-effective when done more often, even if tests costs are higher. Their work is published in Clinical Infectious Diseases. DOI: 10.1093/cid/ciaa1418
Researchers from MIT and the Broad Institute report a CRISPR-based diagnostic test that can detect nearly as many cases as the standard Covid-19 diagnostic. The test—STOPCovid—is based on CRISPR and the SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) method. The test is still in the research phase, but the team submitted a letter to the New England Journal of Medicine outlining their progress. In comparing the second version of the STOPCovid test with the CDC standard two-step test (i.e., RNA extraction followed by RT-qPCR), STOPCovid.v2 reliably detected a viral load that was one thirtieth that detected by the CDC RT-qPCR test. DOI: 10.1056/NEJMc2026172
Meanwhile, researchers from the University of Connecticut announced the "All-In-One-Dual CRISPR-Cas12a" (AIOD-CRISPR) method which enables simple, rapid, ultrasensitive, visual detection of SARS-CoV-2 and is intended for use at home or in small clinics. In a paper published in Nature Communications, the researchers validated the clinical feasibility of the platform using COVID-19 clinical swab samples. Additionally, the researchers used a low-cost hand warmer as an incubator to detect clinical sample results within 20 minutes. DOI: 10.1038/s41467-020-18575-6
In a paper published in the American Journal of Neuroradiology, King's College London researchers found that emergency CT scans used to diagnose stroke also captured enough of the top of the lungs to see a fluffiness known as “ground glass opacification” that signals COVID-19. In the study, 225 patients were examined from three London Hyper-Acute Stroke Units. The emergency stroke scan consisted of a CT of the head and neck blood vessels. The team was able to use changes in the top of the lungs during the emergency scan to reliably and accurately diagnose COVID-19 and the changes also predicted increased mortality. DOI: 10.3174/ajnr.A6832
Kettering General Hospital in the UK performed a clinical assessment of the FebriDx point-of-care (POC) fingerstick blood test to rapidly assess and differentiate viral from bacterial symptomatic respiratory infections. Valid results were available for 47 patients. Overall FebriDx viral sensitivity was 97.1%; the diagnostic specificity of FebriDx and initial SARS‐CoV‐2 molecular test was 100%. The results were published in The International Journal of Clinical Practice. DOI: 10.1111/ijcp.13702
Industry Updates
A group of clinicians from the National Cancer Centre Singapore, Singapore General Hospital, and Duke-NUS Medical School has partnered Biobot Surgical, one of Singapore's pioneers in the field of medical robotics technology, to develop a robot that automates nasal swabbing needed to diagnose COVID-19. Known as SwabBot, the robot reduces swabbers' risk of exposure to the virus, reduces the need for trained manpower, standardizes the consistency of swabs taken, and provides greater throughput of swab tests. SwabBot is a self-administered robot which allows individuals being swabbed to activate and terminate the swabbing process at will. When ready, they use their chin to activate the robot and begin the swabbing process. The robot extends the swab safely and gently through the nose to the back of the nasal cavity, which is typically about 10cm from the nostrils. Press release.
DetectaChem, specializing in portable threat detection solutions used extensively by the U.S. Department of Defense and Homeland Security, has announced that their MD-Bio (MobileDetect Bio) BCP19 Test Pouch for COVID-19 detection successfully passed the initial Deep Dive phase in July 2020 and is currently advancing quickly through Phase 1 of the NIH (National Institutes of Health) RADxSM (Rapid Acceleration of Diagnostics) Tech initiative. DetectaChem's MD-Bio BCP19 Test Pouch is an innovative, high throughput, portable point-of-care test that can produce results for numerous samples simultaneously in 30 mins. The test detects nucleic acids from the SARS-CoV-2 which produces a clear colorimetric reaction to determine positive or negative infection results for active RNA. The solution combines a unique single-use test where the swabbed sample is inserted directly into the pouch combining with reagents, primers and viral transfer medium and then utilizes a propriety, single-button-operation MD-Bio Thermal Heater. The BCP19 Pouch and MD-Bio Thermal Heater are designed from the ground up for maximum ease of use for all point-of-care applications. Press release.
A new research consortium, Reliable Response Data Discovery (R2D2), invites clinicians, researchers, patients and the general public to submit questions that could be answered by COVID-19 patient record data from more than 200 participating hospitals. Questions are submitted and answers are provided via a new web portal: COVID19questions.org. Unlike other patient databases and registries, the R2D2 COVID-19 Questions site allows health systems to maintain control of their own data rather than pool it in a central repository. No patient-level data are ever transmitted outside of each health system, only data aggregates, and the privacy of individuals and institutions is preserved. Through advanced computational methods, complex analyses involving multiple factors can be performed. Since the system queries all patient records, not just those with COVID-19, users can ask questions about how patients with COVID-19 compare to other patients. Press release.
In a collaborative research effort between Pacific Northwest National Laboratory and the University of Washington laboratories, the PNNL team established performance for kits from additional manufacturers for use with the Centers for Disease Control and Prevention 2019-nCoV Real-Time RT-PCR Diagnostic Panel to detect and inactivate the virus. The team’s work addresses severe shortages of extraction reagents, which are having an impact on the work of many testing labs across the nation. The scientists studied the ability of the kits to extract the RNA from the virus, a process that makes the virus easier to measure, and confirmed that the kits inactivate the virus – making it safe for widespread testing and analysis. Proper extraction of the virus from a sample is a critical step in the testing process, and labs cannot test patients without these kits. By showing that additional kits can be used for COVID-19 testing, the scientists have helped improve access and availability of diagnostic testing. Press release.
AusDiagnostics has launched their new
Puryx extraction kit product line. AusDiagnostics was the first Australian manufacturer to produce a PCR (Polymerase Chain Reaction) test for SARS-CoV-2 in January 2020. The tests have been used in most of the public hospitals in Sydney and Melbourne for the past six months, plus various laboratories in other states, as well as overseas in the UK, US and Europe. The Puryx product line, which is manufactured at AusDiagnostics’ Sydney headquarters in Mascot, encompasses kits that extract pathogen derived nucleic acids from patient samples to prepare them for subsequent laboratory detection of infections and other pathogens, including testing for COVID-19.
Press release