May 1, 2020 | The diagnostics community has focused its attention on COVID-19, providing new research and tools to shed light on the virus. New insights include smartphone-based testing, digital pathology software, and more.
In a study published in the Journal of Molecular Diagnostics, researchers in Korea describe a novel method that may enable decentralized facilities to deliver faster test services for COVID-19 to more people. Diagnosis currently relies mainly on methods involving reverse transcription quantitative PCR, but their capacity is limited by the availability of high-level facilities and instruments. The new assay uses a one-step nucleic acid amplification method called RT-LAMP (reverse transcription loop-mediated isothermal amplification) to detect genomic RNA of SARS-CoV-2. Step one was to identify promising LAMP primer sets targeting genomic regions specific to this virus. Researchers then optimized RT-LAMP reactions for each of the two identified primer sets and evaluated the limit of detection and specificity to other coronaviruses. Assays in the study were able to detect as few as 100 copies of SARS-CoV-2 RNA and no cross-reactivity of RT-LAMP assays to other human coronaviruses was observed. Test throughput may increase by coupling the primer sets with crystal violet colorimetric detection, the primer sets were used as the starting point and coupled with crystal violet colorimetric detection. The reaction can be performed and interpreted with a simple instrument, such as a drying oven or water bath. DOI: 10.1016/j.jmoldx.2020.03.006
A multi-institutional study led by researchers at the University of Illinois at Urbana-Champaign and published by Lab on a Chip has demonstrated an inexpensive yet sensitive smartphone-based testing device for viral and bacterial pathogens that could reduce the pressure on testing laboratories during a pandemic such as COVID-19. The roughly $50 smartphone accessory identifies pathogens in about 30 minutes. The unit is comprised of a small cartridge containing testing reagents and a port to insert a nasal extract or blood sample, and clips to a smartphone. Reagents inside the cartridge break open a pathogen's outer shell to gain access to its RNA. A primer molecule then amplifies the genetic material into many millions of copies in about 10 or 15 minutes, and a fluorescent dye stains them and glows green when illuminated by blue LED light, which is then detected by the smartphone's camera. The study began with the goal of detecting a panel of viral and bacterial pathogens in horses (harmless to humans), including those that cause severe respiratory illnesses like those seen with COVID-19. Researchers say the device could be ideally suited for rapid testing of passengers before getting on a flight and people going to a theme park or attending large events. They are now working to eliminate steps in getting all needed reagents into the cartridge. DOI: 10.1039/D0LC00304B
Radiology and vascular medicine experts in The Netherlands authored a special report appearing in Radiology that outlines prevention, diagnosis and treatment of complications stemming from blood clots in patients with COVID-19. Clinicians worldwide face this new severe infectious lung disease with no proven therapies. Based on recent reports that demonstrated a strong association between elevated D-dimer levels and poor prognosis, concerns have risen about thrombotic complications in patients with the novel coronavirus. Recent observations suggest that respiratory failure in COVID-19 is not driven by the development of the acute respiratory distress syndrome alone, but that microvascular thrombotic processes may play a role. This may have important consequences for the diagnostic and therapeutic management of these patients. Recommendations include strict thrombosis prophylaxis, close laboratory and appropriate imaging monitoring with early anti-coagulant therapy in cases of suspected venous thromboembolism; and use of prophylactic-dose heparin, chest CT, CT pulmonary angiography and routine D-dimer testing for diagnostic and therapeutic management as dictated by a patient’s symptoms and risk profile. DOI: 10.1148/radiol.2020201629
Researchers from the Icahn School of Medicine at Mount Sinai have developed a serological test to help determine the real rate of SARS-CoV-2 infection, understand individuals' antibody responses to the virus, and identify people who are potentially immune to re-infection. In a paper published in Current Protocols in Microbiology, they provide a step-by-step directions that other researchers can follow to replicate the test, which involves expressing and purifying segments of a key SARS-CoV-2 protein that are then used to detect the presence of antiviral antibodies. DOI: 10.1002/cpmc.100
A multi-institutional study published in the American Journal of Roentgenology found that Siemens Healthineers' AI-Rad Companion (which examines chest scans) provides results comparable with traditional lung function tests—meaning, artificial intelligence could serve as backup to radiologists' eyes. It marked the first step toward possibly using chest scans to quantify the severity of the lung disease and track the progress of treatment. The program can also create a 3D model of patients’ lungs, showing the existing damage, which could aid doctors trying to impress upon patients the necessity of making changes. The next phase of research will examine whether the AI software, which automatically looks for problems across multiple organ systems, finds things that humans miss. In response to the COVID-19 pandemic, efforts are now underway to start training the software in the detection and characterization of COVID-19-related lung changes. This could potentially provide physicians with a tool to better differentiate the non-specific lung findings of COVID-19 pneumonia from other infectious or inflammatory lung disorders and more objectively quantify the extent of disease. DOI: 10.2214/AJR.19.21572
In a study conducted at Germany’s Saarland University Hospital, and published in The Lancet Infectious Diseases, virologists have shown that sample pooling can massively increase coronavirus testing capacity when the infection rate is low. The pooling of samples before testing is a well-established and safe procedure in blood banking, which researchers adapted and tested for use in coronavirus diagnostics. Samples from as many as 30 individuals can be pooled and tested together in a single tube using sensitive molecular biological detection methods. Only if the pool result is positive do the samples need to be tested individually. The new procedure has been used at the hospital since mid-March to successfully protect vulnerable patients from infection by asymptomatic SARS-CoV-2 carriers and, more recently, to screen around 22,000 residents and staff at nursing and residential care homes in Saarland—a huge collaborative effort involving numerous partners. DOI: 10.1016/S1473-3099(20)30362-5
Researchers at The First Affiliated Hospital of Nanchang University in China have reported a significant and positive relationship between the amount of virus present in a throat swab sample and the severity of COVID disease. They also found a negative correlation between SARS-CoV-2 viral load and lymphocytes that fight infection. The results were based on samples taken from 76 patients with mild and severe COVID-19 and published in Viral Immunology. DOI: 10.1089/vim.2020.0062
Researchers at Massachusetts General Hospital have developed a breakthrough, web-based imaging platform to more easily view, compare and analyze medical images for a wide range of diseases, including COVID-19. The Open Health Imaging Foundation (OHIF) web viewer was originally developed for use in cancer imaging research and clinical trials and provides performance typically available only from installed software. The free, open-source extendable platform is already being used by projects worldwide and is interoperable, commercial grade, user-friendly and requires less technical support than a typical commercial product. It can also be run in a web browser from any computer without having to download software. The platform has been downloaded more than 8,500 times and has been translated into several languages. Among its new uses: a platform in Australia providing education to radiologists worldwide on COVID-19 appearances on CT scans, chest X-ray artificial intelligence programs for diagnosis of COVID-19 in South Korea and a medical image viewer being used to quickly and securely diagnose COVID-19 from multiple sites across Brazil. A description of the OHIF viewer has been published in the Journal of Clinical Oncology: Clinical Cancer Informatics. DOI: 10.1200/CCI.19.00131
A proof-of-concept study published in Analytical Chemistry describes a quick, sensitive test for antibodies against the coronavirus in human blood that could help doctors track a person's exposure to the disease and confirm suspected COVID-19 cases that tested negative by other methods. The assay is based on lateral flow immunoassay (LFA), a technique used for home pregnancy tests, but with so much more sensitive fluorescence-based detection than some other LFAs that results can be read by the naked eye. The new assay was used on seven serum samples from COVID-19 patients and 12 samples from people who had tested negative for the disease by reverse transcriptase-polymerase chain reaction. It correctly diagnosed all seven samples as positive, as well as an additional negative case that had suspicious clinical symptoms, in only 10 minutes per sample. DOI: 10.1021/acs.analchem.0c00784
Cytovale has expanded its partnership with the Biomedical Advanced Research and Development Authority (BARDA), part of the office of the Assistant Secretary for Preparedness and Response at the U.S. Department of Health and Human Services, to conduct a pilot study for Cytovale’s Rapid Sepsis Diagnostic System for patients with potential respiratory infections, including those with SARS-CoV-2, responsible for COVID-19. By looking at the structure of immune cells through high-speed imaging, machine learning and microfluidics, Cytovale’s patented technology can diagnose sepsis in under 10 minutes with the goal of enabling timely and accurate triage in the emergency department, filling a crucial unmet need in rapid sepsis diagnosis. BARDA is continuing to fund advanced research and development activities to support the FDA 510(k) clearance for the Cytovale Rapid Sepsis Diagnostic System. BARDA and Cytovale are demonstrating a continued commitment to their public-private partnership, first announced in October 2019, with BARDA now contributing an additional $3.83 million of the $5.9 million total estimated cost to continue validation and advanced research, including the pilot study of COVID-19 patients. Cytovale will fund the remaining research and development costs for this study. Press release.
Proscia has made available the Concentriq Dx digital pathology software for use in reviewing and reporting of digital pathology slides in the United States. Concentriq Dx, which is CE-marked for use in primary diagnosis in Europe, will support the need for remote pathology in the United States brought about by the COVID-19 pandemic. The current practice of pathology tethers pathologists to microscopes in physical laboratory spaces. By limiting access to these laboratories, the COVID-19 pandemic has crippled pathology operations, disrupting the ability to serve patients. This has created urgency around the adoption of digital pathology, which enables remote case review, to provide timely diagnosis. Recognizing this urgency, the FDA has introduced guidance on a policy to help expand the availability of remote digital pathology devices in an effort to facilitate pathology services while reducing healthcare personnel contact and risk of exposure to COVID-19. Press release.
Huntsville Hospital, HudsonAlpha Institute for Biotechnology, and iRepertoire, a diagnostic technology company located on the HudsonAlpha campus, are studying local patients diagnosed with COVID-19 under a Huntsville Hospital IRC approved protocol to learn how the human immune system responds to the SARS-CoV-2 virus, with hopes for developing an effective treatment for the disease. Area participants who have been recently diagnosed with COVID-19 will be recruited by a research coordinator to participate in the study. The patients will provide blood samples at four time points over a series of weeks in order to gauge how their immune system is responding to the SARS-CoV-2 virus. Researchers at HudsonAlpha and iRepertoire hope the results of the study can be used to find and test possible treatments or cures for COVID-19 by using antibodies identified in these patients. Press release.
OU Medicine, University of Oklahoma Health Sciences Center and Oklahoma Medical Research Foundation (OMRF) have collaborated to create a new test for COVID-19 using technology and reagents from Fluidigm Corporation. The test is intended for large-scale testing of patients across the OU Medicine healthcare system, with the capacity to test 180,000 samples over the next 90 days. OU Medicine has a lab certified under the Clinical Laboratory Improvement Amendments, making it eligible to create its own diagnostic test, and has also applied for Emergency Use Authorization for the test from the FDA. The testing platform will produce results in about six hours. OMRF's experience with Fluidigm's microfluidics technology and its Fluidigm Biomark HD system was a crucial component in the creation and validation of the test. The FAA Civil Aerospace Medical Institute in Oklahoma City also provided a Biomark HD system for use in the testing. Rapid, high-capacity testing is critical for contact tracing and will help the state determine when and how Oklahomans can begin returning to work and their daily lives following the peak of the pandemic. Press release.
A research team at the Suzhou Institute of Biomedical Engineering and Technology of the Chinese Academy of Sciences recently developed an on-site nucleic acid detection system for quick identification of the SARS-CoV-2 virus. The system is based on hybrid capture immunofluorescence analysis and requires only 20 μl of swab or sputum samples, making it easy and convenient to use. A qualitative result is available in 45 minutes. The instrument is portable and can be stored and transported at normal temperature. The National Medical Products Administration has approved the test kit and granted it a medical device product registration certificate in March (the detecting instrument used in the system was similarly certified in 2017). The system also obtained Conformité Européenne certification a few weeks ago. It could soon be in use both in the EU and China. Press release.
Biomedical engineers at Duke University are adapting a rapid testing platform originally designed to detect Ebola to see whether it can be repurposed for COVID-19. The D4 assay is a self-contained diagnostic test that gets inkjet-printed on a small glass slide and detects low levels of antigens from a single drop of blood or throat- or nose-swab sample. In previous studies, the experimental test was shown to detect a variety of biomarkers as accurately as the most sensitive diagnostic tests on the market, but at a much faster rate. Researchers have shown a proof-of-concept by detecting a biomarker of the SARS-Cov-2 virus and the next step would be to validate this with patient samples. The tool has both detection antibodies (tagged with a fluorescent marker) and capture antibodies (primed to find the antigens specific to a pathogen) printed on its surface, and a handheld scanner is used to look for lights indicating the presence of the antigen. Since the assay is printed on a polymer brush coating, non-target proteins don’t attach to the slide's surface and create “background noise” that would make low levels of target proteins harder to detect. Testing with COVID patient samples could begin in the next few months. The lab has been working with synthetic versions of the proteins expressed by SARS-CoC-2 rather than the live virus. Press release.
Alveo Technologies and Janssen Pharmaceuticals and collaborating to advance Alveo’s be.well platform of analyzers, nasal swabs and cartridges for the detection of viral infectious diseases, including Respiratory Syncytial Virus (RSV) and potentially SARS-CoV-2. Alveo will use a phased approach to first gain Emergency Use Authorization (EUA) for a SARS-CoV-2 assay, followed by a multiplex assay for home use. Alveo will receive financial support as well as technical and regulatory counsel from Janssen relating to the regulatory submission of the be.well platform, which is designed to diagnose a range of viral infections. Press release.
A team of materials scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) have built a text-mining tool to help the global scientific community synthesize the mountain of scientific literature on COVID-19 being generated every day. The COVIDScholar tool uses natural language processing techniques to not only quickly scan and search tens of thousands of research papers, but also help draw insights and connections that may otherwise not be apparent. It was developed in response to a call to action from the White House Office of Science and Technology Policy. A prototype of COVIDScholar was up and running within about a week and a little more than a month later had collected over 61,000 research papers—about 8,000 of them specific to COVID-19 and the rest on related topics—and is getting more than 100 unique users every day via word of mouth. New journal articles on the coronavirus are now being published at the rate of 200 per day, which the sophisticated search engine automatically grab, clean up and make searchable. Its creators are now working with researchers in Berkeley Lab's Environmental Genomics and Systems Biology Division and UC Berkeley's Innovative Genomics Institute to improve COVIDScholar's algorithms to discover new connections within the data. The tool runs on the supercomputers of the National Energy Research Scientific Computing Center (NERSC), located at Berkeley Lab, and the online search engine and portal are powered by the Spin cloud platform at NERSC. Press release.
The multi-agency Research Luxembourg COVID-19 Task Force has developed a large-scale voluntary testing strategy making a diagnostic test accessible to the entire population of Luxembourg (in some cases, several times). It will be the world’s first country to have a complete overview of the number of infected citizens. The overall objective is to avoid a second wave of infected people and introduction of a new lockdown. The strategy consists of expanding capacity to 20,000 tests per day, with the population being divided into contingents rather than being considered collectively. Restrictions of the current lockdown will be lifted for people who test negative, while those who test positive must enter isolation and their contacts traced, tested and quarantined to break the chain of infection. Press release.
Researchers at the Wyss Institute at Harvard University have designed a new, fully injection-molded nasopharyngeal swab that can be manufactured quickly and inexpensively at high volume to help address the nationwide and international shortage of swabs for COVID-19 testing and research. The swabs are moving into human trials at SUNY Downstate Medical Center in New York and Translational Genomics Research Institute and expected to be completed next week; they’re also in preclinical evaluation at six additional hospitals. Data from the two trials will be used to inform larger trials with COVID-19 patients, and California-based medical device manufacturer IPB, Inc. will ramp up production of the new swabs to reach 200,000 per day by May 15. The Wyss team effectively built a medical device company from scratch. Press release.
Two startups based in the state of São Paulo, Hoobox and Radsquare, have jointly developed fever-detecting technology (called Fevver) based on artificial intelligence (AI) that is being used at Albert Einstein Jewish Hospital in São Paulo to reduce the risk of coronavirus transmission. People who approach the hospital’s front desk have their temperature taken remotely by a computer vision system installed in a nearby column. Consisting of a thermal camera and armed with facial recognition algorithms, the system scans people's face and measures their temperature automatically. When it detects a fever, the AI software sends a smartphone alert to the duty nurse who will quickly activate the hospital's triage protocol and possibly isolate the person. Results have been so positive that the system will now be installed in other parts of the hospital to measure the temperature of visitors and staff. There is also strong interest coming from industrial firms that want to monitor employees' temperature to reduce the risk of workplace transmission of the virus. Hoobox and Radsquare are supported by healthcare startup incubator Eretz.bio, operated by the Albert Einstein Jewish-Brazilian Charitable Society. Press release.