January 29, 2021 I New diagnostic assay allows testing and genomic surveillance simultaneously, a portable and bifunctional electrical detector for SARS-CoV-2, 1 in 3 infected asymptomatic, genetic factors that predict higher risk of developing pneumonia, and nearly 60% of transmission could be avoided with 14-day quarantine adherence. Plus: Melatonin produced in lungs could be used as a prognostic biomarker and machine learning predicts COVID-19 patient outcomes.
Research News
Federated learning is being employed by Mount Sinai researchers to examine electronic health records to better predict COVID-19 patient outcomes. The technique trains an algorithm across multiple devices or servers holding local data samples without infringing on patients’ privacy rights. The researchers implemented and assessed federated learning models using data from electronic health records at five separate hospitals to predict mortality in COVID-19 patients and then compared the performance of the model against ones built using data from each hospital separately. They found that the federated models demonstrated enhanced predictive power and outperformed the local models at most hospitals. This study is published in the Journal of Medical Internet Research – Medical Informatics. DOI:10.2196/24207
The capacity of the lungs to synthesize melatonin (MEL-Index) could be used as a prognostic biomarker to detect asymptomatic carriers of SARS-CoV-2, say researchers at the University of São Paulo (USP). Their study found that melatonin produced in the lungs acts as a barrier against SARS-CoV-2, blocking the expression of genes that encode proteins in cells serving as viral entry points. The hormone, therefore, prevents infection of these cells by the virus and inhibits the immune response so that the virus remains in the respiratory tract for a few days and then leaves the host, say the researchers. They used RNA sequencing data to quantify the level of expression of 212 COVID-19 signature genes in 288 samples from healthy human lungs. The researchers correlated these gene expression levels with MEL-index. They then were able to determine that when the MEL-index was high, the entry points for the virus in the lungs were closed, and vice-versa. This study is published in Melatonin Research. DOI:10.32794/mr11250090
University of Nebraska Medical Center researchers have developed ultra-absorptive nanofiber swabs that could reduce the number of false-negative tests by improving sample collection and test sensitivity. The researchers used an electrospinning technique to make 1-cm-long cylinders composed of aligned nanofiber layers, which they coated with a thin layer of gelatin and bonded to plastic swab sticks. In lab tests, the porous nanofiber cylinders absorbed and released more proteins, cells, bacteria, DNA, and viruses from liquids and surfaces than the cotton or flocked swabs commonly used for COVID-19 testing. Upon further investigation, the researchers found that their nanofiber swabs reduced the false-negative rate and detected SARS-CoV-2 at a 10-times lower concentration when compared to the cotton and flocked swabs. They hope that this advancement not only allows for more accurate and sensitive COVID-19 testing but will also have far-reaching potential in diagnosing other diseases. This work is published in Nano Letters. DOI:10.1021/acs.nanolett.0c04956
Scientists in China have developed an accurate, fast, and portable bifunctional electrical detector for COVID-19. The new detection system consists of a plug-and-play packaged biosensor chip and a home-developed electrical measurement machine. The method was validated using clinical samples collected from several patients with COVID-19 infection, as well as healthy individuals, and the test results showed full agreement with those of polymerase chain reaction (PCR)-based optical methods. The entire process, precluding the extraction of samples from oropharyngeal swabs, requires approximately 10 minutes. The detection system can also detect SARS-CoV-2 IgM and IgG antibodies with an ultra-low limit of detection (LOD). This new assay is described in a paper published in Science China Materials. DOI:10.1007/s40843-020-1577-y
1 in 3 people infected with SARS-CoV-2 are asymptomatic, a new study published in the Annals of Internal Medicine has found. Researchers reviewed 61 studies and reports including over 1.8 million individuals to determine this finding, which builds upon a previous review of a more limited data set that also determined that a significant portion of infections were asymptomatic. The authors suggest that widespread at-home testing to include even those without symptoms could help to identify infected individuals before transmitting the virus unknowingly, as about half of new infections are believed to be caused by people who are pre-symptomatic or asymptomatic. DOI:10.7326/M20-6976
Vanderbilt University Medical Center (VUMC) researchers, along with their colleagues, have identified genetic factors that increase the risk for developing pneumonia to help identify patients with COVID-19 at greatest risk for this life-threatening complication. The researchers conducted genome-wide association studies (GWAS) of more than 85,000 patients whose genetic information is stored in VUMC’s BioVU biobank. They identified nearly 9,000 cases of pneumonia in patients of European ancestry and 1,710 cases in patients of African ancestry. After further analysis, the research team linked the gene that causes cystic fibrosis (CF) and European ancestry and the mutation that causes sickle cell disease (SCD) in patients of African ancestry as the strongest pneumonia associations. After removing patients with CF and SCD, they then pinpointed a pneumonia-associated variation in a gene called R3HCC1L in patients of European ancestry, and one near a gene called UQCRFS1 in patients of African ancestry. They believe these findings could be applied to identifying patients with high risk of severe pneumonia to enable early interventions. They have published this work in the American Journal of Human Genetics. DOI:10.1016/j.ajhg.2020.12.010
59% of SARS-CoV-2 transmission may be prevented by completing the World Health Organization (WHO) recommended 14-day quarantine period after exposure to a confirmed COVID-19 case, a new UK modeling study predicts. The study’s model assumes that quarantine adherence levels are moderate, with 67% of people completing the recommended 14-day isolation period after testing positive for COVID-19 and 50% of contacts of confirmed cases completing 14 days of quarantine. A similar proportion of transmission could be prevented with only a 7-day quarantine (assuming the same level of adherence) if a COVID-19 test is performed on the seventh day of isolation and those people who receive a negative result are released, the model predicts. This study is published in The Lancet Public Health. DOI:10.1016/S2468-2667(20)30308-X
A new study published in Cardiovascular Innovations and Applications finds that high levels of inflammatory biomarkers are associated with a higher risk of cardiac injury in patients with severe COVID-19. For this study, data was collected on 91 patients with a confirmed diagnosis of severe COVID-19 and the relationship between cardiac injury and inflammatory biomarkers was analyzed. Researchers determined that the levels of inflammatory biomarkers in patients who experienced cardiac injury was generally higher than the levels of those without cardiac injury. They also found interleukin-2 receptor (IL-2R) and comorbidities, such as hypertension and coronary heart disease, to be independent risk factors for cardiac injury in severe COVID-19 patients. DOI:10.15212/CVIA.2019.1264
Industry News
OraSure Technologies’ OMNIgene ORAL (OME-505) saliva collection device has received authorization from Health Canada for use as a component in molecular diagnostic tests for the detection of SAR-CoV-2. Diagnostic labs and COVID-19 test kit providers in Canada now have access to this non-invasive saliva collection device to facilitate expansion of their COVID-19 testing programs. In addition to this authorization from Health Canada, the saliva collection device also has Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) and has a CE marking for in vitro diagnostic use, including for use in COVID-19 testing in the European Union. Press Release
Clear Labs announced the availability of the Clear Dx Whole Genome Sequencing (WGS), the first automated WGS solution that determines the complete RNA sequence of the SARS-CoV-2 genome in less than 24-hours with only minutes of hands-on time. The Clear Dx platform is powered by next generation sequencing (NGS), robotics and cloud-based analytics, and as a result, their WGS can more easily determine the nature of virus transmission by differentiating virus strains and monitoring mutations that lead to variants. In addition to WGS, the platform also features the Clear Dx SARS-CoV-2 Diagnostic Assay, which has received EUA, that allows labs to perform diagnostic screening and genomic surveillance simultaneously. Press Release
A new machine learning tool, developed by a team of John Hopkins University biomedical engineers and heart specialists, warns doctors several hours before patients hospitalized with COVID-19 experience cardiac arrest or blood clots. The team developed the algorithm with more than 100 clinical data points, demographic information and laboratory results obtained from the JH-CROWN registry that John Hopkins established to collect COVID-19 data from every patient in the hospital system. Other variables were also added that they discovered from other doctors and preprint papers. For example, the team did not anticipate the electrocardiogram (EKG) data would play a critical role in the prediction of blood clotting, but once it was added to the algorithm, the ECG data became one of the most accurate indicators for the condition. This paper is published on the preprint website MedRxiv. Paper
The Association for Molecular Pathology (AMP) has formed the AMP COVID Response (ACR) Steering Committee to help coordinate and communicate the organization’s continued efforts to guide diagnostic testing during the ongoing COVID-19 pandemic and to prepare for future emerging outbreaks. The new ACR Steering Committee consists of prominent clinical molecular laboratory professionals who have been actively involved in the response to the COVID-19 pandemic. This new committee will build upon the organization’s current cross-functional efforts, which include assessing ongoing laboratory needs, formulating strategies, and developing guidelines to advance clinical practice. Press Release
OraSure Technologies, Inc. announced that Chronomics Limited has selected the OMNIgene ORAL saliva collection device as a component of its SARS-CoV-2 PCR test. Chronomics Limited will supply its test for the United Kingdom’s “Test to Release for International Travel” program, which enables travelers to England to purchase a COVID-19 test privately from providers including Chronomics. Travelers who receive a negative test result can reduce their self-isolation period. The project is part of the UK’s plan to use COVID-19 testing to reduce the spread of the virus. Press Release