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Nanoparticle Positive Controls, Wastewater Surveillance System, Robotics Platform Screens Thousands At Once: COVID-19 Updates

March 5, 2021 I Axillary adenopathy observed in some women after vaccination, specialized DNA probes analyze RNA sequences with more precision, new approach to pooled testing, elevated neutrophil biomarkers could predict severe outcomes, and two new calculators assess risk of in-hospital mortality or need for mechanical ventilation Plus: Coronavirus-like nanoparticles could serve as new positive controls for COVID-19 testing and a wastewater surveillance system in San Diego proves to be efficient and cost-effective.


Research News

Coronavirus-like nanoparticles, developed by nanoengineers at the University of California San Diego, could serve as simpler and reliable positive controls for COVID-19 testing. In their study, published in Biomacromolecules, the developers of these new positive controls list several advantages. They explain that these coronavirus-like nanoparticles do not need to be kept cold, are easy to manufacture, do not pose a risk of infection to the people running the tests, and can be included in the entire testing process from start to finish – just like a patient sample. The new positive controls are essentially tiny virus shells, made of either plant virus or bacteriophage, that house segments of coronavirus RNA inside. The RNA segments include binding sites for both of the primers used in the polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) tests. The researchers are now looking to partner with an industry to implement this technology. DOI:10.1021/acs.biomac.0c01727

A new mostly-automated early alert system that uses high-throughput analysis of wastewater samples to identify buildings where new COVID-19 cases have emerged has been developed by engineers at the University of California San Diego. Authors of the study, published in mSystems, report that this wastewater surveillance system is fast, cost-effective, and sensitive enough to detect a single case of COVID-19 in a building that houses nearly 500 people. A positive test triggers an alert that is sent to residents of the building where the sample was collected, and they test themselves using kits from a vending machine. After a pilot experiment showed that the system reliably reported new cases in individual buildings, the researchers scaled up and began surveillance of over 2 million people who live in San Diego county. DOI:10.1128/mSystems.00045-21

Toronto researchers have designed a robotics platform that accurately screens thousands of COVID-19 samples at once, reports a new study published in Nature Communications. The next-generation, ultra-high-throughput sequencing platform, called C19-SPAR-Seq, designed at the Lunenfeld-Tanenbaum Research Institute (LTRI) at Sinai Health, has a sensitivity rate greater than 95% in positive cases during peak onset, according to the study. Researchers report that the new platform is also cost-effective. Each test costs only about $8 USD and runs thousands of samples at once with a turnaround time of about 24 hours. DOI:10.1038/s41467-021-21653-y

A new study, published in the Journal of Clinical Microbiology, compared the Abbott BinaxNOW rapid antigen test for COVID-19 to PCR testing and found that the rapid test detected almost all adults who tested positive by PCR if they had symptoms that lasted seven days or less. In symptomatic children with less than seven days of symptoms, the test detected about 85% of true positive cases. The study was led by Boston Children’s Hospital and the Massachusetts Department of Health and included 1,380 adults and 928 children who came for testing at a large drive-through community testing program in an area with a high rate of COVID-19 at the time. Each participant received a nasal swab for BinaxNOW and another for PCR. The researchers also determined that symptomatic adults generally had higher viral loads than symptomatic children, which may explain why some of the symptomatic infections in children were missed by the rapid test. In asymptomatic adults, the rapid test detected about 70% of cases compared with 65.4% in children. Authors of the study add that they do not recommend the BinaxNOW test for use in adults or children with symptoms lasting longer than seven days. DOI:10.1128/JCM.00083-21

Yale University researchers have uncovered a series of biomarkers associated with white blood cell activation and obesity that may predict severe outcomes in COVID-19 patients. The researchers used proteomic profiling to analyze samples taken from 100 patients who developed varying degrees of COVID-19 severity. Blood samples were collected on the patients’ first day of admission. They also analyzed clinical data from over 3,000 additional COVID-19 patients within the Yale New Haven Hospital system. They found that five proteins (resistin, lipocalin-2, HGF, IL-8, and G-CSF) were elevated in the COVID-19 patients who later became severely ill. According to the researchers, these elevated neutrophil biomarkers were evident before any severe symptoms appeared, and all of the COVID-19 patients who were admitted or transferred to the intensive care unit had elevated neutrophil activation markers. These biomarkers remained low for the patients who never developed severe disease and none of the patients with lower neutrophil biomarker levels died. These findings are published in Blood Advances. DOI:10.1182/bloodadvances.2020003568

Two new calculators for predicting which COVID-19 patients are at the highest risk of in-hospital mortality or requiring mechanical ventilation have been developed and validated by Massachusetts General Hospital (MGH). The team compiled clinical information from over 1,000 COVID-19 patients and followed these patients to the end of their hospital course. The researchers used a combination of past medical history, vital signs, and laboratory results at the time of patient admission and developed two models that can differentiate between risk of death and mechanical ventilation. Their two separate risk stratification models, known as VICE (Ventilation in COVID Estimate) and DICE (Death in COVID Estimate) scores, uncovered different predictive factors. VICE factors included diabetes, oxygen saturation of the blood, C-reactive protein and lactate dehydrogenase. DICE factors included age, male sex, coronary artery disease, diabetes, body mass index, platelet count, and a variety of inflammatory and infectious markers. Clinicians can input clinical values into these online calculators for COVID-19 patients upon admission to determine which ones may need the most intensive care and management. This work is published in EClinicalMedicine. DOI:10.1016/j.eclinm.2021.100765

A new approach to pooled COVID-19 testing could prove to be highly effective, according to Harvard T.H. Chan School of Public Health researchers and their colleagues. The researchers developed a population-level mathematical model of SARS-CoV-2 transmission to simulate viral load distributions representing real data sampled from population surveillance. They then used this model to identify optimal pooled testing strategies under different scenarios. Using the model, testing efforts could be tailored to the available resources within a community to maximize the number of infections identified using as few tests as possible. Even in labs with substantial resource constraints, the team created simple pooled testing schemes that could identify as many as 20 times more infected individuals per day compared with individual testing. This research is published in Science Translational Medicine. DOI:10.1126/scitranslmed.abf1568

Rice University engineers have developed a stamp-sized microfluidic chip that can measure the concentration of SARS-CoV-2 nucleocapsid (N) protein in blood serum from a standard finger prick. The nanobeads bind to the SARS-CoV-2 N protein, a COVID-19 biomarker, in the chip and transport it to an electrochemical sensor that detects minute amounts of the biomarker. According to the engineers, COVID-19 can be diagnosed in 55 minutes or less with the help of these programmed magnetic nanobeads and a diagnostic tool that plugs into a cell phone. The team found that their new method paired with a Google Pixel 2 phone and a plug-in potentiostat was able to deliver a positive diagnosis with a concentration as low as 230 picograms for whole serum. This work is published in ACS Sensors. DOI:10.1021/acssensors.0c02561

A team from John Hopkins Medicine is developing a technique to scan biological specimens, including saliva or specimens obtained with nasal swabs, using specialized DNA probes that analyze RNA sequences with more precision. The probes can detect specific RNA sequences of viruses and other disease-causing pathogens. The researchers report that a key feature of the newly developed test is its ability to analyze and detect the many subtle changes that can occur in the SARS-CoV-2 viral genome, or variants, such as those first identified in the United Kingdom and South Africa. They have published a report on the development and application of this test (cRASL-seq) in the journal Modern Pathology. DOI:10.1038/s41379-020-00730-5

An article published in the American Journal of Roentgenology describes the clinical and imaging features of axillary adenopathy detected during screening or diagnostic breast imaging after recent COVID-19 vaccination to inform the development of follow-up recommendations. The author of the study reviewed electronic medical records to identify women with post-COVID-19 vaccination adenopathy found from December 2020 to February 2021. In total, 23 women exhibited axillary adenopathy on the same side of the vaccinated arm on screening or diagnostic breast imaging. 13% were symptomatic (axillary lump with possible tenderness). The researcher suggests that this study highlights axillary adenopathy ipsilateral to the vaccinated arm with Pfizer-BioNTech or Moderna COVID-19 vaccine as a potential reactive process with which radiologists should be familiar. DOI:10.2214/AJR.21.25651


Industry News

Luminex has received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration (FDA) for a new expanded version of its NxTAG Respiratory Pathogen Panel (RPP) that includes the SARS-CoV-2 virus for high-throughput respiratory testing. The new test is a combination of the company’s original NxTAG RPP, an FDA-cleared in vitro diagnostic for syndromic respiratory infection testing, and SARS-CoV-2. The NxTAG RPP + SARS-CoV-2 Assay is expected to detect new variants of the novel coronavirus. Press Release

Eisai announced that it will support the construction of an efficient testing framework for COVID-19 in Kenya. CA Medlynks, in collaboration with the government of Meru County in Kenya, will support the setup of PCR testing laboratories, along with securing the necessary equipment for testing and training of screening technicians. Currently, Meru County must send their samples for COVID-19 testing to the capital city of Nairobi, which is very time intensive. Eisai has committed the equivalent of $1 million in aid over one year to support the controlling of the spread of COVID-19 in Africa, along with prevention of delays of elimination activities for neglected tropical diseases (NTDs). Eisai has begun providing personal protective equipment (PPE) to core hospitals in Africa for research and therapies for infectious diseases, as well as masks and sanitizer for the resuming of mass drug administrations in Kenya for the elimination of NTDs. Press Release

Kaya17 Inc. receives CE Mark approval for its rapid COVID-19 antigen test. The company’s test kit is light and portable, and Kaya17’s novel cartridges process saliva samples in minutes allowing hundreds of tests per hour with only a few readers. The saliva test can detect very early stage and asymptomatic infections and has shown 98% sensitivity and 90% specificity. The company’s test is also pending EUA approval. Press Release

The National Institutes of Health (NIH) has funded a new study to assess the performance and usability of a smartphone app paired with the Quidel QuickVue At-Home COVID-19 Test, which has received EUA from the FDA for use with a prescription. More than 200 participants have already enrolled in the study, which involves daily testing for a two-week period. The MyDataHelps app provides step-by-step instructions for taking the test and also provides an independent confirmation of test results, although the users can interpret the results on their own. The research aims to understand how the users interact with these apps and where they find value in them to inform future advancements in at-home COVID-19 testing. The antigen test gives results in 10 minutes using a nasal swab sample that is placed in a test tube followed by the addition of a test strip and results are read similar to a pregnancy test. Press Release

New England Biolabs (NEB), in collaboration with the ARTIC Network, has developed three new NEBNext ARTIC SAR-CoV-2 kits based on ARTIC Network’s validated protocols on epidemiological changes to the virus and optimized them for accurate and reliable sequencing of the SARS-CoV-2 virus on Illumina® and Oxford Nanopore Technologies® (ONT) platforms. The kits are specifically designed with balanced primers for uniform genome coverage and accept a wide range of SARS-CoV-2 genome copies with the same RT conditions. The kits, developed with the homebrew scientist in mind, were built upon a well-established ARTIC workflow and provide accurate, reliable sequencing results of the virus, making it ideal for core labs and research institutions. Press Release

Frontline workers at Norfolk and Norwich University Hospitals (NNUH) will begin weekly testing using a new saliva-based assay in an effort to cut down COVID-19 transmission rates. The new LAMP test only requires a simple saliva sample once weekly, rather than a nose swab, and positive results do not require an additional confirmatory PCR test. The tests measure genomic RNA, which is no longer detectable once an individual is no longer infectious. The samples will be analyzed at the Earlham Institute (EI) and results will be available on the same day. The joint effort will potentially break the chain of transmission and reduce infection rates among staff and patients. Press Release

University of California San Diego has been awarded $33 million by NIH for five COVID-19 diagnostic projects. The projects will span over four years and range from managing a large data center to expanding testing in disadvantaged communities. The award is part of the Rapid Acceleration of Diagnostics (RADx) initiative that aims to address the nation’s need for innovative solutions in diagnostic technologies that are people-centric, and utilize expertise in infectious diseases, informatics, data science, clinical pathology, bioengineering, and other related areas. Press Release

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