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CRISPR Diagnostics, A Plan for Reagent Shortages, Community Testing: COVID-19 Updates

November 13, 2020 | Stanford’s CRISPR-on-a-chip diagnostic, new diagnostic kit with DIY reagents, and recommendations to boost UK testing services. Plus, Oxford and Thermo Fisher join forces, Massachusetts school district plans weekly COVID-19 surveillance, and a new antibody test from EUROIMMUN.

Research Updates

A University of Oxford team conducted an electronic health record network cohort study to assess whether a diagnosis of COVID-19 (compared with other health events) was associated with increased rates of subsequent psychiatric diagnoses. The researchers used the TriNetX Analytics Network, a global federated network that captures anonymized data from electronic health records in 54 health-care organizations. They found that in patients with no previous psychiatric history, a diagnosis of COVID-19 was associated with increased incidence of a first psychiatric diagnosis in the following 14 to 90 days compared with six other health events. The association was greatest for new diagnoses of anxiety disorders, insomnia, and dementia. The incidence of any psychiatric diagnosis in the 14 to 90 days after COVID-19 diagnosis was 18.1%. The results are published in The Lancet Psychiatry. DOI: 10.1016/S2215-0366(20)30462-4

Researchers at Karolinska Institutet in Sweden have explored all COVID-19 research published during the initial phase of the pandemic. To obtain an overview of the more than 60,000 publications on COVID-19 in PubMed, the team used a machine learning technique that enables them to map key areas of a research field and track the development over time. The present study, published in the Journal of Medical Internet Research, includes 16,670 scientific papers on COVID-19 published from 14 February to 1 June 2020, divided into 14 different topics. The most common research topics were health care response, clinical manifestations, and psychosocial impact. Some topics, like health care response, declined over time, while others, such as clinical manifestations and protective measures, showed a growing trend of publications. Protective measures, immunology, and clinical manifestations were the research topics published in journals with the highest average scientific ranking. The countries that accounted for the majority of publications (the USA, China, Italy and the UK) were also amongst the ones hardest hit by the pandemic. DOI: 10.2196/21559 

A Stanford team combines microfluidics, on-chip electric field control, and CRISPR to directly address limitations of current CRISPR diagnostic methods. Their method, published in PNAS, involves ITP-based nucleic acid extraction from raw sample, isothermal reverse transcription and amplification, and then a CRISPR assay enhanced by ITP with a total assay time of around 30 min to 40 min (from raw sample to result). DOI: 10.1073/pnas.2010254117

Meanwhile, a team from King Abdullah University of Science & Technology (KAUST) published their simple COVID-19 test kit, iSCAN, in Virus Research. iSCAN combines virus amplification with a CRISPR-Cas system for effective SARS-CoV-2 detection. To use iSCAN, nasopharyngeal swab samples are incubated with DNA primers and enzymes that can amplify SARS-CoV-2 genetic material for half an hour. This process is referred to as RT-LAMP. Once enough viral RNA is amplified, a droplet containing the enzyme Cas12 is added to the mix and left for another 15 minutes. This enzyme only recognizes viral RNA belonging to SARS-CoV-2, overcoming an issue with RT-LAMP, where false amplification and cross-contamination can be a problem. Significantly, the test reagents can be manufactured by labs on site. DOI: 10.1016/j.virusres.2020.198129

In a single-center, retrospective cohort analysis of hospitalized coronavirus disease 2019 (COVID-19) patients, a team from Brigham and Women’s Hospital investigated whether inflammatory biomarker levels predict respiratory decline in patients who initially present with stable disease. Examination of C-reactive protein (CRP) trends reveals that a rapid rise in CRP levels precedes respiratory deterioration and intubation, although CRP levels plateau in patients who remain stable. Increasing CRP during the first 48 h of hospitalization is a better predictor (with higher sensitivity) of respiratory decline than initial CRP levels or ROX indices (a physiological score of respiratory function). CRP, the proinflammatory cytokine interleukin-6 (IL-6), and physiological measures of hypoxemic respiratory failure are correlated, which suggests a mechanistic link. DOI: 10.1016/j.xcrm.2020.100144 

More investment and important changes are needed to boost UK testing services, to tackle the COVID-19 pandemic and build a diagnostics service that will head off future UK health challenges, says a meeting report published by the Academy of Medical Sciences. The report highlights that the UK did not have an established national testing system at the start of the COVID-19 pandemic, so new systems had to be put in place rapidly. The Academy of Medical Sciences recommends enhancing collaboration across the NHS, universities and industry to make best use of their combined strengths, making sure that local laboratories can play their part in COVID-19 testing and support national approaches, developing and adopting more innovative ways of testing for COVID-19, adopting a more flexible approach to regulation, and providing longer term testing contracts. PDF of the Report


Industry Updates

The University of Oxford has launched a new rapid testing laboratory and are partnering to jointly developed Thermo Scientific Omnipath Combi SARS-CoV-2 IgG ELISA test detects and quantifies antibodies against the coronavirus and increases the University of Oxford’s testing capacity to up to 50,000 tests per day. Oxford researchers are already using the new fully automated testing platform to provide weekly UK wide data for the Office of National Statistics as part of the national COVID-19 Infection Survey. In addition, the equipment further enhances Oxford’s capacity to quantify the response to vaccines accurately and on a large scale as part of our ongoing clinical trials of the Oxford coronavirus vaccine to assess vaccine performance. Press release.

Precision Genetics has chosen Isohelix GeneFix DNA/RNA saliva collection kits as its preferred collection device and added saliva collection to their existing portfolio of validated Covid-19 testing options submitted under Emergency Use Authorization (EUA) by the Food and Drug Administration. Press release

Mirimus has announced a partnership with the Wellesley Public Schools system in Wellesley, Mass., to enable weekly COVID-19 surveillance testing of all staff, high school and middle school students using its pioneering SalivaClear COVID-19 pooled saliva testing platform. The SalivaClear platform is composed of three key elements—saliva-based sampling, pooled testing and gold-standard PCR molecular diagnostics—that, when combined, enable frequent, high-quality, high-throughput, low-cost detection of SARS-CoV-2, the virus that causes COVID-19. Weekly testing of a portion of Wellesley Public Schools (WPS) staff using SalivaClear began October 13, was expanded to include all staff the following week, and has now been expanded to include all high school and middle school students. Rather than test each individual student and employee separately, a time and resource intensive process, saliva samples are combined, or pooled, to substantially reduce the number of tests. Press release.

EUROIMMUN, a PerkinElmer company, has launched the Anti-SARS-CoV-2 QuantiVac ELISA (IgG) to quantify IgG antibodies against the SARS-CoV-2 S1 antigen. The assay is available for countries accepting the CE mark, and the Company plans to file a request for this product with the U.S. Food and Drug Administration for Emergency Use Authorization (EUA). This quantitative test kit applies a recombinant S1 subunit of the SARS-CoV-2 spike protein, enabling detection of IgG antibodies. These antibodies have been the focus of vaccine development programs as well as discussions about possible immunity in previously infected individuals. With this new ELISA assay, EUROIMMUN is providing a product to support careful evaluation of an important antibody subgroup enabling standard curve-based quantification of the anti-S1 IgG antibody concentration. Press release


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