Coronavirus Solutions: High Performance Computing, Testing, Clinical Trials Tools, Nursing Solutions, and More

April 6, 2020

April 6, 2020 | The biotech and life sciences communities are rallying around the scientific challenges presented by the novel coronavirus pandemic. Here we gather the latest efforts, updates and tools made available to and for the bio-IT community including the updated SARS-CoV-2 genome browser, COVID-19 High Performance Computing Consortium, BGI’s testing efforts in Israel, Sema4’s testing efforts in New York and Connecticut, and more. (For a previous list of free tools available to the bio-IT community conducting COVID-19 and SARS-CoV-2 research, see here.) –The Editors

The browser team at the UC Santa Cruz Genomics Institute has launched a new landing page for resources related to the COVID-19 pandemic, including the SARS-CoV-2 Genome Browser and lung gene expression datasets on the UCSC Cell Browser. The UCSC Genome Browser team posted the SARS-CoV-2 genome assembly on the browser in early February and has now posted the first release of novel coronavirus annotation data. The SARS-CoV-2 Genome Browser now includes the following data annotation tracks NCBI Genes, Nextstrain Genes, UniProt Protein Annotations, Immune Epitope Database and Analysis Resource (IEDB) Epitopes, RT-PCR Primers, Nextstrain Variants, Nextstrain Clades, and Multiz Alignment & Conservation. Press release

A task force of NVIDIA computer scientists has joined the COVID-19 High Performance Computing Consortium, which brings together leaders from the U.S. government, industry and academia to accelerate research using the world’s most powerful HPC resources. The consortium’s objective is to accelerate development of effective methods to detect, contain and treat the coronavirus. It will support researchers by providing access to 30 supercomputers with over 400 petaflops of compute performance. The NVIDIA team has expertise across a variety of critical domains, including AI, supercomputing, drug discovery, molecular dynamics, genomics, medical imaging and data analytics. It is led by Ian Buck, vice president and general manager of Accelerated Computing. “The COVID-19 HPC Consortium is the Apollo Program of our time,” Buck said in a blog post. “Not a race to the moon, this is a race for humanity. The rocket ships are GPU supercomputers, and their fuel is scientific knowledge. NVIDIA is going to help by making these rockets travel as fast as they can.” NVIDIA Blog Post

Sema4 is now performing rapid molecular testing for the detection of SARS-CoV-2, the coronavirus responsible for COVID-19. Sema4 is partnering with the state of Connecticut and regional healthcare providers to address the pressing need for high-throughput testing, including regular screening of medical personnel and other high-risk populations. Doctors in Connecticut and New York are able to order the test. Sema4 is processing samples in its state-of-the-art clinical laboratory, which can analyze 6,000 COVID-19 tests per week and return results within 24-48 hours. In addition to patient testing, Sema4 is involved in several COVID-19-focused research programs. Sema4 seeks to accelerate the development of quantitative, serum-based antibody tests, which will not only help healthcare providers understand the extent of SARS-CoV-2 infection, but will also identify people who have previously been exposed to the virus and developed immunity, some of whom may be appropriate as blood donors that can be used to treat the sickest SARS-CoV-2-infected patients. The company will also utilize its sophisticated whole genome sequencing to track the evolution and spread of SARS-CoV-2 and will combine this with multi-dimensional patient data to build predictive modeling for clinical outcomes. More information.

Medable and MRN have announced a global alliance to bring shared capabilities to decentralized clinical trials. Specifically, Medable will empower MRN’s home clinical trial specialists to conduct home and remote visits using Medable’s Trial-Fit Telemedicine solution to enable remote patient monitoring, medication administration, patient care, and clinical assessments. These capabilities are especially important for clinical trial continuity in spite of widespread shelter-in-place initiatives due to COVID-19. MRN is the largest international provider of specialist community clinical trial support, helping patients participate in trials while remaining in their homes. Medable’s Trial-Fit Telemedicine solution can be used by participants to connect virtually with trial site coordinators, investigators, or other care professionals anywhere in the world. The app consents patients in their native language; provides real-time video capabilities on a single platform that is 21 CFR, Part 11 compliant; removes the burden and cost of travel for on-site clinical visits; and increases patient safety in light of COVID-19 infection rates. The app can be deployed in one week or less for use in existing trials. Press Release

CluePoints has launched a complimentary COVID-19 risk management package. With the FDA, EMA, PMDA and MHRA issuing specific guidelines as a result of the coronavirus, the CluePoints package will help meet these new recommendations and address additional study risks. The platform includes a widely-used online Risk Assessment and Control solution that can be leveraged for performing risk planning and mitigation activities addressing inherent risks during this crisis. Many clinical trials are facing key challenges, including an increase in missed patient visits, missed assessments, missed study treatments and increased dropouts. Studies are encountering IP supply chain disruptions, recruitment issues and slower site responsiveness. There are gaps in reporting adverse events, less frequent interactions with patients and reduced on-site monitoring visits. The relative scope and impact of these common risks will vary by study, as will the proposed mitigations. The CluePoints COVID-19 package incorporates a special coronavirus-specific Risk Assessment template that includes a set of relevant risk categories and associated considerations gleaned from the regulatory guidance documents issued by FDA, EMA, PMDA and MHRA. Further, CluePoints provides recommendations regarding risk controls in the form of specific COVID-19 Key Risk Indicators (KRIs) and will assess each study position before offering advice. More information.

With the immediate need to expand hospital beds and construct makeshift hospital facilities during the pandemic crisis, Jeron Electronic Systems is supplying large nurse call systems to turn convention centers and similar temporary spaces into patient care facilities during this pandemic. Supporting these quick facility conversions, Jeron has a ready-to-ship Emergency Nurse Call packaged to add nurse call to these temporary locations. The Emergency Nurse Call system instantly alerts caregivers to routine and urgent calls from both patients and other staff throughout the nursing unit or even across the facility. Jeron’s network of certified distributors remain open and able to assist with the installation process.  If it is not possible for technicians to be on-site, the pre-packaged systems can be installed by anyone with basic electrical wiring knowledge. Press release

BGI and Israeli medical technology company AID Genomics have announced a partnership to build an emergency testing laboratory in Gaza. The two companies have received approval for the lab from Israeli and Palestinian authorities to perform 3,000 COVID-19 tests daily for Gaza residents. BGI will provide the testing via its HuoYan Labs solution. AID Genomics will lead localized fundraising efforts and provide necessary equipment and personnel for the lab, which is expected to cost millions of dollars. AID Genomics' parent company AID Group will lead the donation alongside Mammoth Foundation, a non-profit organization in Shenzhen, China to donate and organize fundraising in China for the Gaza lab operation. Prospective donors may contact AID Genomics in Israel. Press release. BGI also launched a partnership with MyHeritage to set up a COVID-19 testing lab in Israel that aims to be fully operational by April 9. Upon its launch, the new laboratory will process 10,000 tests daily, and shortly after will increase capacity to 20,000 a day, Israel-based MyHeritage said on Monday. The current daily testing capacity in Israel is just over 5,000. Reuters via New York Times

Applied Biology and Brown University researchers have concluded that the androgen receptor may be implicated in COVID-19 mortality risk; therefore, human type II pneumocytes androgen sensitivity should be tested as a potential treatment marker. The team led by Carlos G. Wambier, MD, PhD Director of Cosmetic Research at the Department of Dermatology of the Alpert Medical School of Brown University and Andy Goren, MD Chief Medical Officer at Applied Biology and Medical Advisor to the Department of Dermatology of the Alpert Medical School of Brown University along with a team of collaborators from other institutions submitted their discovery to publication in the medical journal Dermatologic Therapy (DOI: 10.1111/dth.13365).

AgileBio has announced new COVID LabCollector + Lab Service Management (LSM) Pack that will increase the speed and efficiency in COVID-19 tests management. LabCollector LIMS developed by AgileBio is ready to join hands with the testing labs to increase the rapidity and efficiency of COVID-19 tests and its management thereby helping to eradicate the COVID-19 global pandemic. To address that effort, AgileBio is offering a COVID LIMS pack with its main software LabCollector + LSM (Lab Service Management) + I-Collector automation + 2D rack scanner connectivity to any COVID-19 testing facility with free hosting for one year. The LabCollector COVID-19 pack is a mix of software components and all the needed service to bring labs online quickly. It also includes free online hosting for one year for LabCollector. Labs can now manage the COVID-19 samples from reception to result reporting, inventory for reagents & supplies, biobanking of COVID-19 samples with 2D Rack Scanners and much more with COVID-19 LC + LSM pack. More information.