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TGen, Amgen, CeMM, And More: Bio-IT Community Rallies Against COVID-19



April 10, 2020 Coronavirus research, tools and offerings are advancing at a breakneck pace. The SARS-CoV-2 virus is serving as a rallying cry across the bio-IT landscape inspiring creative new solutions, partnerships, and ideas to address the outbreak, treat and prevent the disease it causes, and address the life adjustments of our new normal. Here are some of the free tools, new solutions, and research this week.

Industry News

The Translational Genomics Research Institute (TGen), an affiliate of City of Hope, The Pathogen and Microbiome Institute at Northern Arizona University and the Ecology and Evolutionary Biology Department at the University of Arizona have formed the Arizona COVID-19 Genomics Union to track the COVID-19 coronavirus by harnessing the power of state-of-the-art technology and "big data" analysis. Scientists will sequence samples from COVID-19 patients to analyze the virus' genetic codes, track its different strains, show where each sample originates from, where it may have been transmitted and—possibly—uncover critical information for diagnostics, anti-viral drug targets and vaccine development. Press release.

Amgen and Adaptive Biotechnologies are combining expertise to discover and develop fully human neutralizing antibodies targeting SARS-CoV-2 to potentially prevent or treat COVID-19. The mutually exclusive collaboration brings together Adaptive's proprietary immune medicine platform for the identification of virus-neutralizing antibodies with Amgen's expertise in immunology and novel antibody therapy development. Neutralizing antibodies defend healthy cells by interfering with the biological function of an invading virus. These antibodies may be used therapeutically to treat someone currently fighting the disease and can be given to people who have heightened risk of exposure to SARS-CoV-2, such as healthcare workers. Press release.

Researchers from the Center For Molecular Medicine Of The Austrian Academy Of Sciences (CeMM) have released SARS-CoV-2 genomes from Austrian patients. Initial sequence analysis of the 29,900 nucleotide-long SARS-CoV-2 genomes from Austria revealed on average 6 mutations different to the reference genome isolated in Wuhan. The observed number of mutations is in line with other recently reported SARS-CoV-2 genomes. Most of the observed mutations lead to changes in viral proteins, providing evidence for positive selection pressure and evolution within the human population. Assessing the actual impact of these mutations for the virus life cycle and its interactions with both the host and the immune system will be within the scope of future investigations. Press release.

IRB Barcelona's Structural Bioinformatics and Network Biology Laboratory has joined forces with Amazon to develop the Chemical Checker, a computational tool that would help process academic literature on COVID-19. Using artificial intelligence, this tool will "read" articles and extract all relevant information related to the molecules and treatments studied. Through a limited review of the most relevant scientific literature, researchers at IRB Barcelona have so far identified more than 150 compounds that are potentially active against COVID-19. Results are already available at https://sbnb.irbbarcelona.org/covid19/. The experience Amazon has with text-mining, machine learning and natural language understanding has allowed the automatic analysis of scientific articles to be incorporated into the Chemical Checker at a fast pace. Chemical Checker and results.

Flinders University researchers working with Oracle Cloud technology and vaccine technology developed by local company Vaxine, are testing a vaccine candidate against the SARS-CoV-2 coronavirus responsible for the COVID-19 pandemic. Oracle was tapped for technical collaboration, access to an expanded research community, and cloud infrastructure that helped enable the rapid design of the novel COVID-19 vaccine candidate. The Australian team used computer models of the spike protein and its human receptor, ACE2, to identify how the virus was infecting human cells, and then were able to design a vaccine to block this process. Press release.

Through the end of 2020, Sandia National Laboratories is offering any U.S. person nonexclusive, fast-track licenses free of charge to more than 1,000 patented technologies. The goal of the Rapid Technology Deployment Program is to enable licensees to invest their full resources into combating the COVID-19 pandemic and its economic effects.

Japan is putting its flagship supercomputer Fugaku to work in combatting the pandemic by giving priority to COVID-related research selected by the Japanese Ministry of Education, Culture, Sports, Science and Technology. Installation of the new supercomputer began in December and isn’t scheduled to go into full-fledged open use until 2021, but some of the nodes are going into trial use as of April 1. Press release.

Latest from the Literature

A collaborative in vitro study led by Monash University's Biomedicine Discovery Institute (BDI) in Melbourne, Australia, with the Peter Doherty Institute of Infection and Immunity (Doherty Institute), has shown that an anti-parasitic drug already available around the world kills the virus within 48 hours. The drug, Ivermectin, stopped the SARS-CoV-2 virus growing in cell culture within 48 hours. Ivermectin is an FDA-approved anti-parasitic drug that has also been shown to be effective in vitro against a broad range of viruses including HIV, Dengue, Influenza and Zika virus. The study was published online in Antiviral ResearchDOI:10.1016/j.antiviral.2020.104787

A multidisciplinary team of scientists at The University of Texas Medical Branch (UTMB) at Galveston have developed a reverse genetic system that allows researchers to make SARS-CoV-2 in the lab and manipulate it in a petri dish—speeding the development and evaluation of vaccines, diagnose infected patients and explore evolution of the virus. The system has been used to label the virus so infected cells turn green, creating a high-throughput test significantly reducing the time it takes to evaluate and bring candidate vaccines to market. UTMB is making the technology available to academia and industry researchers working to quickly develop COVID-19 countermeasures. On-campus scientists will now deploy the technology for blood-based diagnostic testing. The study will be published in Cell Host & Microbe. DOI:10.1016/j.chom.2020.04.004

The receptor for SARS-CoV-2 is abundantly expressed in certain progenitor cells that normally develop into respiratory tract cells, according to scientists at the Berlin Institute of HealthCharité - Universitätsmedizin Berlin and the Thorax Clinic at Heidelberg University Hospital. The discovery, which will be published in The EMBO Journal (DOI:10.15252/embj.20105114), emerged from an examination of samples from non-virus-infected patients using used single-cell sequencing technology. An additional, preliminary finding was that receptor density on the cells increased with age and was generally higher in men than in women. Dell was responsible for the reduced processing time needed to sequence 60,000 single cells.

A University of Ottawa biology professor believes stray dogs—specifically dog intestines—may be the origin of the current SARS-CoV-2 pandemic. His study involved examining full-length betacoronavirus genomes that have been deposited into GenBank, a National Institutes of Health genetic sequence database. Evidence will be published in Molecular Biology and Evolution (http://dx.doi.org/10.1093/molbev/msaa094). While study findings are of vital interest in the current world health crisis, they more broadly suggest that viral evolution can be revealed by looking at the interaction of host defenses with viral genomes.

Researchers in the UK and Germany report in PNAS a phylogenic network of 160 SARS-CoV-2 genomes, revealing three major types of variants—one found predominantly within East Asia and the other two in Europeans and Americans. The network reconstructs documented routes of infection and might be used to trace unknown infection sources that can then be quarantined to prevent recurrent spread of the disease worldwide. DOI:10.1073/pnas.2004999117

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