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

TheTranslational Genomics Research Institute(TGen),an affiliate of City of Hope,The Pathogen and Microbiome Institute at Northern Arizona Universityand the Ecology and Evolutionary Biology Department at theUniversity of Arizonahave formedthe Arizona COVID-19 Genomics Union totrack the COVID-19 coronavirusby 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 andpossiblyuncovercritical information for diagnostics, anti-viral drug targets and vaccine development.Press release.

AmgenandAdaptive Biotechnologiesarecombiningexpertise to discover and develop fully human neutralizing antibodies targeting SARS-CoV-2 to potentially prevent or treat COVID-19. The mutually exclusive collaboration brings togetherAdaptive'sproprietary 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 theCenterForMolecular MedicineOfTheAustrian AcademyOfSciences (CeMM) have released SARS-CoV-2 genomesfrom 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 Laboratoryhas 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 athttps://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 Universityresearchers working withOracle Cloudtechnology and vaccine technology developed by local companyVaxine,are testing avaccine candidate against the SARS-CoV-2coronavirus responsible for the COVID-19 pandemic.Oracle wastapped 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 teamused 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 Laboratoriesisofferingany U.S. personnonexclusive, fast-tracklicensesfree of chargetomore than 1,000 patentedtechnologies. Thegoal of theRapid Technology Deployment Programisto enablelicensees to invest their full resources into combating theCOVID-19pandemic and its economic effects.

Japanis putting itsflagshipsupercomputerFugakuto work in combatting the pandemicby giving priority toCOVID-relatedresearch selected by the Japanese Ministry of Education, Culture, Sports, Science and Technology. Installation of the new supercomputer began in December and isnt scheduled to go into full-fledged open useuntil2021, but someof the nodesare going intotrial useas of April1.Press release.

Latest from the Literature

A collaborativein vitrostudy led byMonash University's Biomedicine Discovery Institute(BDI)in Melbourne, Australia, with thePeter Doherty Institute of Infection and Immunity(Doherty Institute), has shown that ananti-parasitic drugalready 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 inAntiviral Research.DOI:10.1016/j.antiviral.2020.104787

A multidisciplinary team of scientists atThe University of Texas Medical Branch(UTMB)at Galveston have developedareverse genetic systemthatallows researchers tomake SARS-CoV-2 in the lab and manipulate it in a petri dishspeeding thedevelopmentandevaluation ofvaccines, diagnose infected patients and exploreevolution ofthe virus.The system has been used tolabel the virussoinfectedcellsturn green,creatingahigh-throughputtestsignificantly reducing the time it takes to evaluate and bring candidate vaccines to market.UTMBis making thetechnology available to academia and industry researchers working to quickly developCOVID-19countermeasures. On-campus scientistswill nowdeploy the technology forblood-based diagnostictesting.Thestudy willbe publishedinCell Host & Microbe. DOI:10.1016/j.chom.2020.04.004

Thereceptor for SARS-CoV-2 is abundantly expressed in certain progenitor cellsthatnormally develop into respiratory tract cells, according to scientistsattheBerlin Institute of Health,Charit-UniversittsmedizinBerlinand the Thorax Clinic at Heidelberg University Hospital. The discovery, whichwillbe published inThe EMBO Journal (DOI:10.15252/embj.20105114),emerged from anexamination ofsamples from non-virus-infected patientsusing used single-cell sequencing technology.An additional, preliminary finding was that receptor density on the cells increased with age andwasgenerally higher in men than in women.Dellwas responsible for the reduced processing time needed to sequence 60,000 single cells.

AUniversity of Ottawabiology professor believesstray dogsspecifically dog intestinesmaybe theorigin of the current SARS-CoV-2 pandemic.Hisstudy involved examining full-lengthbetacoronavirusgenomes that have been deposited into GenBank, a National Institutes of Health genetic sequence database.Evidence willbepublishedinMolecular Biology and Evolution(http://dx.doi.org/10.1093/molbev/msaa094). While study findings are of vital interest in the current world health crisis, theymore broadly suggest that viralevolution can be revealed bylooking at theinteraction of host defenses with viral genomes.

Researchersin the UK and GermanyreportinPNASa phylogenic network of 160SARS-CoV-2genomes, revealing three major typesof variantsone found predominantly within East Asia and the other two in Europeans and Americans.The networkreconstructsdocumented routes of infectionand might be used to trace unknown infection sourcesthatcan then be quarantined toprevent recurrent spreadof the disease worldwide.DOI:10.1073/pnas.2004999117

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