PIPP Phase I: Develop and Evaluate Computational Frameworks to Predict and Prevent Future Coronavirus Pandemics

Once a novel coronavirus or a new variant is detected, how likely would the novel coronavirus or new variant transmit from person to person, and how sick could patients become? What kind of new coronaviruses could cause future pandemics? Knowing the answers to these questions can help nations make proper strategic decisions. The dilemma is how to predict the behavior and pathogenic severity of new viruses as early as possible. A team of researchers thinks they have found ways to answer these questions by developing new artificial intelligence software tools to predict the virus's behaviors based on its genome sequence. This team of researchers recognizes the potential bias in machine learning applications and the need to increase diversity in the future artificial intelligence workforce. Leveraging their expertise in genomics, data science, artificial intelligence, genetics, infectious disease, chemical engineering, public health, and communication, this team of researchers will organize training workshops and activities providing culturally responsive teaching of artificial intelligence, data science training to teachers, and context-relevant coding experiences to high school students. The team will promote public trust in science and discernment of misinformation through community outreach. This research team will prototype a deep learning model based on biological knowledge and hypotheses that can predict viral pathogenic fitness from genomic sequences to test the potential rules for viral pathogenicity. The team will explore several methods to correct the sampling bias in viral genomic surveillance in order to accurately estimate the fitness of a viral strain. The team will investigate the mutation and recombination profiles in all available bat coronavirus genomes from the Southeastern Asia and build a prototype geospatial model to predict the recombination probability for all available bat coronaviruses. Leveraging their expertise in genetics and macromolecular structure modeling, the team will test a few candidate genes in SARS-CoV-2 for potential pathogenic rules. Based on the outcomes of these pilot projects, the team will be able to estimate the pathogenic fitness of an emerging SARS-CoV-2 variant or another novel coronavirus. This award is supported by the cross-directorate Predictive Intelligence for Pandemic Prevention Phase I (PIPP) program, which is jointly funded by the Directorates for Biological Sciences (BIO), Computer Information Science and Engineering (CISE), Engineering (ENG) and Social, Behavioral and Economic Sciences (SBE). This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.