Rapid: Collaborative Research: Agile and effective responses to emerging pathogen threats through open data and open analytics

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The same types of questions arise during every emergent viral outbreak regarding its origin, its evolution, the manner of spread, and how to detect and mitigate it. Many, if not all, of these questions depend on rapid and reliable genomic analysis of diverse viral sample sequences by multiple laboratories. Early viral investigation is often impaired lack of reproducibility, rigor, and data/analytic sharing; the current investigation of COVID-19 is no different. Essential questions such as the extent of intra-host genomic variability (indicative of adaptation or multiple infection), viral evolution (selection, recombination), transmission (phylogentic and phylogeographic) cannot be answered reliably if researchers cannot trust/replicate the source data and analytical approaches. The goal of this award is to develop, deploy, and continuously update viral genomic analysis workflows to enable the analysis and monitoring of viral evolution and dynamics for SARS-CoV-2, and to use the lessons learned to prepare capacity for future outbreaks. Bioinformatics workflows for critical tasks in investigating COVID-19 and future viral outbreaks will be developed and COVID-19 deep sequencing data will be analyzed and shared openly via Galaxy and Datamonkey to facilitate and accelerate evolutionary discovery and enable the study of and response to inevitable future infectious disease outbreaks. In an age of digital connectivity, open and accessible shared data and analysis platforms have the potential to transform the way biomedical research is done, opening the way to ‘global research markets’, where competition arises from deriving understanding rather than access to samples and data. By enabling any researcher with an Internet connection to perform the same analyses as are done by top-flight research groups in resource-rich countries, this award will deliver critical components to resource limited settings, which are often those that are first and disproportionately affected by viral outbreaks.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.