Newborn infants are particularly vulnerable to neurotropic infections of coxsackievirus which can potentially cause serious central nervous system (CNS) diseases such as meningitis and encephalitis. Coxsackievirus is also capable of persisting in the host CNS for extensive periods of time; however, the mechanism by which the virus evades clearance by the host remains unclear. In vivo models of coxsackievirus infection have previously revealed that the virus isolated from persistent infection is not infectious, suggesting the evolution of the virus over the course of infection. In order to disaggregate the effects of the adaptive immune response and other complicating factors from the actual infection of the central nervous system, we therefore wish to develop and utilize an in vitro model of Coxsackievirus infection using Neural Progenitor and Stem Cells (NPSCs) and a recombinant Coxsackievirus B3 expressing enhanced GFP (eGFP). In developing and utilizing this model we hope to explore the interaction between the host innate immune response and the virus and the impact of these interactions on the evolution of the virus and the development of disorders in the infected host CNS

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.