From tracking outbreaks to dissecting the biology of pathogens, infectious diseases experts are using Terra to share data, distribute tools, and accelerate research
“The ability to share data and distribute best-practice analysis tools with fully reproducible tutorial examples is a game-changer for public health labs.”
Daniel J Park, PhD, Viral Genomics Group Leader
The COVID pandemic has demonstrated the importance not only of sharing infectious disease genomic data quickly and widely, but also of standardizing analysis methods to ensure that data can be aggregated across global surveillance networks. Terra’s unique combination of data sharing, computing capabilities, and collaboration features enables Viral Genomics Group members to analyze and share their datasets, analyses, and workflows between each other and with their public health partners, and the scientific community.
The Viral Genomics Group and their partners analyzed 772 complete SARS-CoV-2 genomes from early in the Boston area epidemic, revealing numerous introductions of the virus, a small number of which led to most cases. Their manuscript describes the detailed analysis of two superspreading events; one in a skilled nursing facility and the second at an international business conference, with significantly different consequences, suggesting varying transmission dynamics in superspreading events. These results show how genomic epidemiology can help understand the link between individual clusters and wider community spread.
Viral diseases have an enormous impact on human health worldwide. Genomic technologies are providing researchers an unprecedented capability to study the viruses that cause disease and their interactions with infected hosts. The Broad Viral Genomics Group, led by Professor Pardis Sabeti, aims to pioneer the application of genomic data to address the crucial unanswered biological questions in viral disease, to build better tools for detecting and tracking viruses as they spread, and to foster a community of researchers who are empowered to use them to reduce the burden of disease worldwide.
772 viral genomes sequenced from cases in Massachusetts outbreak by the Broad Institute, plus over 5,000 viral genomes from global connection in the GISAID database
Reproducible workflows for viral assembly and classification, sequence submission to NCBI Genbank, and phylogenetic tree construction with NextStrain
This public workspace contains data from all of the viral samples that were sequenced in the Boston outbreak study. The analytical workflows are included in the workspace and preconfigured with the analysis parameters used in the study, so anyone can clone the workspace and reproduce the analysis as it is described in the manuscript.
COVID-19 genomic data and workflows for viral genomic analysis (used for training)
Cross-tissue expression analysis of factors associated with SARS-CoV-2 cellular entry (single-cell RNAseq)