The genome of the SARS-CoV-2 virus is emerging as key information source for outbreak tracing, forecasting how the virus mutates and clinical decision making. This page summaries our actives in supporting genomics being used for public health decision making.

Overview of the activities undertaken by CSIRO's transformational bioinformatics team. Image credit @MindsEyeCCF 

Monitoring: Visualising genomic virus signatures

H&B’s eHealth research team has developed a new bioinformatics approach to support the Australian Centre for Disease Preparedness in choosing the right viruses isolate for testing vaccine candidates. Accepted in Transboundary and Emerging Diseases Journal [1], the approach combines large volumes of internationally available virus genomes and machine learning with laboratory observations and epidemiological insights to choose an isolate that is representative of the currently circulating and likely emerging versions of the virus. It embodies CSIRO’s strength of moving at speed while honouring the scientific process of peer reviewed, transparent publications.

Based on this work, we have build a freely available visualisation page for tracking the genomic signature and their distances between virus isolates.  A GitHub issue tracker is maintained and monitored to allow community volunteers to contribute.

Webpage for viewing the genomic distances of all GISAID entires in a Phylogenetic-tree-free approach.

Tracking: Robust sharing and continuously analysing genomic data

Based on the difficulties we experienced in doing the genomic signature work, we propose a cloud-based architecture for sharing and continuously analysing SARS-Cov-2 sequences. Covid Beacon is based on our serverless Beacon (sBeacon) work and it enables the sharing of insights without having to give up ownership or access control of the contributed data itself. The cloud-native architecture allows the economical scaling to potentially millions of data-points and provides an appropriate environment for highly sensitive clinical data.  A GitHub issue tracker is maintained and monitored to allow community volunteers to contribute.

Cloud-native scalable and privacy preserving framework for analysing COVID-19 data

Diagnostics: CRISPR-based Diagnostics

Based on our CRISPR target-site detection tools, we built a webpage for designing CRISPR-targets that are able to differentiate between similar viruses that would form false negatives and combine variations that should be flagged as positives.  

SAUTE: Webservice for optimizing CRISPR-diagnostics sgRNAs
[1] Bauer, DC, Tay, AP, Wilson, LOW, et al. Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS‐CoV‐2 outbreak. Transbound Emerg Dis. 2020; 67: 1453– 1462. DOI: 10.1111/tbed.13588 blog