All Communicable Diseases Genomics Network (CDGN) member laboratories have established or have access to capacity to undertake SARS-CoV-2 whole-genome sequencing and analysis for their jurisdiction.
As a network, members are collaborating to develop protocols and processes that can support and enable national COVID-19 pathogen genomics and enhance surveillance activities across jurisdictions. Leveraging an established a national microbial genomics data sharing agreement signed by all member laboratories, the network also has longstanding relationships with jurisdictional and national governments to meaningfully assist with the COVID-19 pathogen genomics response.
On Thursday, 1 October 2020, the Australian Health Protection Principal Committee (AHPPC) endorsed the Framework for SARS-CoV-2 data sharing and analysis using the AUSTRAKKA system developed by the CDGN, that provides a mechanism for public health laboratories to rapidly share genomic data and request for genomic analyses.
How does SARS-CoV-2 genomic sequencing work?
Genomic sequencing, a laboratory procedure that determines the order of bases in the genome of an organism, provides a very precise fingerprint that can help link cases to one another, allowing outbreaks to be detected and solved sooner. Bioinformaticians, microbiologists and genomic epidemiologists review genomic sequencing data by comparing the reconstructed genomes to those of other cases (locally and/or internationally), to determine how related the genomes of each SARS-CoV-2 cases are. This information is then used in conjunction with epidemiologic data to link cases to one another, allowing outbreaks to be detected and solved sooner.
There are five basic steps involved in the genomic sequencing workflow for RNA viruses, such as SARS-CoV-2, in a laboratory:
RNA extracted from the diagnostic sample
RNA converted into complementary DNA (cDNA) for further processing, as it is easier to process and more stable
cDNA amplification (generates many copies of the cDNA for sequencing)
Genome sequencing – time taken varies significantly depending on method and platform used
Sequencing data processed to reconstruct the SARS-CoV-2 genome
Bioinformaticians, microbiologists and genomic epidemiologists review genomic sequencing data by comparing the reconstructed genomes to those of other cases (locally and/or internationally), to determine how related the genomes of each SARS-CoV-2 cases are. This information is then used in conjunction with epidemiological data to link cases.
Figure 1 Example SARS-CoV-2 sequencing workflow using an iSeq or MinION sequencing platform, https://www.frontiersin.org/articles/10.3389/fmicb.2020.571328/full
Whole-genome sequencing proficiency testing programs
CDGN has an ongoing collaboration with the Royal College of Pathologists of Australasia Quality Assurance Program (RCPAQAP) to develop whole-genome sequencing (WGS) proficiency testing programs (PTP). PTPs are designed to evaluate the analytical laboratory performance with regard to specific laboratory practices such as microbial genomics, and are an critical component of the establishment of high-quality and accurate pathogen genomics capacity in Australia.
Currently CDGN is supporting the development of PTPs for SARS-CoV-2 and bacteria by providing advice, bioinformatics expertise and support to the QAP. In mid-February 2021, the SARS-CoV-2 PTP was made available for public health laboratories utilising genomic technologies across Australia. This activity is funded by the Australian Government’s Department of Health.
This work builds on the deployment of Australia’s first WGS PTP, a pilot which was undertaken in 2018 and 2019, developed in partnership with the RCPAQAP and CDGN. The pilot assessed the participating laboratories’ capacity to sequence two isolates and analyse the genomic data in accordance with their established protocols. Ten public health laboratories participated in the pilot PTP, supporting the development of an approach to implement essential quality assessment and quality control measures for WGS.
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