Improving the approach to viral sequencing in pandemics like COVID-19

Dr Ash Porter, Dept Microbiology & Immunology, shares her recommendations for the sustainable use of viral genomics at scale.

Dr Ash Porter, Research Officer in the Department of Microbiology and Immunology, recently spoke to Cosmos Magazine about the need for a better approach to the way virus testing is handled during pandemics.

Earlier this month Ash co-authored an opinion paper that was published in PLOS Genetics titled ‘New rules for genomics-informed COVID-19 responses – Lessons learned from the first waves of the Omicron variant in Australia’ that called for a better approach to viral sequencing in pandemics like COVID-19. The paper highlights that such changes in approach are necessary to avoid overwhelming health and viral surveillance systems.

Ash works with Dr Sebastian Duchene and his group, with their project focusing on uncovering how different environmental and ecological variables drive the emergence of COVID-19 variants.

“I am currently working on the evolutionary dynamics of SARS-CoV-2, including how Variants of Concern are evolving, the geographical importation/exportation of lineages and applying epidemiological information into evolutionary models.”

In speaking to Cosmos, Ash explained that with the continued evolution of the SARS-COV-2 virus that causes COVID-19, Australia’s high level of sequencing carried out during the national case peak has not continued.

“Doing lots and lots of sequencing is not really possible anymore,” she said. “We just have so many cases now that we can’t sequence the proportion that we used to and having more and more genomes may not correlate to having better results.”

Genome sequencing has played an important role throughout the pandemic; it has allowed researchers to connect a SARS-CoV-2 samples to ancestral strains, effectively charting a viral family tree, and this has been used to guide public health policies.

Ash's proposal is for a more selective approach to testing and sequencing, rather than the randomised genomic profiling of samples acquired from large-scale testing during COVID-19’s big bursts in 2020 and 2021. This new strategy would provide those working in the field the best opportunity to analyse the evolution of viruses during a pandemic.

This approach is broken into sequencing ‘streams’ where those who fit into specific groups such as cross-border travellers, those living in vulnerable settings such as aged care or outbreak communities, or vaccinated people who have a breakthrough infection, would be prioritised. This would enable the tracking of potentially high-impact variants and their movements.

The second stream involves ‘representative’ sampling – sequencing a proportion of positive cases to contextualise the background prevalence of viral lineages circulating within communities. “To have a set of cases that are being sequenced from those specific areas of interest might help better, than broad, random sequencing,” Porter said. The third stream would involve sampling wastewater and animal populations.

These systems are definitely applicable to other pathogens out there and I think the way we deal with SARS-CoV-2 is going to be representative of how we deal with future pandemics.

Ash also shared the importance of metadata collection including information such as vaccine status, travel history, disease severity, previous or current medical treatments, and demographic data. When combined with the genomic sequencing, this information could enable experts to determine the movement of viral lineages and diversity within groups, transmission networks, and emerging variants of concern.

“The metadata can prove really helpful in our analysis. It’s been collected at different points of the pandemic. At the very start of the pandemic they [authorities] did a really great job of collecting all the travel history of the positive cases and that led us to do some really interesting analyses with that information.”

“I know that there’s a lot of privacy issues with sharing metadata that might be associated with an individual patient, but I think that’s something we could overcome and be able to share it within Australia and across the globe.”

Importantly, Ash points out that improvements to the methods used in viral genomics has impacts beyond the COVID-19 pandemic.

With climate change and urbanisation, we’re at more risk of zoonotic spillover and emerging infectious disease. So, it’s not going to be problem that goes away.

Read the full article in Cosmos Magazine here.

Ash also featured in a related Cosmos article, New COVID-19 variants have landed in Australia.