Lessons learnt from COVID-19 shed light on future pandemic preparedness – The Peter Doherty Institute for Infection and Immunity

In an opinion piece released today in PLOS Genetics, University of Melbourne Dr Ash Porter, evolutionary biologist at the Doherty Institute, along with a team of researchers from the University of Melbourne Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL) at the Doherty Institute, shares their learnings about the COVID-19 pandemic response and recommendations to prepare for the next phase of the COVID-19 pandemic and future pandemics.

Whilst public health and social measures, quarantine restrictions and vaccination have all been utilised in past and current pandemics, the COVID-19 pandemic is the first to employ genomic sequencing on a massive global scale.

It was an incredible achievement to bring public health genomics to the absolute forefront of the COVID-19 response and realising the dream of making day-to-day public health decisions based on pathogen genomic data, reflects University of Melbourne Professor Ben Howden, Director of the MDU-PHL who leads the team that sequenced 75 per cent of the cases in Victoria in the last two years, and co-senior author of this article.

University of Melbourne Dr Sebastian Duchene, infectious disease computational biologist at the Doherty Institute and co-lead author of this article, explained that extensive analyses of the virus genome data have been key to understand the mechanisms under which variants of concern emerge.

What we found through previous research is that SARS-CoV-2 virus has the ability to momentarily accelerate its evolutionary pace, enabling variants to emerge more rapidly than other viruses.

This highlights the importance of continued genome surveillance efforts, Dr Duchene added.

In this piece, Dr Porter et al. argue that as the virus changes, so should our approach.

When were dealing with a pandemic, we cant just keep going with what weve done. Our strategy to manage it has to change along with the virus, explains Dr Porter.

Dr Porter explains that a more strategic approach to manage COVID-19 and future infectious disease outbreaks would be to combine sequence data with surveillance data and other metadata, such as individual travel history or patient treatment data.

Sequencing isnt the only form of data we have here, we have so many other additional streams of data that we can use; and for many infectious disease outbreaks, its not just human data, its animal data as well, Dr Porter says.

Putting some of our resources towards collecting and sharing that data would be more helpful than just focusing on sequencing.

In reconsidering our sequencing strategies and looking forward, we believe that the sequencing strategy could be further optimised from a modelling perspective to utilise our resources effectively.

Dr Porter stresses that a global, coordinated response for data collection and modelling will be essential, both for the ongoing COVID-19 pandemic and future outbreaks.

Much of the long-term COVID-normal future will be informed by our ability to exploit genomic epidemiology through gathering data about SARS-CoV-2 (both at the sequence and metadata level) and sharing it, Dr Porter says.

1 A genome sequence is a list of the molecules that make up the code of our DNA and RNA, known as the nucleotides A (adenine), C (cytosine), G (guanine), and either T (thymine) for DNA genomes or uracil (U) for RNA genomes. Its like a barcode. Genomic sequencing is the process of identifying the barcode.

Through genomic sequencing, we can see how those pathogens, such as viruses, are changing and spreading through mapping even single changes in the genetic code.

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Lessons learnt from COVID-19 shed light on future pandemic preparedness - The Peter Doherty Institute for Infection and Immunity