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Review of genomics highlights ESR’s crucial role

20 September 2020

Microbial Genomics

ESR welcomes a review published by the Prime Minister’s Chief Science Advisor’s office into the role of genome sequencing in Aotearoa New Zealand’s COVID-19 pandemic response.

The rapid-review conducted over seven days in September by Professor Michael Bunce, calls New Zealand’s adoption of the technology as ‘world leading’. The review describes and explores the role genome sequencing and analysis has played, and may play, in managing the pandemic across Aotearoa.

ESR Chief Scientist Brett Cowan says the review makes some excellent recommendations on how to enhance this area further.

“ESR’s genome investigations have been a key part of the pandemic response and an integral component of ESR’s health intelligence services for the Ministry of Health. We had been utilising genome sequencing and bioinformatics long before the pandemic and investing in technology and expertise.

Obviously, the pandemic has called for higher levels of investment and speed for our scientists to provide solutions in this unique situation. ESR has made sizable investments in genome sequencing, including the purchase of a GridION to enable the fast throughput needed to have rapid impact. MBIE and Ministry of Health investment has allowed further capability to be developed.

The review applauds our efforts thus far, and those of our collaborators, but calls for the science to keep moving and we are living that advice. One challenge has been getting full genomes from samples with low amounts of the virus, for example when tested late in the illness, and right now our scientists are working on protocols that may be able to extract useful genomic information where standard techniques have failed.”

In particular, ESR welcomes the messaging in the review around the speed at which samples are shipped and genomes can be sequenced.

Dr Joep de Ligt says sequencing and analysis are a team effort, “not just across ESR but across New Zealand’s public health sector, to get the samples to us and to wrap the right expertise around its interpretation. We are working with a large number of teams and individuals from across the country, from clinical microbiologists in the laboratories to epidemiologists who contextualise and prioritise the samples and finally phylodynamics experts, to ensure timely analysis and translation to aid public health guidance as it is needed.”

ESR is also committed to the messages around translating this new science to the public. “Sequencing is proving to be a valuable tool for New Zealand,: says Dr De Ligt. "but we also want people to engage and understand it. Providing this information to the public for them to understand and dissect through platforms like NextStrain will help bring understanding and through that trust about the use of these technologies.

"We will be engaging with the Chief Science Advisor’s office to explore more education, communication and engagement with the public.”