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Joep de ligt Matt Storey FINAL

Joep de ligt and Matt Storey

ESR scientists are helping national and global efforts to understand COVID-19 by performing whole genome sequencing on positive samples.

ESR is currently one of three New Zealand laboratories performing diagnostic testing on COVID-19 samples, which detects presence of the SARS-CoV-2, the virus that causes COVID-19. This is done by looking for small parts of the virus genome in the sample.

Scientists Dr Joep de Ligt, Matt Storey and Dr Una Ren were keen to ensure the most complete information was obtained from these positive samples by also sequencing the entire genome.

ESR scientist Dr Joep de Ligt says they saw the sequencing as an opportunity to contribute.

“A number of countries are doing this and New Zealand needs to be one of them. Determining the RNA genome provides very rich information for both surveillance and research purposes,” Dr de Ligt says.

“Sharing of this data is very important; it enables scientists to study how the virus can enter Human cells and informs vaccine development. Health officials and government need accurate data on the virus to allow responding appropriately and keeping Aotearoa healthy and safe. At times like these, of high uncertainty, you cannot underestimate the importance of good quality data and accurate reporting is crucial to keeping everyone informed and safe.”

In accordance with WHO guidelines on testing initial cases, the team generated a complete RNA sequence within two days by using the Oxford NanoPore MinION sequencing technology(external link) and the protocols designed and provided by the ARTIC consortium. ARTIC is Wellcome Trust funded to provide systems for real-time genomic epidemiology of viral outbreaks. All of its tools are open source and available to the research and public health communities.

ESR has uploaded the RNA genome of the virus to the international database for viral sequences, GISAID(external link) to support the global response to COVID-19 and allow data integration through platforms like NexStrain(external link). The results from the sequencing are concordant with the travel history of the patient and could be used to track the disease more accurately in potential future cases.

“ESR has invested in sequencing and bioinformatics capability, so we’re able to use these great international resources to produce these insights within days and contribute to the global response to this disease.” Dr de Ligt says.

ESR is committed to ensuring that the testing that is performed in New Zealand is accurate and reliable, and information gained is shared to help others.

ESR will continue to sequence positive samples as cases progress in accordance to WHO guidelines and in close contact with the Ministry of Health.

Nextstrain visualisation of all genomes available worldwide coloured by group

Nextstrain visualisation of all genomes available worldwide coloured by group. Hadfield et al., Nextstrain: real-time tracking of pathogen evolution, Bioinformatics (2018).

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Joep de ligt Matt Storey FINAL

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Ryan Willoughby
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  • Health science