This website has changed. We hope you can find what you need easily, but items have moved around. If you have trouble finding what you are looking for please let us know.

Contact us

Update: ESR’s genome sequencing - 13 August

13 August 2020

Microbial Genomics
Microreact Tree
Microreact Tree

ESR has undertaken genomic sequencing and analysis of the four positive COVID-19 samples reported on Tuesday.

As discussed by Director-General of Health, Dr Ashley Bloomfield at today’s 1pm media stand-up, we have some preliminary results, but investigations are still ongoing.

ESR Medical Director Dr Virginia Hope says no links have been found with the full sequences obtained from cases in managed isolation and quarantine facilities.

"Sequencing of samples from cases in these facilities continues, with more results available tomorrow. Genome sequences most similar to these cases are from the United Kingdom. Investigations and epidemiological analysis are continuing, including comparisons with Australian genomes."

"Genome sequencing is just one part of the puzzle. It is just one tool in the pandemic response to complement contact tracing and epidemiological investigation. It does not give us all the information we need to understand the origin of cases. The information is used to inform the investigation by public health units, epidemiologists and others working with the Government to trace the origin of these cases and manage their spread."

ESR has been sequencing isolation and quarantine cases in New Zealand for months now, and we are growing our body of knowledge about this novel virus.

"In some cases in New Zealand, the genome of the virus gave us clues that have helped us understand how a person was infected," Dr Hope says. "This process was simpler when cases were linked to clusters where we could have said it may be associated with a certain event and therefore know how the transmission events might have happened. We cannot be sure of what we will find when we look at these new samples, but we will use the data we have already collected to find clues on where the virus might have come from.

"We will also share the viral genomes, where appropriate, with international partners as part of the global response pandemic."

No private patient info will be sent to third parties.

ESR will continue to sequence positive cases as we receive them. We will continue to report to the Ministry of Health for them to share.

"The quicker we receive the specimens, the better the condition of the specimen and the more likely we can identify the genome. Results will be shared through the Ministry of Health and they will update the public," Dr Hope says.

This work is also feeds into a research project. This a collaboration between ESR and Otago University which was allocated $600,000 from the Ministry of Business, Innovation and Employment (MBIE) COVID-19 Innovation Acceleration Fund in May.

The grant allows an international team of scientists to sequence the genomes of all of New Zealand’s positive COVID-19 cases and track how the virus spread across New Zealand.

It is led by ESR lead bioinformatics researcher Dr Joep de Ligt and University of Otago Senior Lecturer and Associate Senior Scientist at ESR, Dr Jemma Geoghegan. Collaborating scientists range from Te Pūnaha Matatini, Auckland, Otago, Massey and Victoria university, as well as Nextstrain, US and UK.