Genetic scientists map spread of Covid-19 in New Zealand

11:15 am on 1 May 2020

Genetic scientists mapping the spread of Covid-19 say that as few as 35 cases may have led to the outbreak here.

3D model design of the novel coronavirus virion

A 3D model of the Covid-19 coronavirus. Photo: Supplied

ESR (Institute of Environmental Science and Research) has been analysing virus samples to try to build a comprehensive picture of how it has spread through the country - and how it has mutated along the way.

The scientists' ultimate goal is to genetically map every single case, which could provide invaluable insights in the fight against the disease.

New Zealand's first Covid-19 case was reported on 28 February - a person in their 60s who had arrived from Iran.

Just one month later, the entire country was in lockdown, with the borders shut tight and all but essential services forced to close.

ESR's head of bioinformatics, Joep de Ligt, said the genomic sequencing that has been carried out so far indicates the outbreak was generated by remarkably few cases.

"At the moment there's at least 35 unique introductions. They've come from all over the world, so we've seen them from Europe, from Iran, from North America," he said.

"This is consistent with what other countries have seen - it was these international travellers who have brought it in during that narrow window before the borders have closed."

The scientists look at Covid-19 samples and, due to tiny mutations that occur as the virus spreads, they are able to trace the chain of transmission and determine their origin.

"It's a bit like Where's Wally? Or Spot the Difference, where you have the picture from the original virus and you compare that [with the picture from new cases] and look for the difference."

Their ultimate goal is to analyse every single case here.

So far they have sequenced 125 samples from the 623 cases that have been sent to ESR.

Dr Jemma Geoghegan from the University of Otago's Department of Microbiology and Immunology has been analysing and interpreting the data.

She said the low number of infected people puts scientists in a good position to build a complete picture of the virus in this country.

"We're in a really unique position to be able to do that. It will provide us with a really amazing data set to help us understand how the virus spread here, what happened when we closed our borders, what happened when we went into level 4 lockdown, for example, and as we begin to lift those lockdown restrictions, what happens to transmission of the virus."

Infectious diseases expert Professor David Murdoch said understanding the genetics of the virus was a hugely helpful supplement to more traditional contact tracing, which could rely on assumptions and people's memories.

"Most of the information we get about identifying the source and how the transmission chain has occurred is through interviews and finding out what people have done and the contacts they've had," he said.

"That's obviously very useful but the genetic material as well gives a different and in many ways much finer detail about the specific strain that people have - where the transmission chain has come from, where the virus may have been imported from and who has had contact with who."

Scientists have obtained the DNA sequence from the first confirmed Covid-19 case and so far there is no evidence to suggest the virus was here before 28 February.

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