What we know about the South African variant of Covid-19

The Northland community case of Covid-19 and two Auckland cases have been confirmed as the highly-transmissable South African variant.

A 56-year-old Northland woman who tested positive on 24 January, more than a week after leaving managed isolation at Auckland's Pullman Hotel. Two other people who tested positive after leaving the same facility have the same variant and results of preliminary genomic sequencing on 27 January showed a link with the Northland case.

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Besides the South African variant involved in New Zealand's cases, others have been identified in Britain and Brazil.

Here's what we know so far about the coronavirus strain:

What is the South African variant?

The South African strain is one of the many mutations of the virus that causes Covid-19.

All viruses change over time, with tiny genetic mutations happening as the virus makes new copies of itself to spread and thrive.

Most are insignificant, some emerge and disappear, and a few can even be harmful to the virus's survival, but some can make it more infectious or threatening to the host.

There are now many thousands of different variants of the pandemic virus circulating. But experts' concerns focus on a small number of these.

The strain first identified in South Africa, and another identified the UK, have changes in the spike protein that the virus uses to infect human cells, which may make them more infectious.

In December, national authorities in South Africa in December confirmed detection of the variant that was rapidly spreading in three provinces, which they named 501Y.V2.

Also known as B.1.351, it is the dominant virus strain in the Eastern and Western Cape provinces of South Africa, and at least 20 other countries have found cases.

On 21 January, before the Northland and Auckland cases, New Zealand had recorded 7 cases of the of the South African variant in managed isolation, the Ministry of Health said.

Is it more dangerous?

The South African variant appears to be more contagious.

University of Otago virologist Jemma Geoghegan said research suggested the South African variant could be up to 50 percent more transmissible.

There is no clear evidence that variant causes much more serious illness for the vast majority of people who become infected.

But because it is more transmissible, more people could be infected, meaning "proportionally there could be more people in hospital, unfortunately, who die", Geoghegan said.

She said it was not clear if the vaccines would be as effective on the new variants because they were created on genetic sequence from about a year ago.

"Early evidence suggests that some of the viruses that have this mutation might be better at reinfecting people that have recovered or even vaccinated."

What do we know so far about vaccines' effectiveness?

Early laboratory tests in Moderna's Covid-19 vaccine suggest it can recognise and trigger antibodies to both the South African and UK variants of the coronavirus, the company has said. However there is a suggestion of a potential earlier waning of immunity to the South African strain, and the company is working on a booster shot to protect against that variant.

Pfizer-BioNTtech are also developing booster shots against various mutations, though a preliminary study showed its vaccine appeared to work against the mutated virus. Scientists tested the Pfizer vaccine against one of the mutations found in the South African variant, called N501Y, using blood samples from 20 people. More studies are needed though, because N501Y is not the only change the South African variant has undergone.

The World Health Organisation says most scientists believe vaccines already approved or in development provide protection against coronavirus variants because they elicit a fairly broad immune response, a host of antibodies and cell-mediated immune responses.

However the WHO, too, is cautious, pointing out that studies are still going on in labs around the world to confirm this.

Watch WHO chief scientist Dr Soumya Swaminathan on vaccines and the coronavirus variants:

What action is NZ taking?

Voluntary Covid-19 saliva testing is being offered to border workers in quarantine facilities, in addition to the regular weekly testing, in response both to the appearance of the more contagious variants and higher infection rates overseas.

The government introduced day 0/1 test and pre-departure testing for all passengers, with the exception of those from Australia, Antarctica and most Pacific Islands, on 15 January.

That is in addition to day 3 and day 12 tests in managed isolation facilities.

At the Pullman Hotel, where the three cases completed managed isolation, staff will no longer be able to work at different facilities, and no new returnees will be placed there, and air conditioning will be left on constantly to flush out air in common spaces.

*This story was first published on 26 January and updated on 28 January to include two new cases of the variant in New Zealand and information on vaccines.

- BBC / RNZ / Reuters / WHO / Ministry of Health / CDC /

UK scientists worry vaccines may not protect against South African coronavirus variant