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This was 2020.

The year of Covid-19

Part II

Know your enemy

How science went to war with Covid-19

It took over a month for the mysterious virus and its disease to be given a name. SARS-CoV-2 refers to the virus, Covid-19 the disease.

The names couldn’t refer to a geographical location, an animal or an individual or group of people, the World Health Organisation (WHO) ordered. It needed to be easy to pronounce and relate to the disease.

“I’ll spell it: C-O-V-I-D hyphen one nine – COVID-19,” WHO director-general Adhanom Ghebreyesus said in February.

It is commonly referred to via its disease name - Covid-19.

“I think SARS-CoV-2 probably doesn’t roll off the tongue quite so well,” University of Auckland microbiologist Dr Siouxsie Wiles says.

CO stands for corona, VI for virus, D for disease, and 19 refers to the first year the virus was discovered, ESR technical lead Lauren Jelley explains.

SARS-CoV-2 is just one of many coronaviruses that have been discovered. Four of them are common coronaviruses that cause colds, and three others are from a virus jumping from an animal reservoir to a human host - SARS-CoV, MERS-CoV and SARS-CoV-2.

WATCH: Dr Siouxsie Wiles, a microbiologist from the University of Auckland, has provided Kiwis with information and advice throughout the pandemic. Here’s what she knows about the virus and why it spread across the globe so quickly. Abigail Dougherty/Stuff

Like SARS-CoV and MERS-CoV, SARS-CoV-2 is spread via droplets produced by coughing, sneezing or talking. The symptoms of the three coronaviruses are also similar, though they vary as each disease increases in severity.

Because of the popularity and relative ease of international travel, Covid-19 spread rapidly around the globe. It was found to have a basic reproduction rate - R-nought (Re) - of 2.5, meaning every one case infected, on average, 2.5 people. In comparison, SARS had a reproduction rate of 2 to 3 and MERS 0.9.

Despite having a lower infection fatality rate, SARS-CoV-2 has killed more than both the SARS and MERS epidemics combined. Professor David Hayman, from Massey University’s school of veterinary science, explains this is because of the silent, asymptomatic transmission that didn’t happen with SARS and MERS.

WATCH: Research by health specialists from Singapore shows evidence that asymptomatic individuals infected with SARS-CoV-2 can inadvertently spread the virus. NXAS

“It’s quite similar to SARS - [that’s the reason it’s called SARS-CoV-2] - but it’s just different enough that it’s that little bit more transmissible.”

Wiles describes this transmission as the genie being released before anyone realises it.

When the genetic sequence of the virus was publicly shared by China in January, the world’s best scientific minds went to work.

The sequence was vital to creating a reliable diagnostic test, treating infections and developing a vaccine.

The pace at which labs experimented on the pathogen was unprecedented.

“We don’t worry about egos, we don’t worry about who’s first, we just care about solving the problem,” microbiology-immunology professor Karla Satchell from Northwestern University in the United States said in January.

Professor Kurt Krause, an infectious disease physician and biochemistry professor at the University of Otago, thinks this evolution of knowledge was the fastest of any pathogen in history. “It’s really been extraordinarily fast … Science has progressed rapidly.”

Thanks to this global collaborative approach, clinical virologists from the national reference laboratory ESR had rapid tests ready to go in just 20 days.

“It was impressive, absolutely, that we had those tests so quickly,” the University of Otago’s Professor David Murdoch says.

“This test was stood up out of nothing, out of thin air,” recalls Dr Ian Town, the Ministry of Health’s chief science advisor.

Dr Joep de Ligt, the bioinformatics and genomics lead at ESR, says the process from when they received the genetic sequence and finished the first test was very rapid, especially when compared to the progress for the SARS and MERS viruses.

“Some of the earlier coronaviruses … had to wait for a year or more for their genome to be publicly available in the first place. So designing tests and those types of things took a lot longer.”

ESR’s Jelley likens the process of developing a suitable test to trying a new recipe for the first time. “To make sure it turns out well you have to give it a go in your own oven and see how it turns out in practice.”

A lot of different combinations were trialled before ESR validated one on January 31.

Having a test available in New Zealand before the first positive case emerged was vital for containment. The exponential growth of the virus abroad meant the scientific community and health experts wanted to be ready for when it eventually breached the border.

“If you miss the first couple of people, it very quickly gets out of hand,” de Ligt says. “So you need to have tests ready before you have your first case.”

The shared sequence also confirmed what Hayman suspected - the virus was zoonotic, meaning it had come from an animal, not a lab as conspiracy theorists speculated.

WATCH: Researchers say the novel coronavirus was not made in a lab, after comparing its RNA sequence to SARS, MERS and other coronaviruses. NXAS

The virus is believed to have derived from bats, but researchers still don’t know if there was another carrier.

“It’s not clear, and it’s definitely not known, if this is a direct jump from a bat to a human, or if it’s a direct jump from a bat to another species and another species to a human,” Hayman says.

Those missing links remain a mystery and may remain unsolved for a while, maybe forever. “There’s so many different animals … how do you find the one that had the virus? We may never know exactly,” Hayman says.

These kinds of spillover events are happening more frequently as humans encroach on wild animals’ territory.

“It could be anything. It could’ve come via pigs. It could’ve come via wild animals. It could’ve come via any route really,” Wiles explains.

“You cannot fight a fire blindfolded. And we cannot stop this pandemic if we don’t know who is infected,” Ghebreyesus said.

New Zealand’s health professionals and lab technicians went to work again.

After the first suspected positive sample was validated at Auckland’s Labplus and confirmed by the team at ESR - who technical lead Jelley described as the “hidden figures” of the pandemic - around a dozen more labs came on board. ESR was then able to turn its focus to cultivating the virus and validating alternative diagnosis methods, like saliva tests.

ESR's "hidden figures" of the pandemic confirmed the first Covid-19 sample in New Zealand. The small Wellington-based team worked collaboratively to confirm the news to the country: Covid-19 had breached New Zealand's borders. ESR

Labs across the country adopted a collaborative approach to process the thousands of samples landing on their desks each day. When capacity was reached at one lab, samples would be picked up by another, allowing for the rapid turnaround of results, which few countries matched.

“That was very well done,” Murdoch says. “I think we’ve offered a service that would be [offered by] very few in the world with the testing. We’re well up there.”

Scientific knowledge of the virus continued to evolve.

ESR’s de Ligt and his team were one of the groups to test genome sequencing designs coming out of labs in Germany, China, the US and the UK. The UK design was released just a week after the sequence was shared publicly by China. Once the testing phase was finalised, they began rolling it out within New Zealand labs.

Whole genome sequencing on positive samples provides researchers with a vital piece of the puzzle. The origins of a case can be matched with existing cases to identify the source of infection, scientists are able to study how the virus enters human cells and effectively progress vaccine developments.

After the first positive sample was confirmed by Jelley and her team, de Ligt’s team had a partially complete genome within 24 hours, and a whole genome just a few hours later. This was the first time the sequencing protocol had been practically performed in New Zealand as it requires a positive sample.

Genome sequencing performed by Dr Joep de Ligt and the team at ESR gave researchers a peak into the origins of an infection. They could then connect cases, identify clusters, and track down the international origins of the virus strain the case was infected with. Rosa Woods/Stuff

A collaborative study by New Zealand researchers found most of the country’s initial cases had lineages originating in North America. Additional research found infections linked to strains in China, Australia, Italy, Germany and the Netherlands as well.

“At times like these, of high uncertainty, you cannot underestimate the importance of good quality data. Accurate reporting is crucial to keeping everyone informed and safe,” de Ligt said after the first sample was genomically sequenced in March.

Just as local researchers drew on publicly shared data to create a test, they gave back to the global scientific community by uploading the RNA genome of the virus to GISAID - an international database for viral sequences - three days after the first case was confirmed.

On the global stage, de Ligt believes New Zealand’s genome sequencing capabilities are “quite far ahead”. Other standout markets are Australia, the UK and Taiwan.

However, there is always room for improvement. De Ligt wants to see genome sequencing adapt and improve as more is learnt about the virus. “It’s not going to be perfect,” he says. “But if we are all aware of that [and] we are doing the best we can, and are detecting those problems and actively fixing them, that is when you get public trust and when you get a system that works.

He also hopes the technology will become a standard of care for all infectious diseases, including influenza, sexually transmissible infections (STIs), and bacterial infections.

WATCH: How were the first Covid-19 PCR tests created? Why do we need to perform genome sequencing? ESR biometrics and genomics lead Dr Joep de Ligt has been at the centre of it all throughout the pandemic. Jack Price/Stuff

“If you even have a sniffle or the slightest sore throat get a test because the sooner we get on top of knowing that someone has the symptoms of Covid-19, the more successful our isolation and contact tracing will be,” Ardern said in April.

Murdoch says the evolution of testing criteria aligned with the evolution of knowledge, and people became more accustomed to seeking a test as soon as symptoms emerged.

Testing rates fluctuated, but spikes correlated with reports of new community cases.

With the first wave, the seven-day rolling average for tests had reached 5303 by the end of level 4 lockdown. When the country dropped down to alert level 1, the weekly average had decreased to 1874.

There was a spike in June when two Covid-positive travellers from the UK were granted leave from managed isolation on compassionate grounds. They weren’t tested prior to leaving. This put an end to a 24-day case-free streak, and resulted in the seven-day rolling average peaking at 7440.

In August, when new community cases in Auckland ended the 102-day case-free streak and started what would become the country’s largest cluster, testing rates climbed again from 1687 tests on the day of the announcement, to 25,005 tests a few days later. Daily testing rates hovered in the tens of thousands for nine consecutive days.

At its peak in August, the seven-day rolling average for tests had reached 20,965.

By December, a quarter of the “team of 5 million” had been tested.

Cumulative tests

“That test has stood the test of time,” Town says.

The prime minister's message for everyone with symptoms, no matter how mild, got through to the masses. Queues continuously formed at testing sites all around the country. David White/Stuff

“There is so much effort that goes behind one swab and one test,” Jelley explains. The number of tests is a small indication of how much work has gone in behind the scenes.

“The more testing that we do, the more chance we have of picking up the virus, putting control measures in place quickly, and stopping the spread of the virus,” she says.

But embarrassing errors were made.

Regular testing regimes for border-facing workers weren’t rolled out. The words of former health minister David Clark in June - “Those borders are the thing that we want to make sure are secure” - came back to haunt him. His sucessor, Chris Hipkins, bore the brunt of the backlash.

“I own that… I’ve owned that every day that I’ve been the minister of health and I’ve been working to fix that,” Hipkins said in August.

Murdoch hopes that mistake will act as a vital lesson.

“There’s always a bit of chaos in a crisis. We hopefully can learn from that experience and do better next time.”

Reviews were conducted, testing regimes were overhauled, but the virus continued to seep through the supposedly watertight borders. A number of cases in November were New Zealand Defence Force (NZDF) staff

Eighteen significant clusters formed around the country, most linked to social gatherings or aged care facilities, a scenario the University of Canterbury’s Dr Arindam Basu describes as “always worrisome”.

New Zealand Covid-19 clusters

Of the four aged residential care facility clusters that emerged, the Rosewood rest home in Christchurch became the deadliest.

The Auckland August Cluster, sparked by a breach at the maritime border, grew to be the largest - 179 people were infected. It could have been more dangerous, but the rapid roll out of restrictions stalled its growth.

While clusters - or networks, as Basu describes them - are incredibly harmful when growing, they can also be helpful. If a cluster is quickly identified and all cases contained, the disease will die out and researchers can learn from it.

“Unfortunately, the more people that have become infected, the more we’ve been able to learn about it,” Wiles says. “Every outbreak that we have allows us to learn something new about the virus.”

Alongside clusters, “super-spreaders” entered the global lexicon as a result of the pandemic.

Super spreader events, like the case that infected dozens of people in a religious cult in South Korea, have a higher reproduction rate than regular cases.

“Sooner than you can say ‘Covid’, you’ll see a number of different clusters emerging all of a sudden,” Basu explains.

It’s not yet known, however, if super spreader individuals are created because of their environment, who they are, or a combination of both, Wiles says.

New Zealand was lucky not to experience this type of rapid spread. “We did a good job [of] quickly containing the clusters,” Basu says.

There was one outbreak, however, that New Zealand and many countries around the world failed to contain and eliminate - the spread of misinformation.

An infodemic was raging across the globe.

At the peak of the pandemic, misinformation whipped around the globe. Conspiracy theorists put blame on 5G technology and shared their unfounded claims on social media. Justin Setterfield/Getty Images

“We’re not just battling the virus,” Ghebreyesus said at a briefing in August. “We’re also battling the trolls and conspiracy theorists that push misinformation and undermine the outbreak response.”

Organised campaigns in New Zealand were spreading what Covid-19 Response Minister Chris Hipkins described as “repeated, deliberate, malicious” lies, while dangerous myths emerged linking 5G to the virus.

Officials here and around the world implored people to only listen to official advice. “We can all play our part in drowning out misinformation by sharing the right information,” Hipkins said in September.

But 12 months on, the scaremongering continues, sometimes spreading quicker and further than official advice, via social media.

“At the speed of light we’re bombarded with misinformation about the vaccine and about treatments and about the utility of social distancing and mask use,” Krause said.

But where regulators struggled to quickly come up with a consistent response to misinformation, there was one key tactic in the fight against the virus itself. It was a harsh and, before 2020, wholly unthinkable response. But where it was done well, it worked.

Proceed to part III

When the World stopped turning

Lockdowns across the Planet

Part I
Part IV
Part V
Part VI