Covid then vs Covid now: The emergence of variants and how the virus has evolved

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  • It's been over a year since the new coronavirus first emerged in Wuhan, China
  • During this period, mutations have led to the emergence of dominant variants that are more transmissible and possibly more deadly
  • Professor Tulio de Oliveira spoke to Health24 about what scientists have learned during this time, and what they still need to know

It’s been a year since the minister of health, Zweli Mkhize, officially announced the first confirmed local Covid-19 case in South Africa.

To date, Covid-19, caused by the SARS-CoV-2 virus, has killed more than 2.5 million people worldwide, derailed economies and turned daily lives upside down.

But this virus that first emerged in the city of Wuhan, China, in December 2019, has rapidly evolved and undergone several significant mutations during the pandemic. 

It is a virus that is “not tired of us”, the World Health Organization's director-general said in November.

'Virus mutates in radical ways'

“We’ve probably learned more and quicker about a pathogen that has been learned in the history of humankind,” Professor Tulio de Oliveira, a bioinformatician and director of genomics surveillance lab KRISP (KwaZulu-Natal Research Innovation and Sequencing Platform), told Health24.

Along with his colleagues, de Oliveira has been providing scientific leadership to the South African government during the Covid-19 crisis.

The speed at which the virus infected people led the entire scientific and medical communities to gear most of their resources and work full-time towards devising a solution to this crisis, he said.

“And then around November, we learned that the virus can mutate in radical ways to create this variant that spreads much quicker and that evades the immune system,” added de Oliveira.

When a virus has many mutations (changes acquired in the virus’s genetic material), they are known as variants of concern (VoC).

Scientists quickly learned that SARS-CoV-2 is a ruthless, indiscriminate and opportunistic pathogen that will not be vanquished unless rapid action is taken.

All viruses mutate, but this was a surprise

Within the past few months, there have been a number of VoC that have surfaced and spread with much higher frequencies, with some possibly more deadly than the original version responsible for first-wave infections.

These include 501Y.V1, first identified in the UK; 501Y.V2, first identified in South Africa (and now the dominant virus); and 501Y.V3, first detected in travellers from Brazil. These variants have since spread to many other countries.

But local scientists have stressed that RNA viruses, such as SARS-CoV-2, mutate all the time. After all, it is their nature to do so as it is key to their survival.

It, therefore, came as no surprise that the virus that emanated in Wuhan underwent multiple mutations during the pandemic.

And as time went on, the virus accumulated mutations and moved further away from the original virus. Mutations are grouped into clades, like the branches of a tree, with the original Wuhan virus as the root, explained Professor Penny Moore, the South African research chair of Virus-Host Dynamics at Wits University and the National Institute for Communicable Diseases (NICD), during a webinar hosted by MedTalkz last week.

But what caught scientists off guard was the large number of mutations accumulated in the spike protein, which has allowed the virus to transmit much faster than the original one, said de Oliveira.

“That was a complete surprise. In South Africa, we were fortunate to identify this quickly, otherwise we would have ended up with a more severe second wave because we wouldn't have been able to respond,” he said.

The bioinformatician previously told News24 that the 501Y.V2 variant was a "wake-up call" for the world to take this virus very seriously.

'Genomic surveillance can fight pandemics'

Without genomic surveillance networks in place, we would arguably be in a much worse situation. Genomic sequencing allows scientists to identify SARS-CoV-2 and monitor how it changes over time into new variants, explains the Centers for Disease Control and Prevention.

“I honestly think that this pandemic was a big proof of concept to show that genomic surveillance is very important in the world. We have shown the ability of this surveillance to fight epidemics and pandemics,” said de Oliveira.

Genomic surveillance has been central to controlling outbreaks, said de Oliveira, because it identified the virus.

It has also been used to develop diagnostics and vaccines, and to understand how the virus transmits around the world.

In South Africa, the national genomics programme commenced in March last year and included the sequencing of the first contact Covid-19 case in the country.

While KRISP is the principal investigative institute for the network of genomic surveillance, it is part of a collaborative network comprising a handful of institutes, including the National Health Laboratory Service, the NICD, the University of Cape Town, Stellenbosch University and the University of the Free State.

“One of the things we showed, and one of the reasons South African science is being praised – not only nationally by our ministers and by the president, but internationally by scientists and funders – is because we have shown that by working together, we can do much more than by working independently,” said de Oliveira.

What scientists learned, and are still learning

A couple of things have been learned during this pandemic, said de Oliveira, including the impact of “super spreader events”, and the importance of facemask wearing and lockdown in limiting the transmission of the virus – although the implementation of the latter proved to have disastrous effects on the economy, he said.

“And we also learned the importance of [partaking in] good vaccine trials,” he added, as participation in these trials means that countries will have data on which vaccines will work and won’t work among their populations. South Africa, for instance, participated in the Johnson & Johnson vaccine trial.

For this reason, this vaccine could be deployed in the country after the announcement of the suspension of the Oxford-AstraZeneca rollout in February.

Controlling the pandemic

Another crucial aspect to getting this pandemic under control is to study the effects of neutralising antibodies against the new SARS-CoV-2 variants – in other words, how well the vaccines and immunity induced from natural infection can protect against the new variants, said de Oliveira.

This is something that has been at the forefront of his and his colleagues work. Earlier this week, de Oliveira and Moore, along with Dr Alex Sigal, a virologist at the Africa Health Research Institute, presented promising results from their latest study on neutralising antibodies, which indicated that people infected with the new variant may be protected against reinfection.

Moreover, the scientists explained that vaccines are now being modified to contain the 501Y.V2 spike. Like the neutralising antibodies elicited through natural infection, the vaccine-induced antibodies will likely provide protection against this variant, and multiple other variants.  

No one is safe until everyone is safe

“Right now, there’s another race to make the Covid-19 vaccines even more effective [against new variants], but what’s also important, and what we’re learning, is something that Professor Salim Abdool Karim regularly says: ‘No one is safe until everyone is safe,’” said de Oliveira.

If we ignore other countries and just focus on eliminating the virus in our own country, we’re going to get further introduction of not only current variants, but potentially new ones, he cautioned.

“And at the moment, the country we as scientists are worried about the most is Brazil. The response is chaotic – it’s the same as the US.

"Their epidemic is at the highest level and they are not controlling the variants, whereas, in the UK and South Africa, we took the variants very seriously and controlled our second wave.

“And so the main thing that we are learning now is that we have to have a global response that doesn’t leave any country behind, and that vaccines have to be distributed to countries that cannot afford them,” he said.

READ | What the latest findings on the 501Y.V2 Covid variant mean for the development of vaccines

READ | Another coronavirus variant detected in SA, but no reason to panic, says KRISP director

READ | Covid-19 vaccine hesitancy is rooted in mistrust – and recent events haven't helped

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