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Moment that mattered: Scientists in South Africa announce the identification of the Omicron variant

A healthcare worker conducts a PCR Covid-19 test at the Lancet laboratory in Johannesburg. 30th November 2021

A healthcare worker conducts a Covid-19 PCR test at the Lancet laboratory in Johannesburg, South Africa, 30th November 2021. Photo: Emmanuel Croset / AFP via Getty Images

For 24 hours Shabir Madhi knew something the rest of the world did not. As former chair of South Africa’s National Advisory Group on Immunization and a senior advisor to the World Health Organization, he had been given advance warning that a potent new variant of Covid-19 had been identified. “I know one of the people that was working on the sequencing and he called me and expressed serious concern that the variant had multiple mutations,” says Madhi. “He was worried that the variant might be antibody evasive, more infectious and might also be able to evade T cell immunity. It was a memorable conversation.”

The concerns over T cell immunity were particularly worrying. Madhi, like many virology experts, believes T cell immunity, induced either by previous infection or vaccination, is the difference between relatively mild symptoms after contracting Covid-19 and the kind of critical illness the world witnessed when the disease first emerged. Despite the apocalyptic warnings, Madhi didn’t panic when his country’s National Institute for Communicable Diseases (NICD) made the findings public the day after the call. “We travelled down the same road a year earlier with Beta,” he says of the last variant identified in South Africa in late 2020. “Then there was panic even though all indications were that T cell immunity was relatively preserved. I believed [when Omicron was announced] that people would’ve learned from one year earlier, but I should have known better. Countries again started to shut their borders to southern African countries.”

Within a week of the NICD releasing the news about Omicron, more than 50 countries had imposed tight border controls for arrivals from southern African countries, particularly South Africa and Botswana, where Omicron was first detected. Madhi believes the move was pointless. “The learnings from Beta were that by the time a variant is identified, it’s been circulating for four to six weeks, by which time it is too late to close borders. Within a few days, those very same countries [that had imposed travel bans] started to identify cases.” Despite the apparent inefficiency of border closures, Madhi can see why they are imposed by governments. “It’s political optics,” he says. “You are damned if you do and damned if you don’t. With the Delta variant, which evolved in India, many countries delayed imposing travel bans and when outbreaks occurred their people asked ‘Why didn’t you shut the border earlier?’ But the reality is that even if they had shut the border earlier, it still would have been too late.”

For South Africa, the latest border closures added pressure to an already struggling economy. “The country was punished for the scientists doing their job well and for being forthright with their findings,” says Madhi. “Tourism is a major driver of the economy and the travel ban came right at the start of summer, peak time. Any further knock to the economy affects people’s livelihoods. It increases our unemployment which already sits at over 30 percent.”

South Africa’s last wave had peaked in early July and had faded away to just a couple of thousand cases a day by early November. By the month’s end, thanks to Omicron, cases had increased by more than 3,000 percent. As the outbreak took hold, Madhi and his colleagues continued their investigations. “What we saw at a very early stage was a welcome surprise,” he says. “Despite the huge amount of infections, hospitals remained relatively empty and ICUs weren’t under pressure. It was just worlds apart compared from anything that we experienced in the earlier waves.”

When Madhi reported a more positive update he found the world wasn’t listening. “I think it’s a form of cultural imperialism, where it’s difficult to accept any good news that comes out from low- to middle-income countries,” he says. “When we released the bad news of Omicron the entire world accepted it overnight. When we started to say ‘hey, it’s not so bad,’ the world seemed to change its mind about the validity of data flowing out of southern Africa.”

Madhi, however, was convinced – and went on a global media blitz. “I went on multiple international news channels and even those that were hosting those interviews sounded very sceptical,” he says. “I would have thought that the world was at the stage where it wanted to get some good news. Everyone just felt that this was a disaster in the making, rather than accepting that there might be some light at the end of the tunnel here.”

Madhi says that the news is only positive for populations with high levels of immunity. “We’ve seen a massive difference in experience in Hong Kong and New Zealand, and those are two examples of places that were able to contain the spread of earlier variants, but are now experiencing a surge of cases of Omicron,” he says of the wave the countries experienced in March 2022. “The mortality rate in New Zealand is subdued, but in Hong Kong it is just through the roof.” Madhi believes that this contrast shows not that Omicron is a less serious disease than previous variants but that vaccines and immunity developed through previous infection have had a major effect. He points out that the vaccination levels in people above the age of 70 is much lower in Hong Kong than New Zealand. “I don’t buy into the school of thought which says that Omicron is less virulent,” he says. “I really believe that what we’re experiencing now is a change in the trajectory of the pandemic, driven by the [rising levels of] immunity.”

The disparity between how rich and poor countries have reached this level of immunity makes Madhi visibly angry. “Immunity has arisen in high income countries predominantly because of high vaccine coverage and in low-income countries it’s evolved because of natural infection. I’m not arguing the case for natural infection-induced immunity, because it has come at the cost of the loss of 300,000 lives in South Africa,” he says referring to a report on the country’s excess death rate released by the South African Medical Research Council in March 2022, which said that as many as one in every 200 South Africans may have died from Covid-19. “Our mortality rate is among the highest in the world.”

The WHO has targets for 70 percent of the global population to be vaccinated by the middle of 2022, but for Madhi it is too little, too late. “That boat has sailed already,” he says. “Talking of equity of vaccine access in 2022, it’s an academic discussion. In Africa, I believe, 70 to 80 percent of the population have already been infected, and the science clearly demonstrates that previous infection protects against severe disease and death. An equitable distribution of vaccines now is not going to bring back the lives that have been lost when those vaccines were unavailable to a country.”

Over his 30-year career, Madhi has seen the impact of low-income countries being at the back of the queue when it comes to vaccines. “The inequity of distribution and access to life-saving vaccines is not a new phenomenon,” he says. “It took 20 years from the time when the Hib C vaccine became available in the US, to when the majority of the population in low-income countries started to gain access to it. For the pneumococcal vaccine, that 20-year lag was cut to ten years. Ten years means ten million children died from pneumococcus during a time when a vaccine was preventing millions of infections in high-income countries.”

Everything I am seeing suggests we are at the tail-end of this pandemic”

Madhi worries that when the vaccine does arrive in large quantities to Africa it could be reported as a negative news story. “I think over the next few months there will be large volumes of Covid-19 vaccines coming to the continent, largely because they are no longer required in high-income countries,” he says. “But because of natural immunity, governments are not going to be that interested in getting it out to the population and the population are going to be apathetic about receiving the vaccines. So basically, we’ve got millions of dollars of the vaccine that will expire on the continent when they do eventually arrive here.”

Despite his exasperation at the situation, Madhi is cautiously optimistic about the course of Covid-19. “Everything I am seeing suggests we are at the tail-end of this pandemic,” he says. “If a new variant arises, which is able to evade T cell immunity and cause severe disease, then that would be a completely new type of virus which the entire world would need to react and recalibrate to – we’d be going back to March 2020 – but the chances of that happening, in my mind, are extremely slim.”

The professor also believes Covid-19 could play a positive role helping low-income countries, if the world pools its knowledge and continues to invest in science. “The experience of the past two years could strengthen research into HIV and TB – diseases that still have a huge impact in Africa,” he says. “There’s been a phenomenal amount of learning from the research on Covid-19 which can be applied to other diseases moving forward. It depends to what extent high-income countries and governments are willing to sit together to develop an agenda. Unfortunately, it would be naïve to have too much optimism around that hope.”

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