As new Covid-19 variants fuel fifth wave in South Africa, virus becomes a fact of everyday life

South Africa is in the midst of the fifth wave of Covid-19, driven by two variants linked to the Omicron strain, which caused a surge in cases across the world over the winter. Life just goes on.

The country, which has been at the forefront of that first Omicron wave that happened last November, is a model for living with the virus in the long run. For the average South African, the virus has become an everyday fact. Behind the scenes, dozens of scientists closely monitor every move.

Leaders in the US and Europe say the pandemic — which has killed more than six million people worldwide according to official counts — is entering a new, less acute phase. Anthony Fauci, President Biden’s chief medical adviser, recently said the country is moving into a more controlled phase of the pandemic. European Commission President Ursula von der Leyen said last month that the bloc is moving from emergency mode to more sustainable management of Covid-19.

Most of the pandemic-era restrictions have been lifted in the US and Europe, although mask mandates remain on public transport in some places, including Italy and parts of Germany.

South Africa provides some clues as to what the next phase might look like. “We moved to the next stage five months ago,” said Tulio de Oliveira, director of the Center for Epidemic Response and Innovation in South Africa. He was one of the scientists who sounded the alarm about the BA.1 Omicron variant, which swept the world all winter. They also quickly concluded that it wouldn’t be as deadly as previous waves.

The key to South Africa’s ability to quickly detect and analyze new variants is a network of some 200 scientists who must continuously monitor infection levels and new variants, ready to launch detailed investigations if they discover anything unusual. , says Prof. de Oliveira.

Every Friday, Prof. de Oliveira holds a call with nine genomics and diagnostic labs across the country to assess infection levels and the mix of variants that cause them. South Africa carries out routine Covid-19 testing of all hospitalized patients and tests a random selection of patients at six outpatient clinics. It routinely sequences about 400 viral genomes per week to get an idea of ​​the mix of variants responsible for infections. If an area shows an increase in infections or a rise in a new variant, Prof. de Oliveira mobilizes the network of labs to perform full genomic sequencing of many more samples – up to several thousand per week – to get a more detailed picture to get.

On April 1, during their usual Friday call, the genomics and diagnostic labs had noted more infections caused by BA.4 and BA.5 in South Africa’s two most populous provinces: Gauteng and KwaZulu-Natal. Over the weekend, the labs set to work sequencing hundreds more samples, confirming that BA.4 and BA.5 were on the rise.

Since the start of the Covid-19 pandemic in 2020, the scientific understanding of its transmission and prevention has evolved. Daniela Hernandez of WSJ explains which strategies have worked to contain the spread of the virus and which will be obsolete by 2022. Illustration: Adele Morgan

On Monday April 4, Prof. Dr. de Oliveira contacts Alex Sigal, a virologist who runs a lab in the same building as him. Within minutes, Prof. Sigal sent one of his scientists to Prof. de Oliveira’s lab to collect samples of BA.4 and BA.5 and began investigating whether the variants could evade the immune defenses of vaccination or previous infections.

On April 29, Prof. Sigal and his collaborators shared their findings. They found that BA.4 and BA.5 were able to evade the immune defenses of people who were either vaccinated or previously infected with BA.1 to some extent and likely trigger a fifth wave of infection. The results have not yet been peer-reviewed.

“We are advising the government that there will be a wave, but we do not expect it to translate into high rates of deaths and hospitalizations,” said Prof. de Oliveira.

The end of the pandemic will not be as clear-cut as the beginning, epidemiologists and global health experts say. Eradication of SARS-CoV-2 is likely out of the question because immunity to vaccination or previous infection declines, periodically giving the virus new opportunities to cause new waves of infection. The virus also mutates, leaving open the possibility of a future strain causing more serious disease or evading existing immunity.

The global picture is mixed. In Hong Kong, where few had been exposed to the virus due to a strict ‘zero-covid’ strategy, and vaccination rates were low, including among the elderly, the Omicron wave recently made the death rate one of the highest caused by any country. also throughout the pandemic. China’s zero-covid strategy has also led to a strict lockdown to quell the rising number of cases in Shanghai, seriously disrupting global trade.

The head of the World Health Organization called on China to rethink its strategy to eradicate Covid-19 cases in the country, as a rare challenge to a member state’s domestic Covid policy. Photo: Fabrice Coffrini/AFP/Getty Images

For much of the world, however, the virus has been suppressed through a build-up of immunity and the development of effective treatments. Global weekly deaths are at their lowest level since March 2020, according to the World Health Organization.

“Maybe we won’t know until it’s over, sometime after it’s over,” said Peter Piot, a professor of global health at the London School of Hygiene and Tropical Medicine. He expects the virus to cause increasingly shorter waves of infection that are less severe thanks to the build-up of population immunity through vaccination and previous infection. The pandemic can be considered ‘over’, he says, when there is hardly any transmission for most of the year and hardly anyone ends up in hospital or dies.

As in South Africa – where Prof. de Oliveira says about 91% of the population has antibodies to Covid-19 from vaccination or previous infection – population immunity is high in the US and much of Europe. In December, nearly 95% of people aged 16 and older in the U.S. had antibodies to Covid-19 through infection or vaccination, according to a study based on samples from blood donation centers across the country. In the UK, about 99% of adults have antibodies, according to an April estimate by the country’s Office for National Statistics.

The Omicron BA.1 variant of SARS-CoV-2 sparked an explosion of cases in many parts of the world over the winter. Other members of the Omicron family, such as BA.2, BA.4 and BA.5, continue to cause high infection rates around the world. The WHO said at a recent briefing that the number of cases is rising in more than 50 countries. But in places where most people have been vaccinated or have already had Covid-19, high transmission is not associated with commensurate levels of hospitalization and death.

As evidence grew that population immunity had dampened Omicron’s toll, many governments began to dismantle their pandemic defenses. The UK stopped providing free Covid-19 rapid tests to the population last month and severely restricted access to lab tests. Many countries are relaxing travel restrictions.

Global health experts warn countries should continue to monitor the virus closely so they can be prepared to step up emergency measures in the event that a dangerous new strain emerges. Prof. dr. de Oliveira says the goal of South Africa’s approach is to generate key scientific data before a wave hits to better steer the public health response. The genomic labs there saw the emergence of BA.4 and BA.5 two weeks before the infections started to rise, giving Prof. Sigal’s team a head start to analyze the variants.

South Africa’s ability to detect and respond quickly to infectious disease outbreaks stems from its decades of experience dealing with dangerous pathogens such as HIV and tuberculosis. Those diseases could also hold a lesson about the long-term future of Covid-19 as it moves beyond a pandemic and becomes an endemic disease, meaning it has established itself in the human population. “We have endemic HIV and tuberculosis from which many people die,” says Prof. de Oliveira. “Endemic doesn’t mean it isn’t lethal.”

write to Denise Roland at Denise.Roland@wsj.com

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