South Africa is in the midst of its fifth wave of Covid-19, fueled by two variants related to the Omicron strain that fueled a surge in cases around the world over the winter. Life goes on as normal.
The country, which was at the forefront of that first wave of Omicron that took hold in November last year, is a model for living with the virus long-term. For the average South African, the virus has become a monotonous fact of daily life. Behind the scenes, dozens of scientists closely follow his every move.
US and European leaders say the pandemic, which has killed more than six million people worldwide by official counts, is entering a new, less acute phase. Anthony Fauci, President Biden’s top medical adviser, recently said the country is transitioning to a more controlled stage of the pandemic. European Commission President Ursula von der Leyen said last month that the bloc was moving from emergency mode to more sustainable management of Covid-19.
In the US and Europe, most pandemic-era restrictions have been lifted, though mask mandates remain in place in some places, including Italy and parts of Germany on public transportation.
South Africa provides some clues as to what the next stage might look like. “We moved into the next phase 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 spread across the world during the winter. They also quickly determined that it would not be as deadly as previous waves.
Key to South Africa’s ability to quickly detect and analyze new variants is a network of some 200 scientists tasked with continuously monitoring infection levels and new variants, ready to launch a detailed investigation if they spot anything unusual, says Professor de Oliveira. .
Every Friday, Prof. de Oliveira makes a call with nine genomics and diagnostic laboratories throughout the country to review the levels of infection and the combination of variants that cause them. South Africa routinely tests all hospitalized patients for Covid-19 and tests a random selection of patients at six outpatient clinics. He routinely sequences around 400 viral genomes a week to get a sense of the mix of variants responsible for infections. If any area shows a spike in infections, or an increase in a new variant, Prof. de Oliveira mobilizes the network of laboratories to perform whole genome sequencing of many more samples, up to several thousand per week, to get a bigger picture. detailed.
On April 1, in the usual Friday call, genomics and diagnostics 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, labs went to work sequencing hundreds more samples, confirming that BA.4 and BA.5 were on the rise.
On Monday, April 4, Prof. de Oliveira contacted 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 work to determine whether the variants could circumvent 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 could, to some extent, evade the immune defenses of people who had been vaccinated or previously infected with BA.1 and would likely generate a fifth wave of infection. The results have not yet been peer-reviewed.
“We are warning the government that a wave will come, but we do not expect it to translate into high mortality and hospitalization figures,” said Prof. de Oliveira.
The end of the pandemic will not be as clear as its beginning, say epidemiologists and global health experts. Eradication of SARS-CoV-2 is likely out of the question because immunity from vaccination or previous infection wanes, periodically giving the virus new opportunities to drive new waves of infection. The virus also mutates, leaving open the possibility of a future strain that causes more severe disease or can bypass existing immunity.
The global picture is mixed. In Hong Kong, where few had been exposed to the virus due to a strict “covid zero” strategy and vaccination rates were low, even among the elderly, the Omicron wave recently pushed death rates to one of the lowest. highs suffered by any country throughout the pandemic. China’s zero covid strategy has also led to a strict lockdown to suppress the rising number of cases in Shanghai, seriously disrupting world trade.
However, for much of the world, the virus has been hit by a buildup 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.
“We may only know when it ends sometime after it ends,” said Peter Piot, a professor of global health at the London School of Hygiene and Tropical Medicine. He expects the virus to cause shorter and shorter waves of infection that are less severe thanks to the population’s buildup of immunity through vaccination and prior infection. The pandemic could be considered “over,” he says, when there is hardly any transmission for most of the year, and hardly anyone ends up in the hospital or dies.
As in South Africa, where Professor de Oliveira says around 91% of the population has antibodies to Covid-19 from previous vaccination or infection, population immunity is high in the US and much of Europe. . As of December, nearly 95% of people over the age of 16 in the US had antibodies to COVID-19 from infection or vaccination, according to a study based on samples from blood donation centers across the country. In the UK, around 99% of adults have antibodies, according to an April estimate from the country’s Office for National Statistics.
The Omicron BA.1 variant of SARS-CoV-2 caused an explosion of cases in many parts of the world during the winter. Other members of the Omicron family, such as BA.2, BA.4 and BA.5, continue to generate 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 already had Covid-19, high transmission is not accompanied by commensurate levels of hospitalization and death.
As evidence mounted that population immunity had mitigated Omicron’s toll, many governments began dismantling their defenses against the pandemic. Last month, the UK stopped providing free rapid tests for Covid-19 to the population and severely restricted access to laboratory tests. Many countries are relaxing travel restrictions.
Global health experts are warning that countries need to monitor the virus closely so they can be prepared to step up emergency measures should a dangerous new variant take hold. Professor de Oliveira says the goal of the South African approach is to generate key scientific data before a wave hits to better guide the public health response. Genomics labs there detected the increase in BA.4 and BA.5 two weeks before infections started to rise, giving Professor Sigal’s team a head start in analyzing the variants.
South Africa’s capabilities to rapidly track and respond to infectious disease outbreaks stem from its decades of experience with dangerous pathogens such as HIV and tuberculosis. Those illnesses may also hold a lesson about the long-term future of Covid-19 as it transitions from a pandemic to an endemic disease, meaning it has taken hold in the human population. “We have endemic HIV and tuberculosis that kill many people,” says Prof. de Oliveira. “Endemic doesn’t mean it’s not deadly.”
write to Denise Roland at [email protected]
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