Africa’s daily count of new coronavirus cases has soared to unprecedented levels, as the more contagious Delta variant drives an aggressive third wave of infections through a population largely unprotected by vaccines.
The continent’s daily tally of new cases has increased for seven weeks in a row, surging more than 20% in the past week alone to reach 46,528 by July 9, according to our World in Data. Almost half these cases have been recorded in SA, which has seen hospitals in Gauteng breach capacity and weekly excess deaths from natural causes in the province reach their highest levels since the pandemic began.
With no sign of the epidemic abating, President Cyril Ramaphosa announced on Sunday that the stringent coronavirus restrictions implemented two weeks ago would remain largely unchanged for at least another fortnight, bar easing the curbs on restaurant trade and the reopening of gyms and fitness centres.
The million-dollar question is why the virus is once again ripping through SA’s population, despite the large proportion of people who have previously been infected, says the government’s top coronavirus adviser, Koleka Mlisana, head of academic affairs, research and quality assurance at the National Health Laboratory Service.
A recent study by the SA National Blood Service found 47.4% of the blood donor samples analysed between January and May contained SARS-CoV-2 antibodies, signalling prior infection with the virus that causes Covid-19.
“We should have a significant number of people who are protected. But emerging data shows even though people may have been previously exposed to Beta (or other variants), they may be susceptible to Delta. That is a big concern,” says Mlisana.
A laboratory study published last week in Nature found Delta was better at escaping antibodies made in response to natural infection with the Alpha variant, and local scientists have flagged similar concerns about potentially limited protection conferred by prior infection with Beta.
Delta was first identified in India last October and has now been detected in more than 100 countries, including SA. In the past two months it has rapidly displaced older variants and now accounts for 80% of the samples sequenced by the Network for Genomic Surveillance in SA, according to Tulio de Oliveira, director for the KwaZulu-Natal Research and Innovation Sequencing Platform.
“Beta caused a devastating second wave in SA and the region. We have now seen a continuous replacement of Beta with Delta, associated with an exponential growth in infections,” he said during a recent briefing hosted by the World Health Organization (WHO).
There is no data to suggest Delta causes more severe illness than other variants, but recent research by the National Institute of Communicable Disease (NICD), published in The Lancet, has drawn attention to the risk to patients when cases surge and hospital services are overwhelmed.
The researchers found increased in-hospital mortality during SA’s second wave, which they attributed in part to patients being unable to obtain the care they required. Their finding was in stark contrast to the experience of many other countries, which reported lower hospital death rates in their second waves, as treatments improved over time.
Those risks are once again playing out in Gauteng, which saw average daily Covid-19 hospital admissions reach a record high of 722 a day in the fortnight to July 3, according to the NICD. During the same period, average in-hospital deaths from Covid-19 reached 163 a day, almost double the average rate recorded in the previous fortnight.
The evolution of SARS-CoV-2 into the Delta variant, with its increased transmissibility and apparent ability to evade antibodies generated by prior infection, combined with a hefty dose of Covid-19 fatigue and marginal vaccine coverage, has created a perfect storm, says Marc Mendelson, head of the division of infectious disease and HIV at UCT.
“After the country’s first two waves, we saw a slide backwards towards mass super-spreading events. When you have increased transmission — first with Beta, and now with Delta — you are going to see a lot more cases,” he says.
Beta is estimated to be 50% more transmissible than the original coronavirus lineage detected in Wuhan, China, while Delta is up to 60% more transmissible than Beta.
SA’s serially delayed vaccination drive — which, after a slew of unexpected setbacks, got off to a slow start with the over-60s in mid-May — came too late to prevent the third wave and is still not progressing fast enough to alleviate hospital admissions, says Mendelson. “We are not rolling out vaccines fast enough, even in urban centres, and we are seeing a lot of vaccine hesitancy, even among the elderly [who are most at risk of severe disease],” he says.
Recent UK data shows full vaccination with the Pfizer-BioNTech shot, which is one of the two Covid-19 jabs being administered in SA, confers 96% protection against severe illness and death from Covid-19 caused by the Delta variant, he says.
The Johnson & Johnson jab offers better protection against Delta than it does against Beta, for which it was 85% effective at preventing severe disease, according to research released by the company last week. “If vaccines had been rolled out at scale two months earlier, Gauteng would not be in the situation it is in now,” says Mendelson.
Scientists expect SARS-CoV-2 to continue evolving, raising the prospect that new-generation shots adapted to new variants may soon be required, says Mlisana. “While we need to procure as many vaccines as possible and catch up, we also need to look to the future. We need to think about what is likely to be in the pipeline, and ensure we have a stake in these vaccines as they come out,” she says.
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