Coronavirus variant in South Africa sparks fear of faster spread, possible reinfection

South African doctors and researchers struggling with a second wave of Covid-19 cases are beginning to understand the role that a new coronavirus variant could play in the new rise of infections.

The total confirmed cases of Covid-19 in South Africa passed one million this week. The 60 million country recorded 17,710 new infections on Wednesday, higher than any daily case load seen during the first spate of infections, which peaked in July.

Doctors say they need to ration oxygen and that they do not have the manpower to do the best practice care, such as turning patients on their stomachs. One-third of coronavirus tests return positive, indicating that the actual number of infections is likely to be much higher.

South African researchers first discovered the new coronavirus variant in November – which shows similarities to a variant found in the United Kingdom in December – and it quickly became dominant in the coronavirus hotspots in the country. According to the researchers, the South African variant has the same mutation as the British scientists said that the variant there could be significantly more contagious than other versions of the virus.

South African researchers say they have also found changes in the virus’ structure, which in earlier laboratory tests has led to increased resistance to antibodies in people who have recovered from Covid-19.

However, researchers have said that human behavior is still the main reason for the new boom in Covid-19 cases. Millions of South Africans have traveled in recent weeks to see family across the country, while tens of thousands have flocked to restaurants, bars and beaches during a festive season that overlaps with the country’s most important summer holiday.

South Africa’s daily confirmed Covid-19 cases, averaging seven days

Source: Johns Hopkins CSSE

“The variant is likely to play a very small role” in the recent increase in infections in South Africa, said Jinal Bhiman, the leading medical scientist at the National Institute of Communicable Diseases in Johannesburg, who is studying the new variant. . But Bhuran said, “it could also be a perfect storm.”

Several countries have banned travel to and from South Africa over concerns about the spread of the new variant. In the past week, laboratories in Finland, the United Kingdom, Japan, Australia and Switzerland have found the South African variant in coronavirus tests performed there. Researchers in neighboring Zambia said on Wednesday that the South African variant now also appears to be the dominant virus there.

It is unclear whether the mutations may affect the effectiveness of Covid-19 vaccines.

Richard Lessells, a specialist in infectious diseases at the KwaZulu-Natal Research Innovation and Sequencing Platform, or KRISP – the group of scientists who sequence the South African variant – said that its discovery coincided with another worrying development: doctors reports more patients, including health professionals, testing positive for Covid-19 a second time after having it in the first wave.

“We are really concerned, and therefore we need to do the research to understand this variant as quickly as possible,” Dr Lessells said.

Dr Lessells and doctors treating Covid-19 patients in South Africa said they had not yet been able to prove whether these repeated positive tests were true reinfections – which according to many scientists are extremely rare – or the revival of an earlier disease. . South Africa’s public healthcare system generally only tests people who have Covid-19 symptoms.

To complicate the problem, most South African laboratories do not store coronavirus test samples for more than a few weeks, which means that it is almost impossible to ascertain whether a new infection results from another variant of the virus.

Excessive health workers are at high risk of getting Covid-19 a second time because of exposure to sick patients and because stress can weaken their immune systems.

A liquor store in Johannesburg was closed on Tuesday in a week when South Africa recorded its one millionth case of Covid-19.


phill magakoe / Agence France-Presse / Getty Images

“What we’re looking at is a very dark hockey here, where no one understands what’s in it,” said John Black, who heads the Infectious Diseases Division at Livingstone Hospital in Port Elizabeth. the city hit hardest by the second wave of South Africa. . Dr. Black said a small number of his patients tested positive again, more than three months after their first positive test.

At Tygerberg Hospital, the main public hospital treating coronavirus patients in Cape Town, doctors see both patients and healthcare professionals test positive again within three months of a previous infection, a spokesperson said. What doctors do not know, she said, is whether these recurring positive reactions are due to true reinfections, or that some people carry the virus longer. Health officials are currently investigating whether they can isolate the new variant of the new test samples, the spokesman said.

An in-house doctor at another public hospital in Cape Town interviewed by The Wall Street Journal said four of her fellow students recently tested positive for a second time after getting Covid-19 early in the first wave. Another doctor at a maternity hospital in another South African hotspot said she herself tested positive again this week after having Covid-19 symptoms for the second time since August.

A document outlining a new coronavirus testing strategy, released on Tuesday by the Western Cape province – one of the regions where the new variant is currently believed to dominate – warned of the risk that people catch Covid-19 for a second time. .

“Concerns about the greater likelihood of transmissibility and the possible resistance to neutralizing antibodies suggest that a second infection with Covid-19 is more likely than previously predicted,” says the document viewed by the Journal.

Doctors in South Africa do not know whether repeated positive test results are due to reinfection or to people who carry the virus longer; a mobile test unit at OR Tambo International Airport on Wednesday.


luca sola / Agence France-Presse / Getty Images

According to the document, people who show Covid-19 for a second time after recovering from a previous infection should be tested again after 30 days, rather than waiting for the 90 days previously advised. It says that people who test positive again should also receive an antibody test to confirm whether they have a true second infection, because an antibody test can indicate whether a patient is acutely infected and or antibodies due to an older disease is.

Meanwhile, South African researchers are developing a live version of the new virus, which will be used to test how the new variant responds to blood drawn from people who have recovered from a Covid-19 infection and from people who ‘ received a Covid-19 vaccine. . “We should know more within a week or more,” Dr Bhiman said.

Like the British variant, the South African variant has an extremely large number of mutations, including eight on the ear protein through which the virus attaches to and infects human cells. One of these mutations, called 501Y, is the same mutation that scientists in the UK have said could make the variant contagious.

Another, called E484K, showed in laboratory tests that it increased resistance to laboratory-made antibodies and serum from the blood of recovered Covid-19 patients, said Dr. Lessells said.

“The mutation probably changes the formation of the protein, so that the antibodies cannot grip it well,” said Dr. Lessells said. But even if more advanced tests on the live virus confirm antibody resistance, he adds, Covid-19 vaccines should elicit a broader immune response that goes beyond antibodies.

Dr Lessells and other researchers also stressed that measures such as wearing masks and social distance will still stop the spread of the new variant.

South African researchers believe that the new variant probably originated in the coastal city of Port Elizabeth, which was hit hard by the first and second wave of infections. One theory is that the extraordinarily large number of mutations could be caused by a long-term infection suffered by an immunocompromised person, such as a patient undergoing chemotherapy.

“There is strong evidence that this new variant originated as a result of immune pressure,” Dr Bhiman said.

Port Elizabeth and other regions where the new variant is now believed to be dominant have had a large number of people with antibodies due to earlier coronavirus infections during the first wave. Dr Bhiman said it may have contributed to making the new variant dominant over variants of the virus that do not have these mutations.

Write to Gabriele Steinhauser at [email protected] and Benjamin Katz at [email protected]

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