Southern Africa hoped it was through the worst of Covid-19. Then the Delta variant arrived

By David McKenzie, CNN

Patients are crammed into every corner of the hospital’s emergency room ward. They lie on beds and gurneys, or sit slumped in wheelchairs. Many suck on oxygen, but nobody talks. Some die while waiting for a bed.

On the worst nights in Johannesburg, currently in the grips of a terrible wave of infections, medics at one hospital must turn away ambulances carrying Covid-19 patients. It may be a diversion order more common to mass casualty events, but 16 months into the pandemic here, Covid-19 is a mass casualty event.

“It’s devastating, it’s soul destroying. We are trained to save lives, but you revert to that wartime mentality. You revert to becoming numbed, you revert to becoming blunted,” said a senior doctor at a major public hospital in South Africa’s largest city.

“Patients are being brought in in cars with desperately ill patients who have been turned away from other hospitals with no beds.”

Like many healthcare workers CNN has spoken to during the crisis here, they did not want to be identified for fear of reprisals from the government.

“The third wave has been far more devastating, far more overwhelming,” the doctor said.

The disease is no respecter of status, with authorities announcing Friday that the city’s mayor had died of Covid-19 in hospital.

“It is my sad duty to confirm that the Executive Mayor of the City of Johannesburg, Cllr Geoffrey Makhubo has indeed succumbed to Covid-19,” said acting Executive Mayor and Member of the Mayoral Committee Eunice Mgcina via the official Twitter account of the city’s authorities.

“We had hoped that the Executive Mayor would beat the virus and return to work and lead the city as we face this pandemic that has devastated lives and livelihoods. Our heartfelt condolences go to his wife, daughters, mother and the rest of his family, friends and comrades,” added Mgcina.

No more cheering

In the early days of the fight against Covid-19, South Africans cheered healthcare workers in neighborhoods across this city. Since then there have been more than 2.1 million confirmed cases in the country, and over 63,000 deaths — making it one of the worst-affected countries in the region per capita. Excess deaths suggest the toll is much higher.

The applause stopped months ago, but the impact of Covid-19 is at its worst right now.

Sixteen months into the pandemic here and doctors describe a system beyond its breaking point — with insufficient beds and barely enough oxygen. Sometimes the only time a bed opens is when a patient dies.

“There are patients that are dying while they are waiting to be seen, while they are waiting to go to the ward. Because the resources are just being overwhelmed by the onslaught of patients,” the doctor said, an assessment corroborated by paramedics and other physicians.

Sometimes patients will die when entering a hospital no matter what the level of care, they say. But this wave means tough choices have to be made and the best care can’t always be given.

The explosion of cases and deaths, as well as renewed lockdowns across the region have come as a surprise to many public health experts. With low rates of vaccination in South Africa, they did expect another wave, but some scientists thought that the very worst was over.

After all, the southern African region was hit by a first wave and battered by a second wave driven by the more infectious Beta variant discovered by South African scientists. The thinking was that a level of immunity in much of the population might dampen future spikes.

The caveat given was always that a new variant could emerge, but few anticipated an even more transmissible variant like Delta that would dominate so quickly.

“When you get a new variant, you can roughly think of it like getting a new virus. A lot of the progress you have made through people getting exposed will get reduced,” said Dr. Humphrey Karamagi, the leader of the World Health Organization (WHO) Africa regions data, analytics and knowledge team.

First discovered in India and responsible for an overwhelming spike in cases and deaths on the sub-continent earlier this year, the Delta variant is now present in countries throughout the world.

The variant has so far been detected in at least 10 African countries, with a high prevalence observed in southern and eastern Africa, according to WHO.

On Thursday WHO Regional Director for Africa Matshidiso Moeti said the variant continues to “gain speed and new ground in countries.” New cases on the continent have increased for the seventh consecutive week while vaccination rates remain low, said Moeti.

“Africa has just marked its worst pandemic week ever,” she said. And the situation is set to worsen.

“The next couple of months are going to be very difficult on the continent as we see the spread of the variant,” added Moeti.

The rapid spread of variants on the continent poses a major threat to Africa’s population, of whom 16 million have been fully vaccinated — less than 2% of the continent’s population, added Moeti.

Displacing and dominating

Karamagi said Delta’s greater transmissibility and its ability to reinfect people with previous Covid infections helped drive the spike in the region. And while countries like the United Kingdom are seeing surges in Delta infection, their widespread vaccination coverage should provide some protection from severe illness.

Vaccination coverage is still exceptionally low on the African continent — fertile ground for a new variant like Delta.

Countries have been hit by the slowdown in the vaccines coming from the COVAX vaccine alliance, because of India’s decision to stop importing to the facility. And, in South Africa’s case, a reticence to make bilateral deals with vaccine manufacturers early on.

“It was surprising how quickly the Delta variant took over,” said Tulio de Oliveira, who until recently led the team at KRISP, a genomics surveillance center in Durban. “The growth seems to be much, much faster than the Beta variant. Within weeks here it seemed to be dominating and displacing the Beta variant.”

Within hours of the variant’s discovery, the country’s Covid task force decided to put the country back into a strict lockdown, de Oliveira said. But by then, Delta was already raging in Gauteng province, much of the rest of the country, and the wider region.

Asked by CNN about the lack of space in hospitals and the deaths of patients while they waited for a bed, the Gauteng Department of Health responded by sharing presentations that show expanded bed space in the city over the past few months.

Private hospitals are also packed to capacity with surgeons and other non-physicians volunteering for rounds in the Covid-19 wards.

But doctors here blame a fire at one of the city’s biggest hospitals and the decision to close one of its major field hospitals at Nasrec before the third wave as significant failures. Also, beds need staff.

“Beds are just a piece of furniture, you need staff and oxygen, nurses and supplies,” said a physician who helped set up Nasrec and spoke on the condition of anonymity because they still work within the state sector.

Overcoming natural barriers

In recent weeks, one of the worst-hit countries in the world has been Namibia, South Africa’s neighbor to the northwest and a tragic example of the power of the new variant.

In 2020, Karamagi and his team of data scientists at WHO’s African headquarters in Brazzaville, Republic of the Congo, had predicted that Covid-19 would have a very different trajectory in parts of the continent than in countries like the US, Italy, and the UK, where cities were brought to their knees.

Unlike the dire predictions of a catastrophe in Africa, with Covid-19 overwhelming weak health systems, their modeling suggested a mixed picture with some countries escaping the worst because of a young population and so-called “socio-ecological” factors.

Namibia would seem an ideal example: A large country for its population of around 2.5 million, with a generally warm climate, and limited large-scale movement of people relative to other countries.

“Namibia has had three waves. The first two waves were quite small and health measures brought them under control. But this wave is very high. You can see the effect of the transmissibility of the virus,” said Karamagi.

The presence of the Delta variant was only confirmed by government scientists this week, but by then it was one of the worst-hit countries on earth, despite renewed lockdowns.

“At every hospital you have 25 to 30 people on a waiting list. The system is overloaded, prominent people are dying because they can’t get a bed,” said Dr. Danie Jordaan a well-known general practitioner who works in the country’s capital, Windhoek, and the coastal city Swakopmund.

“You have come to a point where they need to decide who will make it. Elderly patients are being pulled out of ICU knowing that it will kill them to give someone younger a chance,” he said.

In Windhoek, the state mortuary has been completely overwhelmed. Video clips seen and authenticated by CNN show bodies in white bags stacked three deep in the facility.

“What they are having to do now is use a rotation system, swapping bodies kept in the freezers overnight with those lying in the corridors in the morning and then doing it again in the afternoon to prevent thawing,” a person familiar with the operations at the mortuary told CNN.

Namibia’s presidential spokesman confirmed that the mortuary in Windhoek was at full capacity.

“Our mortuaries had been designed to deal with deaths under normal circumstances and we are now dealing with exceptional circumstances. This is not a challenge that is unique to us, COVID-19 has put pressure on health systems across the globe,” said Dr. Alfredo Hengari, adding that they have created additional capacity in order to deal with the emergency.

Making space when there is none

The situation is so bad in Namibia, doctors like Jordaan must resort to treating patients at home. The same is happening in Gauteng, the epicenter of this wave in South Africa, but just on a much larger scale. And sometimes home care is just not enough to keep sick patients alive.

“Delta has caused a whole lot of chaos, a whole lot of patients are suffering, their oxygen levels are dropping drastically daily — there are patients that are suffering and there is no space in hospital, there is no ventilators available. It’s complete chaos,” said Mohammed Patel, a paramedic with Pulsate EMS.

Patel and paramedics throughout the city are working with charity Gift of the Givers. In its warehouse, filled with the food and emergency supplies they deploy to crises all over the world, a team loads oxygenators into the back of a pickup.

They distribute them to patients across the province to lessen the load at hospitals. Covid-19 is unlike any emergency they have ever dealt with.

“The difference is when you go to a war zone or a natural disaster, you have an idea of the level of damage, what the disaster is. But this is very unpredictable. We have never seen anything like this before,” said Dr. Yakub Essack, the medical coordinator of Gift of the Givers.

But with hospitals at full capacity in both the public and private sector, the charity has gone a step further and built, in five days, a 20-bed clinic for patients who can’t find a bed.

Patel and his team enter a house in Lenasia, a suburb south of Soweto, to find a 67-year-old patient who tested positive for coronavirus 17 days ago. After he gets up to walk, an oximeter shows that his oxygen concentration levels drop into the 60s. Healthy adults should have a reading in the nineties.

“We are going to get you through, OK,” Patel tells the patient. He is the first patient to arrive at the community center-come-clinic attached to a mosque. Patel is confident he will make it now.

But in the hospitals across Johannesburg patients are still struggling through this Delta wave, and the doctors and nurses are suffering with them.

Doctors do say that sometimes patients won’t make it into the wards, even with the best facilities.

But just this week, the doctor we spoke to said that their hospital was struggling to wrap the bodies quickly enough to free up space.

“Patients are looking to us, they are relying on us to do our best, but it isn’t good enough. There is a that sense no matter how much I do, it is going to be the same thing tomorrow and the next day and the next day and the next day,” they said.

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CNN’s Bethlehem Feleke and Niamh Kennedy contributed to this story. Reporter John Grobler contributed reporting from Windhoek.