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What South Africa is seeing in its omicron outbreak

One of the country’s top health journalists on omicron, early case and hospitalization data, and the West’s travel bans.

Medical scientists prepare to sequence Covid-19 omicron samples at the Ndlovu Research Center in Elandsdoorn, South Africa, on December 8. The center is part of the Network for Genomic Surveillance in South Africa, which discovered the omicron variant.
Jerome Delay/AP

Mia Malan has been covering the emergence of the new omicron coronavirus variant from the ground in South Africa.

She is the editor-in-chief at the Bhekisisa Centre for Health Journalism, which focuses on solutions-based health analysis and reporting in South Africa — a position that gives her firsthand access to the country’s pandemic data and the South African scientists and health leaders who are on the front lines. Her Twitter threads have been essential as the world races to find answers to some of the big questions about the variant: How transmissible is it? How dangerous is it? How do vaccines hold up?

So far, the data and the anecdotes point to cautious — cautious — optimism on the most important question of disease severity. Some hospitals say a lot of the people who have been classified as hospitalized with Covid-19 were actually being admitted for something else. Fewer patients so far are ending up in the ICU on oxygen, compared to prior waves. Primary care doctors also say their patients seem to recover quicker.

“Of course, that’s anecdotal, but that’s the general feeling,” Malan told me in an interview over Zoom. “That line is pretty consistent across the country. There hasn’t been an institution that’s come out and said, ‘No, it’s completely different in severe cases.’”

But the one thing everybody also says: “We need more data.” Any optimism about more mild illness is tempered by the early indications that omicron transmits faster than the delta variant that is currently dominant in the US and much of the world. The average number of daily new cases in South Africa has shot up, from 350 on November 1 to 13,500 on December 8, and the great majority of new analyzed cases are the omicron variant.

With 55 percent of the global population, and 40 percent of the US, still not fully vaccinated, a lot of people are vulnerable if a more contagious version of the virus starts spreading widely.

The South African government is ramping up the incentives, both the carrots and sticks, to get people vaccinated. The health department was rocked by a corruption scandal in the middle of Covid and trust in institutions has fallen generally, allowing misinformation to flourish, Malan says; the country has inoculated about 31 percent of its overall population, much less than the US and most of Europe.

But while South Africans scramble to reassess their holiday plans and scientists seek answers to omicron, the country is also enduring travel bans from the United States and wealthy European countries. That includes the UK, which South Africa hoped would be the source of travelers and expats coming to the country to enjoy a summer Christmas.

That is a blow to families hoping to reunite and to the country’s economy. Travel bans also make it harder for South African scientists to get the supplies they need to conduct their research on omicron, as Malan reported in a recent story.

Our conversation is below, edited and condensed for clarity and length.

Dylan Scott

How would you describe the situation in South Africa right now compared to prior waves? What is the government doing to respond?

Mia Malan

There is a lot of confusion currently, because of the timing of this wave. It arrived just as people were making their holiday plans. It’s the big annual holiday of the year, and people are not sure what to do now. We don’t know everything about this variant yet. Should they go to the places they booked or should they stay? Most people didn’t have a holiday last December, and they really wanted to go. People thought things were going back to normal now and clearly that’s not the case.

This is also our first wave with a fair proportion of people vaccinated, about a third of adults. Now there’s a division emerging between people who want to be vaccinated and those who don’t. Vaccinated people tend to accuse unvaccinated people of making the environment unsafe for them. Unvaccinated people talk more about: “What are my rights?”

But our government strategy is changing. Last December, we just locked down again. This time around, we have vaccines now. So you either lock down the country or you say people can move around and you make sure they’re safe. That can be done with vaccines.

The vaccination rate is not increasing at the rate the government would like it to increase, so they are starting to do things like incentives. They initially had vouchers, equivalent to about $7. But that was too small, so they’ve doubled them now. They’ve started with more pop-up sites.

But the big thing now is regulation, which is going to be vaccine mandates.

A man looks into his vaccination card as people wait in line to receive their Covid-19 vaccines in Johannesburg, South Africa, on December 8.
Emmanuel Croset/AFP via Getty Images

Dylan Scott

With the caveat that it will still take more time to reach confident conclusions, what are the most important data points on omicron so far, in your view?

Mia Malan

The complexity with the data at the moment is it’s so early on in the outbreak. The one thing we can’t yet say is how sick are people going to get. It looks like they’re not getting so sick, but it takes time to get sick and die and we have not had enough time for them to die yet, essentially. It’s really the beginning of the data.

We do have data from Gauteng province, where the outbreak in South Africa started, and we have more data from our version of the CDC, the National Institute for Communicable Diseases. Both sets of data show that hospitalized patients are younger. People above 50 were admitted mostly to hospitals previously, now there are more people younger than 50.

What we don’t know yet is: Is this because of how omicron affects young people or is it because younger people are less vaccinated than older people in South Africa? Is it that older people don’t get sick because they’re vaccinated and it’s just the younger people left?

Or is it because during the time omicron started to circulate, young people were still in school? They were the people who congregated. It started in universities. Because omicron is so transmissible and they were in groups, was it easier for the virus to reach them?

One interesting thing about the data from a hospital system in the Gauteng province is three-quarters of the patients who were admitted in the first two weeks to hospitals in the area had no idea they had Covid. They went there for something else. That is an indication there weren’t symptoms. We could then think there are a lot of asymptomatic cases and it might cause milder disease.

We’re also seeing, in terms of the age profile in Gauteng, that the youngest patients between zero and 5 years old are becoming a larger proportion of admissions. We don’t yet know why that is. But what’s interesting is of those kids who got admitted, almost all of their parents were unvaccinated. We don’t yet know what that means, but it’s something our CDC points out. And among teenagers who get admitted, they’re almost all unvaccinated.

We know for a fact it’s spreading faster. But we don’t know yet what proportion of cases is people getting Covid for the first time and what proportion is reinfection, which means the variant is escaping the immune system at least to some extent.

Based on the new Pfizer data and South Africa’s hospital admission data so far, it does look like any immunity escape has a lot more effect on protection against infection, as opposed to protection against falling significantly ill. Our scientists think omicron is unlikely to have a big impact on the latter, based on prior variants that didn’t really reduce the effectiveness for serious illness.

Dylan Scott

In terms of disease severity, with the same caveat that it’s early, what’s the attitude among the medical establishment in South Africa?

Mia Malan

There’s a lot of anecdotal evidence, some general practitioners will go on TV and talk about their patients. Almost all of them would say they are seeing patients that are far milder, that recover quicker. Hospitals are saying people are being discharged sooner, fewer people need oxygen, fewer people end up in ICU, with far fewer complications, and far lower death rates.

Of course, that’s anecdotal, but that’s the general feeling. That line is pretty consistent across the country. There hasn’t been an institution that has come out and said, “No, it’s completely different in severe cases.”

I think we’re going to start to see a lot of lab data, not just from us but from everywhere. That’s the one thing everyone says: We need more data.

Dylan Scott

What about kids? How worried are your public health officials about them?

Mia Malan

They just don’t know. Nobody really knows what the reason is.

What is comforting, however, is in the Gauteng cases, none of the kids died. They did not fall very seriously ill. And they mostly got admitted because they had other illnesses. Something else was wrong with them.

Experts think this could be another indication of how transmissible the variant is. Because in the previous waves, they did not get this level of incidental Covid patients. It could be so transmissible that these hospitalizations are just a reflection of the fact that so many people have already contracted it.

I would love to give you a certain answer. But no one knows.

Dylan Scott

You’ve reported recently on the travel restrictions imposed on South Africa. What have the consequences been for the country?

Mia Malan

A travel ban means our economy in terms of tourism is severely impacted. The time you choose to go to a country is summer generally and a holiday. That is the time now in South Africa, and a lot of people from Europe were going to come here, especially people from the UK. All of those things have been canceled, and hotels have to give their money back.

Then there is the family impact. We have lots of first- and second-generation South Africans who came from Britain, and that means they can get a passport, and that means many of them have moved there for various reasons. There’s a lot of South Africans in England. They couldn’t visit their families last December, now they can’t get in this year. It’s people who see their children once a year or once every two years. And all of that is gone.

I also think colonization has had such a large aftereffect. The way in which people from Western countries are used to treating people from Africa and other developing countries is really atrocious. It’s a lot of pretending that we’re partners, equal partners, but we’re not. If the one half has the money and the other half receives the money, it’s hard to have an equal partnership.

But the way in which the Western world has behaved with vaccines is not okay. It’s a symptom of what’s already there. I find it outrageous a Western country can justify the hoarding of vaccines by arguing they also donate vaccines to less developed countries. France will let one of their own people who passed through here off the plane, but not an African. Canada won’t accept our PCR tests.

To be treated like this, it’s patronizing. The Western world must consciously change their behavior. The way that you treat the African countries is a reflection of what you really think. And I’m a very privileged person in South Africa. With whiteness comes a lot of privilege. If you’re Black in Africa, there is so much discrimination against you and so much counting against you.

I think it would be wonderful if we used Covid to change that a bit. Will it change? I don’t think so. I think it’ll just continue how it’s always been.

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