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First detected in South Africa, omicron cases are rising rapidly there


South Africa alerted the world to the omicron COVID variant last week. Since then, case counts have reached nearly 3,000 a day in South Africa. Professor Wolfgang Preiser is head of medical virology at Stellenbosch University. He and his team are closely tracking the variant, and he spoke with me from South Africa about what they've learned.

Why are we seeing these variants of interest in South Africa in particular - omicron this year, beta last year? What's the reason for that?

WOLFGANG PREISER: One potential explanation might, of course, be that we are looking very actively. We have the system in place. We are doing it systematically across the country. So I think the chances of anything slipping through are very slim. So we would see it if it is there, and we do see it.

One of the hypotheses why, perhaps, South Africa is prone to generating new variants is we are the country with the world's largest population of HIV-positive individuals. And even though our antiretroviral drug treatment program is fairly advanced and fairly successful, that still leaves tens of thousands of individuals immunosuppressed. And we have seen, in our lab and in other labs, that patients with profound immunosuppression who become infected with the SARS coronavirus are often unable to clear that infection. And therefore, the virus keeps replicating within these individuals. The immune response is not able to clear it. It's too weak.

This is, I have to stress, at this stage, pure speculation. It's a hypothesis. But we have by no means proven neither that this new variant, omicron, actually originated in South Africa, nor have we demonstrated that it actually originated in the way that I just described, in a long-term HIV-infected individual.

MARTÍNEZ: Professor, what's the makeup, if you know, of the people who are being infected? Are they vaccinated? Are we talking about reinfections here?

PREISER: I don't have a very good overview of that. The reason being that, you know, we sequencing labs around South Africa are frantically analyzing samples as we speak. What I do know is that these early outbreaks in Gauteng were largely younger people and therefore also healthier people that one would not expect to be at high risk of severe infection. And, indeed, from the information available so far, most of the cases seem to have rather mild course, which is, of course, good. Does, however, not mean, by any means, that this virus is not able to cause also severe disease should it affect people who belong to the risk groups.

Otherwise, our vaccination rate is very low, unfortunately. Therefore, it's probably likely that it would have infected also vaccinated individuals. Whether those are more likely to become infected through a breakthrough infection than with another strain of the virus, I cannot say at this stage.

MARTÍNEZ: Has omicron overtaken other variants in South Africa? Is it the most dominant one?

PREISER: Not yet, to my knowledge. But again, we are observing a highly dynamic situation. And in my own province here in the Western Cape - that's the area around Cape Town - we found the first case of omicron in a sample dated about two weeks ago. And from then, it has been spreading so much that - on the background of still very low numbers, but we fear that a fourth wave is coming. It now constitutes the majority of newly infected people. So it looks as if its transmission dynamics is very high.

What we saw, almost to the week, a year ago is the emergence of the beta variant here in South Africa. It overtook the previously predominant virus strains and became our majority virus and, in turn, was displaced earlier this year, by the arrival of the delta variant. So we've seen this before, that new variants may be better at spreading in the human population and may displace previous ones.

MARTÍNEZ: I saw how President Cyril Ramaphosa says that South Africa won't be adding new restrictions, but he's putting an emphasis on vaccinations. He's talking about making it mandatory in some places. Professor, is that the best path forward? Is South Africa's current response good enough?

PREISER: As scientists, we are concerned that over the past few weeks, we have been quite lax with our restrictions. So clearly, there is a need to strengthen that. The vaccination is, of course, the key. I know that everyone will never be vaccinated. But when a very large proportion is vaccinated, the risk for these variants to emerge and also the risk they pose should they emerge, it would be vastly diminished.

MARTÍNEZ: The United States and the European Union have imposed travel restrictions, and even countries in Africa, such as Rwanda and Angola, have done the same. Are travel bans effective on this?

PREISER: I can sympathize with the knee-jerk reaction that if you hear there is something new and potentially nasty, you want to keep it out. The problem is that South Africa, at this stage, feels very much the victim of their own good deeds. We have this surveillance system. We have maximum openness. The results were publicized the moment we were sure about it. And this is actually enabling other countries to look out for it.

But the effect is that the travel bans are devastating now our second tourism season for international tourists. I would very much hope the world can move to a cleverer system. I think a good regime of travel checks, testing before flying, at arrival and maybe shortened quarantine with obligatory negative PCR before release would be as effective as these very blunt total travel bans that cause a lot of damage and are not very precise instruments.

MARTÍNEZ: Professor Wolfgang Preiser, head of medical virology, Stellenbosch University. Professor, thank you.

PREISER: It was a great pleasure. Thank you very much, indeed. Transcript provided by NPR, Copyright NPR.

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