In November 2020 amidst the Covid-19 pandemic, Dr. Sikhulile Moyo and Prof. Tulio de Oliveira discovered the omicron variant. The two scientists shared their findings immediately with the World Health Organization (WHO). Yet, instead of being praised for their scientific achievement and due diligence, countries – among them the United Kingdom, the United States, and many European countries – reacted by putting in place harsh travel restrictions for Southern Africa. The negative effects, economic and otherwise, were felt strongly, while the measures themselves were ineffective, as the variant had already been circulating before the discovery. We spoke to the two scientists about their discovery and experiences.
Elisabeth Massute: First, congratulations to you both on your discovery and on receiving the German Africa Award 2022. The discovery of the Omicron variant was a milestone in the Covid-19 pandemic. At what stage did you two notice that the variant would be significantly different to the others and likely to be more transmittable?
Dr. Moyo: As part of usual quality assurance, we noticed that cases clustering away from lineages we have seen in Botswana and was not also seen elsewhere in Africa. We immediately alerted the Ministry of Health by email and called it “an unusual lineage”. We then shared our sequences in an international database (“GISAID”). We also discussed these findings with our colleagues in South Africa (Professor Tulio’s team) who had seen these same patterns. You could also immediately see the exponential rise in the number of cases – from below 5 percent of the population to above 15-20 percent. Looking at the mutations that were there, looking at the way the virus had changed, we used to get around 10 or fewer mutations, and now we were getting around 32 or more. Of course, some viruses had been studied before in terms of predicting transmissibility and others were not. Therefore, I think it was really apparent that this was a new type of lineage of the virus.
Dr. de Oliveira: What we do – and have done in the past – is that we look where that virus mutated from and make a big circle on the map. Then we request samples from around 100 different clinics from within a radius of a few hundred kilometers. Samples are then sent to my laboratory so that they can be sequenced very fast. We first noticed the variant with many mutations on a Tuesday afternoon, and immediately called an urgent meeting. By Wednesday morning the samples had arrived and we did all the sequencing. We found the same variants in over a hundred clinics at the same moment and knew this variant had the potential to spread fast. At that time, there were almost no Covid-19 infections in South Africa. We had followed the same procedures when we had the Beta and Delta variants but it was not the same. The other variants were widespread at the time of discovery. However, when we discovered the omicron variant there were only a few cases. We communicated our findings with the minister of health and highlighted that we had found the same variants in a hundred different clinics not related to each other and that that it looked serious.
The ministry of health then informed our president and WHO. The whole process – from looking at the initial virus to all the validation and characterizations, to communication with the government and WHO about it becoming a variant of concern – took less than 72 hours.
Both countries – South Africa and Botswana – did not have many infections at that time, but it was a very important time to prepare the hospitals in case the numbers should rise. And that’s what we did. What ended up happening is that we had a low mortality rate because we were alerted. The hospitals were prepared, and we rolled out booster vaccinations for the healthcare workers.
Dr. Moyo, what went through your head when you realized how the other countries were reacting, for example with travel bans, after you shared the information?
Dr. Moyo: I think that for me it was a rollercoaster ride because you think, as a scientist, you’re making a contribution to the community. It was really a surprise and a shock to see the response from the international community, to be honest. This was not expected after being almost 18 months into the pandemic. You expect that now that we are really global village in terms of public health and mode of transmission is well known that interventions will be coordinated between countries and regions to be effective. We know viruses do not respect the color of the passport you have, then it could be anywhere within a few hours – and that’s what exactly happened. It was already spreading in many other countries before it was detected in Botswana and South Africa. The virus could have come from anywhere. So, for our countries to be blacklisted within a few hours was definitely not the best approach and led to severe economic consequences and delays in health related commodities. My country was waiting for vaccines. And just imagine, in the middle of rolling out vaccines from your vaccine program, your flights are shut down, and you can’t get medicine and important goods because it is being hindered due to a virus, a variant, a lineage that already exists. I think that was unfortunate and I believe that no one wants to do that again.
And do you, Dr. de Oliveira, think that global leaders have learned from this mistake and the mistakes that were made in this pandemic? Not only regarding the travel bans, but also regarding the inequitable vaccine distribution that was just mentioned?
Dr. de Oliveira: Have global leaders learned from this? The answer is that we do not know. What we know is that politicians usually have a very short memory. At the moment, people are just trying to forget about the pandemic After the variant was studied, we saw that 80 percent of the Omicron cases in Africa were introduced from North America and Europe. It was exactly the opposite: We had blamed Africa for introducing the variant, and that would have been possible even if we had the travel ban, but it was the opposite. So when we detected the BA.4 and the BA.5 variants we didn’t get a travel ban. It seems like the world is learning that punishing a country for scientific discovery is not a smart idea. First, it does not stop pathogens, especially highly transmissible ones such as Covid. Second, you risk that countries and scientists that discover a pathogen will keep quiet next time. And that could derail global health. I think the main thing that the world has to learn is not to punish the discovery of pathogens, but the opposite: How to incentivize quick discoveries and learn the actions of pathogens and how to provide financial support and help. For example, help doctors and nurses respond to control epidemics while they are emerging because, in the end, that saves lives and can protect the global economy. Give courage and support to countries to help them make scientific discoveries that can be of global importance.
Do you think global leaders learned that changes need to be made in terms of vaccine distribution?
Dr. de Oliveira: This pandemic was characterized by an extreme level of nationalism, discrimination, and selfishness. We saw in the beginning of the pandemic hoarding of personal protection equipment and reagents for diagnostic tests and later the hoarding of vaccines: Countries such as Canada horded eight times the amount of vaccines it needed. And in the last few months, they have been dumping vaccine stockpiles that are soon to expire. What we learn is that when we have a global problem, a selfish and nationalistic response is ineffective. Countries in the European Union, the UK or the United States have waves and much more severe outbreaks because they were very selfish and forgot that if you have a global problem, a global response would be more effective. What we hope is that they learn from the process. We are just lucky because we have been working for decades against another very discriminated disease: HIV/AIDS. We have thick skin and we learned that quick identification, transparency, and activism can make a difference to save lives. We ended up saving hundreds of thousands of lives in our countries and helped the world to prepare due to a quick identification of variants, but we felt that we were not completely supported, but instead punished.
Dr. Moyo: We learned from working on HIV for many years. Look at Botswana and other countries in Southern Africa, the number of people they’ve managed to put on therapy, the levels of viral suppression – the elimination of HIV infections there is among the top in the world. So those regions should be incentivized with true collaboration. With very few resources, great science is happening there nevertheless. Africa is a region to invest in and do science. I think one of the lessons as well – in terms of vaccine production – is that Africa is beginning to wake up and say “Hey we can’t be depending on the Global North to purchase all the vaccines.” It will take us time, but I think we need to start doing things for ourselves.
Germany and other richer nations are now making investments in the expansion of vaccine production in African countries. They are positioning or handling intellectual property rights, such as for patents for example. So from your point of view on the pandemic, what needs to change, not only in terms of production, but also in terms of knowledge transfer to be able to ramp up that production more efficiently and more equitably?
Dr. de Oliveira: It’s good that we are, in fact, developing the infrastructure to produce mRNA vaccines in South Africa. I participated in the South African bid for the hub, which Germany has been a very strong supporter of. That’s one of the reasons why we are here for the award ceremony: to expand the support, collaboration, and relationship between Southern Africa and Germany to be able not only to produce vaccines, but also to quickly identify and characterize pathogens. We have a strong interest in what we call the “climate amplified” diseases and epidemics.
In relationship to intellectual property, it was really sad that after one of the biggest vaccine companies in the world made billions of dollars in profits, they decided that it was not enough. For me, that’s called human greed. They maintained all the patents and wouldn’t share. For example, instead of investing in or supporting technology transfer, one of the big companies became the biggest sponsors of the US Open tennis tournament, together with Rolex. It seems that they have a lot of money to spend on expensive sports events, but they had no interest in transferring their technology or supporting the development of vaccines and therapeutics, which has been restricted so far.
Most of the time, the vaccines were hoarded and didn’t get to Southern Africa and Africa in the first place. Other times, we had to pay more than the developed countries, all the new vaccines were being developed with Omicron lineages and sub-lineages that we discovered. So not only did they not support us financially or morally, but they openly punished us. Yet, they’re using our scientific discovery to produce vaccines that give companies high profits. We have to really think of a way to incentivize sharing of data that can be of crucial importance to the world.
Dr. Moyo, focusing on your work before Covid-19 – which was during the age of AIDS, mostly on AIDS as far as I’ve read – what would you say HIV should have taught us in this pandemic in terms of being better prepared for Covid-19? And do you see parallels from your work?
Dr. Moyo: One of the most important lessons was to set up a pathogen genomics platform that was responsive in real time to HIV, and not only for HIV but for other pathogens as well. We learned a lot in terms of making sure that we adapted the technology and developed methods to quickly sequence the whole of HIV. That technology was a tipping point for us in responding to Covid-19. But we also learned with HIV how to make sure that our findings don’t remain in the lab and that we remain at the forefront of the public health response. For the first few cases of Omicron, for example, within 24 hours that cluster was investigated. We wanted to be helpful from the start, so we gathered information of the entire country using similar systems that were built on HIV.
I think that is how we learned to be transparent with data and I think it’s important for building trust. The international community knows that if we discover something, we wouldn’t hide it in the lab. That’s an important lesson that we learned as well from HIV.
Dr. de Oliveira, Covid-19 is not our only problem. I would also like to ask about your other work – the effects of the climate crisis on public health. Why do you think these developments are so dangerous? And is this the next big problem that we are facing as a global community?
Dr. de Oliveira: Not only is it the next big problem, but it’s a big problem everywhere in the world, but particularly in the Global South. For example, one of the reasons why our team could do so well with genomic surveillance on SARS-CoV-2 is because we participated in the response from all the emerging epidemics in Brazil and South America. We had very large outbreaks of Zika, Dengue. We have had the worst outbreaks of yellow fever in the past 100 years in Brazil, in the West Nile. These are viruses that are not very well known by the public yet, but these are viruses that have been amplified by climate change or climate extreme events.
We see that these pathogens are spreading around the world, but we also see that they are evolving and can potentially start using another mosquito, called the culex mosquito, which is very widespread. We are going back to what we did for years in the response to emergent viruses in Latin America, Brazil, and Africa to now create a global network to try to work together – not just in the Global South. This network should be led by the Global South because they’re the ones who have experience in responding to these kinds of epidemics. We hope that we have shown the world with SARS-CoV-2, for example, that we can identify variants more quickly than in the rest of the world or through the experience on the ground of the clinical staff.
One thing that we know is that our environment is being damaged very quickly, but also that this damage is helping pathogens to spread further and evolve. That’s how we can help the world.
Coming to the last question, you both touched on this a couple of times already, but in Germany, at a societal and political level, there are still many blind spots and even ignorance, I would say, when it comes to the expertise of African scientists and researchers. Do you think that by winning this award, through your popularity with your discovery, that you can contribute to a growing visibility of African expertise?
Dr. Moyo: Definitely. We appreciate the German Africa Foundation because I believe that there were many people in the world nominated to receive the prize. For us to be chosen was a demonstration of the recognition that there is science happening in Africa, and we demonstrated the highest scientific integrity. We didn’t hoard the data. Not once, not twice, but from Beta in South Africa to Omicron and to BA.1 to BA.4/BA.5, we still released the data, even after we were punished and showed the highest level of scientific integrity: from modest resources to high-level science in generating massive amounts of data in Africa. Not only that, we also demonstrated through collaborations in African countries that we can work together, meaning that we are open to working with the Global North. But what’s important is to do the science where we have the most infections. I think that’s part of the discussions that we’re having this week. Of course, we have a lot of infectious diseases, and in other areas we are given benefits from the Global North. Having true collaborations on both sides is very important. The German Africa Foundation and the people of Germany have noted that there is so much work being done in Africa. There are so many contributions being made to the new vaccines, Omicron-adapted vaccines. Where’s that data coming from? I think that’s a true testimony that there is true science happening in Africa. It can only get better with more resources, investment, and true collaboration on both sides.
Dr. de Oliveira: We know that there is much discrimination against Africa and that many members of the public and politicians and even fellow scientists would not believe that Africa can contribute to science. Personally, I do not think that South Africa can lead on the production of rockets or satellites or GPS, because those things have been developed for decades in the Global North. But on infectious diseases, we have much more experience than the Global North. For example, the labs at Stellenbosch University are potentially some of the most advanced labs in the world for studying infectious disease pathogens.
In summary, there are three areas in which I believe Africa can lead in science in the world: infectious diseases, human genomics, and biodiversity. It would be a wake-up call to the world to realize that this is for their own advantage because we can help to protect the whole globe. As our example shows, countries can be discriminated against. They can put up borders, they can build fences, but viruses, bacteria, and pathogens will not respect them.
Thank you so much for your time. Congratulations again on your discovery. All the best for your future research, and thank you for telling people about it.
Dr. Sikhulile Moyo is Laboratory Director at the Botswana-Harvard AIDS Institute Partnership (BHP) and is Research Associate with the Harvard T.H. Chan School of Public Health. The BHP is the leading national institution for HIV/AIDS research, training, and capacity-building in Botswana. Specializing in the human immunodeficiency virus HIV, Moyo, who grew up in Zimbabwe and moved to Botswana 25 years ago, has made a number of significant contributions to studies on the prevention of mother-to-child transmission of HIV during his career. In addition, he has been responsible for monitoring HIV incidence, and has conducted research on HIV mutations associated with drug resistance. Thanks to this work done by the Scientists at the Botswana Harvard AIDS Institute Partnership, their laboratory was able to perform real-time genome sequencing in the wake of the Corona pandemic.
Prof. Tulio de Oliveira is Director at the Centre for Epidemiology (CERI) at Stellenbosch University; Director and Co-Founder of the KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) at the University of KwaZulu-Natal; and Director of the South African Network for Genome Surveillance (NGS-SA). Born and raised in Brazil, de Oliveira attended the Nelson Mandela School of Medicine at the University of KwaZulu-Natal, where he obtained his master’s and doctorate. A bioinformatician, he is one of South Africa’s leading researchers and embodies the face of South African excellence in his field in various capacities, including as professor of bioinformatics at the School for Data Science and Computational Thinking at Stellenbosch University and as lecturer at the College of Health Science at the University of KwaZulu-Natal.