Prof. Walter Jaoko’s responses to media queries on the new Omicron virus during an AfriSMC press briefings on What Scientists know about the new Covid-19 variant. Prof Jaoko is the Director KAVI-Institute of Clinical Research, University of Nairobi

 Why is the new variant called Omicron?

The naming of these variants are based on the Greek alphabets. So why is this one called Omicron? If you look at the Greek alphabet it starts with Alpha, Beta, Gamma, Delta and so on. Then the next two Greek alphabets were Nu and Xi. But Nu was skipped because it can confuse with new so the World Health Organization (WHO) did not want people to confuse this variant with a “new” virus so they skipped Nu. The next Greek alphabet was Xi but it was skipped because Xi is a common Chinese name so for example the Chinese premier is known as Xi Jinping and WHO did not want to have any offence to cultural, social, national or ethnic groups. And the next Greek alphabet after Xi is Omicron, and it’s for that reason that the current variant of concern is called Omicron.

What do the scientists already know about the Omicron variant?

The genetic number that the Omicron variant has been given is B.1.1.529. It was first identified in South Africa on 25th November 2021. It’s actually disputable whether it was identified in South Africa or Botswana because the samples were from both countries. To date, there are over 60 countries that have reported Omicron cases. In some countries, like Kenya, Rwanda, Saudi Arabia, Belgium, Nigeria, Ghana, Israel, and many other countries, it has just been identified amongst travelers. However, there are some countries where there is evidence of local transmission. By this we mean there are people who’ve not gotten into contact with anybody who has travelled from Southern Africa, but they have been identified as having been infected by the Omicron variant. The countries include the UK, the US, Canada, India, Spain, Australia, Germany, Norway, Iceland and a few other countries.

Originally, researchers had seen about 30 mutations but now there is evidence that there could even be up to 50 mutations on the spike protein. The spike protein is the structure that the virus uses to attach onto a human host and, therefore, infect the body. Most of the vaccines currently in use are based on this spike protein to be able to develop what we call an immunogen. This is what is injected into the body as the vaccine and then the body produces antibodies to fight the suspected infection. Many mutations raise possibility that the variant might escape either the current natural immune responses that are generated after becoming infected and recovering from infection or that are generated from getting the vaccine. If this happens there might be reduced efficacy of treatment even with antibodies.

There is something called use of convalescent plasma, where somebody who has become infected with COVID-19 and recovers, their blood is taken and used to produce their plasma, that is rich in antibodies against the virus, and which is then used to treat people with severe COVID-19 disease. So, if there’s enough mutation on the surface of the spike protein, then we will not be able to use convalescent plasma that contains these antibodies to treat people with severe COVID-19 disease. It is also possible that if there’s sufficient changes on the spike protein, it might even be able to avoid detection using the diagnostic techniques that we currently have. Scientists are investigating this possibility.

Is Omicron more dangerous than other COVID-19 variants

Delta quickly overtook all its predecessors in the world; but Omicron is more transmissible than all the other variants. It is possibly causing more severe disease in unvaccinated people than the previous variants, but at the moment there is no evidence that Omicron is more lethal. In fact, it seems to be even less lethal than the Delta. And if this is proven to be the case, it is actually a good thing that we can have a less lethal variant coming to displace the more lethal one. However, studies are still going on to show whether this is the case. At the moment, there is no evidence to show that the Omicron variant will outsmart the current COVID vaccines that are being used globally.

Looking at the infections we were having from the three waves in South Africa, by the beginning of December, the infections were really going down and then they started rising up with the emergence of Omicron variant. So, it seems that the transmission of the Omicron variant is actually more aggressive, and it is responsible for the current wave in Southern Africa. Specifically, in South Africa, the Omicron variant is now the dominant variant, having displaced the Delta variant.

We’ve seen a sharp increase in COVID cases in the last one month. We have also noticed that there seems to be an increase in the number of new infections among people who have already previously been infected and recovered. Although we know that people can be re-infected with COVID-19 more than once, the numbers usually are much less compared to what we are seeing now with the Omicron variant.

We also know that although Omicron variant seems to be spreading much faster than the Delta variant, it seems to cause milder illness compared to the Delta variant. Delta variant had severe presentation including loss of taste and smell but the Omicron variant currently, seems to only present as cough, sore throat but not with difficulties in breathing, and no loss of taste and smell associated with Delta variant. These are early or preliminary findings. We need to gather more information to prove that is the case.

However, it should be noted that the number of people being infected in South Africa are mainly young people who are less likely to become severely infected. The question to ask is what if Omicron begins to infect older population, will the symptoms remain as mild as being seen currently? We also know that most people who have been hospitalized with Omicron are people who have not been fully vaccinated. This may suggest that vaccination is still preventing people from getting the variant.

Will the current approved vaccines be effective against Omicron?

It is unlikely that the Omicron variant will not respond to COVID-19 vaccines. This is because the vaccines that have been developed for COVID-19 stimulate two arms of the immune response in the body. They produce antibodies that fight the infection but also produce what we call T-cell response. This is cellular immune response which produces white blood cells that attack the virus infected cells in the process killing both the virus and the infected cell. So, because mutations are happening in the spike protein, it might blunt the antibody response but will not blunt T-cell responses. Thus, it is envisaged that the vaccine will continue to work either partially even if it is affected or it will work fully because the cellular arm of the immune response is not affected unlike the antibody responses. This has been seen with the previous mutations. For example, in South Africa, when the Beta mutant was found not to be responding to the vaccine, it wasn’t that the response was zero, it’s only that it was lowered. One of the things we know for sure is that with regards to preventing severe disease and death, the vaccines work irrespective of the mutations. Therefore, unless Omicron behaves differently, it is expected to behave similarly.

Are there any ongoing studies on the new variant?

We are doing more studies as scientists to get more evidence to show whether this Omicron variant is more transmissible. We have some evidence from South Africa but we need to see whether this is replicated all over the world. We also need to know whether there’s any evidence developing that it might cause severe disease. At the moment we know that symptoms are less severe than the Delta variant, but we’ll continue to observe and to do investigations to see whether that remains the case.

With regards to vaccines we still need to check and be sure that the vaccines are effective. What we know up to now is that they are still effective against severe disease and death from all the variants identified so far. We therefore have no reason to doubt that they will continue to remain effective against the Omicron variant.

We also need to check if there’s any escape in detection of infection. We know that the PCR test that is currently being used is able to detect all infections, including Omicron. But, we are not sure yet about the ability of other tests, such as the antigen detection technique being used also in clinical practice, to remain effective in detecting the variant. We need to continue doing investigations and studies to see whether these other tests are also still effective in detecting Omicron variant.

With regards to COVID-19 treatment, there is no change. This remains the same globally. Nevertheless, we need to keep on doing studies to see whether Omicron variant, or any other variant for that matter, still respond to the current treatment regimes.

Will people who have already been vaccinated require boosters to fend off Omicron?

As mentioned earlier, vaccines that we have currently stimulate two arms of the immunity, namely, the cellular and humeral/antibodies responses. It is for this reason that none of the vaccine we are currently using has been shown not to be effective against any of the mutations we have had so far.

The worst that can happen from the evidence that we have so far is lowered but not lack of immune response. We are still doing more studies so it could be that this would be the first mutation that would escape vaccines. So far, we don’t have any evidence for that.

As we generate more evidence on the effectiveness of COVID-19 vaccine against this particular variant, there are two things that can happen in the event that we find the vaccines are not as effective. We can make a recommendation for a booster dose using current vaccines in the event that it is found that that there is inadequate protection by the generated immune responses.

The second thing for the vaccine manufacturers to do, is to tweak the vaccine we currently have so that we add additional immunogens. This is done by looking at the mutation on the surface of the variant and then designing an immunogen that when given to the body would stimulate antibodies targeting that part of the variant that has mutated. Pfizer and Moderna are already considering doing this.

Even though early studies show that it could be less severe, is there a danger that we might have more people with weak immunity getting infected and leading to more deaths?

We don’t know for sure. It is possible but we don’t have any evidence for that at the moment. For example, if that was the case South Africa also has a lot of elderly people and those with co-morbidities but Omicron variant has not been seen to cause severe diseases in these populations to an extra degree compared to the Delta variant.

These are still preliminary findings. Probably it will start doing that, but we do not know yet. We just have to keep on observing. South Africa is doing a splendid job in updating the world on what they are seeing. It is young people who are largely being infected and it is not causing severe disease in them. We’ll have to wait and see whether it will start changing and causing more severe disease and especially in people with lowered immunity.

How fast can they be able to develop the improved vaccines with enough immunogens to deal with this new mutant if at all there will be need for that?

That is the beauty of the platform that Moderna and Pfizer are using called the messenger RNA. It is a new technology that they can use to develop this very fast. In a matter of weeks.

Since scientists have found 50 mutations, does it mean that they are waiting for a variant to become dangerous so that they can alert us or they are always working on these new COVID variants before it gets dangerous?

Scientists are not waiting for a variant to become dangerous before they alert the world. Sequencing of every new infection involves looking at the genetic makeup of that variant. It isn’t that this Omicron has been mutating over time, so it has one mutation, then a second and you keep on counting and then you say now that it has reach more than 30, we report to the world. The sequencing done at once revealed the more than 30 mutations on the spike protein.

When such mutations are noted, the first questions that comes to mind is if these mutations are making the virus more easily spread, causing more severe disease or escaping vaccines. Mutations are not always bad, in fact, there are many infections that die out because of mutations. The variant changes but it can do so to its disadvantage. Some infections just die on their own even without a vaccine because the virus mutated but the new variant that came was less easily spread and was causing less severe disease.

It is therefore important to be aware that every time there is a new variant it does not necessarily mean that it is going to be more dangerous. But we cannot predict that until studies show that. It is always better to err on the side of caution.

Are the major vaccine manufacturers still studying it so that they can develop a vaccine?

Any vaccine manufacturer will be wasting their time and resources if they are developing a vaccine against something that is not easily spread, causing severe disease or hospitalization and even death. That is why scientists have to first of all see whether this particular variant is of that concern for manufacturers to develop a vaccine against it. There is no point just developing vaccines for every mutant that you see. First, it is not scientifically making sense and secondly, it is not economical. Why would you just develop a vaccine for something that would not require one? That is the wisdom of all vaccine manufacturers. It has to be something that requires development of vaccine.

In order to travel you have to be vaccinated, so for those travelers found positive of the Omicron variant, does it mean it escaped the vaccine?

It is not true that every country requires people to be vaccinated for travelling. But we should also remember that the purpose of the vaccine is not to prevent you from becoming infected. It is very important that scientists and reporters of science let the world, our audience, to always know that the primary purpose of vaccination is not to prevent us from getting infected with the virus. That is a bonus in the event that it occurs. Vaccines are said to be 95, 80 or 75 percent efficacious meaning that you still have a risk of becoming infected.

The aim of vaccination is to prevent you from getting severe disease that requires hospitalization, ICU treatment or ultimately causing death. Therefore, the fact that you have been vaccinated, doesn’t mean you will not be infected. Some of these people who have tested positive on arrival in airports of certain countries, only required one to be vaccinated to enter the countries and so there were people who had not been tested for COVID-19 in their own countries before travelling. However, with the coming of Omicron variant, they have now introduced an additional requirement for testing before travelling to these countries and in addition some countries now require testing of people on arrival. That is how the countries have found infected people.

Will countries shy away in reporting genomic surveillance for fear of being crucified like South Africa is?

The World Health Organization (WHO) said it has been totally unnecessary to crucify South Africa; there has been discrimination which is obvious. Some countries such as the Netherlands, Israel, Hong Kong and Belgium had people testing positive for Omicron but countries like the UK did not ban flights from those countries. So, the question that people are asking is why only South Africa was affected. And not only that, but why even countries neighboring South Africa where the variant had not been identified were affected. It is quite obvious to anyone that there is no scientific justification at all for the measure Western countries took against the Southern Africa countries.

Regarding shying away from reporting new variants, scientists are governed by ethics and are unlikely to keep such information to themselves just because of possible repercussions. In fact, South Africa has repeatedly been showing how the current COVID-19 wave is being driven by Omicron. If the country was afraid of what the world would do to or think about them, they would not be telling us how fast COVID-19 driven by Omicron variant is spreading in South Africa. When you find something that is important for the world, you cannot keep it to yourself. Doing that would not ethical. Although there may be governments that would not want their scientists to report emergence of new variants, I’m sure the scientists will do the right thing.

Is expert reaction on AstraZeneca being associated with clotting of blood pushing people to prefer other vaccines?

Previously on the same platform, I’ve given a number of press briefings on this issue of blood clots with regards to the AstraZeneca and Johnson & Johnson vaccines. As I said before, this issue has largely been exaggerated.

This issue of clots was largely reported in Europe, where blood clots are more common than other parts of the world even without getting COVID-19 vaccination.  Those getting the clots after COVID-19 vaccines were largely young people. However, the risk of getting blood clots after receiving a COVID-19 vaccine is quite low. Only two out of a million people vaccinated. Some drugs, such as female hormonal contraceptives, are associated with a much high risk of getting blood clots but we’ve never stopped using them. One needs to weigh the risks of getting side effects of the vaccine against its benefits and then decide for themselves whether to get vaccinated or not. The benefits by far outweigh the risk. We should remember that the best vaccine against COVID-19 is the one you have access to.

 We are yet to see any studies telling us about the side-effect of the vaccines on the people who have been vaccinated. Is there any research being done in Africa?

Actually, pharmacovigilance surveillance is being done repeatedly in Africa but mostly by governments. This is coordinated by ministries of health. Anybody receiving the vaccines are observed for 20-30 minutes, and before being released, they are asked to report any problem they may experience after that to a health facility, where there are forms that are filled and uploaded into the national surveillance system. Based on this information, we know that there have been very few people who have had side effects that prevented them from going to work. Majority of the people vaccinated have had only mild side effects such as pain at the injection site, mild fever, joint pains, headaches etc.

So far is there any data that shows whether the vaccines had any effects on children as well as pregnant and lactating mothers?

At first, we did not have evidence of the vaccines’ efficacy in children and lactating mothers because the groups were not included in clinical trials/testing of the vaccines. Children were excluded from these studies, and for women participate in the trials they had to be non-pregnant, use an effective contraceptive method to prevent getting pregnant, and to be non-lactating. However, more recent studies have shown COVID-19 vaccines to be safe in these populations. The issue of giving COVID-19 vaccines to pregnant women needs special mention. We know that pregnant women are at a greater risk of getting very severe COVID-19 disease, and it is, therefore, in their best interest to be vaccinated against the disease.

With regards to giving COVID-19 vaccines to children, it should be noted that initially the vaccines were tested in people aged 18 years and above except for Pfizer vaccine that included 17-year-olds. Since then vaccines have been tested in children. Initially this was done in children aged 12 years and above, and then in the younger children (5-11 years). They have been found to be safe in children. However, children are still not being given COVID-19 vaccines in resource-limited countries, such as Kenya, because these countries do not have enough vaccines to include them. For this reason, these countries are prioritizing vaccinating adults who are the ones at the greater risk of getting severe COVID-19 disease leading to hospitalization, ICU admission and death. When these countries get sufficient vaccines, they will include children in their national COVID-19 vaccination schedules.

There was a rallying call from Africa’s heads of state supported by the Africa CDC to come up with a vaccine, what is the status of Africa’s quest to develop its own vaccine?

The African Union recognizes that African countries don’t have resources and what they are trying to do is to put regional centres for making vaccines. The amount of money required for this is not easily available. What they are now thinking of is to have one hub in the East Africa region, another in the West Africa region, another in the North Africa region and so on. It is envisaged that this will enable countries to put their resources and expertise together and build the required infrastructure.

With this COVID-19, are we seeing more mutations in the future?

Yes, we’ll continue to see mutations. We need to understand that viruses always mutate. As long as we have transmission of SARS-COV, the virus that causes COVID-19, we will always have mutations. As to whether the mutations will cause variants of concern, that is a different issue. As to whether those mutations are lethal, more easily transmitted or escaping vaccines that’s a different story.

The only way to stop mutations is to stop transmission of the virus by applying known effective public health measure we’ve been talking about in addition to vaccination.

Lastly, what should countries do to contain Omicron?

Countries should continue to enhance surveillance, keep on sequencing any new infections that they have so that we can better understand the circulating variant. As long as the virus is being transmitted, we will continue to see mutations being developed. As long as the variant moves from one person to another, it will keep on making mistakes, and it will keep changing its surface. As a result, we will expect to see more variants.

We also need to report initial cases or clusters of infections in our respective countries to WHO. In this regard, South Africa should actually be commended for doing a lot of virus sequencing and alerting the world that there’s a new variant. South Africa should not be condemned because they were the first ones to identify the variant. The fact that you identify a variant in a country doesn’t mean that the variant started there. There are many countries that are not doing as much sequencing as South Africa and thus the world should not blame South Africa for being a source of the Omicron variant. It is not true that it is the source. Furthermore, each country should continue to do investigations, laboratory assessment to improve the understanding and the impact of any new variants, not only Omicron.

The world globally should address the inequities of access to COVID-19 vaccine because if we vaccinate people everywhere, transmissions will be reduced and the developments of variants of the virus would greatly reduce. It is the sure way of stopping the development of virus mutations.

But what should we do as individuals? This is a question I’ve been asked before. Should we change our public health measures? The answer is “no”. Wearing of well-fitted mask, washing of hands, physical distancing, use of proper ventilated rooms if you are staying or working indoors, avoiding crowded places, sneezing in the elbows and getting vaccinated are known public health measures that will stop transmission of any covid transmitting virus irrespective of the variant.

Compiled by Faith Atieno

Edited by Daniel Otunge and Sharon Atieno

Reviewed and approved by Prof. Walter Jaoko