With new Covid-19 variants being identified, FORBES AFRICA speaks to renowned bioinformatician Professor Tulio de Oliveira of KRISP to discuss South Africa’s role at the forefront in variant identification, and why there is hope on the horizon.
PROFESSOR TULIO DE OLIVEIRA is director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in South Africa, and at the coalface of research to combat the Covid-19 pandemic.
He is known for leading the team that first identified the Beta variant of the virus in December 2020 – the same team has identified another new variant currently termed C.1.2 here in South Africa.
Currently, the Variant of Concern dominating the rise in cases globally is the Delta variant, which has allowed massively increased transmissibility. Another Variant of Interest is the Mu, which is being closely followed by the World Health Organization (WHO).
Q. What is the difference between a Variant of Interest and a Variant of Concern?
A. When we look at variants, we as scientists keep a close eye on these changes because the mutations mean that it might have increased neutralization of vaccines, or for example be transmitted more quickly and take over. A Variant of Interest is one that we are interested in looking at because it’s a variant that seems to be growing, but it’s not definitive – the Lambda variant in Peru for example. The spread of this variant was relatively slow so it wasn’t upgraded to a Variant of Concern.
A Variant of Concern is the next stage in that mutations that a variant might have is allowing it to grow very quickly – such as the Alpha in Western Europe during the second wave, the Delta Variant here in South Africa, which is dominating the third wave of infections.
The new Mu variant has been identified as a Variant of Interest, but potentially, it may not become a Variant of Concern because it seems to be not as transmissible.
We also monitor lineages which you can think of as a third category; there are thousands and thousands of these, but we don’t define them as a variant because they are not spreading very fast.
We have a handful of lineages around the world being examined – such as C.1.2 – and if these progress, they will then become a Variant of Interest, then Variant of Concern.
Q. There are a number of Covid-19 variants around and many seem to be identified in South Africa – what is the reason for this?
A. We have variants identified for a few reasons. One is that you see more variants when there are higher levels of transmission. For example, no variants have
originated in New Zealand and Australia because their transmission rates are so low.
Another reason is virus transmission in immune-compromised individuals – we saw this in the Alpha variant in the United Kingdom with variants in cancer patients.
There is a similar suspicion that this might be the case with the Beta variant and C.1.2. in South Africa due to HIV [prevalence] – because someone’s immune system is already so low, once they are infected with Covid-19, this infection could last in them for a hundred days and the virus could evolve.
Obviously, another reason we think plays a role is the rate of vaccination – people who are vaccinated will clear the virus much more quickly so there is less likelihood of mutation.
Our ability to detect variants and identify them in South Africa is also because we have excellent funding and infrastructure for genomic surveillance. We have a history of TB, HIV – we’ve learned that this surveillance is very important in identifying the source of an epidemic and intervention. We have experience in working with epidemics and strong support for science and innovation – some of the best examples in the world are Denmark, Australia, New Zealand, the United Kingdom, and South Africa.
Q. If you had a message for people reading this, what would that be?
A. The main message I would have is that we should increase our rate of vaccination. We should also improve our HIV treatment program to make sure people who get infected can clear the infection.
It’s quite simple. You’ve got to know the enemy in order to fight. It’s important to identify the variants that spread more quickly so we can inform governments and guide the public health response. If a variant isn’t identified here, it will be identified when it is found somewhere else, and that can be even more damaging.