South Africa and Africa could become a hotbed of new SARS-CoV-2 variants if we don't take care, a top bioinformatician at Stellenbosch University (SU) has warned.
Speaking at the Annual Academic Day of SU's Faculty of Medicine and Health Sciences (FMHS), Professor Tulio de Oliveira said that unlike other countries, South Africa had experienced “very distinct waves" of infection, each of which allowed the virus to evolve further.
De Oliveira, who recently joined the university to set up a new institute aimed at understanding and controlling epidemics and pandemics, received international acclaim for his team's work of identifying a new variant of the virus in South Africa. As professor of bioinformatics, he will hold a joint appointment in three different environments – the School of Data Science and Computational Thinking, the FMHS and the Faculty of Science. He will establish a new national institute – provisionally named the Centre for Epidemic Research, Response and Innovation (CERI) – to advance the understanding of epidemics in Africa and the global south.
In his address entitled Emergence and Spread of New Variants of SARS-CoV-2, De Oliveira said the Network for Genomic Surveillance in South Africa, had started producing genomes as early in March and had even sequenced the first case in the country. The team have continued to produce genomes throughout the various waves of the pandemic.
Through its research the team has also found evidence that prolonged infection in immunocompromised individuals is one mechanism for the emergence of new SARS-CoV-2 variants.
They have also demonstrated that there are “multimutational escape variants" in an individual with advanced HIV and prolonged failure to take antiretroviral therapy (ART), and that the replication of SARS-CoV-2 in the body was terminated shortly after the introduction of effective ART.
For this reason, De Oliveira recommended that people with HIV should be on effective ART, particularly if they also acquire Covid-19.
“People living with HIV should be prioritized for Covid-19 vaccination, and more research is needed to optimize vaccination strategies for people with advanced HIV and other immunosuppressive conditions," he said.
The need to prioritize Covid-19 vaccination in people living with HIV is so important that he and his team had informed both the South African president and the health minister about it.
“It is going to be very important to also increase the ART program and HIV diagnosis as soon as possible," he stressed.
De Oliveira said the first wave of the pandemic had created sixteen novel lineages of SARS-CoV-2 in South Africa. These had usually been created by superspreader events in the country. The team had been able to learn how the variants emerged, how they were introduced into South Africa and how they spread.
“In November-December 2020, a new lineage emerged that completely dominated infections in South Africa and went to displace all the other lineages present in the country. This lineage not only dominated all the infections, but it spread extremely fast."
Similarly, the second wave had also seen a large number of mutations which gave rise to a new lineage of the virus and allowed it to be more transmissible in humans as well as in animals. New lineages also emerged during the third wave. “This virus surprises us every week."
De Oliveira said there are now multiple cases in the literature of prolonged infections in immunocompromised individuals.
“We have learned that SARS-CoV-2 evolved very fast in a suppressed host." An examples of this had been found in a paper from Boston in the United States of a long-infected individual that could not clear the virus for at least 150 days, and that, when sequencing the virus, had found a “large accumulation of mutations … that was characteristic of various variations and mutations. Another individual in the United Kingdom had shown a similar case, and who is believed to have “caused the alpha variant there."
In South Africa, De Oliveira and his team studied a 36-year-old female patient with Covid-19, who was also HIV-positive and had “really bad adherence to ART". She stayed positive for Covid-19 for 216 days, during which there had been a “massive evolution" of the virus.
“What we saw in this individual is that this virus is not only mutating, but gaining and losing mutations. This indicates that if you have individuals that cannot clear the virus for so long – especially if they are immune suppressed – you are going to allow this virus to evolve very fast inside them which can give rise to new variants."
This had led to the conclusion that there is good evidence that prolonged infection in immune-compromised individuals is one of the mechanisms for the emergence of SARS-CoV-2 variants.
“If we do not take both the HIV and SARS-CoV-2 epidemics in South Africa and Africa seriously, we may risk that Africa can become a factory of variants," he said.
Photo credit: PIXABAY
