Why South Africa gets so many Covid-19 variants of concern
One possible reason South Africa presents Variants of Concern of the coronavirus that causes Covid-19 might be because of the high number of people with severely compromised immune systems in the country.
Virology experts told The Conversation that despite an advanced antiretroviral treatment programme for people living with HIV, numerous individuals in South Africa have advanced HIV disease and are not on effective treatment.
The assumption is that some degree of “immune pressure” (which means an immune response that is not strong enough to eliminate the virus yet exerts some degree of selective pressure which “forces” the virus to evolve) creates the conditions for new variants to emerge.
While scientists do not know for sure, and much remains to be learnt, several clinical cases have been investigated that support this hypothesis.
It should be noted that new information about the recently-discovered Omicron variant is being released at a rapid rate, and the article below was written before the World Health Organisation had officially designated the variant with its Greek letter name.
An Omicron variant case was also subsequently reported in Belgium that was reportedly detected in a young woman travelling from Egypt who had no known links to South Africa.
According to the BBC, Belgian media reported that the patient was unvaccinated, had travelled from Egypt via Turkey, and developed mild flu symptoms 11 days after landing.
The original article from The Conversation is reproduced below.
Since early in the COVID pandemic, the Network for Genomics Surveillance in South Africa has been monitoring changes in SARS-CoV-2. This was a valuable tool to understand better how the virus spread. In late 2020, the network detected a new virus lineage, 501Y.V2, which later became known as the beta variant. Now a new SARS-CoV-2 variant has been identified, known as B.1.1.529. To help us understand more, The Conversation Africa’s Ozayr Patel asked scientists to share what they know.
What’s the science behind the search?
Hunting for variants requires a concerted effort. South Africa and the UK were the first big countries to implement nationwide genomic surveillance efforts for SARS-CoV-2 as early as April 2020.
Variant hunting, as exciting as that sounds, is performed through whole genome sequencing of samples that have tested positive for the virus. This process involves checking every sequence obtained for differences compared to what we know is circulating in South Africa and the world. When we see multiple differences, this immediately raises a red flag and we investigate further to confirm what we’ve noticed.
Fortunately South Africa is well set up for this. This is thanks to a central repository of public sector laboratory results at the National Health Laboratory Service, (NGS-SA), good linkages to private laboratories, the Provincial Health Data Centre of the Western Cape Province, and state-of-the-art modelling expertise.
In addition, South Africa has several laboratories that can grow and study the actual virus and discover how far antibodies, formed in response to vaccination or previous infection, are able to neutralise the new virus. This data will allow us to characterise the new virus.
Again, we do not know. The known cases include individuals who had been vaccinated. However we have learnt that the immune protection provided by vaccination wanes over time and does not protect as much against infection but rather against severe disease and death. One of the epidemiological analyses that have commenced is looking at how many vaccinated people become infected with B.1.1.529.
The possibility that B.1.1.529 may evade the immune response is disconcerting. The hopeful expectation is that the high seroprevalence rates, people who’ve been infected already, found by several studies would provide a degree of “natural immunity” for at least a period of time.
Ultimately, everything known about B.1.1.529 so far highlights that universal vaccination is still our best bet against severe COVID-19 and, together with non-pharmaceutical interventions, will go a long way towards helping the healthcare system cope during the coming wave.
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