Scientists modelling SARS-CoV-2 variant transmission dynamics in South Africa find common characteristics related to transmissibility and immune evasion, according to their report published today in eLife.

Their findings highlight the need for more proactive planning and preparedness for future variants of concern (VOCs), including the development of a universal vaccine that can block SARS-CoV-2 infection as well as prevent severe disease.

As with many places, by February 2022, South Africa had experienced four distinct pandemic waves caused by the original (or ancestral) SARS-CoV-2 virus and three VOCs — Beta, Delta and Omicron.

“These repeated pandemic waves have been driven by new VOCs that erode prior immunity from either infection or vaccination, increase transmissibility, or a combination of both,” explains study author Wan Yang, Assistant Professor of Epidemiology at Columbia University Mailman School of Public Health, New York, US. “Although laboratory and field studies provide insights into variant epidemiological characteristics, quantifying the extent of immune erosion and changes to transmissibility for each VOC is challenging.”

To better understand the characteristics of the different COVID-19 VOCs, the team developed a mathematical model using weekly case and death data from nine South African provinces, from March 2020 to end of February 2022, to reconstruct SARS-CoV-2 transmission dynamics.

They validated their model using three independent datasets and found that estimated cumulative infection rates roughly matched serology data over time, and the estimated number of infections matched with the number of hospitalisations for all four pandemic waves caused by the ancestral, Beta, Delta and Omicron variants. Modelled infection numbers also matched with death rates from the ancestral, Beta and Delta waves, but less so for Omicron, because by this stage prior infection and vaccinations reduced the number of infected people suffering from deadly outcomes.

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