Summary Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have been key drivers of new pandemic waves of coronavirus disease 2019 (COVID-19). To better understand the variant epidemiological characteristics, here we apply a model inference system to reconstruct the transmission dynamics of SARS-CoV-2 in South Africa, a country that has experienced three VOC pandemic waves (i.e., Beta, Delta and Omicron BA.1) by February 2022. We estimate key epidemiological quantities in each of South Africa’s nine provinces during March 2020 to February 2022, taking into account changing detection rates, seasonality of infection, non-pharmaceutical interventions and vaccination. Model validation shows that the estimated underlying infection rates and key parameters (e.g. infection detection rate and infection mortality risk) are in line with independent epidemiological data and research. Additionally, hindcasts capture pandemic trajectories beyond the model training period. These detailed and validated model inference estimates enable quantification of both the immune erosion potential and transmissibility of the three major VOCs of SARS-CoV-2, i.e., Beta, Delta, and Omicron BA.1. These findings help elucidate the changing dynamics of COVID-19 and inform future public health planning. |
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A model of COVID-19 dynamics in South Africa reveals the epidemiological characteristics of the main SARS-CoV-2 variants of concern and highlights their potential to cause new outbreaks.
Their findings highlight the need for more proactive planning and preparation for future variants of concern (VOC), including the development of a universal vaccine that can block SARS-CoV-2 infection and prevent severe disease.
Like 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 infection or vaccination, increase transmissibility, or a combination of both,” explains study author Wan Yang, assistant professor of epidemiology at the Mailman School of Public Health. from Columbia University, New York, USA. “Although laboratory and field studies provide information on variant epidemiological characteristics, quantifying the extent of immune erosion and changes in transmissibility for each VOC is challenging” .
To better understand the characteristics of 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 the end of February 2022, to reconstruct the transmission dynamics of the SARS-CoV-2.
They validated their model using three independent data sets and found that the estimated cumulative infection rates roughly matched the serology data over time, and the estimated number of infections matched the number of hospitalizations for all four pandemic waves caused by the ancestral variants, Beta, Delta and Omicron. The modeled infection numbers also matched the mortality rates of the ancestral, Beta, and Delta waves, but less so for Omicron, because at this stage prior infection and vaccinations reduced the number of infected people suffering fatal outcomes.
Using data that emerged at the time of the new variants, Delta and Omicron, the model was also able to retrospectively predict the Delta and Omicron waves before the real-life spike in cases and deaths caused by these VOCs. The team found that the model accurately predicted the remaining trajectories of cases and deaths in most of the nine provinces.
After validating their model, they used it to estimate the epidemiological characteristics of each VOC, including infection detection rates, infection mortality rates, population susceptibility and transmissibility, and compared these dynamics across provinces. These “model inference estimates” were then used to quantify immune erosion and increased transmissibility for each VOC.
They found that the Beta variant eroded immunity among about 65% of people previously infected with the ancestral SARS-CoV-2 and was 35% more transmissible than the original virus. This finding was supported by the experience of previously infected participants in one of the vaccine trials, who had a similar susceptibility to the Beta variant as those who had no previous infection.
Estimates for Delta varied between provinces, but overall the variant eroded immunity from prior infection or vaccination by about 25% and was 50% more transmissible. This aligns with a reported reinfection rate of 27.5% observed during the Delta wave in Delhi, India.
Finally, for Omicron, estimates varied but consistently highlighted its higher known transmissibility than previous VOCs. The authors estimated that Omicron was approximately 95% more transmissible than ancestral SARS-CoV-2 and eroded immunity by 55% (previous infections and vaccines).
These results illustrate that high prior immunity to SARS-CoV-2 does not exclude new COVID-19 outbreaks, as neither prior infection nor current vaccination completely blocks infection of a new variant.
Multiple SARS-CoV-2 variants of concern and interest have emerged in the two years since the pandemic began, and it is challenging to predict the frequency and direction of future viral mutation, especially levels of immune erosion, changes in transmissibility and innate diseases, say Yang and co-author Jeffrey Shaman, professor and director of the Climate and Health Program at Columbia University’s Mailman School of Public Health.
They add that so far, VOCs except Alpha have produced some degree of immune erosion, and later VOCs, such as Delta and Omicron, are more genetically distinct from earlier variants, making them more capable of causing reinfection despite various prior exposure and vaccination. Given this pattern, the authors suggest that a universal vaccine that can block SARS-CoV-2 infection and prevent severe disease is urgently needed.
