What is the impact of the SARS-CoV-2 omicron wave in South Africa?

A study published in the journal Science Translational Medicine has described the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), population-level immunity, and the impact of the omicron wave in South Africa.

Study: SARS-CoV-2 transmission, persistence of immunity, and estimates of Omicron’s impact in South African population cohorts. Image Credit: PHOTOCREO Michal Bednarek/Shutterstock


The omicron variant of SARS-CoV-2 was detected for the first time in South Africa in November 2021. Before its emergence, South Africa experienced three distinct waves dominated by wildtype SARS-CoV-2 with D614G mutation, beta variant, and delta variant, respectively.

Compared to previously circulating viral variants, omicron exhibits a heavily mutated genome, making the variant immunologically superior to evade population-level pre-existing immunity (herd immunity) induced by prior infections and vaccination.

In the current study, scientists have determined the long-term dynamics of SARS-CoV-2 in two household groups from a rural and an urban region in South Africa. Both groups were followed over 13 months.

Specifically, the scientists have estimated the robustness of cross-reactive immunity induced by consecutive waves of SARS-CoV-2 variants. They have recreated the landscape of herd immunity in South Africa before the emergence of the omicron variant, as well as determined the impact of the omicron wave in the same population.     

SARS-CoV-2 epidemiology in South Africa

The study was conducted in a rural region and an urban region situated in two South African provinces. The study population included 1200 individuals living in 222 households. Only 10% of the study population were fully vaccinated during the study period.

At enrollment (baseline), the seroprevalence of anti-SARS-CoV-2 nucleocapsid antibodies was 1.1% in the rural region, which increased to 7%, 25%, and 39% after the first (D614G), second (beta), and third (delta) waves, respectively. The infection rate was almost 60% in this region.

In the urban region, the seroprevalence was 14% at enrollment, which increased to 27%, 40%, and 55% after the first, second, and third waves, respectively. The infection rate was almost 70% in this region.

Dynamics of viral RNA shedding

Household exposure to the virus primarily depends on the levels of viral RNA shedding among family members.

The analysis of viral RNA shedding dynamics revealed that all three variants have similar characteristics, represented by a short proliferation stage and a longer clearance stage.

The prevalence of symptomatic infection among household members was 13%, 16, and 18% for SARS-CoV-2 D614G, beta, and delta variants, respectively. The peak viral shedding timing coincided with the timing of symptom onset, indicating that significant viral shedding occurs before symptom onset.

Further analysis revealed that symptomatic infections are characterized by high viral load. The highest viral load was observed in delta infections, followed by beta and SARS-CoV-2 D614G infections. Notably, household members with previous infections exhibited significantly reduced levels and duration of viral shedding upon reinfection.

Risk of SARS-CoV-2 primary infection and reinfection

A positive correlation was observed between household exposure intensity and risk of SARS-CoV-2 infection. This association was stronger in the proliferation stage than in the clearance stage. The delta variant showed the highest infectiousness, followed by beta and D614G variants. 

Regarding the protective efficacy of pre-existing immunity, the findings revealed that prior infection provides 92% protection against reinfection for the first three months, which reduces to 87% after nine months.

The lowest risk of infection was observed among older adults aged over 65 years during the D614G wave. During the delta wave, the risk was highest among children and adolescents aged 6 to 18. In addition, an increased risk of infection was observed among obese individuals and those residing in urban regions.

Impact of omicron wave in the urban region

The scientists developed mathematical models to evaluate the trajectory of omicron waves as well as the viral dynamics in the urban region.

The model projections revealed that omicron has a growth advantage of 0.338 per day over delta. The basic reproduction number was also higher for omicron. As expected, a higher infection rate was observed during the omicron wave than during previous waves. More than 40% of the omicron infections were expected to be reinfections and vaccine breakthrough infections.

Using a reference scenario for Omicron’s immune evasion characteristics, the impact of the omicron wave was estimated. The findings revealed that the ratio of omicron versus delta basic reproduction number is 2.4, the infection rate is 69%, the wave duration is 32 days, and the proportion of reinfections and vaccine breakthroughs is 68%.

To understand the robustness of omicron-induced immunity against existing and future variants, mathematical models were developed to project the degree of protection under different exposure conditions (contact rates).

Considering the contact rate of the delta wave, the models predicted that the degree of herd immunity would not be sufficient to prevent a recurring omicron epidemic unless previous omicron infections induce robust and durable protection.      

Considering a 100% higher contact rate, the models predicted that if it reemerged, omicron might cause outbreaks irrespective of the protection induced by prior omicron infections. Overall, these predictions indicate that an induction in contact rates may lead to the emergence of new waves caused by pre-existing or novel viral variants.

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