A study published within 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
Background
The omicron variant of SARS-CoV-2 was detected for the primary 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.
In comparison with 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 present 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. Each 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’ve recreated the landscape of herd immunity in South Africa before the emergence of the omicron variant, in addition to determined the impact of the omicron wave in the identical 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 in the course of the study period.
At enrollment (baseline), the seroprevalence of anti-SARS-CoV-2 nucleocapsid antibodies was 1.1% in the agricultural region, which increased to 7%, 25%, and 39% after the primary (D614G), second (beta), and third (delta) waves, respectively. The infection rate was almost 60% on this region.
Within the urban region, the seroprevalence was 14% at enrollment, which increased to 27%, 40%, and 55% after the primary, second, and third waves, respectively. The infection rate was almost 70% on this region.
Dynamics of viral RNA shedding
Household exposure to the virus primarily will depend on the degrees of viral RNA shedding amongst relations.
The evaluation of viral RNA shedding dynamics revealed that every one three variants have similar characteristics, represented by a brief proliferation stage and an extended clearance stage.
The prevalence of symptomatic infection amongst household members was 13%, 16, and 18% for SARS-CoV-2 D614G, beta, and delta variants, respectively. The height viral shedding timing coincided with the timing of symptom onset, indicating that significant viral shedding occurs before symptom onset.
Further evaluation revealed that symptomatic infections are characterised by high viral load. The very best 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 within the proliferation stage than within the clearance stage. The delta variant showed the best 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 primary three months, which reduces to 87% after nine months.
The bottom risk of infection was observed amongst older adults aged over 65 years in the course of the D614G wave. Throughout the delta wave, the chance was highest amongst children and adolescents aged 6 to 18. As well as, an increased risk of infection was observed amongst obese individuals and people residing in urban regions.
Impact of omicron wave within the urban region
The scientists developed mathematical models to judge the trajectory of omicron waves in addition to the viral dynamics within the urban region.
The model projections revealed that omicron has a growth advantage of 0.338 per day over delta. The fundamental reproduction number was also higher for omicron. As expected, a better infection rate was observed in the course of the omicron wave than during previous waves. Greater 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 grasp 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 wouldn’t be sufficient to forestall a recurring omicron epidemic unless previous omicron infections induce robust and sturdy protection.
Considering a 100% higher contact rate, the models predicted that if it reemerged, omicron might cause outbreaks no matter the protection induced by prior omicron infections. Overall, these predictions indicate that an induction in touch rates may result in the emergence of recent waves attributable to pre-existing or novel viral variants.