Study explores relative reproduction of SARS-CoV-2 omicron variant in South Africa

Recently, a rapidly growing variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appeared in the Gauteng province of South Africa, named Pangolin B.1.1.529 (Omicron). Omicron, which quickly replaced the circulating Delta and other variants, contains as many as 32 remarkable mutations in the tip protein. It was reported that the new variant was identified two months after its emergence – at the end of November 2021. On in December, this pathogen spread globally – spanning 50 countries with genome monitoring capacity.

The Omicron spread in South Africa remained consistently low before the new variant replaced the Delta variant. The reason behind the new epidemic can be explained via examines the transferability of the omicron variant.

Study: Relative reproduction rate of SARS-CoV-2 Omicron (B.1.1.529) compared to delta variant in South Africa.  Image credit: Fit Ztudio / ShutterstockExamination: Relative reproduction number of SARS-CoV-2 Omicron (B.1.1.529) compared to Delta variant in South Africa. Image credit: Fit Ztudio / Shutterstock

A recent study published in Journal of Clinical Medicine presented a modeling result from an analysis of genome monitoring data in the province of Gauteng, South Africa, using an existing estimation technique.

The study

Here, genome monitoring data from the Gauteng province as registered for the Global Initiative on Sharing Avian Influenza Data (GISAID) at the end of November 2021 were used. The study assumed that the effective reproduction number of the Omicron variant – Romicron

The present study was primarily funded by the Japan Agency for Medical Research and Development, among others.


The results showed that Romicron

Transmission benefits of Omicron

Assume that ω the faction was immune at the beginning of the ongoing epidemic in South Africa and €delta

A similar equation applies to the Omicron variant. Then the immune protection against the Omicron variant – €omicron, induced by acquired immunity, in the current scenario, is estimated at €omicron = 1 / ω {1 – k (1 – €delta

The €omicron is probably very small – about 10-20%. It is possible that the transmission advantage of Omicron over Delta could have been obtained by Omicron’s escape mechanism from existing immunity in the population.

Data suggest a reduced neutralization potential against the Omicron variant among previously vaccinated individuals along with an increased incidence of reinfections. However, a four times higher infection rate solely due to increased transmissibility is unlikely.

In addition, Omicron has a significant transmission potential to penetrate the existing flock immunity gained through mass vaccination in many countries. Still, several questions remain unanswered:

  • The clinical severity of infection across age groups and among different populations with underlying health conditions.


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