Study estimates prevalence of SARS-CoV-2 omicron breakthrough infections in South Africa

By Dr. Sanchari Sinha Dutta, Ph.D.Jul 27 2022Reviewed by Aimee Molineux

In an article recently published in The Lancet journal, scientists have described the prevalence of vaccine breakthrough severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa during the period of delta and omicron variant circulation.

Background

The most recently emerged omicron variant of SARS-CoV-2 has been declared a variant of concern (VOC) by the World Health Organization (WHO) on November 26, 2021. Soon after its first detection in South Africa, the variant has transmitted exponentially across the globe, eventually replacing the previously circulating delta variant and sharply increasing the number of coronavirus disease 2019 (COVID-19) cases.

Because of its heavily mutated spike protein, the omicron variant exhibits significantly higher transmissibility and immune evasion ability. Studies conducted in real-world settings have revealed that the variant is capable of escaping COVID-19 vaccine-induced immunity, leading to a sharp increase in breakthrough infections worldwide.

In the current study, the scientists have estimated the prevalence and clinical outcomes of breakthrough SARS-CoV-2 infections in South Africa during delta and omicron circulation.

Study design

The study enrolled healthcare workers in 360 vaccination centers across South Africa. A total of 477,234 participants received a single dose of the adenovirus vector-based COVID-19 vaccine (Johnson & Johnson) between February and May, 2021. In addition, a total of 230,488 participants received a second dose of the vaccine between November and December, 2021.

The study primarily determined the prevalence of vaccine breakthrough infection and COVID-19 related hospitalization and mortality in the study population between February 2021 and January 2022. The breakthrough infection was defined as laboratory-confirmed SARS-CoV-2 infection 28 days or more after vaccination.

Important observations

The study estimated the prevalence of breakthrough infection during the first 74 days of delta and omicron circulation when the participants received a single dose of the vaccine.

The findings revealed that the number of daily infections was 3-fold higher during the omicron period than that during delta period. Similarly, a significantly higher prevalence of breakthrough infections among participants was observed during the omicron period compared to that during the delta period.

The average duration between initial vaccination and detection of breakthrough infection was 98 days during the delta period and 259 days during the omicron period. A significantly lower risk of hospitalization was observed among men and elderly people during the omicron period compared to that during the delta period.

Regarding preexisting health conditions, a 1.5-fold higher probability of having human immunodeficiency virus (HIV) infection was observed among hospitalized participants with breakthrough infection during the omicron period. In contrast, a lower probability of having hypertension and diabetes was observed among participants during the omicron period compared to that during the delta period.

Overall, the proportion of hospitalized participants needing intensive care, oxygen supplementation, or ventilation was lower during the omicron period compared to that during the delta period. The average duration of hospital stay was also significantly lower during the omicron period.

Study significance

The study demonstrates that the omicron variant of SARS-CoV-2 is associated with more vaccine breakthrough infections in South Africa than the delta variant. However, omicron infections are less severe than delta infections in terms of hospital admission and requiring intensive care, oxygen supplementation, or ventilation.

A reduced disease severity observed among healthcare workers during the omicron period could be attributed to a high level of preexisting immunity against SARS-CoV-2 (about 68% seroprevalence) due to vaccination or infection. Thus, this observation is specific to a population with high seroprevalence and might not be generalized to all populations worldwide.   

A sharp increase in breakthrough infections observed during the omicron period could be due to declining vaccine effectiveness or higher infectivity and immune fitness of the omicron variant.

As mentioned by the scientists, the study has certain limitations. Since the study has considered only the first 74 days of the omicron period, the findings might not reflect the full effect of the variant.

Furthermore, there might be an overestimation of the prevalence of COVID-19-related hospitalization among healthcare workers with breakthrough infection because some of the patients received incidental COVID-19 diagnosis while hospitalized for other reasons.