Study: Clinical severity of SARS-CoV-2 Omicron BA.4 and BA.5 lineages in South Africa. Image Credit: CROCOTHERY/Shutterstock

Severity of Omicron BA.4/BA.5 lineages in the South African population

In a recent study posted to the Research Square* preprint server, investigators assessed the clinical severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants.

Study: Clinical Severity of SARS-CoV-2 Omicron BA.4 and BA.5 Lines in South Africa† Image Credit: CROCOTHERY/Shutterstock


The Network for Genomic Surveillance in South Africa (NGS-SA) discovered the new SARS-CoV-2 Omicron BA.4 line in January 2022 and BA.5 in February 2022. These lines were responsible for the arrival of the fifth wave of SARS-CoV-2 infections. Several studies have estimated that the BA.4 and BA.5 lines multiply faster than BA.2. In addition, compared to the BA.1 and BA.2 lines, these BA.4 and BA.5 have been shown to reduce serological neutralization in individuals vaccinated with three doses of the coronavirus disease 2019 (COVID-19)- vaccines.

About the study

In the current study, researchers evaluated the disease severity of infections caused by SARS-CoV-2 Omicron BA.4 and BA.5 lines.

The team conducted a data-linking study in which they obtained individual-level national information from the national COVID-19 case data, SARS-CoV-2 lab test data, and an active surveillance system called DATCOV that monitored data related to hospitalizations due to COVID. -19 in South Africa. The dataset was limited to tests performed with the TaqPath™ COVID-19 Assay.

The team used a combination of the absence of the SARS-CoV-2 spike (S) gene resulting in S gene target failure (SGTF) or the presence of the S gene resulting in S gene target positive (SGTP). according to a period of time according to circulating variants or lineages found through genomic surveillance. The SGTP COVID-19 infections observed between October and November 2021 were categorized as Delta infections, and those between February and April 2022 were categorized as BA.2 infections, while SGTF COVID-19 infections observed between November and January 2022 were categorized as BA. 1 infections, and those found in April 2022 were categorized as BA.4 or BA.5 infections.

The team assessed risk factors for COVID-19-related hospitalization and serious illness in patients hospitalized as a result of COVID-19, comparing BA.4, BA.5 and Delta infections with BA.1 infections. The analysis was performed by controlling for factors related to hospitalization and severity.


The study results showed that a total of 884,379 COVID-19 cases were detected between October 1, 2021 and April 26, 2022. Of those, 16.3% were diagnosed through the TaqPath COVID-19 test. Furthermore, the team noted that based on the presence or absence of the S gene, the SARS-CoV-2 Delta variant caused 1.3% of infections, BA.1 76.6%, BA.2 20 .3% and BA. 4 or BA.5 caused 1.8% of infections.

Among adults 25 years and older, 76.2% of total cases were Delta infections, 81.6% were BA.1, 66.5% were BA.2, and 78.7% were BA.4 or BA.5 . Among children aged five to 18 years, 24.7% of total cases were BA.1 infections, 14.5% were Delta, 9.1% were BA.1, and 13.2% were BA.4 or BA.5 .

Of the COVID-19 patients requiring hospitalization, 13.5% were diagnosed with Delta infections, 4.0% BA.1, 3.3% BA.2, and 4.8% BA.4- or BA .5 infections. In addition, the number of reinfections detected was 9.7% for BA.1, 9.3% for BA.2 and 11.7% for BA.4 or BA.5 patients, compared to 2.9% for Delta patients .

Of the SARS-CoV-2 infected patients whose infecting variant or lineage was known, 3.9% were hospitalized. In addition, 33.4% of patients with known disease outcome developed severe COVID-19 infection, including 57.7% Delta, 33.7% BA.1, 26.2% BA.2 and 27.5% BA.4 or BA.5 patients.

Multivariate analysis showed that compared with BA.1 infection, the probability of developing serious disease was higher in Delta, lower in BA.2, and comparable with BA.4 or BA.5 infection. In addition, compared with patients between the ages of 19 and 24, individuals between the ages of 40 and 59 and 60 years of age were more likely to develop serious disease. Notably, the odds of developing serious disease were lower in women and in individuals who had received one or more doses of the COVID-19 vaccine.

Overall, the study results showed that patients infected with the SARS-CoV-2 Omicron BA.4 or BA.5 lines had a comparable risk of developing serious disease and hospitalization as BA.1-infected patients. The researchers believe the current study could be helpful in planning health care resources and developing vaccination policies.

*Important announcement

Research Square publishes preliminary scientific reports that have not been peer-reviewed and therefore should not be considered conclusive, should guide clinical practice/health-related behavior or be treated as established information.

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