Severity of SARS-CoV-2 infections with Omicron BA.2 variant relative to the BA.1 variant in South Africa

In a recent study posted to the medRxiv* preprint server, researchers estimated the clinical severity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage relative to the BA.1 variant in South Africa.

The SARS-CoV-2 Omicron variant of concern (VOC) was first reported in South Africa in November 2021. Initial reports have suggested that the SARS-CoV-2 Omicron BA.1 variant was linked with a lower incidence of hospital admission and severe form of disease relative to the Delta infection.

Nonetheless, the recently emerged Omicron BA.2 sub-lineage has spread worldwide quickly, including in South Africa. The BA.2 sublineage replaced the BA.1 during the Omicron-driven fourth wave of the coronavirus disease 2019 (COVID-19) pandemic in South Africa and several other nations. However, in-depth data regarding the clinical severity of the Omicron BA.2 variant relative to BA.1 is not yet available.

About the study

In the present study, the scientists evaluated the severity of the SARS-CoV-2 infections with the Omicron BA.2 variant relative to the BA.1 variant in South Africa. 

The team performed data linkages for national COVID-19 case data, SARS-CoV-2 laboratory test data incorporating information from the public sector labs and a large private sector lab, and COVID-19 hospitalizations data at the individual level. Further, COVID-19-related hospitalization data was procured from DATCOV, an active tracking system for COVID-19-related hospital admission in South Africa.SARS-CoV-2 case and test data were collected on January 29, 2022, and COVID-19-related hospital admission data on February 10, 2022. 

The Omicron BA.2 variant lacked the 60 to 70 nucleotide deletions and was inferred as SARS-CoV-2 spike (S)-gene-positive on the TaqPath COVID-19 polymerase chain reaction (PCR) assay, whereas BA.1 had these deletions and was associated with S-gene target failure (SGTF) in the assay. Hence, the SARS-CoV-2 cases identified by the TaqPath COVID-19 PCR assay were classified as S-gene-positive and SGTF and served as a proxy for Omicron BA.2 and BA.1 variants, respectively, in the study.

Risk factors for hospitalization and disease severity of SARS-CoV-2 infections were estimated by comparing subjects diagnosed with the BA.1 and BA.2 variants from December 1, 2021, to January 20, 2022, using two multivariable logistic regression models.

Findings

The results show that 680,555 COVID-19 cases were reported between December 1, 2021, and January 29, 2022, in South Africa. Further, from December 5, 2021, to January 29, 2022, the percentage of S-gene-positive infections in South Africa rose from 3% to 80%. 

Of the 95,470 samples evaluated using the TaqPath™ COVID-19 PCR assay, 3.4% and 3.6% were hospitalized with SGTF and S-gene-positive infections, respectively. Further, the multivariable analysis indicates that the chances of hospitalization did not vary among subjects with the SFTG and the S-gene-positive infections after controlling factors linked with hospital admission in COVID-19.

Further, the factors associated with a high risk of COVID-19-related hospitalization include geographic factors, female gender, those younger than five years, between 40 and 59 years and older than 60 years, and those employed in the public health sector. Nonetheless, the odds of hospitalizations were lower in those aged between 19 and 24 years and working in the private healthcare sector.

The risk of severe COVID-19 was comparable among hospitalized subjects with SARS-CoV-2 Omicron BA.1 and BA.2 infections after controlling factors linked with the severe form of COVID-19. Those with comorbidities, aged between 40 and 59 years and older than 60 years, were associated with high risks of the severe form of COVID-19 relative to those aged between five and 12 years, female gender, and recipients of at least one dose SARS-CoV-2 vaccines. 

Conclusions

The study findings connotate that during the Omicron-dominated fourth SARS-CoV-2 pandemic wave in South Africa, a comparable number of people were hospitalized and developed severe COVID-19 among those infected with the Omicron BA.1 or BA.2 variants. This shows that while the Omicron BA.2 variant may have a competitive edge over BA.1 in some situations, the clinical profile of the disease remains identical between them.

However, since South Africa probably varies from other settings as it has a high degree of prior immunity induced by natural SARS-CoV-2 infections, studies assessing the severity of the Omicron BA.2 variant in additional clinical settings are warranted.

The limitations of the present study include restrictions to samples analyzed using the TaqPath™ COVID-19 PCR assay, possible biases of geographical information, and entitling S-gene-positive infections as a proxy for the Omicron BA.2 variant, which might have resulted in misclassification with other SARS-CoV-2 non-Omicron strains. Additionally, vaccination status was only known for the hospitalized SARS-CoV-2-infected individuals and was dependent on self-reporting, and re-infection was most likely under-reported because of inadequate testing.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Shanet Susan Alex

Shanet Susan Alex, a medical writer, based in Kerala, India, is a Doctor of Pharmacy graduate from Kerala University of Health Sciences. Her academic background is in clinical pharmacy and research, and she is passionate about medical writing. Shanet has published papers in the International Journal of Medical Science and Current Research (IJMSCR), the International Journal of Pharmacy (IJP), and the International Journal of Medical Science and Applied Research (IJMSAR). Apart from work, she enjoys listening to music and watching movies.