A tentative assessment of the changes in transmissibility and fatality risk associated with Beta SARS-CoV-2 variants in South Africa: an ecological study

ABSTRACT

The circulation of SARS-CoV-2 Beta (B.1.351) variants challenged the control of COVID-19 pandemic. The numbers of COVID-19 cases and deaths and SARS-CoV-2 sequences in South Africa were collected. We reconstructed the variant-specified reproduction numbers (R t) and delay-adjusted case fatality ratio (CFR) to examine the changes in transmissibility and fatality risk of Beta over non-Beta variants. We estimated that Beta variants were 41% (95%CI: 16, 73) more transmissible and 53% (95%CI: 6, 108) more fatal than non-Beta variants. Higher risks of infection and fatality might lead to increasing volumes of infections and critical patients.

Impacts

• The circulation of SARS-CoV-2 Beta (B.1.351) variants, which were firstly reported in South Africa, challenged the control of COVID-19 pandemic.

• Using the national-wide COVID-19 cases and SARS-CoV-2 sequences data, Beta variants were estimated 41% more transmissible and 53% more fatal than non-Beta variants in South Africa.

• Higher risks of infection and fatality might lead to increasing volumes of infections and critical patients.

KEYWORDS:

• COVID-19
• beta variants
• South Africa
• reproduction number
• case fatality
• statistical modeling

Ethics approval and consent to participate

The number of COVID-19 cases and deaths and SARS-CoV-2 sequences data are collected via public domains, and thus neither ethical approval nor individual consent is applicable.

Availability of materials

All data used in this work are publicly available.

Acknowledgments

The SARS-CoV-2 genetic sequences were retrieved from the global initiative on sharing all influenza data (GISAID) at http://platform.gisaid.org/ (accessed on 15 July 2021). The complete acknowledgment table could be found online via GISAID. We thank the contributions of the submitting and the originating laboratories, and colleagues for helping collected the sequences data.

Author’s contributions

Conceptualization: SZ. Methodology: SZ. Software: SZ. Validation: SZ. Formal analysis: SZ. Investigation: SZ. Resources: SZ. Data Curation: SZ. Writing - Original Draft: SZ. Writing - Review and Editing: SZ, and ZP. Visualization: SZ. Supervision: MHW. Project Administration: SZ. Funding acquisition: ZP. All authors critically read the manuscript, and gave final approval for publication.

Disclosure statement

MHW is a shareholder of Beth Bioinformatics Co., Ltd. Other authors declared no competing interests. The funding agencies had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; or decision to submit the manuscript for publication.

Additional information

Funding

ZP was supported by the Natural Science Foundation of China [82073673, 11961071], the National S&T Major Project Foundation of China [2018ZX10715002-004-002, 2018ZX10713001-001], and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). MHW was supported by the National Natural Science Foundation of China [31871340, 71974165], Health and Medical Research Fund, the Food and Health Bureau, The Government of the Hong Kong Special Administrative Region [COVID190103, INF-CUHK-1], and the Chinese University of Hong Kong Grant [PIEF/Ph2/COVID/06, 4054600].