An Overview of the South African COVID-19 Subvariant Outbreak

Non-Sponsored Content

INFECTIOUS DISEASE

Medical writer: Christy Leung | Last updated: 17 June 2022 | In: COVID-19, SARS-CoV2, Infectious Disease

Article Keywords

SARS-CoV-2, infectious diseases, omicron, Subvariants, South Africa, COVID-19

The first reported case of Coronavirus Disease 2019 (COVID-19) was reported in China on 17^th November, 2019.¹ The disease is caused by SARS-CoV-2 virus, and the circulating strains have varied periodically since the outbreak, beginning with the wild-type strain. The Alpha and Delta variants appeared in late 2020, while the Omicron variant appeared in November 2021.² The increase in variants can be attributed to viral spike protein mutations and immune evasion, causing mass infections even as the population’s immunity increases.³ Notably, the wild-type strain was relatively less transmissible; each subsequent strain increased in transmissibility, from Alpha to Delta, now to Omicron variants.² Omicron is currently the world’s dominant strain; in particular, B.1.1.529, BA.2, BA.4 and BA.5 are the significant subvariants of concern in South Africa. All four subvariants belong to the Omicron lineage.⁴

After its emergence in late 2021,⁵ subvariant B.1.1.529 dominated South African COVID-19 infection in January 2022, and BA.2 was dominant in February and March 2022.⁶ Strains BA.4 and BA.5 became a regional public health concern in April 2022, accounting for 73% and 94% of South Africa’s COVID-19 cases in April and May, respectively.⁶ Omicron sub-lineages BA.4 and BA.5 sub-lineages of Omicron cause disease severity similar to previous Omicron strains, but they are more contagious and are considered “game-changing sub-lineages” due to their F486V mutation.⁷ In addition to “escaping” and reducing the effectiveness of neutralising antibodies from previous vaccinations and infections,⁸ the F486V mutation increases the affinity of angiotensin-converting enzyme 2 (ACE-2) receptors for SARS-CoV-2, the cellular entry point,⁹ and causes immune-mediated damage and subsequent multi-organ injury.¹⁰This immune evasion mechanism allows BA.4 and BA.5 to transmit at high rates and infect even those who have been recently vaccinated or infected.¹¹

Overall, the COVID-19 hospitalisation and mortality rates in South Africa are 13.5% and 2.60%, respectively.¹²The nation’s hospitalisation rate during the Delta wave was 10.0%, higher than during the Omicron wave through January 2022 (8.3%) and 13 June 2022 (5.97%).^12,13The in-patient case-fatality ratio (CFR) during the Delta wave was 26.4%, higher than in the Omicron wave through late January 2022 (10.7%). The lower hospitalisation rate and CFR in in-patients during the Omicron wave compared to the Delta wave can be explained by the increasing immunity of the population to previous vaccinations and infections.^11,14 Regionally, a third of the cases originate from the small but densely populated province of Gauteng, which is the home to the main cities of Pretoria and Johannesburg.^11,12

Currently, the antibody escape mechanisms of BA.4 and BA.5 make them the “fittest” subvariants which can “survive” better and infect further than their predecessors.^7,11 This, together with the resumption of air traffic, explains the rapid spread of BA.4 and BA.5 subvariants in Europe, North America and Australasia in recent months.⁴ Coupled with the scientists’ postulation that new strains will be discovered every six months in the future,¹⁵total eradication is unlikely and unrealistic. Instead, the global community should aim to prevent serious consequences and deaths from COVID-19, by working together toward population-wide vaccination and personal hygiene education.^11,16 Eventually, as the disease severity and transmissibility vary across COVID-19 strains, countries may require more efficient testing and viral gene sequencing for more accurate strain and sub-lineage monitoring, healthcare burden predictions, and timely resource allocation.¹⁷

Reference

South China Morning Post. Available online. https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back. Last accessed: 7 June 2022.

Yale Medicine. Available online. https://www.yalemedicine.org/news/covid-19-variants-of-concern-omicron. Last accessed: 7 June 2022.

Nature. Available online. https://www.nature.com/articles/d41586-021-03619-8. Last accessed: 15 June 2022.

European Centre for Disease Prevention and Control. Available online. https://www.ecdc.europa.eu/en/news-events/implications-emergence-spread-sars-cov-2-variants-concern-ba4-and-ba5. Last accessed: 15 June 2022.

European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern as of 25 May 2022. Available online. https://www.ecdc.europa.eu/en/covid-19/variants-concern. Last accessed: 15 June 2022.

The National Institute for Communicable Diseases. Available online. https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/sars-cov-2-genomic-surveillance-update/. Last accessed: 15 June 2022.

European Centre for Disease Prevention and Control. Available online. https://www.ecdc.europa.eu/en/news-events/epidemiological-update-sars-cov-2-omicron-sub-lineages-ba4-and-ba5. Last accessed: 15 June 2022.

Cao Y, et al. BioRxiv. 2022.

Nature. Available online. https://www.nature.com/articles/d41586-022-01069-4. Last accessed: 15 June 2022.

Iwasaki M, et al. Inflammation. 2021;44(1):13-34.

Madhi AS, et al. N Engl J Med. 2022;386:1314-26.

The National Institute for Communicable Diseases. Available online. https://www.nicd.ac.za/latest-confirmed-cases-of-covid-19-in-south-africa-13-june-2022/. Last accessed: 15 June 2022.

Jassat W, et al. Lancet Glob Health. 2022;10(7):e961-9.

Harvard T.H. Chan School of Public Health. Available online. https://www.hsph.harvard.edu/news/press-releases/omicrons-milder-severity-due-to-population-immunity/. Last accessed: 15 June 2022.

Nature. Available online. https://www.nature.com/articles/d41586-022-01240-x. Last accessed: 15 June 2022.

Moghadas SM, et al. Clin Infect Dis. 2021;73(12):2257–64.

United States Agency for International Development. Available online. https://www.usaid.gov/tajikistan/press-releases/feb-28-2022-usaid-builds-covid-19-genomic-sequencing-capability. Last accessed: 15 June 2022.

Achieving the Best Outcomes under COVID-19 Endemicity

Inactivated and mRNA COVID-19 vaccines in patients with autoimmune rheumatic diseases – A city of two tales

Late but sinister post-COVID-19 conditions: new-onset rheumatic diseases

COVID-19 Infection and Subfertility: A Subtle and Debatable Complication

Previous Next

17 May 2023

Achieving the Best Outcomes under COVID-19 Endemicity

30 January 2023

Inactivated and mRNA COVID-19 vaccines in patients with autoimmune rheumatic diseases – A city of two tales

Disclaimer

This article is not medical advice. Patients should seek personal assessment by a licenced specialist. Physicians are recommended to read the full publication(s) as cited in the article before making medical decisions. This article does not supersede nor replace the published article(s).