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Latest on new Covid variant discovered in SA

Photo by Martin Sanchez on Unsplash

The South African government confirmed on Thursday, 25 November, that it has detected the new Coronavirus variant Omicron in the country.

This variant was discovered through collaborative efforts with private laboratories and the Network for Genomic Surveillance in South Africa (NGS-SA) members. NGS-SA is a network of laboratories, scientists and academic institutions that have been established to monitor changes in SARS-CoV-2, the virus that causes COVID-19, since March 2020.

The National Institute for Communicable Diseases (NICD) has since developed frequently asked questions for the Omicron mutated SARS-CoV-2 lineage.

What is the Omicron lineage?

On 22 November 2021, the NGS-SA detected a group of related SARS-CoV-2 viruses in South Africa named the Omicron lineage.

Omicron has been detected in Gauteng at relatively high frequency, with more than 70% of genomes sequenced from specimens collected between 14 and 23 November 2021 belonging to this lineage. This lineage possesses a high number of mutations previously seen in other COVID-19 variants of interest (VOI) or variants of concern (VOC) but also other novel mutations.

What did NGS-SA do with the information?

The World Health Organisation (WHO) and the Department of Health were alerted to this lineage earlier this week.

The NGS-SA is continuing to monitor the frequency of this lineage, and laboratory tests to assess the functional impacts of these mutations are underway. However, the virus has not fulfilled the WHO criteria for VOC or VOI. This will be revisited, especially as the virus spreads and data is accumulated.

How do the C.1.2, Beta or Delta variants differ from the B.1.1.529 lineage?

While the Omicron lineage shares a few common mutations with the C.1.2, Beta and Delta variants, it also has several additional mutations. Presently, the Omicron lineage is relatively distinct from the C.1.2, Beta and Delta variants and has a different evolutionary pathway.

Does infection with Omicron result in similar symptoms as with other variants?

Currently, no unusual symptoms have been reported following infection with the Omicron variant and as with other variants, some individuals are asymptomatic.

What are the implications? Will these mutations affect vaccine effectiveness, disease severity, and transmissibility?

SARS-CoV-2, like all viruses, changes with time, with mutations that afford the virus some kind of advantage being selected for in recent infections.

While some of the mutations in the Omicron lineage have arisen in other SARS-CoV-2 variants of concern or variants of interest, NGS-SA is being cautious about the implications, while they gather more data to understand this lineage.

Work is already underway to look at the immune escape potential of Omicron in the laboratory setting. A real-time system to monitor hospitalisation and outcome associated with Omicron has since been established.

Based on the understanding of the mutations in this lineage, scientists believe that partial immune escape is likely, but vaccines may still offer high levels of protection against hospitalisation and death.

What about other new variants?

Scientists expect new variants to continue to emerge wherever the virus is spreading.

Vaccination remains critical to protect communities at high risk of hospitalisation and death, to reduce strain on the health system, and to help slow transmission.

This must be in conjunction with all the other public health and social measures.

The public is advised to remain vigilant and continue to follow COVID-19 protocols and non-pharmaceutical interventions, which are proven to prevent the spread of the virus. (Source: SAnews.gov.za)

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