The Network for Genomics Surveillance in South Africa (NGS-SA), which includes the NICD, UKZN, UCT and SUN, has been monitoring changes in SARS-CoV-2, the virus which causes COVID-19, since March 2020.
NGS-SA recently detected a new lineage, which is a group of mutated viruses, of SARS-CoV-2 in the Eastern Cape, Western Cape and KwaZulu-Natal Provinces. This lineage possesses between 10-20 mutations that were not previously seen in viruses from South Africa prior to September 2020.
What does this mean?
SARS-CoV-2, like all viruses, mutates with time. Between March and September 2020, this virus mutated at a relatively slow rate, as evidenced by over 2,000 sequences from across 8 of the 9 provinces. However, from late September 2020, this virus has accumulated several mutations that have not previously been seen in South Africa.
Scientists at the NICD, UKZN and UCT are working on testing what impact all these mutations have on virus growth, virus sensitivity to antibodies, and binding to human cell receptors.
What is currently known:
One of these mutations increases binding to the human cell receptor, which could make it easier for the virus to infect.
Two of these mutations reduce virus sensitivity to some antibodies, meaning that these antibodies may not be as effective against this new mutated lineage, compared to the original (un-mutated) lineage.
What are the implications?
We are being cautious about the implications until the necessary experiments are performed. The public is encouraged to remain vigilant and to continue to follow COVID-19 protocols by wearing masks (which covers the nose, mouth and chin), regular washing or sanitising of hands, cleaning surfaces frequently, and maintaining 1.5m distance from others. These interventions continue to be effective in preventing the spread of all SARS-CoV-2 viruses.
Will these mutations affect test sensitivity?
These mutations will not affect PCR testing sensitivity. The mutated lineage from the Eastern Cape has already been detected in over 150 samples using South Africa’s current repertoire of real-time PCR tests. In addition, the tests typically detect at least two or three different SARS-CoV-2 gene targets, which serves as a backup in the case of a mutation arising in one.
Culled from NICD
