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 of coronavirus, being a group of mutated strains of SARS-CoV-2 in the Eastern Cape, Western Cape and KwaZulu-Natal Provinces. This evolved lineage possesses between 10-20 mutations not previously observed in strains from South Africa, prior to September 2020.
SARS-CoV-2, like all viruses, mutates with time and 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, the virus accumulated several mutations previously not observed in South Africa.
Scientists at the NICD, UKZN and UCT are testing what impact all these mutations have on virus growth, virus sensitivity to antibodies, and binding to human cell receptors.
According to the National Institute for Communicable Diseases, one of these mutations increases binding to the human cell receptor, which could make it easier for the virus to infect—a concerning development which sees the commercialisation of COVID-19 vaccines, being more pressing than ever.
In support of the demand for vaccines, two of these mutations reduces virus sensitivity to some antibodies, meaning that antibodies may not be as effective against this new mutated lineage, compared to the original (un-mutated) strain.
But it is worth noting, 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.
Bare the following in mind; People all expected this virus to be the next Bubonic plague, but in reality, it appears to be a persistent slow gainer. But, unlike in bygone years, we have medical science on the verge of delivering vaccines, globally—all we have to do, is wash our hands, practice social distancing and be healthier people until then.
Authors: Quinton Boucher and Calvin Swemmer
Edited: Calvin Swemmer