Covid-19 variant responsible for second wave may have emerged from Eastern Cape
Cape Town – The coronavirus variant that became dominant in parts of South Africa towards the end of 2020 may have emerged from the coast of the Eastern Cape after the first wave.
This according to a study by an international group of scientists recently published in the prestigious journal, Nature.
The rapid displacement of other Sars-CoV-2 lineages in multiple regions indicates that this variant has an advantage over these other strains, possibly owing to increased transmissibility and/or its ability to avoid the immune system.
Professor Carolyn Williamson from UCT’s Division of Virology, National Health Laboratory Services (NHLS), and a lead member of Network for Genomic Surveillance in South Africa (NGS-SA), said the study was preceded by a call she received from Professor Tulio de Olivera, the head of NGS-SA.
“He was worried as he had found a new variant with an unexpected number of mutations in the spike protein – a region included in most vaccines.
“At UCT, we rapidly sequenced viruses and found more than half the viruses transmitted in the Western Cape contained these mutations, and by December this virus had essentially replaced the previously circulating variants, ” said Williamson.
“This rapid emergence suggested this variant was better at spreading, and subsequent data showed that it could also affect vaccine efficacy.”
The second wave of the Sars-CoV-2 epidemic in the country began around October 2020 and was notably rapid in parts of the Eastern Cape, Western Cape and KwaZulu-Natal, prompting an intensification of genomic surveillance.
“A new Sars-CoV-2 variant (501Y.V2 / B.1.351) was identified by the NGS-SA through the analysis of 2 882 Sars-CoV-2 whole genomes from South Africa, collected between March 5 and December 10, 2020.
“The data suggested that the new variant emerged around August 2020 in Nelson Mandela Bay, becoming the dominant lineage in the Eastern Cape, Western Cape and KwaZulu-Natal by the end of 2020,” said Williamson.
She noted that the 501Y.V2 variant is defined by eight mutations in its spike protein.
“One of these mutations, N501Y, is also present in a variant identified in the UK (B.1.1.7) and is associated with enhanced binding to the human ACE2 receptor.
“Another mutation, E484K, has been associated with resistance to neutralising antibodies. The distribution and spread of 501Y.V2, along with insights from genomic analysis, suggest that the variant may be more transmissible than other Sars-CoV-2 lineages.”
“However, the full import of the mutations is not yet clear and requires further study,” she said.
Professor Koleka Mlisana, the executive manager for Academic Affairs, Research & Quality Assurance at the NHLS, said: “The NHLS laboratories played an important role in acting quickly in the discovery of the new variant as we could quickly sample hundreds of health-care facilities.
“We found that the NGS-SA allowed South Africa to quickly and accurately identify the 501Y.V2 variant. We now want to continue working together to expand this technology to other important pathogens in the country, such as HIV, TB, and the Hepatitis virus,” Mlisana said.
De Oliveira added: “This was the first paper that described the 501Y.V2 variant. Since the discovery of the variant, scientists in South Africa have worked relentlessly to advance the science.”
“Novel results show that people recently infected with 501Y.V2 produce broad neutralising antibodies that neutralise 501Y.V2 and other variants.
“The focused and collaborative way that South African scientists worked to understand this variant has been inspiring and exciting.”