Through genomic surveillance of samples collected in Angola a new variant was discovered in Tanzanian travellers. Picture: File
Through genomic surveillance of samples collected in Angola a new variant was discovered in Tanzanian travellers. Picture: File

KZN team discovers most mutated Covid-19 variant

By Nathan Craig Time of article published Apr 4, 2021

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Durban - The KwaZulu-Natal Research Innovation and Sequencing Platform team has discovered the most mutated Covid-19 variant, with experts calling for further support of genomic surveillance.

Local scientists submitted a report late last month on Angola’s first genomic surveillance results.

Professor Tulio de Oliveira, KRISP’s director, said the variant was discovered in three Tanzanian travellers in Angola, which was worrying as little to no Covid-19 data was being released by Tanzania.

“It has 31 amino acids mutations, 11 spike protein mutations and three deletions in the N-terminal domain. When compared with other variants of concern (VOC) and variants of interest (VOI), this is the most divergent one. We reported this as a new VOI given the constellation of mutations with known or suspected biological significance, specifically resistance to neutralizing antibodies and potentially increased transmissibility. Whilst we have only detected three cases with it, this warrants urgent investigation as the source country, Tanzania, has a largely undocumented epidemic and few public health measures in place to prevent spread within and out of the country,” De Oliveira said.

Infectious diseases specialist, Richard Lessells, KRISP group leader, said it had not crossed the borders into South Africa.

“So far we have identified only the three sequences of this variant, and to the best of our knowledge it hasn't been reported from any other country. We have received additional samples from Angola and are currently generating and analysing data. Of course we hope that we won't find it in other Angolan sequences. We have no idea if it is still new or has been the dominant variant in Tanzania, and that's why we call for urgent attention as we really need to get a better understanding of the virus and the epidemiology in Tanzania,” Lessells said.

Following the discovery of the 501Y.V2 VOC the Network for Genomic Surveillance in South Africa partnered with the Africa Centres for Disease Control and Prevention and the African Society of Laboratory Medicine through the Africa Pathogen Genomics Initiative to strengthen SARS-CoV-2 genomic surveillance in order to rapidly characterize the spread of current and other emerging VOCs and VOIs.

A pre-print manuscript titled: “A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa” was published on health sciences pre-print server medRxiv.

It was a collaboration between authors from the KRISP team, Angolan health ministry, Africa CDC, the Oswaldo Cruz Foundation, the University of Oxford and University of Cape Town.

According to the global Covid-19 tracker by the Centre for Systems Science and Engineering at Johns Hopkins University in the US, Tanzania has not experienced a Covid-19 death let alone new cases since since May 2020.

Throughout the pandemic the Tanzanian President John Magufuli, who died last month speculated from Covid-19, has denied the pandemic and dismissed Covid-19 vaccines.

Tanzania stopped releasing data on Covid-19 infections and opened up the economy, including the resort island of Zanzibar. The stance taken by Magufuli garnered much criticism from neighbouring nations and the World Health Organisation as evidence has suggested many citizens had contracted the virus.

De Oliveira said: “When I spoke with health minister Zweli Mkhize, who was briefed, he mentioned that our country is not in a position to comment on this as this involves two other health departments (Angola and Tanzania) and we followed all the discussions with the appropriate diplomatic process via the Africa Union and Africa CDC.”

Co-chair of the Ministerial Advisory Committee on Covid-19, Professor Koleka Mlisana, said: “We advise the South African national department of health and can therefore not comment on how other countries respond to the pandemic, as the MAC.”

Sunday Tribune

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