Scientists investigating ‘highly mutated’ Covid variant detected in travellers from Tanzania

‘We will continue to work logically through the experiments to characterise the variant and will share those results as soon as we have them’

Scientists are investigating a coronavirus variant thought to have originated in Tanzania that has acquired 34 mutations, making it the most genetically diverse Covid-19 virus detected to date.

The variant was identified in three people who had flown from Tanzania to Angola in mid-February. Since then, no more cases have been picked up by health authorities.

It has been labelled a variant of interest (VOI) due to its broad “constellation of mutations,” some of which feature in the UK, South Africa and Manaus variants.

The VOI was reported in a non peer-reviewed research paper written by scientists at the Universities of Oxford and Cape Town, the Angola Ministry of Health, Africa Centres for Disease Control and Prevention, and research body KRISP.

Because of the “largely undocumented epidemic” within Tanzania, which has “few public health measures in place”, the authors have expressed their concern that the variant may have spread beyond the three identified travellers.

“We still have very little information about Tanzania – the only information we get is when a virus is sequenced somewhere else in the world from someone with recent travel from Tanzania,” Dr Richard Lessells, one of the paper’s authors, told The Independent.

“So that's a very small number of sequences. So essentially we have no idea how prevalent this variant was or is within Tanzania.”

The variant carries 14 mutations within its spike protein – the part of the virus responsible for gaining entry to human cells.

It has acquired the E484K mutation associated with resistance to neutralising antibodies, and “there is also the P681H that is seen in the UK variant, that might contribute to increased transmissibility,” said Dr Lessells.

Through evolution, the structure of the Sars-CoV-2 spike protein has mutated to make it easier for the virus to bind with and penetrate our cells, as seen with the UK variant.

In some cases, as with the South Africa variant, it has mutated to become less recognisable to neutralising human antibodies which would normally attach to the virus’s spike protein and block its entry.

This type of mutation therefore allows Sars-CoV-2 to slip past the first line of immunological defence in people who have been vaccinated or previously infected, enabling the virus to carry on circulating.

However, the defining characteristics of these variants and others are the result of their collective mutations, rather than the singular genetic changes, like E484K, which have dominated headlines in recent months.

At the time Dr Lessells’ paper was published, the variant from Tanzania was “the most divergent virus that had been characterised” by scientists.

“Of course, there is a lot of sequencing being done now and lots of variants popping up all over the place, so difficult to be sure now,” Dr Lessells added.

His team in Cape Town is now working to determine whether antibodies generated by previous coronavirus infections are capable of neutralising the variant.

The variant is grown in a lab from the virus sample that was originally sequenced. “Then we test it against a pool of convalescent plasma specimens that we have collected here in South Africa,” Dr Lessells said. “We should have results in the next week or two.”

Depending on those findings, the team may then test the virus against blood plasma taken from people who have received the Covid-19 vaccines, giving an indication of its ability to evade artificially-induced immunity.

Dr Lessells admitted that he was “concerned” by the emergence of the variant “because we don't know whether it might be circulating more widely in Tanzania, and there is a possibility that this variant could have some effect on the vaccines”.

“We will continue to work logically through the experiments to characterise the variant and will share those results as soon as we have them,” he said.

For now, there is confidence that the current generation of vaccines will be able to offer high levels of protection against hospitalisation and death from the different known variants in circulation.