What do we know about the South African variant of Covid?

The South African variant, like the new UK variant, contains a mutation known as N501Y which is believed to make the virus more contagious than older variants. The South African variant also contains other mutations of concern, including E484K and K417N. These two mutations are thought to explain why the South African variant appears to be better able to evade neutralising antibody responses by the body.

Recent results from the Novavax Covid vaccine trials support this concern: while the vaccine had 95.6% efficacy against the original coronavirus and 85.6% against the UK variant, it had an efficacy of only 60% against the South Africa variant.

Experts say there is, at present, no sign that the South African variant results in more severe disease, or different symptoms.

How widespread is the South African variant in the UK?

On 24 January, the health secretary, Matt Hancock, announced that 77 cases of the South African variant had been detected in the UK, and that these were linked to people entering the country from overseas. On Monday 105 cases of the South African variant were announced.

But Public Health England (PHE) has said that cases are no longer confined to people who have recently entered the country, with 11 cases picked up among those with no such travel history – in other words, the variant is now spreading between people in the community. PHE said the South African variant had been found in such circumstances in eight different areas of England.

Unlike the UK variant, known as B117, which can be identified through PCR tests because of the particular mutations it contains, the South African variant, 501Y.V2, cannot be distinguished from other variants in this way – instead it is spotted by genetic sequencing by the Cog-UK consortium.

This consortium is analysing 5%-10% of swabs from people testing positive for Covid, meaning not all cases of the South African variant are spotted, although it is expanding its efforts.

“The numbers that we count are only those ones that we have sequenced, so we will underrepresent how many are out there,” Prof Sharon Peacock, director of Cog-UK, told the Guardian, adding that the team are sequencing between 15,000 and 20,000 genomes a week.

With just over 232,000 coronavirus genomes sequenced by Cog-UK since they started, that suggests – as a rough estimate – that under 0.05% of cases in the UK have involved the South African variant.

Where else has it been found?

To date the South African variant has been found in more than 30 other countries, including Austria, Belgium, Kenya, the United Arab Emirates and Japan. In some of those countries, including Belgium, cases of community transmission have been detected.

The UK is one of the countries with excellent genetic surveillance of coronavirus variants: the South African variant, and other variants of concern, might be common in countries with poorer surveillance but simply not have been picked up.

Was community spread inevitable, or did the UK fail to crack down quickly enough?

Peacock said the control of any new variant of concern requires strict adherence to lockdown rules, as well as measures such as hand washing and maintaining physical distance to prevent transmission, as well as careful consideration of border controls, including the use of quarantine.

With travel bans and strict quarantine in place, the chance of a new variant from abroad being spread within a community is greatly reduced. But once a variant has entered local settings, it is a different matter.

“We know that this variant is also likely to be more transmittable and we have seen how the UK B117 has transmitted rapidly in the UK, so it is likely that this variant will also be transmitted in the community,” said Prof Kamlesh Khunti at the University of Leicester, who sits on the government’s scientific advisory group for emergencies (Sage) and the Independent Sage committee.

Travel to the UK is now banned for people who have recently been in certain countries, including South Africa, while those returning from such countries will soon have to quarantine in hotels.

Some say the move comes too late. Gabriel Scally, visiting professor of public health at the University of Bristol and a member of Independent Sage, said it was “grossly irresponsible” that the government’s new quarantine measures were not up and running and did not apply to all those entering the UK.

Nicola Davis, a UK based virology expert. The article published in The Guardian