Authorities all over the world have have shown alarm at a new coronavirus variant detected in South Africa, with the European Union and the United Kingdom among others quickly tightening border controls as more is being found out about the mutation.
Hours after the UK banned flights from South Africa and neighbouring countries and asked travelers returning from there to quarantine, the World Health Organization (WHO) cautioned against hasty measures, and a South African scientist labelled London’s decision a symptom of “vaccine apartheid”.
This latest variant named Omicron by the World Health Organization is the most heavily mutated version discovered so far -and has been described as “horrific”.
It is early days and the confirmed cases are still mostly concentrated in one province in South Africa, but there are hints it may have spread further.
Infections in South Africa had risen steeply in recent weeks, coinciding with detection of the variant.
What is known
The variant has been named Omicron by the World Health Organization, following the pattern of Greek code-names like the Alpha and Delta variants.
It is also heavily mutated. Prof Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa, said there was an “unusual constellation of mutations” and that it was “very different” to other variants that have circulated.
In a media briefing Prof de Oliveira said there were 50 mutations overall and more than 30 on the spike protein, which is the target of most vaccines and the key the virus uses to unlock the doorway into our body’s cells.
Zooming in even further to the receptor binding domain (that’s the part of the virus that makes first contact with our body’s cells), it has 10 mutations compared to just two for the Delta variant that swept the world.
The main concern is that this virus is now radically different to the original that emerged in Wuhan, China. That means vaccines, which were designed using the original strain, may not be as effective.
Some of the mutations have been seen before in other variants, which gives some insight into their likely role in this variant.
Prof Richard Lessells, from the University of KwaZulu-Natal in South Africa, said: “They give us concern this virus might have enhanced transmissibility, enhanced ability to spread from person to person, but might also be able to get around parts of the immune system.”
There have been many examples of variants that have seemed scary on paper, but came to nothing. The Beta variant was at the top of people’s concerns at the beginning of the year because it was the best at escaping the immune system. But in the end it was the faster-spreading Delta that took over the world.
Prof Ravi Gupta, from the University of Cambridge, said: “Beta was all immune escape and nothing else, Delta had infectivity and modest immune escape, this potentially has both to high degrees.”
It is still early to draw clear conclusions, but there are already signs that are causing worry.
There have been 77 fully confirmed cases in Gauteng province in South Africa, four cases in Botswana and one in Hong Kong (which is directly linked to travel from South Africa). Israel and Belgium have also reported cases.
However, there are clues the variant has spread even more widely.
This variant seems to give quirky results (known as an S-gene dropout) in the standard tests and that can be used to track the variant without doing a full genetic analysis.
That suggests 90% of cases in Gauteng may already be this variant and it “may already be present in most provinces” in South Africa.
But this does not tell us whether it spreads faster than Delta, is any more severe or to what extent it can evade the immune protection that comes from vaccination.
It also does not tell us how well the variant will spread in countries with much higher vaccination rates than the 24% of South Africa that is fully vaccinated, although large numbers of people in the country have had Covid.
The WHO says it would take weeks to determine how effective vaccines were against the variant, which was first identified this week.
Travel restrictions
The US, European Union and the United Kingdom and an increasing number of countries have temporarily halted flights from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi.
Germany, Italy, Israel, Japan, Kenya and Singapore have also restricted travel.
