South African scientists have identified a new version of the coronavirus this week that they say is behind a recent spike in Covid-19 infections in Gauteng, the country's most populous province. It's unclear where the new variant actually arose, but it was first detected by scientists in South Africa and has also been seen in travellers to Hong Kong and Botswana.
A World Health Organization panel has named the variant Omicron and classified it as a highly transmissible virus of concern — the same category that includes the predominant delta variant, which is still a scourge driving higher cases of sickness and death in Europe and parts of the United States.
South Africa's Health Minister Joe Phaahla said the variant, now titled Omicron, was linked to an “exponential rise” of cases in the last few days, although experts are still trying to determine if the new variant is actually responsible.
From just over 200 new confirmed cases per day in recent weeks, South Africa saw the number of new daily cases rocket to 2,465 on Thursday. Struggling to explain the sudden rise in cases, scientists studied virus samples from the outbreak and discovered the new variant.
On Friday, the World Health Organisation was convening a group of experts to assess the data from South Africa.
Why are scientists worried about Omicron?
It appears to have a high number of mutations — about 30 — in the coronavirus’ spike protein, which could affect how easily it spreads to people.
Read: Living with Covid
Sharon Peacock, who has led genetic sequencing of Covid-19 in Britain at the University of Cambridge, said the data so far suggest the new variant has mutations “consistent with enhanced transmissibility”, but said that “the significance of many of the mutations is still not known.”
Lawrence Young, a virologist at the University of Warwick, described the variant as “the most heavily mutated version of the virus we have seen”. He said it was concerning that although the variant was only being detected in low levels in parts of South Africa, “it looks like it's spreading rapidly.”
What's known and not known about Omicron?
We know that Omicron is genetically distinct from previous variants including the beta and delta variants, but we do not know if these genetic changes make it any more transmissible or dangerous.
South African scientists have noticed a surge of cases, but we don't know if the new variant is responsible and it will take weeks to sort out if vaccines are still effective against it.
So far, there is no indication the variant causes more severe disease. South African experts said that as with other variants, some infected people don't have any symptoms.
Even though some of the genetic changes in Omicron appear worrying, it's still unclear if the virus will pose a significant public health threat. Some previous variants, like the beta variant, initially concerned scientists but didn't end up spreading very far.
Francois Balloux, director of the Genetics Institute at University College London, said it was impossible to make any predictions about whether or not the virus was more dangerous or infectious based on its genetic make-up alone.
How did this new variant arise?
The coronavirus mutates as it spreads and many new variants, including those with worrying genetic changes, often just die out. Scientists monitor Covid-19 sequences for mutations that could make the disease more transmissible or deadly, but they cannot determine that simply by looking at the virus.
They must compare the pattern of disease in outbreaks to the genetic sequences and sorting out whether there is an actual connection can take time.
Peacock said the variant “may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve", in a scenario similar to how experts think the alpha variant — which was first identified in England — also emerged, by mutating in an immune-compromised person.
Are the travel restrictions being imposed by some countries justified?
Maybe. As of noon Friday, travellers arriving in the UK from South Africa, Namibia, Botswana, Lesotho, Eswatini and Zimbabwe will have to self-isolate for 10 days. European Union nations also moved quickly on Friday to try to stop air travel from southern Africa.
Given the recent rapid rise in Covid-19 in South Africa, restricting travel from the region is “prudent”, said Neil Ferguson, an infectious diseases expert at Imperial College London.
Balloux of University College London said that if the new variant turns out to be more infectious than delta, the new restrictions will have little impact but that they could still buy the UK some time to boost vaccination rates and roll out other possible interventions.
What happens next?
The WHO panel drew from the Greek alphabet in naming the variant omicron, as it has done with earlier, major variants of the virus.
Even though some of the genetic changes appear worrisome, it was unclear how much of a public health threat it posed. Some previous variants, like the beta variant, initially concerned scientists but did not spread very far.
Medical experts, including the WHO, warned against any overreaction before the variant was thoroughly studied. But a jittery world feared the worst after the tenacious virus triggered a pandemic that has killed more than 5 million people around the globe.
Variants of interest — which currently include the mu and lambda variants — have genetic changes known to affect things like transmissibility and disease severity and have been identified to cause significant clusters in multiple countries.
Variants of concern — which include alpha, beta and delta — have shown they can spread more easily, cause more serious disease or make current tools like vaccines less effective.
To date, the delta variant remains by far the most transmissible form of Covid; it accounts for more than 99 per cent of sequences shared with the world's biggest public database.
Header image: People with masks walk in a shopping mall in Johannesburg, South Africa, Friday, Nov 26. — AP