12
NEWS
12
CORONAVIRUS
On Monday morning, four long days
before anyone had heard of the Omicron
variant, an announcement was made by
the health department in Pretoria, one of
South Africa’s capital cities.
A cluster of new Covid cases had
emerged at Tshwane University of Tech-
nology, which health officials assumed
had been caused by an increase in social-
ising in the run-up to Christmas. TheYes, the new variant is worrying, but
scientists are preparing our defences
nearby townships of Atteridgeville,
Mamelodi and Soshanguve were also see-
ing rising numbers of infections. Cases in
the city and surrounding area had risen
four-fold in a week. By the end of the
week it was clear this surge not only
threatened to envelop South Africa, but
also marked the most worrying develop-
ment in the pandemic since the Delta var-
iant emerged from India last spring.A constellation of mutations
While officials in Pretoria were worrying
about resurgent cases in student dorms,
in nearby Botswana scientists were grow-
ing concerned about an unusual set of
Covid samples taken from three patients.
The test samples, the first of which dated
back to November 11, revealed a brandnew variant, displaying an unprece-
dented 50 mutations. Scientists were
startled: this was not just a gradual shift,
it was an evolutionary leap. Worryingly, a
fourth sample with the same genetic
sequence was recorded in Hong Kong
from a patient who had travelled from
South Africa.
The new variant — at that point
unnamed — was particularly concerning
because the spike protein, the protrusion
on the outside of the virus, had 30 muta-
tions. By comparison, the Delta variant,
which ripped across the world in the
spring, only had 13 spike mutations. Such
a dramatic evolution has two significant
ramifications. Firstly, the key vaccines in
use — Pfizer, Moderna and AstraZeneca —
work by teaching the immune system torecognise the spike protein. If the spike
protein has significantly changed, anti-
bodies might no longer recognise it quite
so well. Our hard-won immunity might
be side-stepped.
Secondly, ten of the mutations seen in
the new variant were on the receptor-
binding domain, the specific part of the
spike protein that attaches to human
cells. Delta has only two such mutations.
The better the ability to attach to cells,
the theory goes, the more transmissible
the virus is. And the more transmissible it
is, the faster it will spread.Joining the dots
Tom Peacock, a virologist at Imperial Col-
lege London, was one of the first outside
southern Africa to spot the implications.Omicron’s mutations suggest it could be fast-spreading and able to evade vaccines — but let’s not panic just yet
But while he was concerned about the
number of mutations and the “horrific
spike profile”, he initially took a meas-
ured approach. Tweeting on Tuesday, he
said: “Worth emphasising this is at super-
low numbers right now in a region of
Africa that is fairly well sampled.”
But scientists in South Africa were join-
ing the dots, and realised the surge in Pre-
toria was caused by the same mysterious
mutation spotted in Botswana. Within a
couple of days it had become apparent
that Peacock’s “super-low” numbers
were in fact a lot, lot higher.
The speed with which this link was
made is remarkable. Last year it took two
months for scientists to realise that a mys-
terious spike in cases in Kent was caused
not by socialising, as first thought, but bythe new Alpha variant. It took even
longer for the Delta variant, which
emerged at around the same time in
India, to be recognised.
This time the reaction was immediate.
Within hours the UK had put South Africa
and five bordering countries onto its
travel red list. A senior UK government
scientist that night described it as “the
worst variant we have seen so far”.
On Friday the World Health Organisa-
tion labelled it a “variant of concern” and
gave it the name Omicron, after the 15th
letter of the Greek alphabet. Cases were
reported in Belgium and Israel. Some £
billion was knocked off the value of the
London stock indexes as the market pan-
icked. By the weekend Omicron had
reached our shores.BEN
SPENCER
Science EditorHOLLIE ADAMS/GETTY IMAGES; DENIS FARRELL/AP