[A South African tip led to the discovery of mutations around the
world. With infections skyrocketing, “it’s a race against
time.”] [[link removed]]

AS CORONAVIRUS MUTATES, THE WORLD STUMBLES AGAIN TO RESPOND  
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Matt Apuzzo, Selam Gebrekidan and Apoorva Mandavilli
January 9, 2021
The New York Times
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_ A South African tip led to the discovery of mutations around the
world. With infections skyrocketing, “it’s a race against time.”
_

Greenacres Hospital was among the Netcare hospitals in South Africa
where doctors spotted an unexplained spike in cases in October.,
Samantha Reinders for The New York Times

 

DURBAN, South Africa — Doctors and nurses at a South African
hospital group noticed an odd spike in the number of Covid-19 patients
in their wards in late October. The government had slackened its
lockdown grip, and springtime had brought more parties. But the
numbers were growing too quickly to easily explain, prompting a
distressing question.

“Is this a different strain?” one hospital official asked in a
group email in early November, raising the possibility that the virus
had developed a dangerous mutation.

That question touched off a high-stakes genetic investigation that
began here in Durban on the Indian Ocean, tipped off researchers in
Britain and is now taking place around the world. Scientists have
discovered worrisome new variants of the virus, leading to border
closures, quarantines and lockdowns, and dousing some of the
enthusiasm that arrived with the vaccines.

Britain has been particularly overwhelmed.
[[link removed]] Infections
and hospitalizations have skyrocketed in recent weeks since that
country discovered its own variant of the virus, which is more
contagious than previous forms. By one estimate, the mutated virus is
already responsible for more than 60 percent
[[link removed]] of
new infections in London and surrounding areas.

By one estimate, the mutated virus is already responsible for more
than 60 percent of new infections in London and surrounding areas.
Andrew Testa for The New York Times

The coronavirus has evolved as it made its way across the world, as
any virus is expected to do. But experts have been startled by the
pace at which significant new variants have emerged, adding new
urgency to the race between the world’s best defenses —
vaccinations, lockdowns and social distancing — and an aggressive,
ever-changing foe.

The new variant pummeling Britain has already been found in about 45
countries [[link removed]], from
Singapore to Oman to Jamaica, but many countries are effectively
flying blind, with little sense of how bad the problem may be.

Long before the pandemic emerged, public health officials were calling
for routine genetic surveillance of outbreaks. But despite years of
warnings, many countries — including the United States
[[link removed]] —
are conducting only a fraction of the genomic studies needed to
determine how prevalent mutations of the virus are.

Denmark, which has invested in genetic surveillance, discovered the
variant afflicting Britain in multiple Danish regions and recently
tightened restrictions. The health minister compared it to a storm
surge, predicting that it would dominate other variants by
mid-February.

And as countries go looking, they are discovering other variants, too.

With the world stumbling in its vaccination rollout
[[link removed]] and
the number of cases steeply rising to peaks that exceed those seen
last spring, scientists see a pressing need to immunize as many people
as possible before the virus evolves enough to render the vaccines
impotent.

Preparing residents for vaccinations at a nursing home in Reims,
France, on Friday. Andrea Mantovani for The New York Times

“It’s a race against time,” said Marion Koopmans
[[link removed]], a
Dutch virologist and a member of a World Health Organization working
group on coronavirus adaptations.

The vaccine alone will not be enough to get ahead of the virus: It
will take years to inoculate enough people to limit its evolution. In
the meantime, social distancing, mask-wearing and hand-washing —
coupled with aggressive testing, tracking and tracing — might buy
some time and avert devastating spikes in hospitalizations and deaths
along the way. These strategies could still turn the tide against the
virus, experts said.

“We do know how to dial down the transmission of the virus by a lot
with our behavior,” said Carl T. Bergstrom
[[link removed]], an evolutionary biologist at the
University of Washington in Seattle. “We’ve got a lot of agency
there.”

Yet in the course of the pandemic, governments have often proven
reluctant or unable to galvanize support for those basic defenses.
Many countries have all but given up on tracking and tracing.
Mask-wearing remains politically charged in the United States, despite
clear evidence of its efficacy. Cities like Los Angeles have been
gripped by a spike in cases linked to Christmas festivities
[[link removed]],
and national public health officials are bracing for surges
[[link removed]] elsewhere,
driven by people who ignored advice and traveled during the holidays.

Family members mourn the death of Gilberto Arreguin, who died from
complications of Covid-19, in Los Angeles in late December.  Alex
Welsh for The New York Times

Much remains unknown about the new variants, or even how many are
sprouting worldwide. Scientists are racing to sequence enough of the
virus to know, but only a handful of countries have the wherewithal or
commitment to do so with any regularity.

The rapid spread of the new variants is a reminder of the failings and
missteps of major countries to contain the virus earlier. Just as
China failed to stop travelers from spreading the virus before the
Lunar New Year last year, Britain has failed to move fast enough ahead
of the new variant’s spread. Britain lowered its guard during the
holidays, despite a rise in cases now known to be linked to a variant.
And just as China became a pariah early on in the pandemic, Britain
now has the unfortunate distinction of being called Plague Island
[[link removed]].
[[link removed]]

The spread of the variant lashing Britain has left some countries
vulnerable at a time when they seemed on the brink of scientific
salvation.

A case in point: Israel. The country, which had launched a remarkably
successful vaccine rollout, tightened its lockdown on Friday after
having discovered cases of the variant. About 8,000 new infections
have been detected daily in recent days, and the rate of spread in
ultra-Orthodox communities has increased drastically.

A HODGEPODGE OF RESPONSES

The variant discovered in Britain, known as B.1.1.7, has 23 mutations
that differ from the earliest known version of the virus in Wuhan,
China, including one or more that make it more contagious, and at
least one that slightly weakens the vaccines’ potency. Some
experiments suggest that the variant spreads more easily because
mutations enable it to latch more successfully onto a person’s
airway.

Dr. Bergstrom and other scientists were surprised to see this more
transmissible variant emerge, given that the coronavirus was already
quite adept at infecting people.

But other experts had warned from the start that it would only be a
matter of time before the virus became an even more formidable
adversary.

“Every situation we have studied in depth, where a virus has jumped
into a new species, it has become more contagious over time,”
said Andrew Read [[link removed]], an
evolutionary microbiologist at Penn State University. “It evolves
because of natural selection to get better, and that’s what’s
happening here.”

Much of the global response has focused on shutting out Britain, with
a hodgepodge of national restrictions that harken back to the early
reactions to the epidemic.

The closed port at Dover, England, last month.  Andrew Testa for The
New York Times

China has banned flights and travelers from Britain. Japan took an
even harsher measure, banning entry to nonresident foreigners from
more than 150 countries.

Others like India and New Zealand are allowing some flights from
Britain but require passengers to have two negative tests — one
before departure and another after arrival. Australia is sticking with
its policy of requiring hotel quarantines and testing for
international travelers.

Experts say that countries should focus instead on ramping up
vaccinations, particularly among essential workers who face a high
risk with few resources to protect themselves. The longer the virus
spreads among the unvaccinated, the more mutations it might collect
that can undercut the vaccines’ effectiveness.

That is why, when the World Health Organization working group saw the
first data on the variant circulating in South Africa on Dec. 4,
everyone took notice.

“Your next question immediately is: Can the vaccines still protect
us if we get viruses with these mutations?” said Dr. Koopmans, who
was in the meeting.

For now, the answer seems to be yes, said Jesse Bloom,
[[link removed]] an
evolutionary biologist at the Fred Hutchinson Cancer Research Center
in Seattle. Dr. Koopmans agrees.

Doctors, nurses and health care assistants began receiving the
coronavirus vaccine at a hospital in Piacenza, Italy, in December.
Alessandro Grassani for The New York Times

The variants that have emerged in South Africa and Brazil are a
particular threat to immunization efforts, because both contain a
mutation associated with a drop in the efficacy of vaccines. In one
experiment, designed to identify the worst-case scenario, Dr.
Bloom’s team analyzed 4,000 mutations, looking for those that would
render vaccines useless. The mutation present in the variants from
both Brazil and South Africa proved to have the biggest impact
[[link removed]].

Still, every sample of serum in the study neutralized the virus,
regardless of its mutations, Dr. Bloom said, adding that it would take
a few more years before the vaccines need to be tweaked.

“There should be plenty of time where we can be prospective,
identify these mutations, and probably update the vaccines in time.”

‘These Variants Will Spread’

That sort of surveillance is precisely what led to the discovery of
the new variants.

Liza Sitharam, a nurse and infectious disease specialist in coastal
South Africa, was among those who first noticed a small cluster that
was quickly bulging.

“We’d have five cases and then it’d double really quickly,”
she recalled. The raw numbers weren’t alarming, she said, but
“there was something just not looking right.”

Her boss at the Netcare hospital group, Dr. Caroline Maslo, figured
that with the country’s borders open, business travelers from German
auto companies had perhaps brought in a European variant of the virus.
She sought help from Tulio de Oliveira,
[[link removed]] a
professor and geneticist at the Nelson Mandela School of Medicine in
Durban who had studied viral variants during the first Covid-19 wave.

Prof. Tulio de Oliveira, a geneticist at the Nelson Mandela School of
Medicine in Durban. Joao Silva/The New York Times

Soon, his lab was analyzing swabs, shipped on ice by courier
overnight. On Dec. 1, he emailed a British scientist, Andrew Rambaut
[[link removed]], and asked him to review
some of his early findings: a series of strange mutations on the
virus’s outer surface.

Dr. de Oliveira, a Brazilian-South African scientist who sports long
hair and a surfer vibe, shared his findings at a Dec. 4 meeting of the
World Health Organization working group. All took notice because of
the variants’ potential to disrupt the vaccine’s effectiveness.

Days later, Dr. de Oliveira recalled, Dr. Rambaut emailed him with a
discovery of his own: British scientists had scoured their databases
and found a similar but unrelated mutation that appeared linked to a
cluster of infections in the county of Kent.

Coming two weeks before Christmas, Dr. de Oliveira immediately thought
of the Lunar New Year early in the pandemic, when millions of people
in China traveled far and wide for the holiday, some carrying the
virus.

“It was crystal clear,” Dr. de Oliveira said in an interview.
“These variants will spread nationally, regionally and globally.”

Dr. Rambaut and colleagues released a paper on the variant discovered
in Britain on Dec. 19 — the same day that British officials
announced new measures. The variant had apparently been circulating
undetected as early as September. Dr. Rambaut has since credited
[[link removed]] the South
Africa team with the tip that led to the discovery of the variant
surging in Britain.

Public health officials have formally recommended
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type of swift genetic surveillance and information-sharing as one of
the keys to staying on top of the ever-changing virus. But they have
been calling for such routine surveillance for years
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with mixed results.

“The message was very clear, that this is the way surveillance has
to go,” said Dr. Josep M. Jansa
[[link removed]], a senior
epidemiologist at the European Centre for Disease Prevention and
Control [[link removed]]. Just as Covid-19 exposed
flaws in the world’s pandemic plans
[[link removed]] a
year ago, the hunt for new variants is exposing gaps in surveillance.
“We’re learning,” he said. “Slowly.”

At Los Angeles International Airport in December. Variants will spread
with travelers. Ariana Drehsler for The New York Times

Britain has one of the most aggressive surveillance regimens,
analyzing up to 10 percent of samples that test positive for the
virus. But few countries have such robust systems in place. The United
States sequences less than 1 percent
[[link removed]] of
its positive samples. And others cannot hope to afford the equipment
or build such networks in time for this pandemic.

In Brazil, labs that had redirected their attention from Zika to the
coronavirus had discovered a worrisome mutation there as early as this
spring. But little is known about the variants circulating in the
country, or how quickly they are spreading.

“We just don’t know because no one is either sequencing or sharing
the data,” said Dr. Nuno Faria 
[[link removed]]at Imperial College and
Oxford University, who coordinates genomic sequencing projects with
colleagues in Brazil. “Genomic surveillance is expensive.”

As the virus continues to mutate, other significant variants will
almost certainly emerge. And those that make the virus hardier, or
more contagious, will be more likely to spread, Dr. Read said.

“The faster we can get the vaccines out, the faster we can get on
top of these variants,” he said. “There’s no room for
complacency here.”

_Matt Apuzzo reported from Durban, South Africa, and Brussels, Selam
Gebrekidan from London, and Apoorva Mandavilli from New York.
Reporting was contributed by Thomas Erdbrink; Melissa Eddy from
Berlin; Isabel Kershner from Jerusalem; Manuela Andreoni from Rio de
Janeiro; Christina Anderson from Stockholm; Amy Chang Chien and Amy
Qin from Taipei, Taiwan; and Jennifer Jett and Tiffany May from Hong
Kong._

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