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Variants


SCIENTIST WHO FIRST SEQUENCED OMICRON WORRIED BY SPEED OF CHANGE

By
Janice Kew
+Follow
December 4, 2021, 2:27 PM GMT
 * Evolution of omicron in an animal host is being considered
 * First samples taken from diplomats who traveled together

What Science Is Looking for in Omicron Research


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The speed at which the omicron variant appears to have accumulated its unusual
pattern of mutations is a concern, according to Sikhulile Moyo, the scientist
who first detected the new strain that has quickly spread across the world. 

The velocity of the mutations also raises questions about how the variant
evolved and adds to the puzzle of how transmissible the variant may be. 




Moyo, director for the Botswana Harvard HIV Reference Laboratory and a research
fellow at Harvard T.H. Chan School of Public Health, said in a briefing on
Friday that viruses don’t accumulate mutations in a single step. Given the
global lack of adequate sequencing of the coronavirus, it’s very hard to get a
good grasp of how early the omicron variant developed.  



“We are still trying to understand how so many mutations arose for omicron in a
short space of time,” he said. “If you look at the previous lineages, if you
look at alpha, if you look at beta, you can see that the mutations accumulated
over time.”



One of the theories is that this strain developed in an immuno-compromised
person that harbored the virus for much longer than normal. Still, Moyo
cautioned that there is no evidence for this. Another hypothesis being looked
into is whether it could have been transferred from people into an animal host,
adapted to that host relatively quickly and then moved back into humans.

When Moyo first sequenced the sample, taken on Nov. 11 from foreign diplomats
who had traveled together to Botswana, the variant it most closely resembled was
B.1.1.263. That variant is known as the U.A.E lineage and was first detected in
early April 2020.  



When he looked more closely at B.1.1.263 he saw that strain had less mutations
and ruled out what he was seeing as being the same. After asking for more
information from Botswana’s health department about the people from whom the
positive samples had been taken, Moyo and his team deposited their findings into
an international database on Nov. 23. A few hours later, a separate group in
South Africa reported similar findings, followed by another group in Hong Kong
that deposited a partial genome. 



Omicron Up Close: South Africa’s Experts Tell Their Stories



With omicron’s sheer number of changes, Moyo initially thought this would be a
weak virus, he said. Instead, it seemed to be able to replicate quickly and
evade parts of the immune system, causing a higher risk of reinfection. 


More from

Apple Delays Office Return; Germany Rations Shots: Virus Update
Canadians Told to Avoid Traveling Abroad as Omicron Spreads
Omicron's Surge Is Turning London Into a Ghost Town
U.K. Faces Inevitable Surge in Hospital Cases From Omicron

In South Africa, daily confirmed Covid-19 cases have almost quadrupled from
Tuesday as the variant spread across the country, showing how contagious the new
strain may be.

“We hope that as data is coming in, people are going back to their freezers and
they are pulling out old samples,” he said. Some scientists have done just that
and have found that the omicron lineage was already circulating as early as
October.

One of the big questions that scientists are trying to answer is how effective
vaccines are against the omicron variant. That could be determined in a matter
of weeks, in part, thanks to Moyo and his team’s fast response and transparency
in sharing what they found with the world.

“I was enjoying the contribution that we have made in terms of this discovery,
and how it might have averted a number of deaths,” he said. “But when you open
the news, we’re also sad to see the number of countries closing their borders,
shutting flights, a number of people, you know, tweeting and saying you
scientists, what have you done, you’ve closed our Christmas and I believe that’s
not how scientists should be rewarded.”



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