April 20, 2024

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Where did such “WEIRD” COVID Omicron variant come from?

Where did such “WEIRD” COVID Omicron variant come from?


Where did such “WEIRD” COVID Omicron variant come from?



On December 1st, researchers published a study in “Science” discussing the fifth “concerning mutant” Omicron (Omicron), where it came from, and how it evolves, and its emergence is important for avoiding the future. What are the lessons for the dangerous variants?


On Wednesday, the US CDC reported the first case of Omicron variant infection, and the patient has been vaccinated with two doses but not a booster shot, which further reflects the spread of the variant strain.


Scientists have given three possible answers:

  • The virus may spread and evolve in a population with little surveillance and sequencing;
  • It may also be conceived in patients with chronic COVID-19 infection;
  • Or it may have evolved in a non-human species, and recently it has spread from this species back to humans.


The low vaccine coverage rates in South Africa and Botswana “provide a fertile environment” for the evolution of this variant, and the global vaccine inequality now seems to be retribution.


The Centers for Disease Control and Prevention (CDC) announced on Wednesday that it has confirmed the first case of Omicron variant infection in the United States.


According to reports, the case returned to the United States from South Africa on November 22 and has already received two doses of Moderna vaccine.


The patient developed mild symptoms and is currently improving, and has been in isolation since the test was positive. CDC said all close contacts have been traced and the test results are all negative.


This fact further confirms that this strain has spread to most parts of the world. As of  on December 2, the mutant new coronavirus Omicron strain has spread to 27 countries and regions around the world, including Australia, Germany and other places.


This mutant strain did not first appear in South Africa, but South Africa noticed this unusual phenomenon. The epidemic quickly spread from a few people to thousands of people, and spread to other cities in South Africa.


To this end, South Africa quickly began research. South African researchers said that the Omicron strain seems to be more easily spread than its previous generations.

The amount of mutations in the virus is very high, not only easy to produce immune escape, Omicron can be said to be the most ferocious and worst mutated strain of COVID-19 in history.

California Governor Gavin Newsom wrote on Twitter: “There is no reason to panic, but we should remain vigilant. This means vaccinations, booster shots, and masks indoors.”




“Omicron” is coming so fiercely that many people are worried, so where does this mutant come from?


Since South African scientists announced last week that they had discovered a disturbing new variant of SARS-CoV-2, the world has been anxiously awaiting clues about how it might change the trajectory of the pandemic.

However, if it is not so urgent, then where and how Omicron evolves, and what lessons its appearance has for avoiding future dangerous variants, this is a huge mystery.


Where did such "WEIRD" COVID Omicron variant come from?

Obviously, Omicron did not develop from early mutant strains, such as Alpha or Delta. On the contrary, it seems to evolve in parallel in the dark.

Emma Hodcroft, a virologist at the University of Bern, said that Omicron is so different from the millions of publicly available SARS-COV-2 genomes that it is difficult to determine its nearest relatives.

It is likely to be isolated from other strains very early, she said: “I think this will go back to mid-2020.”


This raises a question: where are Omicron’s “predecessors” lurking for more than a year.

Scientists have basically seen three possible explanations: The virus may spread and evolve in a population with little surveillance and sequencing.

It may also be conceived in patients with chronic COVID-19 infection.

Or it may have evolved in a non-human species, and recently it has spread from this species back to humans.


On December 1, researchers published an article titled “Where did ‘weird’ Omicron come from?” in “Science”, which sparked heated discussion:


Where did such "WEIRD" COVID Omicron variant come from?

Christian Drosten, a virologist at the Charité University Hospital in Berlin, agrees with the first possibility. He said: “I don’t think this evolved in South Africa, where a lot of sequencing is going on, but in other parts of Southern Africa during the winter wave.

There are many infections that have lasted for a long time. For this virus to evolve, it really requires huge evolutionary pressure. “


But Andrew Rambaut of the University of Edinburgh does not understand how the virus has been hidden in the crowd for so long.

He said: “I’m not sure that anywhere in the world there is a virus isolated enough to spread for such a long time without appearing everywhere.”


On the contrary, Rambaut and others believe that this virus is most likely to develop in patients who are chronically infected with COVID-19, possibly in people whose immune response is impaired by other diseases or drugs.

When Alpha was first discovered at the end of 2020, the mutation appeared to have acquired many mutations at the same time, which led the researchers to hypothesize a chronic infection.

This idea is supported by sequencing SARS-CoV-2 samples from some chronically infected patients.


Richard Lessells, an infectious disease researcher at the University of KwaZulu Natal, said: “I think the evidence to support it is getting stronger.” Lessells and his colleagues described a case in a preprint. Young women in South Africa were infected with uncontrollable HIV and carried SARS-CoV-2 for more than 6 months.

The virus accumulated many of the same changes as the variant of interest, and this pattern also appeared in another patient with a longer SARS-Cov-2 infection.


The cause of the “abnormal” Omicron in South Africa is likely to be closely related to the high prevalence of AIDS in the region

. Statistics show that the HIV infection rate in South Africa exceeds 13% (a total of about 8 million people).

The infection rate for women aged 15 to 49 is over 21%, and the infection rate for adult men of the same age is about 18%.


Lessells said that in order to stop one possible source of future mutation, “what we need to do is bridge the gap in the HIV treatment cascade.

Therefore, we need to allow everyone to be diagnosed, we need to allow everyone to receive treatment, and we need to allow those who are currently receiving ineffective treatment to receive an effective treatment plan. “


But Drosten said that the experience of immunosuppressed patients with chronic influenza and other viruses contradicts Omicron’s hypothesis.

Mutations in evading the immune system do occur in these people, but they are accompanied by a series of other changes that reduce their ability to spread from person to person.

“These viruses have low applicability in the real world.” This is because over time, the mutations that allow the virus to survive in one person may be the same as the mutations needed to best spread from one person to the next. Very different.


Jessica Metcalf, an evolutionary biologist at the Institute for Advanced Study in Berlin, is not sure whether this is the case for SARS-CoV-2. “I think one of the reasons this virus performs so well is that better binding of ACE2 (its receptor on human cells) helps spread within and between hosts.”

However, for now, she agrees with Drosten’s view that Omicron is most likely to spread and evolve in a hidden population.


Some people believe that the virus may be hidden in rodents or other animals, rather than humans, and therefore has undergone different evolutionary pressures to select new mutations.

“The genome is really weird,” Kristian Andersen said, referring to its confounding mutations, many of which have never been seen in other variants before.


Mike Worobey, an evolutionary biologist at the University of Arizona, said: “The interesting thing is how crazy it is.”

Although Worobey tends to use immunosuppressants as the source of Omicron, he pointed out that according to recent preprints, 80% of the white-tailed deer sampled in Iowa from the end of November 2020 to the beginning of January 2021 carried SARS-CoV- 2.

“This really makes me wonder if other species will be chronically infected, and over time, this may create this selective pressure.”


Aris Katzourakis, an evolutionary biologist at the University of Oxford, said that it is too early to rule out any theories about the origin of Omicron, but given the large number of human infections, he is skeptical of the animal scenario.

“If we successfully suppress the virus, I will start to worry more about the animal’s host, and then I will be able to see where it might hide.”


Many global health leaders have used the emergence of Omicron to focus the world’s attention on the huge gap between COVID-19 vaccination in rich and poor countries.

In a speech at the World Health Assembly on Monday, Richard Hatchett, head of the Epidemic Prevention Innovation Alliance, said that the low vaccine coverage rates in South Africa and Botswana “provide a fertile environment” for the evolution of the variant.

The global response is characterized by global inequality, and this inequality is now being retributed.


However, some scientists say that there is little evidence to support this claim. Katzourakis said: “If we had more vaccinations in Africa, we wouldn’t have this idea: I hope this is true, but we really have no way of knowing.”

Currently, the lessons learned from Omicron are as unknown as their origins.




Where did such “WEIRD” COVID Omicron variant come from?

(source:internet, reference only)

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