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Saved Stories – None: Third homegrown coronavirus variant found in U.S. as researchers say first emerged in Texas in MAY

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Researchers have discovered the third new variant of the coronavirus in the U.S. and say it could end up being the most easily transmissible one yet.

A team from Southern Illinois University Carbondale traced the earliest appearance of new variant, called  20C-US, to Texas in May 2020.

The variant carries several mutations, including to the spike protein, which the virus uses to enter and infect human cells.

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Scientists say the variant has not spread significantly beyond the country’s borders, but that is most highly prevalent in the Upper Midwest. 

What’s more, the variant makes up nearly 50 percent of all genomes sequenced between November 1 and December 30, meaning it is likely very widespread.

‘We predict that 20C-US may already be the most dominant variant of SARS-CoV-2 in the U.S.,’ the team wrote in a pre-print article

‘The ongoing evolution of 20C-US, as well as other dominant region-specific variants emerging around the world, should continue to be monitored with genomic, epidemiologic, and experimental studies to understand viral evolution and predict future outcomes of the pandemic.’

20C-US is now one of the growing list of mutations discovered in countries such as the UK, South Africa and Brazil.

The news comes just one day after Ohio researchers announced the first discovery of two homegrown variants – one virtually identical to a variant that emerged in the UK and the other completely unique to the U.S. and dominant in the capital of Columbus.

Researchers from from Southern Illinois University Carbondale have found a third new variant of the coronavirus, called 20C-US, first detected in Texas in May 2020. Pictured: Odessa Regional Medical Center nurse Teresa Armendariz tests a person for COVID-19 at the West Texas Horse Center in Odessa, Texas, December 8

Researchers from from Southern Illinois University Carbondale have found a third new variant of the coronavirus, called 20C-US, first detected in Texas in May 2020. Pictured: Odessa Regional Medical Center nurse Teresa Armendariz tests a person for COVID-19 at the West Texas Horse Center in Odessa, Texas, December 8

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Researchers from from Southern Illinois University Carbondale have found a third new variant of the coronavirus, called 20C-US, first detected in Texas in May 2020. Pictured: Odessa Regional Medical Center nurse Teresa Armendariz tests a person for COVID-19 at the West Texas Horse Center in Odessa, Texas, December 8

Genome sequencing revealed an uptick of the new variant in July 2020 (left) and, between November 1 and December 31, it made up 50% of all U.S. genomes (right)

Genome sequencing revealed an uptick of the new variant in July 2020 (left) and, between November 1 and December 31, it made up 50% of all U.S. genomes (right)

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Genome sequencing revealed an uptick of the new variant in July 2020 (left) and, between November 1 and December 31, it made up 50% of all U.S. genomes (right)

Led by Dr Keith Gagnon, an associate professor of chemistry and biochemistry at SIU, the team first noticed the possibility of the new variant while looking at genome sequencing data from Illinois.

‘The data kind of jumped off the page when we looked at it, so we then started looking at national data, and later worldwide genome sequence data,’ Gagnon said in a news release.  

Viral genomes has been sequenced from samples taken beginning in March 2020 to the present day. 

‘The data kind of jumped off the page when we looked at it, so we then started looking at national data, and later worldwide genome sequence data,’ Gagnon said in a news release.  

The team began sequencing viral genomes from samples taken beginning in March 2020 to the present and one variant became more pronounced than the rest. 

To see if it was present at the the national level, researchers randomly subsampled 3.3 percent of U.S. genomes available on the global genomic database GISAID. 

The earliest appearance was found from a sample taken in the greater Houston area of Texas on May 20, 2020.

Following the variant over time, there was a notable expansion in the variant’s presence in July 2020, which coincides with America’s second wave of the pandemic, in states such as Wisconsin and Illinois. 

However, between November 1 and December 31, almost 50 percent of all sequenced genomes from the U.S. are the new variant.

Researchers suggest this means 20C-US has ‘surpassed 50 percent penetrance to become the most dominant variant in the U.S.’

The variant has not spread significantly beyond U.S. borders and is most highly prevalent in the Upper Midwest (above)

The variant has not spread significantly beyond U.S. borders and is most highly prevalent in the Upper Midwest (above)

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The variant has not spread significantly beyond U.S. borders and is most highly prevalent in the Upper Midwest (above)

Researchers say the virus has several mutations, including two to the spike protein, which it uses to enter and infect cells. Pictured: CDC illustration of the coronavirus

Researchers say the virus has several mutations, including two to the spike protein, which it uses to enter and infect cells. Pictured: CDC illustration of the coronavirus

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Researchers say the virus has several mutations, including two to the spike protein, which it uses to enter and infect cells. Pictured: CDC illustration of the coronavirus

However, it has a high prevalent in the eastern and Midwestern regions and has no t spread widely to the western half of the U.S. 

‘It’s here. We found it. It’s definitely home-grown and widespread, and we’re the first to characterize it,’ Gagnon said.  

20C-US has been reported in other countries including Australia, Israel, Mexico, New Zealand, Poland, Singapore, Taiwan and Thailand, but at low levels.

The first mutations the virus showed were in genes related to virus particle maturation – a process by which a virus breaks from a host cell and activates to infect more cells – and the  processing of viral proteins.

Gagnon says these are all important for virus production.

Since then, the new variant has formed two new mutations in the spike protein, which demonstrates that it is evolving. 

Evidence is lacking, but the team says the combination of reduced case-fatality rates and a rise in COVID-19 infections suggests the new variant is highly transmissible but only causes a midl illness. 

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Dr Daniel Jones, of The Ohio State University Wexner Medical Center, who discovered the Columbus variant told DailyMail.com the Illinois variant ‘looks closely related but not exactly identical.’

Jones said this means the two sets of researchers – in Ohio and Illinois – are likely tracking variants from the same outgrowth.

With the first doses of newly approved vaccines being administered across the national, Gagnon said it is unknown whether the variant will impact its effectiveness. 

‘Based on the mutations so far, I don’t think it will significantly impact the vaccine’s effectiveness,’ he said.

‘The catch is that the virus continues to evolve, and since May, it has acquired three mutations, and two of them are in the spike protein, one of which might affect antibody binding. There are a lot of unknowns.’ 

Both Pfizer and Moderna have been testing their vaccines against the international variants and say they expect the jabs to provide protection.  

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