The original coronavirus strain has almost disappeared in the US. One chart shows how variants took over.

covid delta variant
A mobile COVID-19 vaccination center in Bolton, England, on June 9, 2021.

  • Coronavirus variants have largely replaced the original strain, rendering it essentially obsolete.
  • The Alpha variant took over as the US’s dominant strain in April. Delta could replace it soon.
  • Scientists aren’t sure whether more contagious variants will evolve from the dominant ones.
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Viruses will do what it takes to survive – even if it means killing off an older, weaker self and replacing it with a more transmissible strain.

For the first several months of the pandemic, however, the coronavirus had no need to become more dangerous: The virus was doing a good job of spreading, with each new infected person passing it to an average of two to three others. At the time, scientists hoped that the original strain of the virus, known as the “wild type,” was already contagious enough that it wouldn’t evolve further.

But as the pandemic swelled and more people got infected, the coronavirus had more opportunities to replicate, and therefore mutate, incurring small, random changes in its genetic sequence. Most mutations are harmless, but every so often a distinct set yields new properties – a variant.

Scientists now estimate that variants have almost completely replaced the original strain in the US, rendering it essentially obsolete.

“Pretty much all the virus that’s circulating right now has one of these variants that make it differ from the original strain that first took off across the world,” Tyler Starr, a postdoctoral research fellow at the Fred Hutchinson Cancer Research Center, told Insider.

The chart below shows how a few variants have dominated the US since February. More than 200 less prevalent strains, including the original version of the virus, are listed as “other.”

The Alpha variant, first identified in the UK in September, became prevalent in the US from February to April, going from 27% to 70% of all circulating strains. It’s about 50% more transmissible than the original strain, according to the Centers for Disease Control and Prevention. Meanwhile, the share of other coronavirus strains (including the original) fell from 20% to 4%.

By May, Alpha had a strong competitor: Delta. An analysis from Public Health England found that the Delta variant was associated with a 60% increased risk of household transmission compared to Alpha, though more recent estimates suggest that difference is closer to 40%.

From May to June, Delta grew from less than 3% of all circulating strains in the US to more than 20%. It’s poised to become the US’s dominant strain within weeks.

“Basically everywhere, once Delta gets there, it does overtake something like the Alpha variant,” Starr said. “That is evidence that, to some degree, it is more transmissible.”

Could an even more contagious variant replace Delta?

variant lab
Researchers sequence coronavirus samples at the University Hospital of Badajoz in Spain on April 15, 2021.

So far, Starr said, coronavirus variants – even Delta – aren’t fundamentally different from the wild type.

“These mutations might be slightly modifying things like transmissibility,” he said, but “that trait was there in the original virus and it’s just being altered slightly.”

In fact, some scientists wonder if the virus is nearing “peak fitness,” the point after which it no longer mutates to become more infectious.

Delta is by far the “fittest” variant to date, according to the World Health Organization. In addition to being more transmissible than other strains, it may also be deadlier: Researchers in Scotland found that getting infected with Delta doubled the risk of hospital admission relative to Alpha. (Previous studies have suggested that the Alpha variant may be 30 to 70% deadlier than the original strain.) Vaccines, of course, significantly lower that risk for both variants.

“Delta is absolutely going up the fitness peak – whether it’s at the top, I think that’s very hard to say until we just don’t see any further change,” Andrew Read, who studies the evolution of infectious diseases at Pennsylvania State University, recently told Insider.

“If Delta takes over the world and nothing changes,” he added, “then we’ll know in a while – a year or two – that it is the most fit.”

But Starr thinks the virus probably won’t ever stop mutating.

“As people continue to get immunity, the virus will continue to evolve to be able to transmit and infect people,” he said. “But at the same time, we’ll have that low-level immune reaction that makes it a much less severe thing over time.”

It’s still possible that an entirely new lineage might replace Delta as the dominant variant, or that two variants – Delta and Alpha, for instance – could combine mutations to produce an even more infectious strain. In the worst-case scenario, the virus could evolve into a “variant of high consequence” – one that’s far more distinct than the variants currently circulating and highly resistant to vaccines. That hasn’t been observed yet.

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SPAC HighCape Capital soars 140% on deal to buy protein-sequencing firm Quantum-Si

Trader NYSE
Traders work on the floor at the opening bell of the Dow Industrial Average at the New York Stock Exchange on March 18, 2020 in New York.

Shares of special purpose acquisition company HighCape Capital Management LLC exploded as much as 140% on Thursday after the company agreed to buy biotech firm Quantum-Si. 

Quantum-Si has created the world’s first semiconductor chip that can enable protein sequencing and analyze proteins in a digitized format.  

 “DNA sequencing changed medicine and research by revealing what could happen in the body; protein sequencing shows what is happening right now,” ” said Dr. Jonathan Rothberg, Founder of Quantum-Si in a press release.

The transaction was also supported by a $425 PIPE, or private investment in public equity, with participation from Foresite Capital Management, LLC, Eldridge, accounts advised by ARK Invest, Glenview Capital Management, LLC, and Redmile Group, LLC. 

The expected value of the combined company is $1.46 billion. It will trade on the NASDAQ under the ticker symbol “QSI.” 

Quantum Si’s end-to-end solution is on track to launch commercially in 2022 for research use, according to the press release. 

The SPAC merger follows over 130 other blank-check companies that have gone public in 2021 as mania for the funding model continues. For context, in 2020 it took until early October for 130 SPACs to make their debut, according to data from investment firm Accelerate.

In a Thursday CNBC interview, Dr. Rothberg said that it’s not just the SPAC format that’s propelling more biotech companies to receive funding, it’s the “sophistication of investors.” 

“Our PIPE investors understood proteomics. I didn’t have to give them a lecture,” he said. “And so I’d say it’s a combination of the SPAC being there after we worked and spent $200 million to make a semiconductor that sees the molecules of life, and then an educated investor base that normally invests in public companies that knows that this is the future: digitization, artificial intelligence, [and] diagnostics on proteins.” 

Dr. Rothberg is the founder of multiple life science and medical device companies including Butterfly Network, CuraGen, and AI Therapeutics. He is best known for investing high-speed, DNA sequencing.


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