Batch of homegrown coronavirus mutations seen in US

Researchers said Sunday they have identified a batch of similar troubling mutations in coronavirus samples circulating in the United States. They’ve not only drawn attention to them; they’ve come up with a better shorthand for referring to them. They’ve named them after birds.

The mutations all affect the same stretch of the spike protein – the knob-like extension on the outside of the virus that it uses to dock onto the cells it infects, the researchers wrote in a pre-print report. It’s not peer reviewed yet, but researchers are rushing such findings online to share them quickly with other experts.

Critical Care staff carry out a tracheostomy procedure on a Covid-19 patient on the Christine Brown ward at King's College Hospital in London on January 27, 2021.

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The genetic stretch that is mutated, or changed, is called 677. The various changes are so similar that the researchers think evolution favors these particular variants. And it’s in a troubling place, said Vaughn Cooper, director of the Center for Evolutionary Biology and Medicine at the University of Pittsburgh School of Medicine, who worked on the study.

“This stretch of Spike is important because of its proximity to a region key for virulence,” Cooper told CNN via email.

“We actually think these mutations are relatively rare (compared to other types of mutation), but they are disproportionately selected when then occur,” he added.

The team has been reviewing genomic sequences deposited into GISAID, a global database that researchers are using to share genetic information about the virus. It’s where scientists first noticed the rise of troubling new variants such as B.1.1.7, first seen in the United Kingdom, and B.1.351, first seen in South Africa.

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“In late January of 2021, our two independent SARS-CoV-2 genomic surveillance programs, based at the University of New Mexico Health Sciences in Albuquerque, New Mexico and the Louisiana State University Health Sciences Center in Shreveport, Louisiana, each noticed increasing numbers of … viruses carrying an S:Q677P mutation, and that this variant had increased in frequency in samples collected in late 2020 to mid-January,” the researchers wrote.

That shorthand – Q677P– refers to the specific change in the amino acid making up that part of the spike protein.

They’ve identified seven similar mutations at 677 – each one appearing to have arisen independently. They named them after birds to make it easier to identify them.

One, called Robin 1, has turned up in more than 30 US states, predominating in the Midwest, they said. A second “first appeared from a Oct 6, 2020 sample from Alabama and is named ‘Robin 2’ owing to its similarity to the parental Robin 1 sub-lineage,” they wrote. It’s mainly seen in the Southeast. One called Pelican was first seen in a sample from Oregon, and has since turned up in 12 other states as well as Australia, Denmark, Switzerland and India.

Pelican was the first variant that grabbed the attention of the researchers, in part because it was found in nearly 28% of samples from Louisiana and 11% of samples from New Mexico.

“The remaining Q677H sub-lineages each contain around 100 or fewer sequences, and are named: Yellowhammer, detected mostly in the southeast US; Bluebird, mostly in the northeast United States; Quail, mainly in the Southwest and Northeast; and Mockingbird, mainly in the South-central and East coast states,” the research team wrote.

The United States has barely studied the genomic sequences of coronaviruses circulating, so if these variants have turned up so often in databases, they are probably very prevalent, the researchers said. The appearance of so many similar mutations at the same time is “remarkable,” they said.

“These variants were not detected until mid-August 2020, but as of 03 Feb 2021 already account for over 2,327 of the 102,462 genomes deposited to GISAID from the USA,” they wrote. That merits close attention, they said.

Correction: This story has been updated to correct the list of countries where the Pelican mutation has been identified.