Humboldt County Lab Manager Jeremy Corrigan displays the reagents needed to amplify COVID-19 RNA in a test sample.
When Humboldt County Public Health announced Thursday that a new, never-seen-before mutation of the COVID-19 virus had been discovered locally, the news sounded alarming.
And it is. But not for the reasons most initially feared.
Due to vigilance and some luck, the virus variant’s spread was limited to a single assisted living facility, meaning it never entered the broader community, where its tendrils of transmission could have webbed. Instead, it was kept isolated and is believed to have died out, relegated to a blip in virus history. But the variant is also now one blip among many that combine to present a growing body of evidence that COVID-19 continues to mutate, to change, looking for ways, as viruses do, to become more infectious and effective, which in turn raises questions about the long-term effectiveness of vaccinations.
Since June, the local Public Health laboratory has been partnering with the Chan Zuckerberg Biohub, a nonprofit collaboration based in the Bay Area that’s doing genomic sequencing of the COVID-19 virus, sending the biohub positive local samples that contain a robust enough amount of virus to be sequenced.
Late last year, Public Health Laboratory Manager Jeremy Corrigan told the Journal the partnership would help Public Health find links between case clusters to better understand local transmission patterns and also identify mutations. But he said the samples had to be packaged up in batches to be shipped to the biohub, which was fielding samples from all over, so it would take some time to get sequencing results back.
And that’s why Humboldt County is just now learning of this new variant, which has now been found in 16 local cases, all of them tracing back to samples taken at Granada Rehabilitation and Wellness, an 87-bed skilled nursing facility that was the site of a deadly and pervasive outbreak that began Nov. 25 and ultimately infected 100 people with 13 resident deaths.
Public Health Officer Ian Hoffman said Thursday there is evidence to suggest the mutation made the virus more infectious, which may have contributed to its devastating impacts at Granada.
The surface of the coronavirus is spotted with proteins — known as spike proteins — that are made up of chains more than 1,200 amino acids. The virus infects humans when the tip of one of these spike proteins attaches to the surface of a human cell and transfers its genes into the human body, which then replicate and spread. Changes — or mutations, which can happen any time a virus is transmitted and replicates — to any of these amino acids have the ability to alter the virus’ behavior. And numerous mutations have been detected, with varying impacts.
The New York Times recently ran a story about scientists studying seven virus variants found in different parts of the country that all feature the same mutation, a change to the 677th amino acid, in a way that is feared to make the virus more effective in entering human cells. Then there’s the variant in the 452nd amino acid — known as the L452r Variant or the California Variant — that’s become a dominant variant throughout the state and has been found in at least 14 Humboldt County cases. (Scientists still haven’t determined whether this variant is any more or less contagious.) There’s also what’s been dubbed the B.1.1.7 variant that was first identified in the U.K. and has since spread to 62 countries, with some studies suggesting it may be 40 percent more transmissible than the standard variety. This variant includes changes to the 501st amino acid, as well as a constellation of other mutations, the combination of which is believed to be responsible for the increased transmissibility.
Humboldt County’s virus mutation is similar — containing changes to the 501st amino acid — but distinct from the others, according to Hoffman. The mutation is believed to affect the spike protein’s tip, allowing it to bind more easily and tightly to cells, potentially making it more contagious than the standard coronavirus.
“Given some of the laboratory studies that have been done around 501y mutations, it is highly suggested that it is stickier and can bind more to the receptors that allow the virus to enter the cells,” Hoffman said Thursday, adding that could be part of the reason the Granada outbreak spread so quickly and effectively.
Imagine it like walking through a field of burs. There are times of year when the tiny hooks covering the little seeds aren’t fully formed and you might end up with just a few on your pants. But when those hooks or little teeth are fully developed, they can come to coat your pant legs and shoe laces. The spike proteins are similar and it’s believed the mutation to the 501st amino acid is akin to developing those burs, making it more likely any human cells that come into contact with the virus will become infected.
But in Humboldt County’s case, this virus mutation occurred in a relatively controlled setting — a skilled nursing facility — and didn’t find a host to carry it to the broader community. In a press release announcing the finding Thursday, Chan Zuckerberg Biohub Senior Biosecurity Fellow Patrick Ayscue said that’s “remarkable.”
“It’s really a credit to the hard work of local Public Health and their partners,” he said in a release.
As Hoffman stressed in a media availability Friday, there appears to be no ongoing risk associated with the newly discovered variant, as in the months since the Granada outbreak it has not been detected in any other Humboldt County samples.
The discovery does, however, add to a growing body of evidence indicating the virus is continuing to grow and change, sometimes in unexpected ways.
“The coronavirus reproduces inside our body and makes millions of new viruses,” Hoffman said. “Every time it makes a copy of itself, there’s a potential that it can make a mistake in that replication of the genetic code. Those sorts of mistakes can sometimes confer advantages to the genetics of the virus.”
Hoffman stressed that the tools needed to combat virus mutations are the same as those needed to combat the original virus: masking, hand washing, physical distancing and avoiding the intermixing of households. Slowing the virus’ spread reduces chances for it to mutate and change, eliminating its opportunities to grow more contagious and effective. And, Hoffman said, that goes for people who have already been vaccinated, too, as a lot remains unknown about whether the vaccine prevents people from transmitting the virus or how long it remains effective.
While it is so far believed currently approved vaccines will be similarly affective against currently identified virus mutations and variants, more study is needed to be sure and there’s certainly no knowing whether they would be effective against future mutations and variations. In the final question of Thursday’s media availability, the Times-Standard asked Hoffman if it’s likely COVID-19 — and its continued mutations — will be “here to stay” and vaccinations will require yearly boosters to protect against mutations and remain effective.
“Time will tell and studies will tell,” Hoffman said, “but I think that’s probably likely.”