When Sara Sawyer read that there was a new variant of the coronavirus rapidly spreading around the United Kingdom recently, she wasn’t surprised. For the past 15 years, Sawyer, a virology professor at the University of Colorado Boulder, has studied how infectious diseases are transmitted from animals to humans, including how viruses mutate.
What did catch her attention was how much — and how quickly — the new variant, called B.1.1.7, had mutated before European public health officials caught on. “We have of course seen many variants arise,” said Sawyer, who’s also a co-founder of the Boulder-based startup Darwin Biosciences. “There’s no getting away from variants. They are just a side effect of an imperfect duplication of genetic material.”
“Usually what we see are genetic variants that are one or maybe two bases different from things that we have seen before,” she said. “What’s unusual about this variant is it’s not one or two mutations, it is 14 to 17. It’s different than anything we’ve seen before.”
Colorado public health officials on Tuesday identified the United States’ first case of the seemingly more transmissible version of the virus and announced another probable infection on Wednesday. Both people infected are Colorado National Guard personnel who were deployed on Dec. 23 with four others to the Good Samaritan Society nursing home in Simla to provide support during an active COVID-19 outbreak. Neither members of the guard had traveled internationally in the weeks prior, according to public health officials.
Although the symptoms caused by the new variant appear to be the same, preliminary research shows that the B.1.1.7 version of the virus is 50% to 70% more transmissible, according to Eric France, chief medical officer at the Colorado Department of Public Health and Environment.
“So, if you’re ill, instead of only making two or three other people sick, you might actually spread it to four or five people,” France said. “If it’s more transmissible, that means that we’ll have more cases in our communities and the number of cases will rise quickly.”
“This could be overwhelming for our health care systems,” he said.
‘Things are going to get harder, not easier’
As of Wednesday, more than 84,000 vaccine doses had been distributed in Colorado.
During a media briefing on Wednesday, Gov. Jared Polis announced a handful of updates to the state’s vaccination plan, including bumping up to phase 1B people who are 70 or older, teachers, front-line workers, essential government officials, direct care providers for people experiencing homelessness and front-line journalists. Phase 2 now includes Coloradans who are 60 to 69, and people who are high risk between the ages of 16 to 59.
Polis stressed that Coloradans can avoid catching and transmitting the new variant by staying 6 feet from others, avoiding gatherings with people outside the home and washing hands regularly with soap and water. “We have a very easy, simple, low-cost, 50 to 75% effective vaccine available today,” he said. “It’s called a mask — wear one.”
Sawyer said the increased transmission rate is cause for serious public health concern.
“It means that our own laziness at following public health guidelines is now going to become even more painful to us than it was before because we’re going to have a lot more infections, we’re going to have a lot more transmission chains and things are going to get harder, not easier.”
She said there are still a lot of unknowns when it comes to the efficacy of the vaccine against the variant. But she’s optimistic.
“When you get a vaccine, your body does not just make one antibody flavor directed at that vaccine, your body will make a whole repertoire of different types of antibodies,” she explained. “So while you do have some mutations here, it’s not going to affect all of the positions where all of those antibodies bind.”
State lab flagged samples that are suspected variants
On Tuesday, the state lab deployed a team to the nursing home in Simla to test staff and residents. Preliminary results show that the variant is not circulating within the facility, according to Rachel Herlihy, the state’s top epidemiologist with the Colorado Department of Public Health and Environment. “But testing is ongoing,” she added during Wednesday’s news briefing.
Given the detection of the new variant of the COVID-19 virus, Polis is requesting that the Centers for Medicare & Medicaid Services allow the state to temporarily pause visitation for nursing homes until all residents can be vaccinated.
The state lab is still working to confirm if the second Colorado National Guard member has the new version of the virus.
“We anticipate the timeframe to be within the next week. This particular sample was a little bit less strong,” Herlihy said. “So it’s taking a little bit more work to pull out the sequence from the patient sample.”
As of Wednesday, the state lab has sequenced 24 samples that were flagged as suspected variants, according to Emily Travanty, scientific director for CDPHE’s Laboratory Services Division. The two samples from the National Guard members contained the mutation and 12 are still waiting to be sequenced.
The state lab discovered the variant using the same techniques used to identify COVID-19 positive patients: the PCR test, also called a molecular test. The test looks for the presence of three novel coronavirus genes on a nasal swab sample using a lab technique called polymerase chain reaction.
A positive result for COVID-19 infection occurs when at least two out of the three genes are found. The third gene, called the S gene, doesn’t always appear on the PCR test because of the mutations. When this happens, scientists flag the sample as a potential variant.
“To investigate further, we do viral genome sequencing,” Travanty said. “We look at the entire COVID-19 virus genome using next generation sequencing technology to create a complete fingerprint of the viral RNA found in the individual patient sample.”
The sequencing process takes longer than the typical COVID-19 PCR test, which requires a little over a day for the state lab to complete.
“(It) can take three to five days to generate all of the data necessary because we look at every position in the entire viral genome and compare it to known sequences across the country as well as what’s been circulating in Colorado,” Herlihy said.
Higher transmission rate does not mean new version of virus is more deadly
It’s too early to know exactly why the new variant is more transmissible, France said. One hypothesis is that the new version of the virus is able to stick onto human cells more efficiently.
“So if that’s the case, it could take fewer virus particles for a given person to become sick, and any given virus will have a better chance of causing an infection,” France said.
Sawyer said it’s important for people to understand that just because the new version of the virus is spreading faster, it doesn’t mean that it’s more deadly.
“There is a small possibility that what we’re doing here is watching this virus mutate into its more benign, seasonal form,” she added. “So it’s not necessarily a given that it’s mutating into some super virus.”
She used the 1918 flu as an example.
“That virus was actually around for several years after that pandemic,” Sawyer said. “It’s just that it attenuated itself so that it wasn’t as harmful anymore. So there is precedent for what I’m saying. It’s possible.”
She said modern technology is allowing scientists to watch how the virus is changing in real time. “We have a lot of tools now that we did not have at the beginning of this pandemic,” she said. “So I think that we are prepared to handle this variant.”
Sawyer has some hesitations about how quickly some of the vaccines have moved through FDA trials.
“I am a highly vaccinated citizen and I want to be careful about casting any doubt on vaccines. But I think it’s really important that people know that when you do a vaccine trial, you have to look for four things,” she explained. “You look for short-term safety, short-term efficacy — that’s protecting against the virus — long-term safety and long-term efficacy. And in a four-month trial, you can only look at two of those things.”
Given the seriousness of the pandemic and the toll it’s taken around the world, she said the “cost-benefit ratio may still make it worthwhile for elderly people.”
“But can we justify giving first of their class vaccines that have not been ever tested for long-term safety to a bunch of 25-year-old mothers in the world? I don’t know if we can,” she said. “That’s what keeps me up at night.”