They are like the sentinels of the coronavirus pandemic, standing watch with eyes fixed on the horizon, searching for invaders.
These infectious disease guardians — scientists at the Michigan Bureau of Laboratories who do whole genome sequencing of COVID-19 test samples — clanged the warning bells on Saturday.
They alerted state health officials and the public that a new, more transmissible variant of SARS-CoV-2 was detected in a test sample from Washtenaw County.
Called B.1.1.7 or the United Kingdom variant because that’s where it was first identified in September, health officials are concerned about what its arrival in Michigan could mean for case numbers, hospitalizations and deaths.
Although this strain of the virus is not more deadly and isn’t known to make people more severely ill than other previously identified strains, B.1.1.7 spreads more easily.
“It appears to be about 50% more transmissible, or able to spread 50% faster,” said Dr. Adam Lauring, an associate professor of infectious diseases and microbiology at the University of Michigan. “One way to think about it is if one person generally infects two other people on average with coronavirus, with the B.1.1.7 variant, that one person might infect three other people on average. And so scaled up, that can lead to much faster growth of the virus.
“What I always come back to is this: If it spreads faster, that means that there’s going to be more people who are going to get infected and that means that there’s going to be more people who are going to get sick and be hospitalized. And that could mean that there’d be more people who die.
“So even though it’s not really lethal on an individual level, it spreads faster. It’s going to cause more infections and more serious illness and more deaths, so I think that’s the concerning thing,” said Lauring, whose work in whole genome sequencing at U-M accounts for about 2.5% of the total coronavirus surveillance in the nation.
The B.1.1.7 variant was detected Saturday in a COVID-19 test sample from a woman living in Washtenaw County who had traveled to the U.K., according to state health officials.
Two new cases have been identified among the woman’s close contacts, though it still isn’t clear whether they have the same strain. It takes a minimum of five days to fully sequence a COVID-19 test sample to identify the particular strain, said Heather Blankenship, the bioinformatics and sequencing section manager at the state laboratories.
“A lot of times, that is gonna take up to a week because of holidays and weekends and other testing that is going on for diagnostics,” Blankenship said.
The Washtenaw County woman and her close contacts are now all in quarantine, state health officials say.
Some states surge, Michigan keeps watch
So far, the UK strain of the virus has been identified in at least 16 other states.
The U.S. Centers for Disease Control and Prevention announced Friday that the trajectory of the variant’s spread suggests it could become the predominant strain circulating in the U.S. in March.
If that happens, the CDC warned it could “threaten strained health care resources, require extended and more rigorous implementation of public health strategies, and increase the percentage of population immunity required for pandemic control.”
That’s already happening in the UK.
England, Northern Ireland, Scotland and Wales are locked down as hospitalizations and deaths from the virus are soaring. And cases of the B.1.1.7 variant have been detected across many other European countries, leading to curfews in France and extended school closures in Germany.
“We get asked what should we do about this variant,” said the state’s epidemiologist Sarah Lyon-Callo during a news conference with reporters in early January, before it was detected in the state. “I think of it as this virus has kind of stepped up its game a bit in terms of its ability to transmit between people.
“Therefore, we need to step up our game in terms of wearing masks, keeping social distance and staying at least six feet apart from others, avoiding crowds ventilating indoor spaces and washing our hands often.”
And it puts new urgency on vaccinating as many people as possible as quickly as it can be done.
“We obviously want to get the vaccine rolled out as fast as we can to protect people,” Lauring said. “We know what we need to do to control the virus, we’re just going to need to do even better just to sort of achieve the same level of control.
“What concerns me,” he said, “is that we haven’t been doing a good job, and the job just got harder.”
Tighter restrictions were put in place in November in Michigan, closing in-person dining at restaurants and bars, canceling in-person high school and college classes and putting a pause on organized sports.
The measures reduced rising rates of new infections and hospitalizations. The seven-day average of new daily cases dropped on Saturday to 2,350, its lowest point since late October. Since the pandemic began, 535,534 Michiganders have been infected and 13,804 have died, according to state data.
As the case rates and hospitalizations have fallen and vaccines came onto the market, high schools were granted permission to resume in-person classes. Many college campuses are about to reopen to students this week. Indoor entertainment venues and some sports have resumed.
But the appearance of this new, more transmissible strain of the virus puts all that in jeopardy again.
“We are going to be have to be even more careful about some mitigation strategies,” said Dr. Arnold Monto, a professor of epidemiology and global public health at U-M who serves as acting chair of the U.S. Food and Drug Administration’s Vaccines and Related Biological Products Advisory Committee.
He said state public health leaders will have to watch to see whether the B.1.1.7 variant gains a foothold here.
“I think what we are doing is responding by shutting down or opening up based on observation of transmission” is working, he said. “Look at Atlanta, where cases are taking off again. Texas is taking off again. But we’re not. The proof is in the pudding.”
Mutations common, impact of new strains uncertain
All viruses mutate. It’s what they do.
Some mutations help them spread more easily. Others may lead the virus to cause more severe illness. Still other mutations actually keep a particular variant of a virus from replicating and it dies off.
“Having variants pop up is not unexpected,” Monto said. “Actually it’s expected. And it’s a question of where the changes are and what they do to the virus’ behavior. … It’s very clear that the UK one … has what we call a competitive advantage over previous ones, and that’s why it has spread and took over.”
Researchers can sequence the genome of viruses to look for those often tiny changes or mutations and use them to identify how a virus is spreading within communities or families.
Most mutations are small and relatively inconsequential. But sometimes, a significant series of changes can occur that can make a big difference.
Marty Soehnlen, director of infectious disease at the state labs that do the bulk of viral surveillance in Michigan, said her team is always on the lookout for significant changes like those in the B.1.1.7 variant, and can see how the virus spreads from one person to the next based on the mutations.
“From the public health side, we really like it for transmission patterns, figuring out how to investigate our outbreaks,” she said. “We also look at resistance markers or the way that it may change tests. … Will it cause you not to be able to pick up a positive sample? Or in some instances you could use it to develop new interventions, and that could be through drug therapy, for vaccination. It could be all those different things. So you’re constantly looking at those changes and trying to figure out what’s happening.”
Some changes can also make vaccines ineffective, which is why new batches of flu vaccines come out each year, aimed at particular strains that are predicted to be in high circulation for the upcoming season. So far, the research suggests that the current COVID-19 vaccines on the market will still be effective for the B.1.1.7 variant, Lauring said.
Scientists at the Lansing-based labs have run nearly 5,700 samples through the days-long process of whole genome sequencing in the last 10 months, Blankenship said. That makes them among the busiest labs in the country and their work accounts for between 6% and 7% of all coronavirus whole genome sequencing in the United States.
Samples that are sent to the state’s labs come from all over Michigan to ensure surveillance has a widespread geographic base, Soehnlen said, and there’s a particular interest in cases with “unusual clinical presentations. So was it more severe illness? Was it an unusual combination illness? Was there an age difference associated with that case — all those different things so that we can feed that back in for the surveillance data that can be used.”
What they learn about the samples is uploaded to an international database that researchers from around the world can use to learn about the virus.
‘We are extremely proud of the numbers we’ve been able to put out, and we are hoping that we continue to do even more than that,” Soehnlen said. “Obviously, the whole reason that you want to do large numbers is to be able to take good public health actions, and we need data to be able to provide to our epidemiologists so they can do something for our citizens.”
Eleven known coronavirus variants, or clades, characterized by a combination of specific mutations, are spreading around the world right now, Blankenship said.
Of them, 10 have been identified in Michigan. Now that the UK variant has been detected, that means only the B.1351 variant, also known as the South African variant, has yet to be found in samples from Michigan, she said.
“We are starting to hear possible other variants of concern from Japan and Brazil, and we expect that these types of things will be constantly evolving,” she said.
And as the virus continues to change, Blankenship, Soehnlen, Lauring and other sentinels of infectious disease, will continue in their posts, ready to ring the alarm bells once again.
“If you’re working in a public health laboratory, you’re choosing to do something because you see the most interesting of cases and you get to try to help save lives while doing it,” Soehnlen said.
“People have stepped up. Everybody has been doing over time. They do weekends. They do holidays. They do whatever is necessary, and I think that is just a beautiful statement on how much people care.”
Contact Kristen Shamus: [email protected] Follow her on Twitter @kristenshamus.