‘Be very vigilant’: Baker says highly infectious COVID-19 variant is likely already in Mass.

Nicholas McKenzie of Cataldo Ambulance Service conducted a COVID-19 test on Tuesday outside the Randolph Intergenerational Community Center.Craig F. Walker/Globe Staff

Governor Charlie Baker on Tuesday asked residents to redouble their efforts to control the spread of the coronavirus based on the assumption that a new, more contagious form of the virus has arrived in the state, threatening a further surge in cases and deaths.

”There’d be no reason not to [believe it’s here], given the contagious nature of this new variant,” Baker said in Springfield, a day after the first case of the new strain was reported in New York. He reiterated the importance of masks and social distancing and urged residents to be “very vigilant and careful and cautious about our physical engagement with other people.”

Baker’s acknowledgment of the variant’s likely presence in Massachusetts came less than three weeks after officials in the United Kingdom announced the discovery of the dangerous new mutation. As cases surged, health officials worldwide scrambled to halt travel to and from the UK. Truckers spent Christmas waiting in their cabs, barred from crossing into Europe. Flights were grounded. And still, the variant spread, across borders and oceans. It has since been found in more than 30 countries including the United States, where it has been reported in Colorado, California, Florida, and New York.

Baker talks about highly infectious COVID-19 variant

Gov. Baker talked about the new highly infectious COVID-19 variant and said it's likely already in Massachusetts. (Photo by David L Ryan/Globe Staff)

Massachusetts is already in the midst of a surge in COVID-19 cases and hospitalizations, with the state averaging a positive test rate of 8.5 percent. On Tuesday, Boston Mayor Martin J. Walsh announced he will extend restrictions on gyms, museums, movie theaters, and many other businesses for another three weeks, until Jan. 27, saying “we have to do everything we can to get those numbers down.”

No case linked to the variant has been officially announced in Massachusetts, though virologists agree it is almost certainly here. Labs, they say, aren’t screening broadly or quickly enough to detect the variant in Massachusetts.

“There is a high chance that the variant is anywhere and everywhere. But because we’re not looking for it, we don’t find it,” said Dr. Dan Barouch, director of the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center.

Dr. Lindsey Baden, an infectious diseases specialist at Brigham and Women’s Hospital, said he was unaware of any confirmed cases of the new strain in the state. But he too suspects it’s here and believes that other strains of the virus will emerge because that’s what pathogens do: mutate.

“This is a routine problem with infectious diseases,” he said. “Why should SARS CoV-2 be any different? Yes, I’m concerned.”

While highly transmissible, the UK variant is not believed to be more deadly than other versions of the virus, nor does it seem to cause more severe illness. Current vaccines are likely to be effective against it. But the variant’s emergence opens the door to what Harvard epidemiologist Bill Hanage called “a surge on top of a surge.” If cases increase across the board, then more deaths will inevitably follow.

Several groups in Massachusetts are trying to develop strategies to surveil for the UK variant, as well as a similarly worrying strain that seems to be responsible for the second wave of COVID in South Africa. Some experts fear the vaccines may not be effective against the latter strain.

Current methods of searching for the COVID variant mostly involve a laborious process of identifying virus samples that experience something called an “S gene dropout,” a phenomenon that could be an indicator of the new mutation. Once those samples are flagged by groups in Massachusetts, they are sent off to a lab for sequencing. Only then can officials be certain which strain the sample belongs to.

A study published in late December showed a recent rise in samples nationwide exhibiting the “S gene dropout,” suggesting the variant could have entered the United States in the fall.

Dr. Eric Rosenberg, director of the clinical microbiology laboratory at Massachusetts General Hospital, is overseeing a team that has started to screen for the variant. So far, two samples were flagged as potentially harboring the N501Y mutation — a marker of the British and South African COVID variants — but were found to be false alarms when analyzed by the Broad Institute, the Cambridge research center that has sequenced hundreds of samples since December looking for new and known variants.

The Massachusetts Department of Health is also sequencing samples, but state officials did not respond to requests for comment.

Rosenberg’s team intends to screen all positive specimens obtained at Mass. General. But none of the analysis will be done in real time, meaning it may take days or weeks to link a positive test to the variant. Furthermore, the screening method used by Rosenberg’s team uses the same coveted test reagent needed for the basic COVID-19 PCR test, which will be prioritized.

“We don’t sequence as many viruses on a per capita basis as they do in the UK, or as we need to do [to] understand what’s going on. We do some sequencing, sure, but it’s not broad and comprehensive. We analyze less than half a percent of the virus, whereas the UK is closer to five to 10 percent,” said Barouch.

Moreover, the variant underscores the reality that the virus is mutating, sometimes dangerously, even as the world develops strategies to mitigate its spread and treat its disease.

“I think you’re going to see variants originating all over the world. This isn’t a uniquely South African or British experience. It’s only a matter of time before we have a couple of variants that originate in the United States,” said Dr. Michael Osterholm, an infectious disease expert tapped by President-elect Joe Biden’s Transition COVID-19 Advisory Board.

“We have to recognize that we’re just now getting into these very difficult variant situations. Don’t expect it to get any better,” he cautioned. “I think this is only going to get more complicated as time goes on, in terms of variants that emerge that have these potential aspects of increased transmission or the potential to avoid vaccine-related immunity. This is not going to be a one-time phenomenon.”

Osterholm said the infrastructure exists to sequence more widely for variants and potentially stop them before they become too dispersed. But “the network isn’t there to give us a valid, real-time example of what’s going on out there.” The virologists who were contacted said they hope the discovery of the two variants sparks more investment in sequencing.

“This is a wake-up call. It’s clear that we need to improve our capabilities and build something more like the United Kingdom has,” said Dr. Jacob Lemieux, an infectious disease physician at Mass. General and researcher involved with the Broad Institute’s sequencing. “There’s been clear communication from the state level as well as national level public health authorities that this is a priority. But we are starting from a position where there is frankly a lot of work to be done.”

With the highest reported mutation rate for any biological entity, HIV is a prime example of a worst-case scenario of what happens when a virus mutates so quickly that it evades antibodies and therefore thwarts a widely effective vaccine. Almost four decades after HIV first emerged in the United States, scientists today rely on a combination of high-cost pre-exposure prophylaxis and an antiretroviral cocktail to prevent and suppress the virus. Still, roughly 36,400 new infections occurred in 2018. Thankfully, SARS-CoV-2 seems to have a far slower rate of mutation.

But mutations do happen. The two discovered in the UK and South Africa have proved to be alarmingly contagious. Given time and space, further mutations could be of even greater concern. Some might cause more severe disease that doesn’t respond well to promising treatments, like remdesivir or monoclonal antibodies. Some could thwart the diagnostic tests used to identify cases. Others could evade the vaccines, though none have been officially reported to do so yet.

“Do you know what the two most important words of the pandemic are that people don’t tend to use?” said Hanage. “So far.”

Jonathan Saltzman of the Globe staff contributed to this report.