How Minnesota confirmed the nation's first Brazilian COVID-19 variant case

Sean Wang was on his way to get vaccinated against COVID-19 when a co-worker in the state's public health lab called with startling news.

Lab results that January morning suggested a Minnesotan might be the nation's first confirmed case of a more threatening form of the pandemic virus, one that had been wreaking havoc in Brazil.

Wang's reflex was to quickly double- and triple-check the accuracy of the finding, which seemed surprising since so many other states have more obvious connections with the South American nation.

"It was like: Really?" said Wang, who is the sequencing and bioinformatics supervisor for the Minnesota Department of Health. "Since this is from a random sampling pool — to me, it's like a 'bingo' I don't really want to call."

Health officials quickly discovered they had previously conducted a case investigation when the patient tested positive. An interview summary showed the patient had traveled back from Brazil in early January.

The Minnesota Department of Health soon issued a public notice underscoring that travel during the pandemic is risky, because it can enable dangerous new forms of the virus to spread.

The sequence of events shows why whole genome sequencing has emerged as a key tool for spotting pandemic threats — and why Minnesota and other states are scrambling to analyze as many random samples as possible. Because scientists never know what they might find.

"There needs to be a coordinated federal effort for sequencing," said Sara Vetter, interim director of the state's public health lab, via e-mail. "That means more on a national level and more states doing more sequencing. Right now, it's really difficult to understand the big picture, because every state is either on its own or relying on commercial laboratories for sequencing.

"It's getting there," she added, "but it's going to take time."

There are many strains of SARS-CoV-2 that comprise what scientists call the "wild type" virus that's caused most pandemic infections thus far. As the virus has circulated around the globe in the past year, it has mutated in ways that have led to the creation of variant strains.

Whole genome sequencing is a laboratory technique that shows the genetic code of a virus that's infected a patient. That's how scientists can see the difference between wild type SARS-CoV-2 and variant strains, including the subset known as "variants of concern."

These versions of the virus are thought to be more contagious, more likely to cause serious illness or capable of evading immune protection from vaccines or previous illness.

Last year, health officials in the United Kingdom announced that a more contagious form of the pandemic virus called B.1.1.7 was widely circulating in southeast England. Concerns have grown this winter over another variant first identified in South Africa called B.1.351 as well as the variant associated with Brazil, which is called P.1.

Whereas vaccines still seem to work well against the U.K. variant, the South African and Brazilian variants feature a mutation called E484K that is particularly troubling because it apparently lets the virus escape protective immune responses to some degree.

"Right now, Brazil is a total house on fire," Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, said during a March 18 podcast. "P.1 is by far the most important of the variants we're seeing there."

Yet that variant doesn't seem to be spreading rapidly in the U.S. Whereas the Centers for Disease Control and Prevention was reporting more than 5,567 confirmed cases of B.1.1.7 as of March 18, there were just 48 cases at that time of the P.1 variant.

"I don't know what to make of the fact that some of the strains [such as P.1] with that mutation haven't really been taking off everywhere, as one might expect they could be," said Dr. Yonatan Grad, professor of immunology and infectious diseases at the Harvard T.H. Chan School of Public Health. "It's an interesting and puzzling question."

When the U.K. in November raised alarms about B.1.1.7, Minnesota's public health lab started to increase its volume of whole genome sequencing studies, Wang said. Expanding the work is easier said than done, however.

Samples from patients who test positive for SARS-CoV-2 reside with commercial labs that don't have a lot of space to store specimens. So, the state has relied on a partnership where commercial labs agree to retain and share samples — no small task, since those outside labs must analyze whether any given sample is of a quality that allows for sequencing.

Once the state public health lab obtains samples, processing them isn't quick. Workers must perform about a half-dozen steps to prepare specimens for analysis in a sequencer. The machine analyzes 94 samples at a time, but each run takes 40 hours to complete. A high performance computer then performs further analysis.

"It's a multiday process," Wang said. "The effort we need to put in whole genome sequencing is roughly five times more than the regular … COVID clinical test."

When results arrived on the morning of Jan. 25, a lab worker manually examined slides to double-check that the specimen's sequence included 15 of the 17 mutations that are the hallmark of the P.1 strain. Wang, meanwhile, contacted Melanie Firestone, an epidemic intelligence service officer for the Centers for Disease Control and Prevention.

Firestone looked up data and found the patient previously had been interviewed by health officials, and the report showed recent travel to Brazil.

"That was sort of an 'a-ha' moment, where we realized the epidemiology data corresponded so well with the laboratory data," said Firestone, who has been assigned by CDC to work with the state Health Department.

Soon, the message made its way to Dr. Ruth Lynfield, the state epidemiologist. "Our jaws dropped," Lynfield said, "because this was picked up in random surveillance."

Kathy Como-Sabetti, an epidemiologist focused on COVID-19 with the Minnesota Department of Health, added: "Minnesota is not necessarily the geographic location that I would think of as an introduction of a variant known in South America."

If it was surprising, it was also reassuring because the case was connected with travel. Otherwise, the finding might have suggested it was circulating in the community. As of March 18, the state's only other case of P.1 was a household contact of the first case, who also traveled to Brazil.

The patient wound up in the hospital for nine days.

Assessments were conducted for 111 people who provided care at four different facilities, and there were no high-risk exposures such as breaches in use of personal protective equipment, said Amanda Beaudoin, an epidemiologist who co-leads a Health Department group that works on preventing cases among health care workers. Even though there wasn't necessarily a reason to test workers based on standard criteria, 22 of them accepted the state's offer of testing and none tested positive.

"The history of travel to Brazil had raised red flags in every single institution," said Stacy Holzbauer, the other co-lead for health care worker monitoring who also is a CDC epidemiology field officer. "It really served as a teaching point for these health care facilities when we confirmed that it was a P.1 variant — that you always have to be vigilant because you don't know what's coming in the door."