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Scientists reading the genetic blueprints of the new coronavirus, drawn from 250 Wisconsin COVID-19 patients, have discovered two distinct clusters of disease: one in Madison, and the other in Milwaukee. There appears to have been limited mixing between the two viral clusters, said researchers at the University of Wisconsin-Madison.

“The fact that we are not seeing those from one community cropping up in the other community suggests that the stay-at-home orders are working,” said David O’Connor, a UW professor of pathology and laboratory medicine.

Within the two communities, however, the virus has been busy.

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“There’s pretty strong evidence in the testing that there is continued spreading within Milwaukee and within Madison,” said Thomas Friedrich, professor of pathobiological sciences and an expert on pandemic viruses. “That would suggest that if we release people, more people who are infected would mix with uninfected people and we would expect there to be more infections.”

Just as the genetic sequence of a person reveals their inherited traits, strengths and vulnerabilities to disease, the sequence of a virus tells much of its story. Researchers use complex machines to read the sequence of viruses because the information can explain how a virus has evolved, how mild or deadly it is, and why it spreads easily or with difficulty.

Knowing a virus’ sequence can provide a window into targets for treatment and also present a picture of how it may evolve in the months or years to come. With the new coronavirus, we have only seen it for a short time.

Yet more than 16,000 samples of the new coronavirus have been sequenced already across the globe.

“What we are seeing now still represents the virus’ first tentative explorations around the host,” O’Connor said.

He and Friedrich have been sequencing viruses together for more than 20 years and stressed that so far their new coronavirus samples have come from two main areas, Milwaukee and Madison.

“We still don’t know what the viruses in Brown County look like, and we’d really like to know,” Friedrich said.

The Madison researchers are part of the SPHERES program, a national effort led by the Centers for Disease Control and Prevention, to share sequencing information, monitor changes in the virus and provide information to help diagnose and treat COVID-19. The program includes dozens of universities, hospitals, labs and institutions.

The Medical College of Wisconsin will also be participating in the program. Raul A. Urrutia, director of the college’s Genomic Sciences and Precision Medicine Center, said he expects to begin sequencing samples of the virus next week.

He said about 30 to 50 researchers from the Medical College, Marquette University, Marshfield Clinic and the University of Wisconsin-Milwaukee expect to collaborate on studies of the virus’ sequence.

Infectious disease experts only gained the ability to sequence the genetic blueprint of a virus in recent decades. But in the last 10 years, the technology needed to do it has grown much faster and far less costly.

One of the remarkable early scientific accomplishments was the publication of the new virus’ genetic sequence barely a week after doctors first identified the virus. Just six days later, another team ironed out the inaccuracies that often appear in the first draft of a genome.

“No virus has been sequenced this deeply and this quickly,” O’Connor said.   

Knowing the virus’ genetic sequence helps researchers in multiple ways, from finding potential weakness to exploit through treatments, to determining where the virus came from and how it might evolve.

The new coronavirus has a genetic sequence of about 30,000 chemical base pairs — much smaller than the human sequence, which is 3.2 billion base pairs. In 2009, doctors at Children’s Hospital and the Medical College of Wisconsin used about 1.5% of the full human sequence to diagnose and treat a new disease that afflicted a young Monona boy named Nic Volker. They were able to save his life.

The genetic sequences of viruses are constantly changing, but some changes are far more important than others. Researchers look for crucial changes that alter how deadly or how infectious the virus is.

“So far, we don’t have any evidence that any of these different signatures are biologically significant — that any of them make the virus more virulent or more transmissible,” Friedrich said.

These changes can also affect what happens when a person who survived COVID-19 in 2020 becomes infected by a new version of the virus in 2022. A person may still have some portion of the antibodies they used to defeat the virus. However, it is also possible that the 2022 virus will have evolved to slip past the antibodies that worked in 2020.

“Will immunity to the virus last for two years, five years or more? Ask me again in two years,” O’Connor said. “It’s too early to say.”

Mark Johnson has written in-depth stories about health, science and research for the Journal Sentinel since 2000. He is a three-time Pulitzer Prize finalist and, in addition, was part of a team that won the 2011 Pulitzer Prize in Explanatory Reporting for a series of reports on the groundbreaking use of genetic technology to save a 4-year-old boy.

Email him at [email protected]; follow him on Twitter: @majohnso.

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