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How coronavirus’s genetic code can help control outbreaks

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The six British patients seemed to have little in common besides this: Each was dealing with kidney failure, and each had tested positive for the coronavirus.

They were among scores of virus-stricken people showing up at Addenbrooke’s Hospital in Cambridge in the early weeks of April. Had they lived in the United States instead of the United Kingdom, the link that allowed the contagion to spread among them might have slipped by unnoticed.

But the U.K. had done something in the early days of the pandemic that the United States and many other nations had not. It funded a national push to repeatedly decode the coronavirus genome as it made its way across the country. The process reveals tiny, otherwise invisible changes in the virus’s genetic code, leaving a fingerprint that gives scientists valuable glimpses into how the disease is spreading. It’s a cutting-edge technique that was not widely available in prior global pandemics but that researchers believe can help hasten the end of this one.

[The code: How genetic science helped expose a secret coronavirus outbreak]

Experts cite this practice, known as “genomic epidemiology,” as one more tool the United States has failed to fully employ in the fight against the virus. Though it first sequenced the 3 billion-base-pair human genome 20 years ago and spends more on basic biomedical research than almost any other nation, the United States has yet to muster the kind of well funded and comprehensive national effort that could produce a more precise accounting of how covid-19 is infiltrating communities around the country.

In the case of the six British patients, sequencing revealed they had been infected by almost identical sub-strains of SARS-CoV-2, the virus that causes covid-19. Epidemiologists soon determined that all six had visited the same outpatient dialysis clinic on the same day of the week. Many had ridden in the same small transport van that regularly brought patients for treatment from across the surrounding area.

Officials promptly put in place new safety measures, including mandatory masks and intense cleaning of the van and the chairs at the dialysis clinic.

“And, you know, we’ve had no further cases,” said Estée Török, an infectious-disease expert at the University of Cambridge who helped decipher the outbreak. Studying the virus’s genome “helps to highlight cryptic or hidden transmission. That’s the real power of it — you can detect outbreaks and act while they’re happening.”

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Estée Török, an infectious-disease expert at the University of Cambridge, and her colleagues have sequenced and catalogued thousands of viral genomes since the spring. (Photos by Anastasia Taylor-Lind for The Washington Post)

Already, the United Kingdom has sequenced at least 72,529 coronavirus genomes, nearly as many as the rest of the world combined. By contrast, U.S. labs have produced less than half as many sequences as their British counterparts, based on data from the GISAID Initiative, a global database of coronavirus genomes. That’s despite the fact that the United States is battling an epidemic that’s massively larger.

UW Medicine Examines The Coronavirus’s Long-Term Effects

SEATTLE, WA — The University of Washington School of Medicine is helping lead a nationwide study, aiming to learn why some COVID-19 patients experience prolonged symptoms.

One of the researchers is Kelli O’Laughlin, a UW Medicine professor and emergency room physician, who says she has seen some former COVID-19 patients later return to the hospital experiencing severe fatigue and shortness of breath.

“We want to understand the long-term effects of COVID-19 and the ongoing impact it has on people’s lives,” O’Laughlin said. “We are still trying to understand which lingering symptoms are to be expected, how long they will remain and what is causing them.”

Nikki Gentile, another UW professor, said the same trend in “long-haulers” has been also noted by primary care doctors.

“We are seeing a lot of previously healthy, active patients presenting to primary care clinics with shortness of breath, fatigue, decreased exercise tolerance, diminished sense of taste or smell, and/or new or worsening anxiety or depression several weeks, or even months post-COVID-19 infection,” Gentile said.

The New York Times recently reported that some estimates indicate 1 in 3 coronavirus survivors suffer prolonged symptoms. The new two-year study hopes to illuminate why that might be happening across various age groups.

The research, funded by a grant from the Centers for Disease Control and Prevention, will allow UW medical experts to keep tabs on participants who contracted the virus and closely follow their recovery path. Recruitment for the study began on Oct. 1 and will analyze thousands of COVID-19 cases across the nation.

Learn more about the INSPIRE research project online.

This article originally appeared on the Seattle Patch

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