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GeekWire

Genetic sleuths flesh out pandemic’s origin story

Detailed genetic analyses of the strains of virus that cause COVID-19 suggest that the outbreak took hold in Washington state in late January or early February, but went undetected for weeks.

That’s the upshot of two studies published by the journal Science, based on separate efforts to trace the genetic fingerprints of the coronavirus known as SARS-CoV-2.

The studies draw upon analyses of more than 10,000 samples collected in the Puget Sound region as part of the Seattle Flu Study during the early weeks of the outbreak, plus thousands more samples from other areas of the world.

One of the studies was conducted by a team including Trevor Bedford, a biologist at Seattle’s Fred Hutchinson Cancer Research Center who has been issuing assessments of the virus and its spread since the earliest days of the outbreak. The first version of the team’s paper went online back in March and was revised in May, months in advance of today’s peer-reviewed publication.

The other study comes from researchers led by the University of Arizona’s Michael Worobey, who also published a preliminary version of their results in May.

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Cosmic Science

Report lays out a road map for human gene editing

Experts on an international commission are saying it’s too early to tweak the human genome for future generations, but they’re also pointing to the first genetic targets to be tweaked.

The experts’ report, issued today, comes in response to the uproar that arose in 2018 over claims that Chinese researchers had edited the genomes of twin babies in an attempt to reduce their vulnerability to the HIV virus.

Those claims sparked a blizzard of questions about the ethics, legality and efficacy of the experiment. It also sparked efforts to lay down guidelines for the use of recently developed gene-editing tools such as CRISPR to make changes in the human genome that could be passed down to future generations.

In today’s report — prepared with the backing of the National Academy of Medicine, the National Academy of Sciences and Britain’s Royal Society — the 18-member commission says researchers will have to demonstrate that precise genomic changes can be made reliably without introducing unwanted changes. The commission also says no current technologies, including CRISPR, can satisfy that requirement.

Once the state of the art gets to that point, heritable human genome editing should initially be limited to the prevention of serious diseases that are caused by a single gene, the report says. Examples include cystic fibrosis, thalassemia, sickle cell anemia and Tay-Sachs disease.

Even in those cases, gene-editing therapy should be reserved for cases where parents who have a known risk for passing on such a disease have virtually no other options.

“Any initial uses of HHGE [heritable human genome editing] should proceed incrementally and cautiously, and provide the most favorable balance of potential benefits and harms,” Rockefeller University President Richard Lifton, the panel’s co-chair, said in a news release.

Today’s report will feed into the work of a different advisory panel at the World Health Organization, which is drawing up recommendations for governance mechanism that would apply to heritable as well as non-heritable genome editing research and clinical uses.

Those recommendations are due to be issued later this year. It’ll be up to individual countries to incorporate the guidelines as they draw up gene-editing regulations. Today’s report calls for the creation of an independent International Scientific Advisory Panel to track developments in the gene-editing field, as well as an international body to provide further guidance on regulating the field.

Francis Collins, the longtime director of the National Institutes of Health, gave the report his thumbs-up in a tweet:

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GeekWire

How genomics can revolutionize public health

Coronavirus evolutionary tree
A phylogenetic tree tracks the evolution of SARS-CoV-2, the virus that causes COVID-19, as it spread throughout the United States. An orange dot at lower left indicates WA-1, the first confirmed case in the U.S., which was detected in Washington state. (Nextstrain / GISAID Graphic)

From the early days of the coronavirus pandemic, genetic sleuths have been at the forefront in the global effort to monitor SARS-CoV-2, the virus that causes COVID-19. By comparing the molecular fingerprints of different virus samples collected in Washington state, they were able to track down the first signs of community spread in the U.S.

In a paper published today by Nature Medicine, some of the pioneers of genomic epidemiology have laid out a 10-point plan for creating a well-supported scientific ecosystem — not only to fight COVID-19, but to head off future pandemics as well.

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GeekWire

Artist pays tribute to DNA pioneer Rosalind Franklin

Artist Kate Thompson with Rosalind Franklin portrait
Artist Kate Thompson worked samples of synthetic DNA into the ink and acrylic coating for her portrait of DNA pioneer Rosalind Franklin. (University of Washington Photo / Dennis Wise)

On one level, multimedia artist Kate Thompson’s work shows the black-and-white visage of Franklin — the late biochemist whose famous “Photo 51” revealed the double-helix structure of life’s most vital molecule, even though she didn’t get her full share of credit for it.

Look more closely, and you’ll see a mosaic of 2,000 images submitted by the general public as part of UW’s #MemoriesInDNA project.

And if you were to scrape off a few flakes of paint and process them in a DNA lab, you could read out the pixels that make up all of those images and more, translated from the four-letter genetic code of life to the ones and zeroes of digital data.

“This portrait is not only preserving Franklin’s memory, but preserving the data as well, in a form that will be accessible to future generations,” Karin Strauss, co-director of UW’s Molecular Information Systems Laboratory and principal research manager at Microsoft Research, said today in a news release about the art project.

Thompson’s portrait arguably ranks as the most visual and publicly accessible demonstration of mass data storage in DNA, which has been the focus of study at MISL for years.

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GeekWire

Bill Gates touts AI and gene editing for global health

Margaret Hamburg and Bill Gates
Microsoft co-founder Bill Gates makes a point during a Q&A with Margaret Hamburg, board chair for the American Association for the Advancement of Science. (GeekWire Photo / Alan Boyle)

Microsoft co-founder Bill Gates has been working to improve the state of global health through his nonprofit foundation for 20 years, and today he told the nation’s premier scientific gathering that advances in artificial intelligence and gene editing could accelerate those improvements exponentially in the years ahead.

“We have an opportunity with the advance of tools like artificial intelligence and gene-based editing technologies to build this new generation of health solutions so that they are available to everyone on the planet. And I’m very excited about this,” Gates said in Seattle during a keynote address at the annual meeting of the American Association for the Advancement of Science.

Such tools promise to have a dramatic impact on several of the biggest challenges on the agenda for the Bill & Melinda Gates Foundation, created by the tech guru and his wife in 2000.

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GeekWire

Scientists crack the code of mystery DNA

Evolutionary DNA tree
It’s been 80 million years since our our evolutionary branch diverged from mice — so why do we share some fragments of DNA that are essentially unchanged? (Fred Hutch News Service Illustration / Kim Carney)

Why do some strings of genetic code remain virtually unchanged despite tens of millions of years of evolutionary divergence? A newly published study that takes advantage of the gene-editing technique known as CRISPR has found that at least some of those DNA strings are essential to keep healthy cells growing and block the growth of tumor cells.

The research, published today in Nature Genetics, is the “first study finding large-scale importance of these highly conserved elements,” senior author Rob Bradley of Seattle’s Fred Hutchinson Cancer Research Center said in a news release.

Bradley and his colleagues say unraveling the mysteries of those ultra-conserved elements could lead to new avenues for cancer treatment.

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GeekWire

Chinese gene-editing scientist goes to prison

He Xiankui
Chinese researcher He Jiankui discusses his lab’s effort to produce babies whose genes have been altered to protect them from future HIV infection. (The He Lab via YouTube)

Chinese researcher He Jiankui, who stirred up a global controversy last year when he said his experiment produced twin baby girls with gene-edited traits, has been sentenced to three years in prison and ordered to pay a $430,000 fine, the state-run Xinhua news agency reported today.

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GeekWire

Cyrus Biotech and CRISPR gene pioneers team up

Feng Zhang
MIT researcher Feng Zhang will be the principal investigator for the Broad Institute’s collaboration with Cyrus Biotechnology. (HHMI Photo)

Seattle-based Cyrus Biotechnology says it’ll collaborate with the Broad Institute of MIT and Harvard on ways to optimize CRISPR gene-editing techniques for use in developing novel human therapeutics.

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GeekWire

Scientists publish a ‘parts list’ for the brain

Rebecca Hodge with brain
Rebecca Hodge, a senior scientist at the Allen Institute for Brain Science and one of the principal authors of a research study outlining a “parts list” for mouse brains and human brains, holds a section of postmortem human brain that was used in the study. (Allen Institute Photo)

A study led by researchers at Seattle’s Allen Institute for Brain Science lays out a “parts list” for the brain, including a detailed look at the differences between the parts for human brains and mouse brains.

They say the genetic results, published today in the journal Nature, suggest that relying on mice to study how the brains of men and women work could lead neuroscientists down blind alleys.

“The answer may be that you have to go to species that are more similar to humans,” Ed Lein, an investigator at the Allen Institute who’s also affiliated with the University of Washington, told GeekWire.

It’s not that the basic parts list is all that different: The researchers found that most of the 75 different cell types identified in the human brain, based on genetic makeup, are found in the mouse brain as well.

That commonality applies even to cells that the scientists had previously thought might be uniquely human, such as the “rosehip neurons” discovered last year.

But there are significant differences in the way those genes are expressed — differences that have developed over 75 million years of evolution. “The genes themselves haven’t really changed, but their regulation can change a lot,” Lein said.

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GeekWire

Year in Science: Genetic hopes and fears come true

He Xiankui
Chinese researcher He Jiankui discusses his lab’s effort to produce babies whose genes have been altered to protect them from future HIV infection. (The He Lab via YouTube)

In science, it was the best of times, and the worst of times.

2018 was a year when researchers focused in on ways to head off disease by reprogramming a patient’s own cells, but also crossed what many thought were ethical red lines in genetic experimentation. It was the first year in which women won a share of the Nobel Prize for physics as well as for chemistry, but also a year when the #MeToo issue came to the fore in the science community.

And it was the year that marked the passing of British physicist Stephen Hawking, who was arguably the world’s best-known living scientist.

As I look back at 2018, I’m seeing some stories that I missed but ended up featuring prominently in other folks’ year-end recaps. So, to even things out, my top-ten list focuses on five developments that we featured in the course of the last 12 months, and five more that didn’t get much play at the time.

Feel free to use the comment section to cast write-in ballots for the year’s science highlights and low lights. (For example, the sad tale of Tahlequah and the Southern Resident orca population tops The Seattle Times’ year-end list).

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