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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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Scientists design proteins that confound coronavirus

Imagine being able to ward off COVID-19 just by spritzing a nasal spray into your nostrils. It may not be just your imagination: Researchers at the University of Washington have designed a batch of synthetic proteins that could conceivably block the coronavirus behind this year’s pandemic from gaining a foothold.

“Although extensive clinical testing is still needed, we believe the best of these computer-generated antivirals are quite promising,” Longxing Cao, a postdoctoral scholar at UW’s Institute for Protein Design, said in a news release.

Cao is the lead author of a study about the protein-building experiment, published today by the journal Science. It’s the latest innovation to come from the emerging field of protein engineering, and the technique could revolutionize how drugs are developed to counter future pandemics.

It may not be too late to counter COVID-19 as well. “We are working to get improved versions … deployed to fight the current pandemic,” senior study author David Baker, the director of the Institute for Protein Design, told GeekWire in an email.

The technique involves creating small-molecule proteins, or mini-binders, that are custom-designed to latch onto the spiky molecular structures that are scattered around the surface of SARS-CoV-2, the virus that causes COVID-19.

The spikes on the virus do their dirty work by fitting into molecular-scale receptors on the surfaces of cells, much like fitting a key into a lock to gain entry to someone’s house. Once the virus “unlocks” a receptor, it gains entry to the cell, hijacks its chemical machinery and churns out more virus particles to spread the infection.

Baker, Cao and their colleagues used high-powered computers to design more than 2 million candidate proteins that could conceivably gum up the works for the virus’ spike protein. More than 118,000 of the most promising candidates were synthesized and tested on lab-grown cells.

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‘Three Little Pigs’ demonstrate Neuralink’s brain implant

With grudging assistance from a trio of pigs, Neuralink co-founder Elon Musk showed off the startup’s state-of-the-art neuron-reading brain implant and announced that the system has received the Food and Drug Administration’s preliminary blessing as an experimental medical device.

During today’s demonstration at Neuralink’s headquarters in Fremont, Calif., it took a few minutes for wranglers to get the swine into their proper positions for what Musk called his “Three Little Pigs demonstration.”

One of the pigs was in her natural state, and roamed unremarkably around her straw-covered pen. Musk said the second pig had been given a brain implant that was later removed, showing that the operation could be reversed safely.

After some difficulty, a third pig named Gertrude was brought into her pen. As she rooted around in the straw, a sequence of jazzy electronic beeps played through the sound system. Musk said the tones were sounded whenever nerves in the pig’s snout triggered electrical impulses that were picked up by her brain implant.

“The beeps you’re hearing are real-time signals from the Neuralink in Gertrude’s head,” he said.

Eventually, Neuralink’s team plans to place the implants in people, initially to see if those who have become paralyzed due to spinal cord injuries can regain motor functions through thought alone.

Musk said the implant received a Breakthrough Device designation from the FDA last month. That doesn’t yet clear the way for human clinical trials, but it does put Neuralink on the fast track for consultation with the FDA’s experts during preparations for such trials.

Neuralink has received more than $150 million in funding, with roughly two-thirds of that support coming from Musk himself. Today he said the venture had about 100 employees. He expects that number to grow. “Over time, there might be 10,000 or more people at Neuralink,” he said.

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A new way to fight COVID-19 and other viral threats

A team including researchers from Seattle’s Benaroya Research Institute at Virginia Mason has identified a new pathway for protecting cells from deadly viruses — including the coronavirus that causes COVID-19 as well as the Ebola virus.

The technique, described in this week’s issue of the journal Science, takes advantage of a screening technique for seeking out new genes that can prevent infection.

In the newly published study, the research team pinpoints two genes that have already been the subject of biomedical studies. One gene is called the MHC class II transactivator, or CIITA. The second gene is known as CD74 — specifically, a variant known as p41.

Those genes have previously been thought to be involved in conventional immune responses involving T cells and B cells. The new findings, resulting from a screening technique called transposon-mediated gene activation, shed light on a different way in which the genes block infection.

The researchers found that CIITA can induce resistance in human cell lines by activating CD74 p41, which in turn disrupts the processing of proteins on the coat of the Ebola virus protein. That stops the virus from being able to infect its target cell. The same process blocks the entry pathway for an assortment of coronaviruses — including the SARS-CoV-2 virus that’s behind the current pandemic.

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Synthetic proteins use logic to choose which cells to kill

The age of molecular-scale computing is entering a new era, thanks to the development of a system that uses synthetic proteins and Boolean logic to identify cancer cells.

The proteins can lock onto chemical markers on the surface of cells in predetermined combinations, performing the roles of logical AND, OR and NOT gates. It’s similar to the way binary computers do their thing, but with biochemistry rather than electronic bits.

“We were trying to solve a key problem in medicine, which is how to target specific cells in a complex environment,” Marc Lajoie, one of the lead authors of a study published today in the journal Science, explained in a news release.

“Unfortunately, most cells lack a single surface marker that is unique to just them. So, to improve cell targeting, we created a way to direct almost any biological function to any cell by going after combinations of cell surface markers,” Lajoie said.

Lajoie worked on the effort during his stint as a postdoctoral scholar at the University of Washington’s Institute for Protein Design. He’s now co-director for protein and cell engineering at Lyell Immunopharma, a California-based startup aiming to commercialize the technique.

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Cosmic Science

XPRIZE organizes $5M challenge for COVID-19 tests

The nonprofit XPRIZE foundation has assembled a high-powered coalition to take on a high-priority problem: developing high-quality screening tests for COVID-19 that are low-cost and easy to use with a fast turnaround time.

The $5 million XPRIZE Rapid Covid Testing competition is the latest project from the folks who created multimillion-dollar contests for privately financed spaceships, super-efficient cars and real-life equivalents of Star Trek’s medical tricorders.

Among those voicing support for the testing development effort are:

  • OpenCovidScreen, a nonprofit group that numbers researchers from such institutions as the University of Washington and business leaders from such companies as Illumina among its advisers and collaborators. OpenCovidScreen’s partners include ThermoFisher Scientific, Google, Amazon and Ancestry.com. The group’s president and co-founder is Jeff Huber, a former Google executive and co-founder of Grail, a cancer detection startup.
  • A $50 million fund known as the COVID Apollo Project, backed by investors including RA Capital, Bain Capital, Perceptive Advisors, Redmile Group and Samsara Biocapital.
  • Healthcare companies including Anthem, Blue Shield of California, BlueCross / BlueShield of South Carolina and Cambia Health Solutions.
  • California Gov. Gavin Newsom, who said in a statement that he looks forward to “seeing the breakthroughs that arise from this challenge and the countless lives that will be saved as a result.”

Teams can compete in one of four categories, focusing on at-home tests, point-of-care tests, distributed lab tests or high-throughput lab tests. They’ll be asked to develop new tests that produce results within 12 hours of collecting a sample, using minimally invasive procedures.

Winning teams will be required to deploy and conduct a minimum of 500 tests per week at a live testing site within 60 days, and have the potential to scale up their solutions to thousands of tests per week.

Cost of the test should be less than $15, including all materials, with avenues for reducing costs as production is scaled up.

Currently, the cost of COVID-19 testing can range from less than $100 to more than $1,000, depending on healthcare circumstances. What’s more, the turnaround time for test results can extend past a week, due to shortages in supplies and staffing.

“Fast, affordable, and accessible testing is crucial to containing the COVID-19 pandemic and safely reopening schools, businesses and other vital institutions around the world,” XPRIZE CEO Anousheh Ansari said. “XPRIZE Rapid Covid Testing is inspiring the best entrepreneurial and scientific teams to come together to work towards rapid, affordable Covid-19 testing at scale, and ultimately, getting the world up and running again.”

Teams must register by Aug. 31, and the XPRIZE timeline calls for tests to be deployed in a pilot round that runs from Nov. 2, 2020, to Jan. 22, 2021. Winners are to be announced by the end of next January, with scaled-up production planned during the months that follow.

The reaction to today’s announcement was mostly positive. “THIS is what we need right now,” Eric Feigl-Ding, an epidemiologist at the Federation of American Scientists, said in a tweet.

However, the Food and Drug Administration is likely to have the final word on any tests that come out of the competition. And even without the contest, progress is being made on rapid-turnaround COVID-19 tests. There’s a chance that this XPRIZE will be rendered unnecessary before it reaches its climax. It wouldn’t be the first time.

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Elon Musk’s COVID-19 tweets get a reality check

Billionaire Elon Musk knows his stuff when it comes to rockets or electric cars. But does that translate into epidemiological expertise? Not completely, according to Washington state’s coronavirus trackers.

Musk weighed in today with a Twitter response to a GeekWire story that focused on Washington’s rising number of COVID-19 cases as well as Washington Gov. Jay Inslee’s appearance on CBS’ “Face the Nation.”

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Bill Gates sounds the alarm on resurging pandemic

Tech leaders typically use their TED talks to sketch out an optimistic vision of the future, but today Bill Gates used his to warn about a rough autumn ahead due to the continuing coronavirus pandemic.

“There’s good progress … but nothing that would fundamentally alter the fact that this fall in the United States could be quite bad, and that’s worse than I would have predicted a month ago,” he told moderator Chris Anderson during a live-streamed TED2020 Q&A.

Although Gates didn’t mention President Donald Trump by name, he faulted a lack of American leadership for making things worse.

“We need leadership in terms of admitting that we’ve still got a huge problem here, and not turning that into almost a political thing,” he said. “You know, ‘Isn’t it brilliant, what we did?’ No, it’s not brilliant. … We need a leader who keeps us up to date, is realistic, and shows us the right behavior as well as driving the innovation track.”

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COVID-19 tracking system extends its reach

As concerns about a resurgence of the coronavirus outbreak are widening, so is the reach of the COVID-19 tracking platform created by Sentinel Healthcare, a Seattle-based medical data startup.

The app-based platform was rolled out three months ago, just as the pandemic was taking hold, and it wasn’t long before it was picked up by UT Health Austin in Texas to keep track of the symptoms of quarantined patients.

“We’ve now contact-traced and diagnosed many, many patients,” said Sentinel Healthcare CEO Nirav Shah, a neurologist and the former stroke director at Swedish Hospital in Seattle.

As of this week, about 1,600 of the app’s users in Texas have been diagnosed with COVID-19, triggering contact tracing for more than 4,000 people, Shah told GeekWire.

Shah said Sentinel Monitor started registering a spike in the number of cases being diagnosed about two weeks ago. “That ended up being borne out,” he said. “Looking back over the past 10 days … we’ve seen almost a tripling or quadrupling of daily case counts.”

Now Sentinel will be putting its platform to the test closer to home.

Today the company announced a partnership with Era Living, which runs eight retirement communities in the Seattle area. Sentinel will support Era Living in testing and monitoring its more than 900 employees and 1,300 residents for COVID-19. Seattle-based Transpara Health will provide logistical and operational support.

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Scientists will map effects of Alzheimer’s disease

A $40.5 million collaborative research center headquartered at Seattle’s Allen Institute aims to create high-resolution maps of brains ravaged by Alzheimer’s disease, to trace new paths to early diagnosis and treatment.

The center will draw upon expertise not only at the institute, but also at UW Medicine and Kaiser Permanente Washington Health Research Institute. Funding for the next five years comes from the National Institute on Aging, part of the National Institutes of Health.

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