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Human genome sequencing rises to the next level

Twenty years after the first human genome sequence was published, an international research team has kicked the sequencing game to the next level with a set of 64 reference genomes that reflect much higher resolution and more genetic diversity.

Since the Human Genome Project completed the first draft of its reference genome in 2001, decoding the human genetic code has been transformed from a multibillion-dollar endeavor into a relatively inexpensive commercial service. However, commercial whole-genome sequencing, or WGS, often misses out on crucial variations that can make all the difference when it comes to an individual’s health.

“As a metric, 75% of structural variants that are present in that person’s genome are missed by WGS, but are captured by our long-read phased genome assembly,” University of Washington genome scientist Evan Eichler told me in an email. “Such variants are about three times more likely to cause disease.”

Eichler, who was a member of the original Human Genome Project, is one of the senior authors of a study laying out the new set of reference genomes, published today by the journal Science.

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GeekWire

Bad weather slows COVID-19 vaccination drive

They say that the second vaccine shot for COVID-19 is rougher than the first one — and we’re not just talking about the side effects.

As a newly double-vaccinated member of the 65-and-older set, I can vouch for the claim that the side effects can be felt more acutely the second time around: Back in late January, my first Pfizer-BioNTech shot gave me nothing more than a sore arm. This week’s second shot gave me body aches the day after, as if I had been shoveling snow for hours. (Which, come to think of it, I was … a couple of days earlier.)

But that’s nothing compared to the headaches I would have given myself if I had tried to schedule a vaccination this week. I would have been hard-pressed to find an appointment, even with the benefit of websites like WA COVID Vaccine Finder, the Washington State Department of Health’s Vaccine Locator and the Washington State COVID-19 Vaccination Sign Up System.

Jeffrey Duchin, health officer for Public Health – Seattle & King County, acknowledged that it’s been a tough slog for some folks. “I wish we had more vaccine, and had vaccine for everyone,” he said today during a news briefing.

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GeekWire

One man’s quest for the COVID-19 vaccine

Trying to get an appointment for a COVID-19 vaccine on the day that eligibility was expanded to new age groups in Washington state would be a familiar experience to anyone who’s tried to get a hot movie ticket, a cheap airfare or season tickets to Kraken hockey games.

I’ve been through all of those trials, and my efforts to work through the online hiccups and fast-disappearing slots are likely to be replicated in the months ahead as efforts to quell the coronavirus pandemic continue to ramp up.

Bottom line? Sharpen your searching skills, don’t wait for an invitation, and pursue multiple options.

Your mileage may vary, of course. I was just one of thousands of regular folks aged 65 and older who joined the search for the vaccine this week.

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GeekWire

What we need to do to get through a COVID winter

You may want to put off that big holiday dinner. Don’t have your heart set on sending the kids back to school anytime soon. And if you plan to get on a plane, be sure to wear your mask.

Those are just a few of the nuggets of advice that critical-care physician Vin Gupta and computational biologist Trevor Bedford passed along for getting through this winter in the midst of the persistent coronavirus outbreak.

“We’re definitely not ’rounding the curve,’ ” Gupta said.

Gupta and Bedford delivered a data-rich status report on the pandemic today during a virtual GeekWire Summit session moderated by CNBC technology and health reporter Christina Farr.

The bottom line is that it’s still too early to let your guard down, despite what some politicians might claim.

Get the full story on GeekWire.

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GeekWire

Triumphs and tragedies in the vaccine quest

The good news is that Operation Warp Speed, the multibillion-dollar effort to develop vaccines for COVID-19, is moving ahead at a pace that justifies its name.

The bad news is that despite all that effort, the coronavirus outbreak is still likely to be with us next year — and low- to medium-income countries such as India are likely to be hit particularly hard.

“We’re going to probably see a lot of deaths,” said Lynda Stuart, deputy director for vaccines and human immunobiology at the Bill & Melinda Gates Foundation. “It’s going to be a great inequity and tragedy that will unfold.”

Stuart and other experts involved in the vaccine quest laid out their assessment of the road ahead today during the first session of the 2020 GeekWire Summit.

Get the full story on GeekWire.

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Cosmic Science

When pandemics mix with politics, it’s unhealthy

For years, public health officials at the Centers for Disease Control and Prevention have been playing out scenarios for dealing with pandemics, but the one scenario they didn’t count on was that they’d be hamstrung by their own political leaders.

“I don’t think anybody ever thought that that would happen,” said Maryn McKenna, a veteran reporter on infectious diseases. “And yet, seven months into the pandemic here in the United States, that’s pretty much where we are.”

McKenna and others involved in the response to the coronavirus outbreak discussed the role that politics has played in the pandemic, during a presentation organized by the National Association of Science Writers and the Council for the Advancement of Science Writing.

Today’s session served as the kickoff for a free weekly series of online events focusing on COVID-19, offered for journalists as well as the public in conjunction with the annual ScienceWriters conference.

Panelists agreed that mixed messages from the nation’s leaders have hampered efforts to combat the pandemic, which has claimed the lives of more than 200,000 Americans. Just today, Cornell University researchers said their analysis pointed to President Donald Trump as “the single largest driver of misinformation around COVID.”

Such misinformation has taken the form of conspiracy theories about the origins and spread of the coronavirus that causes COVID-19, plus the hype surrounding supposed “miracle” cures and efforts to downplay the seriousness of the outbreak.

Marsha Jones — co-founder and executive director of The Afiya Center, a Texas-based reproductive justice organization — said she’s seen it all before, during the AIDS crisis of the 1980s and 1990s.

“I didn’t think that I would ever see a disease so politicized as HIV was ever again, because for some reason I thought we learned,” she said.

Like the HIV epidemic, the COVID-19 epidemic is dealing a particularly heavy blow to people “who get the least amount of funding, who get the least amount of recognition, who have the worst care,” Jones said.

And even as the outbreak is raging, disadvantaged communities are struggling with the repercussions of systemic racism and urban unrest. “We’re living in a dual epidemic,” Jones said.

Science is suffering along with society, said Peter Daszak, president of the New York-based EcoHealth Alliance. His group became the focus of controversy early in the pandemic because it helped train Chinese virologists in Wuhan, which was the outbreak’s global epicenter.

The training effort was part of a federally funded program called PREDICT, which aimed to anticipate cross-species viral outbreaks. The Trump administration let the program expire last year, just before the first COVID-19 cases came to light — and EcoHealth Alliance faced heavy criticism largely because of unfounded accusations that the virus was unleashed from the Wuhan virology lab.

“It’s the right wing, it’s QAnon, it’s people spending hours in their basements doing ‘research’ on the internet to dig up stuff that sounds like a conspiracy,” Daszak said. “And of course, with so much online presence, the president not only allows that to happen, but also promotes it, and seems to believe it himself.”

Scientists tend to be uncomfortable about getting into the political fray, but Daszak said inaction may no longer be an option. “During the HIV pandemic, science got political, and scientists got political,” he said. “It’s no good keeping quiet. You’ve got to push back, and push back strong, and tell the truth about what’s going on. … If you keep quiet, you’ve just basically consigned science to the trash heap.”

So what is to be done? The panelists said the political outlook could brighten next year. There’s already an effort in the works to get a virus surveillance program called Stop Spillover funded, and Democratic presidential candidate Joe Biden has promised to revive PREDICT.

McKenna said Biden could also reverse cutbacks in public health spending and shore up the CDC’s data-gathering operation.

But politicians aren’t the only ones who can play a role in repairing public policy on pandemics, Daszak said.

“You’re journalists,” he told the online audience. “So get out there and speak the truth, and push back.”

McKenna said it’s crucial for all journalists to be trained to cover the different facets of coronavirus coverage, ranging from biology to business, from epidemiology to education.

“We should rethink the silos within which we exist as journalists … because it’s entirely possible that a science and public health story like the coronavirus pandemic will come in and cut across all those silos, and demonstrate the degree to which we have not trained each other in the mutual knowledge that we all need,” she said.

Daszak said truth-telling shouldn’t be confined to a newsroom setting.

“Go talk to your neighbors and friends,” he said. “And also, you know, the folks with the Trump sign outside their house. Go have a chat with them, see what they think about masks and school openings. Listen to them, and say a couple of things, a couple of facts, nothing heavy, and just let it settle and move away. … We need a societal change in our understanding of things like this pandemic.”

Jones stressed that you don’t need to be a politician — or a journalist, or a public health worker, for that matter — to parry the pandemic.

“The greatest changes don’t necessarily have to happen in the political arena. “There are changes that can happen outside of that, that will inevitably impact what’s happening in the political arena,” she said.

She advised starting with the place where you have the most influence, even if it’s outside the traditional halls of power.

“If that’s at your house, if that’s on your porch, in the park, in the gym — wherever it is that you have the most power, and you can have the most convincing conversation where you’re talking with somebody who can create change, that’s what you do,” Jones said.

From the CDC: How to protect yourself and others

The next presentation in the “COVID-19 Science and Coverage” series is scheduled for Oct. 7, starting at 5 p.m. ET (2 p.m. PT). The theme is “Reporting on the Pandemic.” Panelists include STAT senior writer Helen Branswell; Laura Helmuth, editor in chief of Scientific American; Patrice Peck, creator of the newsletter Coronavirus News for Black Folks; and Zeynep Tufekci, a contributing writer at The Atlantic

Full disclosure: I’m the president of the Council for the Advancement of Science Writing, which is one of the organizers of the series. FiveThirtyEight senior science writer Maggie Koerth, a CASW board member, moderated today’s session. 

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Cosmic Science

Antibody cocktail just might ward off COVID-19

An international research team led by University of Washington scientists has identified two kinds of “ultrapotent human antibodies” that could go into a drug cocktail for guarding against COVID-19.

  • UW’s David Veesler and Vir Biotechnology’s Katja Fink are the senior authors of the study published online today by the journal Science, which highlights two monoclonal antibodies known as S2E12 and S2M11. The antibodies were found to block SARS-CoV-2, the coronavirus that causes COVID-19, from latching onto molecular receptors on cells in hamsters.
  • An analysis of the antibodies’ molecular structure determined that they block the virus by gumming up its characteristic “spike” protein, which has been a target for many of the vaccines and therapies under development to fight COVID-19. Some of the researchers behind the newly published study, including Veesler, reported a similarly promising antibody called S309 in May.
  • Researchers say such antibodies could be combined in a drug cocktail to guard against the virus evolving to evade any single one of the ingredients. A drug that takes advantage of S309’s effect is already being tested in a phase 2/3 clinical trial launched by GlaxoSmithKline and Vir Biotechnology.

The principal authors of the Science study, “Ultrapotent Human Antibodies Protect Against SARS-CoV-2 Challenge Via Multiple Mechanisms,” are M. Alejandra Tortorici of the University of Washington and Martina Beltramello of France’s Pasteur Institute and CNRS. Other UW researchers among the 47 co-authors of the study include Ha Dang, Matthew McCallum and John Bowen.

This report was first published on GeekWire.

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GeekWire

Premonition takes disease tracking to the next level

Five years after launching an experiment to see if advanced sensors and artificial intelligence could spot the signs of a disease outbreak before it happens, Microsoft says it’s ramping up Project Premonition to create an honest-to-goodness biothreat protection network.

The network will involve setting up about 100 sensor stations in Texas’ Harris County, to track swarms of mosquitoes that could transmit diseases ranging from malaria and dengue fever to Zika and West Nile viruses. AI algorithms will analyze that tracking data for the telltale signs of an epidemic in the making, just as weather forecasting programs look for the signs of a storm on the way.

“It will really be almost like a weather map, the likes of which has not really been seen before in the mosquito vector space,” Ethan Jackson, director of Microsoft Premonition, told me.

The expansion of the Premonition program was announced today in conjunction with this week’s annual Microsoft Ignite conference for software developers.

Get the full story on GeekWire.

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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.

Get the full story on GeekWire.

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GeekWire

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.

Get the full story on GeekWire.