Thinking about flying? Here’s what you need to know now - Morning Call

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• Thinking about flying? Here’s what you need to know now - Morning Call
• New CDC-led Genomics Consortium That Harnessed Genetic Sequencing to Track the SARS-CoV-2 Coronavirus includes Clinical Laboratories and IVD Firms - DARKDaily.com - Laboratory News
• Trump Pushing to Open Economy Soon - Outside The Beltway - Mobile Edition

Thinking about flying? Here’s what you need to know now - Morning Call Posted: 28 May 2020 08:49 AM PDT On Friday, the Transportation Security Administration screened 348,673 people at American airports, the most since travel went into a free-fall in mid-March, likely driven by people traveling ahead of Memorial Day weekend. Still, a year ago, more than 2.7 million people were screened, showing just how far the industry has to come back.

New CDC-led Genomics Consortium That Harnessed Genetic Sequencing to Track the SARS-CoV-2 Coronavirus includes Clinical Laboratories and IVD Firms - DARKDaily.com - Laboratory News Posted: 11 May 2020 12:00 AM PDT Medical laboratories are already using gene sequencing as part of a global effort to identify new variants of the coronavirus and their genetic ancestors Thanks to advances in genetic sequencing technology that enable medical laboratories to sequence organisms faster, more accurately, and at lower cost than ever before, clinical pathology laboratories worldwide are using that capability to analyze the SARS-CoV-2 coronavirus and identify variants as they emerge in different parts of the world. The US Centers for Disease Control and Prevention (CDC) now plans to harness the power of gene sequencing through a new consortium called SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance) to "coordinate SARS-CoV-2 sequencing across the United States," states a CDC news release. The consortium is led by the CDC's Advanced Molecular Detection (AMD) program and "aims to generate information about the virus that will strengthen COVID-19 mitigation strategies." The consortium is comprised of 11 federal agencies, 20 academic institutions, state public health laboratories in 21 states, nine non-profit research organizations, and 14 lab and IVD companies, including: Abbott Diagnostics bioMérieux Color Genomics Ginkgo Bioworks IDbyDNA Illumina In-Q-Tel LabCorp One Codex Oxford Nanopore Technologies Pacific Biosciences Qiagen Quest Diagnostics Verily Life Sciences 'Fundamentally Changing How Public Health Responds' Gene sequencing and related technologies have "fundamentally changed how public health responds in terms of surveillance and outbreak response," said Duncan MacCannell, PhD, Chief Science Officer for the CDC's Office of Advanced Molecular Detection (OAMD), in an April 30 New York Times (NYT) article, which stated that the CDC SPHERES program "will help trace patterns of transmission, investigate outbreaks, and map how the virus is evolving, which can affect a cure." The CDC says that rapid DNA sequencing of SARS-CoV-2 will help monitor significant changes in the virus, support contact tracing efforts, provide information for developers of diagnostics and therapies, and "advance public health research in the areas of transmission dynamics, host response, and evolution of the virus." The sequencing laboratories in the consortium have agreed to "release their information into the public domain quickly and in a standard way," the NYT reported, adding that the project includes standards for what types of information medical laboratories should submit, including, "where and when a sample was taken," and other critical details. Even in its early phase, the CDC's SPHERES project has "made a tangible impact in the number of sequences we're able to deposit and make publicly available on a daily basis," said Pavitra Roychoudhury, PhD (above), Acting Instructor and Senior Fellow at the University of Washington, and Research Associate at Fred Hutchinson Cancer Research Center, in an e-mail to the NYT. "What we're essentially doing is reading these small fragments of viral material and trying to jigsaw puzzle the genome together," said Roychoudhury in an April 28 New York Times article which covered in detail how experts are tracking the coronavirus since it arrived in the US. (Photo copyright: LinkedIn.) Sharing Data Between Sequencing Laboratories and Biotech Companies The CDC announced the SPHERES initiative on April 30, although it launched in early April, the NYT reported. According to the CDC, SPHERES' objectives include: To bring together a network of sequencing laboratories, bioinformatics capacity and subject matter expertise under the umbrella of a massive and coordinated public health sequencing effort. To identify and prioritize capabilities and resource needs across the network and to align sources of federal, non-governmental, and private sector funding and support with areas of greatest impact and need. To improve coordination of genomic sequencing between institutions and jurisdictions and to enable more resilience across the network. To champion concepts of openness, standards-based analysis, and rapid data sharing throughout the United States and worldwide during the COVID-19 pandemic response. To accelerate data generation and sharing, including the rapid release of high-quality viral sequence data from clinical and public health laboratories into both the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing All Influenza Data (GISAID) repositories in near-real time. To provide a common forum for US public, private, and academic institutions to share protocols, methods, bioinformatics tools, standards, and best practices. To establish consistent data and metadata standards, including streamlined repository submission processes, sample prioritization criteria, and a framework for shared, privacy-compliant unique case identifiers. To align with other national sequencing and bioinformatics networks, and to support global efforts to advance the use of standards and open data in public health. Implications for Developing a Vaccine As the virus continues to mutate and evolve, one question is whether a vaccine developed for one variant will work on others. However, several experts told The Washington Post that the SARS-CoV-2 coronavirus is relatively stable compared to viruses that cause seasonal flu (influenza). "At this point, the mutation rate of the virus would suggest that the vaccine developed for SARS-CoV-2 would be a single vaccine, rather than a new vaccine every year like the flu vaccine," Peter Thielen, a molecular biologist at the Johns Hopkins University Applied Physics Laboratory, told the Washington Post. Nor, he said, is one variant likely to cause worse clinical outcomes than others. "So far, we don't have any evidence linking a specific virus [strain] to any disease severity score. Right now, disease severity is much more likely to be driven by other factors." That point was echoed by Anthony Fauci, MD, Director of the National Institute of Allergy and Infectious Diseases, in a March 22 interview with CBS News. "I have no doubt it's mutating as all RNA viruses mutate," he said. However, he added, "we have not seen thus far any type of change in the way it's acting." Fast improvements in gene sequencing technology have made it faster, more accurate, and cheaper to sequence. Thus, as the COVID-19 outbreak happened, there were many clinical laboratories around the world with the equipment, the staff, and the expertise to sequence the novel coronavirus and watch it mutate from generation to generation and from region to region around the globe. This capability has never been available in outbreaks prior to the current SARS-CoV-2 outbreak. —Stephen Beale Related Information: Genome Canada Leads $40 Million Genomics Initiative to Address COVID-19 Pandemic COVID-19 Genomics UK Bad News Wrapped in Protein: Inside the Coronavirus Genome How Coronavirus Mutates and Spreads Covid-19 Arrived in Seattle. Where It Went from There Stunned the Scientists 8 Strains of the Coronavirus Are Circling the Globe. Here's What Clues They're Giving Scientists SARS-CoV-2 Genomes Let Researchers Retrace Viral Spread, Mitigation Effects Varied COVID-19 Strains Not a Problem for Vaccines—For Now The Coronavirus Mutates More Slowly Than the Flu, Which Means a Vaccine Will Likely Be Effective Long-Term Response to "On the Origin and Continuing Evolution of SARS-CoV-2"

Trump Pushing to Open Economy Soon - Outside The Beltway - Mobile Edition Posted: 06 May 2020 06:54 AM PDT "Will some people be affected badly? Yes." James Joyner · Wednesday, May 6, 2020 · 61 comments Governors around the country are starting to lift stay-at-home orders in order to re-open the economy. The President is cheering them on while acknowledging that more Americans will die as a result. Bloomberg ("Trump Pivots to 'Phase Two,' Risking More Death to Save Economy") President Donald Trump fixed his course on reopening the nation for business, acknowledging that the move would cause more illness and death from the pandemic but insisting it's a cost he's willing to pay to get the economy back on track. Trump shifted his rhetoric on Tuesday, removing cautionary caveats about when and whether states should reopen and instead presenting the imminent easing of stay-at-home rules as a fait accompli. As governors across the South and Midwest have begun returning people to work, Trump said he's pivoting to "phase two" of the nation's response to the pandemic, a step that will include disbanding the White House coronavirus task force, a group of public health experts that has been advising the administration on how to confront the outbreak. The president has for more than a month clamored for a return to normal, stuck between the devastating human cost of the pandemic and the calamity that has befallen the economy as social-distancing measures pushed more than 30 million people into unemployment in a matter of weeks. Tuesday marked the first time he clearly and unreservedly laid out his own cost-benefit analysis of the situation. "Will some people be affected? Yes. Will some people be affected badly? Yes," Trump said. "But we have to get our country open and we have to get it open soon." On his visit to a Phoenix Honeywell International Inc. factory producing medical masks, Trump encouraged Americans to think of themselves as "warriors" as they consider leaving their homes, a tacit acknowledgment of deep public reservations about reopening the country too soon. The U.S. continues to endure the largest coronavirus outbreak in the world, with about 1.2 million people infected and more than 70,000 killed so far. Speaking separately in an ABC News interview broadcast on Tuesday evening, Trump said closing down the nation was "the biggest decision I've ever had to make." And while as recently as April 22, he criticized Georgia Governor Brian Kemp for reopening salons, barbershops, tattoo parlors and gyms, on Tuesday he was resolute about getting people back to work. "There'll be more death," he said. "The virus will pass, with or without a vaccine. And I think we're doing very well on the vaccines but, with or without a vaccine, it's going to pass, and we're going to be back to normal." "But it's been a rough process. There is no question about it," Trump said. "I think our economy is going to be raging" next year, he added. The map of this is rather stark: While I'm still in lockdown, as are those in the surrounding states, huge swaths of the country are wide open. Let's pretend for the sake of discussion that we had a normal President who made rational calculations after weighing evidence from experts and who had basic human empathy. He would certainly refrain from talking in this manner. And, one imagines, he would be using the bully pulpit to persuade governors and citizens to approach this more judiciously, slowly opening the economy in sectors and areas of the country where it made the most sense rather than simply based on the mood of the governor. We would likely avoid, for example, the bizarre spectacle of Bristol, where the Virginia side of town is still on lockdown and the Tennessee side is wide open. Aside from the vagaries of federalism, there's no rational basis for that kind of thing: either both sides of town should be open or both should be closed. Still, as Sean Trende wrote over the weekend, the rationale for the lockdown has steadily shifted and the current version is unsustainable for the long haul. When we began our foray into quarantine seven weeks ago, there was a unifying and eminently sensible rationale behind it: "Bend the curve." The idea was this: If allowed to go unchecked, COVID-19 would overwhelm hospitals, leaving patients without beds. Short on ventilators, patients would be left to suffocate. In short, by slowing the spread of the virus we would prolong the amount of time it spread through the country, but would reduce the total number of deaths. Moreover, we would buy time for the nation's testing apparatus to ramp up, to produce more ventilators, and to expand hospital capacity. While we're still not testing at adequate levels, we've otherwise achieved those objectives. Trende lays out quite a bit of data in that regard before observing, No states are on anything resembling an exponential growth trajectory, almost all states are past a peak, and most states are substantially so. This would suggest that in many states, the question really should be how to reopen while keeping hospitals from being overwhelmed again. But, for good reason in my view, the goalposts have moved. But in the meantime, there seems to have been a subtle shift in the discourse. Some of this has been a refusal to update prior assumptions – some people seem to believe not much has changed since early March – but other analysts have subtly moved from "bend the curve" to what we might call "crush the curve." Under the latter approach, rather than looking to keep hospitals from becoming overwhelmed, which raises the fatality rate, we should look to avoid all fatalities. If you look at Obama's timeline, you can see this play out in real time: On March 4 he urged people to wash their hands and stay home when sick. On March 12, he defended canceling large gatherings. Three days later he suggested everyone stay home to the fullest extent possible. This was all consistent with the growing conventional wisdom that we needed to close down in order to flatten the curve as the viral spread became more acute in the United States; on March 18 he seemed to endorse the "hammer and dance" strategy, warning of potential multiple rounds of social distancing. But by April 8, he acknowledged that the curve had been bent, but also seemed to suggest that relaxing current policies demanded additional measures to ensure there wouldn't be another breakout. A few weeks later, he retweeted an article that suggested we would need as many as 35 million tests per day before people could return to work. We see this shift expressed in public policy away from reopening as well. In California, for example, the governor closed the beaches everywhere last weekend as warm weather brought thousands of people flocking to the ocean. . This is despite the fact that the evidence that hot, sandy beaches are good places to transmit the virus is not that great and, more importantly, that California appears to have peaked quite some time ago. This isn't to argue that everything in California is going swimmingly, but it is striking that restrictions in the state are moving in the opposite direction of facts on the ground there, especially given the standard of a month ago. It might make more sense to retain restrictions in a place like New York City, but Mayor de Blasio's move to arrest people gathering in large groups seems discordant when cases in New York are receding. Note too the shift in rhetoric: "This is about stopping this disease and saving lives. Period." Those are worthy goals, indeed. Trende shares them, as do I. But he's right that this wasn't the going-in position. But the shift has probably been the most pronounced among pundits. Perhaps the strongest statement of the "crush the curve" point of view comes from an article published in The Atlantic, with the (frankly unhinged) headline "Georgia's Experiment in Human Sacrifice," with the subtitle "The state is about to find out how many people need to lose their lives to shore up the economy." Infections in Georgia appear to be trending downward, and it is beginning to reopen its economy, including gyms and hair salons. The upshot of the title and the article (which avoids the hyperbolic language from the headline) is that people will die as a result of the decision to open early. It seems likely that this is the case, but the idea behind bending the curve wasn't that we would bend the curve until there were no more cases. Indeed, it was expressed that we might end up with a similar number of cases, but that by spreading them out we would lower the number of fatalities. This, then, is something different: The idea that we should use the shutdowns to eradicate the virus as best we can, and that weighing lives against the economy reflects a choice tantamount to sacrificing some portion of the population. Reasonable minds can disagree over whether Georgia has it right (although Colorado, which is reopening amid expanding caseloads, has avoided similar criticism), but this absolutist stance is nonsense. We engage in cost-benefit tradeoffs all the time. As I've noted before, we engage in a similar cost-benefit exercise every year with the seasonal flu. The stakes appear higher here, which weighs heavily on the benefit side of shutting down compared to seasonal flu. The flu also has a vaccine that allows people to protect themselves against some strains, but as parents quickly learn, the efficacy of that vaccine varies wildly from year to year. But, regardless, we ought not pretend that we don't weigh a substantial number of lives against the economy every year, and occasionally make decisions that will undoubtedly "sacrifice" While Trende doesn't say it, the reason for this is obvious: when the status quo was "open for business," governors were under pressure to issue lockdown orders to bend the curve. But, now that the lockdowns are the status quo, governors are under different pressure. On the one hand, lots of people want their life and livelihood back and are clamoring for a re-opening. On the other, almost by definition, more people will get sick and die as a result. And, quite understandably, they don't want to be blamed for that. I don't have a firm view on when, whether, and where to open back up. I don't have enough information to make even a semi-informed guess and am frankly not sure the experts really know enough, either. But I agree with Trende's larger point: that we make these sorts of cost-benefit analyses all the time. To avoid the rabbit holes of comparisons with the flu, driving, or other dangerous but more common practices, let's just stick with COVID-19. We've decided that it's too risky to allow bars and movie theaters—recreational activities where social distancing is next to impossible—to stay open but have declared grocery stores, home improvement stores, delivery services, and a whole host of other commercial activities to be "essential." We're quite literally accepting a much higher degree of risk for those in "essential" industries and their households. And, indeed, workers in those sectors—and, of course, the medical professions—are dying at much higher rates. Trende closes with the politics of the thing: This seems to reflect a wider phenomenon of people being driven into "teams" regarding the shutdown. We've become polarized on the issue, and indeed this polarization is beginning to reflect our underlying politics. This is an unwelcome development. One of the dynamics about team sports is an inability to see the other side's point of view; indeed, that is in many ways the point of teams. As this virus develops, flexibility will be crucial in determining how well we come out of it, and a willingness to listen to the viewpoints of those we don't generally agree with is probably the most important trait we can have. But, as with so many other things, that seems to be one more fatality resulting from this virus. While there are a myriad of explanations for this, including both different information sources and very different lived experiences (the virus is hitting major metropolitan areas very much harder than it is rural areas, at least thus far) one imagines it would be a lot less severe with a normal President. Then again, maybe not. The lockdowns might be generating even more resentment if they were perceived as coming at the behest of Hillary Clinton. It's also worth noting that those of us in the pundit class are bearing a much smaller share of the sacrifice. Most of us can continue our work from the comfort of reasonably nice homes, secure in our paychecks and health coverage, while waiting for Amazon drivers to bring us whatever we need. Again, I don't claim to have a solution here. The infection and death rate in the DC metropolitan area, where I live, are too high to reopen. The governor shut down the schools for the year back in March and extended stay-home orders through June 10 weeks ago. Clearly, we need to be able to adequately test people for infections as a bare minimum for getting back to anything like "normal." But I don't think it's reasonable to wait until we have a cure for the disease, either. It's quite possible we'll never have one.

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