Category Archives: Corona Virus

A broad coalition of US health systems has mobilized to ramp up coronavirus testing in a national effort on a scale not seen since the second world war. But declarations of false victory by the Trump administration and a vacuum of federal leadership have undermined the endeavor, leading experts to warn that reopening the US could result in a disaster.

Interviews with agents on the frontlines of the coronavirus battle lab directors, chemists, manufacturers, epidemiologists, academics and technologists reveal as diverse an application of the legendary American ingenuity as the century has seen.

Test kit manufacturers are running production lines around the clock to triple their output, and triple it again. A private healthcare institute in California has constructed a mega-lab to process thousands of tests daily and deliver the results by text message alert. In smaller labs across the country, microbiologists improvise each day to fill unpredictable supply chain gaps that might leave them without swabs one day, and without crucial chemicals the next.

Its incredible what weve done together over a short period of time, Donald Trump said at a White House briefing this week, praising his administrations response to the pandemic.

But analysts say that without centralized governance and coordination, the national effort remains a competing coalition of state and local outfits hampered by duplicated work, competition for supplies, siloed pursuits of non-transferable solutions and red tape that leaves some labs with testing backlogs and others with excess capacity.

All of which leaves the US without a unified, coherent strategy for testing and contact tracing to contain a virus that does not respect state borders and has already killed more than 60,000 Americans.

Without it, the imminent experiment of reopening the country could be catastrophic, warned Harvard epidemiologist Michael Mina in a conference call with reporters this week.

My concern is that well end up right where we have been, with major cities having healthcare systems that get overrun quickly because of major outbreaks, Mina said.

Im afraid well just end up repeating the past

Meanwhile, as states begin to relax social distancing measures, the Trump administration is spreading dangerous misinformation, denying persistent supply shortages, underestimating the number of Covid-19 cases and exaggerating the margin of safety conferred by the current volume of testing and contact-tracing, experts say.

Weve done more than 200,000 tests in a single day, Mike Pence said at a taskforce briefing this week, in which Trump touted testing as one of the great assets that we have in reopening the US.

But at current testing levels, with only rudimentary plans for contact tracing for new cases, the US will be flying virtually blind as it reopens, said Glen Weyl, a technologist who co-authored a report issued by Harvards Safra Center for Ethics that calls for 5m tests a day by early June.

No, definitely not, you cant open up with that number, Weyl said of Pences announcement. Its not even remotely in the right ballpark. Its off by a factor of 10.

Testing is one of the biggest challenges the coronavirus crisis poses. And as Asian countries that have succeeded in temporarily containing the virus have shown, testing strategy is entwined with the need for contact tracing and isolating confirmed and suspected Covid-19 patients.

There are multiple categories of tests with multiple different modes for sampling, storage and transport. A test might detect the virus itself, detect traces of the virus or detect the bodys reaction to having had the virus. The experience of being tested could be different in each case. One patient might have his or her sinuses probed by a swab at a drive-thru, while another might spit in a tube at home and another give a blood sample at a clinic.

Each test has a different degree of reliability, with different amounts of time and labor required to complete the boomerang curve of sample collection to testing to result report.

We have too many [brands of] tests, and now there are a lot of people who are committed to their tests and they run their tests on their platforms, said Paul Reider, a renowned research chemist in the pharmaceuticals industry who teaches at Princeton University.

We have too many [brands of] tests, and now there are a lot of people who are committed to their tests

If we had an effective administration this is where the federal government comes in they could essentially turn around and say, What we would like to do is, we want one test, maybe two, that are fast, that are accurate, that are scalable and transferable, .

You want a gold-standard test.

In the US, regulatory and administrative hurdles are everywhere, with clinics unable to send samples to private labs that might be out of their usual networks, a lack of protocols for reporting testing data, slow regulatory approval for the use of alternative testing materials, insufficient federal funding to support lab efforts and no central leadership steering the countrys massive laboratory apparatus.

We dont have a system thats ever been built for surveillance, for wide-scale population surveillance or wide-scale testing for people who arent presenting to the hospital or the clinic, said Mina. The demand is just so much larger than our system was built for.

The Trump administrations response to this complicated thicket has been to declare the federal government a supplier of last resort and wish the states luck. Its pretty simple, Trump has said. They have tremendous capacity. We hope to be able to help out.

In an attempt to meet the demand they have encountered, lab scientists have improvised constantly, substituting materials where possible or stacking testing platforms from different manufacturers Roche, Qiagen, Abbott, Hologic, DiaSorin so that if one goes down another can take its place.

The result is that labs have delivered an unprecedented number of tests in record time but with a fraction of the potential efficiency that could be achieved through better coordination, said Reider.

If Jared Kushner wanted to do something decent, and Vice-President Pence, they could try to standardize and distribute nationally a global test, said Reider. At least make it available and let people choose if they want to use it.

The Harvard report called for the establishment of a Pandemic Testing Board akin to the War Production Board that the United States created in World War II. The director of the Center for Infectious Disease Research and Policy (CIDRAP) at the University of Minnesota calls for a new Marshall plan to stand up testing in the US.

But no efforts to create such a central authority are apparent, said Michael Osterholm, CIDRAP director, who described a shortage of reagents, or chemicals used in testing, on his Osterholm Update podcast this week.

We have had a number of our testing laboratories unable to get the needed reagents they couldve and shouldve had to increase testing, Osterholm said. We really need a Marshall plan where the federal government and the private sector get together and decide what are the challenges, what can we do to quickly boost these reagents, what can we do to actually increase the reagent pool?

Demand signal or no, some big private sector players have already moved aggressively. Early on in the crisis, Color, a private healthcare institute that does genomic testing in California, resolved to stand up a mega-lab that is now on the verge of processing 10,000 tests a day, with a goal of expanding that capacity by an order of magnitude, said Othman Laraki, CEO.

The company has since partnered with the city of San Francisco to provide Covid-19 testing for all private-sector and nonprofit essential employees, as well as any resident with symptoms who cannot find testing elsewhere. Next-day results are delivered via email and text-message alerts.

Our thinking was that you needed to have a few massively scaled labs as opposed to having a big sprinkling of small-scale labs, Laraki said. We believe thats the way to build the type of capacity thats needed really to bring the country back to work.

In Minnesota, academics at the state university partnered with scientists at the Mayo clinic, one of the countrys premier labs, to deliver on a challenge by governor Tim Walz to stop coronavirus in the state with comprehensive testing and contact tracing.

We really need a Marshall plan where the federal government and the private sector get together

We just made the decision that were probably going to be on our own and that we need to be ready to care for our patients, said Tim Schacker, vice-dean for research at the University of Minnesota and an architect of the project.

As a first step, the scientists invented a molecular test that was mostly independent of the supply chain problems, Schacker said.

Robin Patel, the president of the American Society for Microbiology, said supply chain issues continue to represent a daily challenge for laboratories, from swabs to chemicals to materials used to extract viral RNA and amplify DNA.

The situation has changed, yes, but its a different situation every day, so using the word improved is I dont think appropriate, she said.

This isnt just an American situation. People throughout the world are dealing with the same issues. The supply chain were talking about is not just an American supply chain, its a worldwide supply chain.

To celebrate Americas reopening, Trump appears to be preparing to hit the road, with plans to visit warehouses and factory sites to advertise the economic comeback he has promised. We built the greatest economy the world has ever seen, Trump said this week. And were going to do it again. And its not going to be that long. OK?

Polling indicates that a majority of Americans does not share Trumps optimism. About two in three Americans think restrictions on restaurants, stores and other businesses are appropriate, and 16% on top of that wanted tighter restrictions, a poll this week from the Washington Post and the University of Maryland found.

Top epidemiologists believe its possible that the US could get some kind of reprieve from the virus in the warmer months ahead. If that happens, the summer could feature the scenes Trump has dreamed about, of packed churches, humming factories, crowded beaches and sold-out flights.

But Trumps dream that the virus will simply disappear is just that a dream, epidemiologists say.

I hope that over the course of the next few weeks to two months, were going to actually see a substantial reduction in transmission, Osterholm said. And if it does, it shouldnt be interpreted that we won, or that somehow were in control.

I hope that the case numbers continue to decrease over time, but Im also very, very aware that theyre coming back, and we just have to remember that.

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No leadership and no plan: is Trump about to fail the US on coronavirus testing? - The Guardian

The World Health Organization extended its declaration of a global health emergency on Friday amid increasing criticism from the Trump Administration about its handling of the coronavirus pandemic.

The move comes exactly three months after the organizations original decision to announce a public health emergency of international concern on Jan. 30. At the time, only 98 of the nearly 10,000 confirmed cases had occurred outside Chinas borders.

But the pandemic continues to grow. More than 3.2 million people around the world are known to have been infected, and nearly a quarter million have died, according to official counts. There is evidence on six continents of sustained transmission of the virus.

All of this has led experts in the W.H.O.s emergency committee to reconvene to assess the course of the outbreak, and to advise on updated recommendations, said Dr. Tedros Adhanom Ghebreyesus, the organizations director-general.

The pandemic remains a public health emergency of international concern, Dr. Tedros said, adding that the crisis has illustrated that even the most sophisticated health systems are struggling to cope with a pandemic.

A rapid rise in new cases in Africa and South America, where many countries have weak health care systems, was alarming, he said. The acceleration is occurring even as the spread of the virus has appeared to slow in many countries in Asia and Europe.

Although people are slowly starting to return to work in China after weeks of lockdowns, businesses, schools and cultural institutions are still shuttered in most parts of the world. The virus has badly damaged the global economy.

Across the United States, governors are struggling to square constituents demands for an end to stay-at-home orders with the consequences of loosening social distancing rules.

Scientific and public health experts have warned that reopening restaurants, movie theaters and malls may lead to a deadly second wave of infection.

Several Republican senators, especially those locked in difficult races, have started shifting the blame for the spread of the virus onto China. Party officials hope that deflecting anger over the human casualties and economic pain in the United States will help salvage a difficult election.

President Trump has embraced the strategy, calling out Chinas misinformation and the W.H.O.s China-centric response in the early days of the pandemic.

He has accused the W.H.O., without evidence, of helping China to obscure the extent of its epidemic in the early days, as well as being slow to release guidelines for precautions against infections.

In fact, the W.H.O. began raising alarms in early January, as soon as it was informed by China of a new, mysterious illness in the city of Wuhan. On Friday, Dr. Tedros insisted that the W.H.O. did not waste any time in traveling to Beijing to discuss with the leadership and to find, to see for ourselves, the situation in China.

In mid-April, Mr. Trump announced he would halt funding to the W.H.O. The United States is by far the organizations largest benefactor.

Dr. Tedros announced Friday that the European Investment Bank would provide grants and financial support to help strengthen global supply chains, and facilitate the distribution of diagnostics, personal protective equipment and other medical supplies.

We look forward to seeing how that type of innovative financing could deliver real results for global health when W.H.O. is advocating health for all, Dr. Tedros said. W.H.O. is deeply grateful to the European Investment Bank for its support and collaboration.

Yet the W.H.O. has still managed the coronavirus crisis as well as it could, and better than the Trump administration has, many experts say.

The W.H.O. helped arrange testing supplies and personal protective equipment for countries in need and held daily news meetings to warn the world that the virus was spreading and that countries should do everything they could to stop it.

At nearly every briefing, Dr. Tedros repeated: We have a window of opportunity to stop this virus. But that window is rapidly closing.

On Friday, Didier Houssin, chair of the W.H.O. emergency committee, said that committee members had made more than 20 recommendations, hoping to reduce disruptions caused by the coronavirus pandemic.

The guidance focuses on mitigating interruptions to the distribution of food and medicines caused by lockdowns, a safe return to work, and resumption of normal air travel. The committee said researchers would continue to look for the animal thought to be the original source of the coronavirus, and to develop potential vaccines and therapies.

We encourage countries to follow W.H.O.s advice, which we are constantly reviewing and updating as we learn more about the virus, and as we learn more from countries about best practices for responding to it, Dr. Tedros said.

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The Coronavirus Still Is a Global Health Emergency, W.H.O. Warns - The New York Times

The Department of Homeland Security study on the effects of heat and sunlight on the coronavirus is undergoing the process for peer review and publication in scientific journals, according to the department.

There is no written report as yet, although the results are being submitted for peer review and publication in scientific journals, a DHS spokesperson told CNN.

DHS' Science and Technology Directorate has been studying theimpacts of environmental conditions on the coronavirus,particularlytheimpacts of temperature, humidity, and sunlight on the virus.

The study came under increased scrutiny after President Trumpsuggested last week during a press briefing that the virus could be treated with sunlight, as well aswhether disinfectants could be used to treat the virus in humans.

During last week's briefing, William Bryan, acting DHS Science and Technology under secretary, discussed the experiments in which, he said, disinfectants like bleach and isopropyl alcohol quickly killed the virus.Trump then mused about whether disinfectantscould be used to treat the virus in humans.

When asked why the department released the results before the final study, a spokesperson said, "We felt it important to share information on the emerging trends that are being identified in our tests," saying that the results are still undergoing a "rigorous scientific review."

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Coronavirus pandemic in the US: Live updates - CNN

The Coronavirus Genome

The coronavirus is an oily membrane packed with genetic instructions to make millions of copies of itself. The instructions are encoded in 30,000 letters of RNA a, c, g and u which the infected cell reads and translates into many kinds of virus proteins.

RNA instructions to make the ORF1a protein

Start of coronavirus genome

Start of coronavirus genome

Start of the

coronavirus

genome

Start of the

coronavirus

genome

In December, a cluster of mysterious pneumonia cases appeared around a seafood market in Wuhan, China. In early January, researchers sequenced the first genome of a new coronavirus, which they isolated from a man who worked at the market. That first genome became the baseline for scientists to track the SARS-CoV-2 virus as it spreads around the world.

Genome Wuhan-Hu-1, collected on Dec. 26 from an early patient in Wuhan

Genome Wuhan-Hu-1, collected on Dec. 26 from an early patient in Wuhan

Genome Wuhan-Hu-1, collected on Dec. 26 from an early patient in Wuhan

Genome Wuhan-Hu-1, collected on Dec. 26 from an early patient in Wuhan

A cell infected by a coronavirus releases millions of new viruses, all carrying copies of the original genome. As the cell copies that genome, it sometimes makes mistakes, usually just a single wrong letter. These typos are called mutations. As coronaviruses spread from person to person, they randomly accumulate more mutations.

The genome below came from another early patient in Wuhan and was identical to the first case, except for one mutation. The 186th letter of RNA was u instead of c.

Genome WH-09, collected on Jan. 8 from another patient in Wuhan

186th RNA letter changed

Genome WH-09, collected on Jan. 8 from another patient in Wuhan

186th RNA letter changed

Genome WH-09, collected on Jan. 8 from another patient in Wuhan

186th

RNA letter

changed:

Genome WH-09, collected on Jan. 8 from another patient in Wuhan

186th RNA letter

changed:

When researchers compared several genomes from the Wuhan cluster of cases they found only a few new mutations, suggesting that the different genomes descended from a recent common ancestor. Viruses accumulate new mutations at a roughly regular rate, so the scientists were able to estimate that the origin of the outbreak was in China sometime around November 2019.

Outside of Wuhan, that same mutation in the 186th letter of RNA has been found in only one other sample, which was collected seven weeks later and 600 miles south in Guangzhou, China. The Guangzhou sample might be a direct descendent of the first Wuhan sample. Or they might be viral cousins, sharing a common ancestor.

During those seven weeks, the Guangzhou lineage jumped from person to person and went through several generations of new viruses. And along the way, it developed two new mutations: Two more letters of RNA changed to u.

Genome GZMU0030, collected on Feb. 27 in Guangzhou

Another RNA letter mutated

This mutation also changed an amino acid

Genome GZMU0030, collected on Feb. 27 in Guangzhou

Another RNA letter mutated

This mutation also changed an amino acid

Genome GZMU0030, collected on Feb. 27 in Guangzhou

Another RNA letter mutated. This mutation also changed an amino acid.

Genome GZMU0030, collected on Feb. 27 in Guangzhou

Another RNA letter mutated. This mutation also changed an amino acid.

Mutations will often change a gene without changing the protein it encodes.

Proteins are long chains of amino acids folded into different shapes. Each amino acid is encoded by three genetic letters, but in many cases a mutation to the third letter of a trio will still encode the same amino acid. These so-called silent mutations dont change the resulting protein.

Non-silent mutations do change a proteins sequence, and the Guangzhou sample of the coronavirus acquired two non-silent mutations.

Amino acid change in the ORF1a protein

Amino acid change in the E protein

Amino acid change in ORF1a

Amino acid change in E

Amino acid change in the E protein

Amino acid change in the ORF1a protein

Amino acid change in the E protein

Amino acid change in the ORF1a protein

But proteins can be made of hundreds or thousands of amino acids. Changing a single amino acid often has no noticeable effect on their shape or how they work.

As the months have passed, parts of the coronavirus genome have gained many mutations. Others have gained few, or none at all. This striking variation may hold important clues to coronavirus biology.

The parts of the genome that have accumulated many mutations are more flexible. They can tolerate changes to their genetic sequence without causing harm to the virus. The parts with few mutations are more brittle. Mutations in those parts may destroy the coronavirus by causing catastrophic changes to its proteins. Those essential regions may be especially good targets for attacking the virus with antiviral drugs.

Total number of amino acid substitutions found in 4,400 coronavirus genomes from Dec. to April

Longer lines may show places where the genome is more tolerant of mutations.

Gaps may show critical spots in the genome that cannot tolerate mutations.

Total number of amino acid changes in 4,400 coronavirus genomes from Dec. to April

Longer lines may show places where the genome is more tolerant of mutations.

Gaps may show critical spots in the genome that cannot tolerate mutations.

Total number of amino acid changes in 4,400 coronavirus genomes from Dec. to April

Longer lines may show places where the genome is more tolerant of mutations.

Gaps may show critical spots in the genome that cannot tolerate mutations.

Total number of amino acid changes in 4,400 coronavirus genomes from Dec. to April

Longer lines may show places where the genome is more tolerant of mutations.

Gaps may show critical spots in the genome that cannot tolerate mutations.

As mutations accumulate in coronavirus genomes, they allow scientists to track the spread of Covid-19 around the world.

On January 15, a man flew home to the Seattle area after visiting family in Wuhan. After a few days of mild symptoms he tested positive for Covid-19. He became the first confirmed case of Covid-19 in the United States.

An X-ray of the patients lungs showed evidence of pneumonia.NEJM

The genome of his virus contained three single-letter mutations also found in viruses in China. They allowed scientists to trace the mans infection to its source.

Genome WA1, collected on Jan. 19 from a man in the Seattle area who visited Wuhan

Genome WA1, collected on Jan. 19 from a man in the Seattle area who visited Wuhan

Genome WA1, collected on Jan. 19 from a man in the Seattle area who visited Wuhan

Genome WA1, collected on Jan. 19 from a man in the Seattle area who visited Wuhan

Identical genomes collected on Jan. 21 in Fujian and Guangdong provinces

Identical genomes collected on Jan. 21 in Fujian and Guangdong provinces

Identical genomes collected on Jan. 21 in Fujian and Guangdong provinces

Identical genomes collected on Jan. 21 in Fujian and Guangdong provinces

Five weeks later, a high school student in Snohomish County, Wash., developed flu-like symptoms. A nose swab revealed he had Covid-19. Scientists sequenced the genome of his coronavirus sample and found it shared the same distinctive mutations found in the first case in Washington, but also bore three additional mutations.

Genome WA2, collected on Feb. 24 from a high-school student in the Seattle area

Genome WA2, collected on Feb. 24 from a high-school student in the Seattle area

Genome WA2, collected on Feb. 24 from a high-school student in the Seattle area

Genome WA2, collected on Feb. 24 from a high-school student in the Seattle area

That combination of old and new mutations suggested that the student did not acquire the coronavirus from someone who had recently arrived from another country. Instead, the coronavirus was probably circulating undetected in the Seattle area for about five weeks, since mid-January.

Since then, viruses with a genetic link to the Washington cluster have now appeared in at least 14 states and several countries around the world, as well as nine cases on the Grand Princess cruise ship.

Genome collected on March 5 from two passengers on the Grand Princess cruise ship

Genome collected on March 5 from two passengers on the Grand Princess cruise ship

Genome collected on March 5 from two passengers on the Grand Princess cruise ship

Genome collected on March 5 from two passengers on the Grand Princess cruise ship

A different version of the coronavirus was also secretly circulating in California. On Feb. 26, the C.D.C. announced that a patient in Solano County with no known ties to any previous case or overseas travel had tested positive.

A sample taken the next day revealed that the virus did not have the distinctive mutations found in Washington State. Instead, it only had a single mutation distinguishing it from the original Wuhan genome. That indicates that it got to California through a separate introduction from China.

Genome UC4, collected on Feb. 27 from a patient in Solano County, Calif.

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How Coronavirus Mutates and Spreads - The New York Times

The tension between private liberty and public health in the United States is hardly new. Americans have demanded the latter in times of plague and prioritized the former in times of well-being since at least the Colonial Era. Politicians and business leaders have alternately manipulated and deferred to that tension for about as long.

In 1701, members of the Massachusetts Bay Colony fought a yearlong political battle to enact the nations first quarantine laws against opponents who said such measures were too severe. In 1918, during the flu pandemic, the mayor of Pittsburgh brought a ban on public gatherings to a swift and premature conclusion over concerns about a coming election.

In 2020, the same tension is back with a vengeance. The nation is under siege from the worst pandemic in a century, and the United States is on track to suffer more deaths than any other industrialized country from SARS-CoV-2, the medical name for the novel coronavirus.

Attorney General William Barr last Monday ordered Justice Department lawyers to be on the lookout for state and local directives that could be violating the constitutional rights and civil liberties of individual citizens. He was talking about state and local orders closing businesses and requiring people to shelter in place to help combat the spread of the virus. The Constitution is not suspended in times of crisis, Mr. Barr said in an April 27 memo.

Yet the same Mr. Barr, early in the outbreak, was seemingly so concerned about its impact that he proposed letting the government pause court proceedings and detain people indefinitely without trial during emergencies effectively suspending the core constitutional right of habeas corpus.

Temporary limitations on some liberties dont seem to concern most Americans at this moment. Polls show that 70 percent to 90 percent of the public support measures to slow the spread of the virus, even if those measures require temporarily yielding certain freedoms and allowing the economy to suffer in the short run.

Indeed, it is wealthy and powerful conservatives and their allies, including President Trump and Fox News, who are driving the relatively small protests demanding a liberation of the states from oppressive lockdowns as opposed to any overwhelming public sentiment to that effect.

Whats more, every country that has managed to get its Covid-19 outbreak under control has done so with measures far more aggressive than anything tried in the United States so far.

In China, South Korea and Singapore, the authorities quickly established comprehensive testing, along with rigorous contact tracing, isolation and quarantine. In the United States, such efforts are still under construction and are proceeding at a snails pace; three-plus months into the crisis, just a tiny fraction of the needed tests, contact tracers and quarantine facilities are operational anywhere.

Civil liberties may feel to some like a second-order problem when thousands of Americans are dying of a disease with no known treatment or vaccine. Yet while unprecedented emergencies may demand unprecedented responses, those responses can easily tip into misuse and abuse, or can become part of our daily lives even after the immediate threat has passed. For examples, Americans need look no further than the excesses of the post-Sept. 11 Patriot Act.

As the nation starts looking ahead to the next phase of its battle against the coronavirus, we need to have a more honest conversation about the extent to which governments may impose restrictions on their citizens that would not and should not be tolerated under normal conditions.

FREEDOM OF SPEECH AND RELIGION

Consider the rights to free speech, association and religious exercise under the First Amendment: These freedoms are central to our self-definition, and yet they have all been infringed on to varying degrees across the country, as states ban gatherings where the virus can spread quickly and easily. In Maryland and Iowa, for example, all types of large events and gatherings, including church services, have been prohibited. (Many other states have exempted religious services from their bans, which raises the separate question of whether the government is impermissibly favoring religion.)

Bans like these are legal, as long as they are neutral and applicable to everyone. A state may not shut down only certain types of events, or prohibit speakers expressing only certain viewpoints. Under Supreme Court precedent, any infringement on speech or religion must be incidental to the central goal of the restriction, which in this case is clear: stopping the spread of the coronavirus.

But even if all these bans are legal on their face, what happens as the 2020 election approaches? Speech and association rights are at their peak in the political context, and Americans will be especially wary of any incursions on those rights in the months or weeks before Election Day. What if a state lifts some restrictions on large gatherings, then reimposes them in the days before an election? That may be necessary if there is another wave of the virus, and yet in a highly polarized political environment, citizens might well distrust official motivations behind a crackdown, and that could generate public unrest.

This is why its so important for the authorities to build that trust now, and to rely openly on scientific consensus when imposing and lifting bans on gatherings and other events.

SURVEILLANCE AND CELLPHONES

Another area of concern is the governments ability to know where we are and whom were with. In normal times, the authorities generally have to obtain a warrant to search your personal property, like a cellphone, or to retrieve its data to find your location.

But giving the government access to all that data carries huge risks. There were already far too many examples of law-enforcement officials abusing their access to cellphone data in the pre-Covid era, taking advantage of revolutions in technology to track people in ways that no one would imaginably consent to. Even if people give their consent to be tracked during the pandemic, governments have a very poor track record of relinquishing new powers once they have them.

The question then becomes: Can cellphone data be used in a way that helps stem the spread of the coronavirus while also being kept out of the hands of the government to avoid abuse, now or down the road?

Apple and Google are in the process of producing an app that would use secret codes to track people through their phones, while leaving the location data on those phones. People who test positive would be given the choice of putting their phone on a list. Other peoples phones could automatically check that list, and if any were within range of the infected person, those people would be notified that they could be at risk.

Fine, in theory. But for a system like this to work, the public needs to buy into it. Enough people have to use these apps to make them effective at least 60 percent of cellphone users, by some estimates and no city or country is anywhere close to that level of adoption. In Norway, only 30 percent of people have downloaded this type of location app.

Another hurdle is that the big technology companies have a poor record of protecting their users private information.

In the end, contact tracing a central feature of any comprehensive public-health response will need to be a cooperative endeavor, involving not only downloadable apps but perhaps hundreds of thousands of human beings, all doing the hard work of direct outreach to find those people at the highest risk of infection.

LIBERATING AMERICA

It would be one thing if the calls to reopen America from President Trump and his allies were part of a coordinated pandemic response strategy by a federal government that had taken strong and science-based measures from the start. But the White House failed to do that at virtually every turn, which makes the current protests ring hollow.

Its possible that at least some of the current lockdowns could have been avoided had the Trump administration led the way back in January when we still had time to take advantage of the information coming out of China and prepare the United States for what lay ahead. In that sense, these devastating shutdowns represent a catastrophic failure of timely government action. Even today, top officials are refusing to take the most basic safety measures. On Tuesday, Vice President Mike Pence toured the Mayo Clinic but refused to follow the clinics requirement to wear a mask. What message does he think that sends to the American people? (On Thursday Mr. Pence visited a plant producing ventilators in his home state, Indiana, and wore a mask.)

In a large self-governing society, civil liberties exist as part of a delicate balance. That balance is being sorely tested right now, and there is often no good solution that does not infringe on at least some liberty. At the same time, the coronavirus provides Americans with an opportunity to reimagine the scope and nature of our civil liberties and our social contract. Yes, Americans are entitled to freedom from government intrusion. But they also have an obligation not to unnecessarily expose their fellow citizens to a deadly pathogen. Protecting Americans from the pandemic while also preserving our economy and our civil liberties is not easy. But its essential.

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We the People, in Order to Defeat the Coronavirus - The New York Times

The ship, which is currently in port in San Diego, was the second US warship to be struck by an outbreak of the pandemic after the USS Theodore Roosevelt aircraft carrier.

The officials said that there are more than 95 cases currently aboard the ship, meaning that almost 30% of the crew has been infected, surpassing the infection rate for the USS Theodore Roosevelt which has seen approximately 24% of its crew infected.

The handing of the outbreak aboard the aircraft carrier led to the firing of the ship's commanding officer, and the resignation of the acting Navy Secretary. It has been the subject of a Navy investigation which is due to be completed on May 27 following an initial preliminary inquiry that officials tell CNN recommended that the aircraft carrier's former captain, Capt. Brett Crozier, be reinstated.

The Navy on Friday stopped providing official daily figures about the number of cases on the Kidd and Theodore Roosevelt, saying that it "will only report significant changes on these vessels and new cases on any other deployed vessels."

On Thursday night, a Navy statement said that official number of active coronavirus cases on the Kidd was 78.

The 20% increase in positive coronavirus cases does not appear to have met the Navy's definition of "significant" information.

The statement Thursday said that the USS Theodore Roosevelt had 1,102 active cases in addition to 53 sailors who have recovered from coronavirus after completing at least 14 days in isolation and two successful negative tests. Three sailors from the ship are being treated in US Naval Hospital Guam for coronavirus symptoms. None of those sailors are in the ICU.

Asked about the new policy, chief Pentagon spokesperson Jonathan Hoffman told reporters at the Pentagon "we wanted to get out of the pattern of providing a daily tracker of minor changes."

"We've now reached a point with both of those ships, particularly with the (Theodore Roosevelt), where we've gone through, the entire crew's been off, the entire crew's been tested, we have the results, the ship has been cleaned, the crew is now returning to the ship. So we believe that we have moved past a point where the daily updates are providing useful information for a public conversation about it," Hoffman said.

"If there was unfortunately an additional outbreak, we would provide information. But we wanted to get out of the pattern of providing a daily tracker of minor changes in this. And I think that's a reasonable place to be," Hoffman added.

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Number of coronavirus cases from second warship outbreak nears 100 as Navy restricts information on pandemic - CNN

A group of nurses from Northwestern Memorial Hospital in Chicago share the moments that have made the long, hard days worth it. USA TODAY

CHICAGO Dressed in jeans, a striped collared shirt and white sneakers emblazoned with the words MADAM and MAYOR on the heels, the 5-foot former prosecutor grooved to the syncopated beat as the first lyrics rang out: Cash on me, like I hit the lottery.

It's not the typical image for a big-city mayor. Especially during the COVID-19 era.

Mayor Lori Lightfoot on Thursday announced Chicago's first-ever citywide celebration of graduating seniors via a video of herself dancingposted to TikTok the most recent in a series of viral social media posts that Lightfoot's office has used to encourage residents to stay home amid the coronavirus outbreak. More than than 22,000 Chicagoans have been infected; 962 have died.

In an exclusive one-on-one interview with USA TODAY, the Chicago mayor talked about the challenges of battling COVID-19 on the political front lines and her personal experience of the outbreak.

Lightfoot, 57, the Windy City's first black woman and first openly gay mayor, has gained national attention for effectively shepherding the nation's third-largest city through the crisis of a generation.Her humor and iron-fisted resolve have provided both welcome levity and comfort for many Chicagoanswatching the citys case count creep upward.

But in a city long dominated by a history of machine politics and mayoral boses, critics warn that Lightfoot is capitalizing on the crisis to consolidate authority at City Hall.

For the new mayor navigating an impossible situation, the outbreak has meantthree months of seeing the inequities within her city laid bare. It'sbeen acrisis colored by loss, resilience and a letter written in orange marker.

"I have a range of emotions,"Lightfoot says. "People are stepping up in really amazing ways . . .But I also recognize that, just as our strength shines through, the vulnerabilities that we all knew about, that we've been working on for years in fact decades those are also flashing like a neon sign."

In Chicago and Detroit: Coronavirus spares one neighborhood but ravages the next. Race and class spell the difference.

Chicago has been held up as an example of how the outbreak is disproportionately affecting communities of color. The city gained national attention in early April when it reported that more than half of its coronavirus patients and about 70% of COVID-19 deaths were among African Americans, even though black Chicagoans make up just 30% of the citys population.

At the time, the city didn't have information about the race or ethnicity of a quarter of all cases. Looking back on the few past months, Lightfoot said that's among her biggest regrets.

"Understanding the disparate impact is really important," Lightfoot said. "I wish we had demanded the demographic information compliance sooner."

Mayor Lori Lightfoot answers a reporters question during a news conference to provide an update to the latest efforts by the Racial Equity Rapid Response Team in Chicago on Monday.(Photo: Tyler LaRiviere/Chicago Sun-Times via AP)

For thousands of Chicagoans, those case counts aren't just statistics they're family, friends, nurses, doctors. For Lightfoot, it was a man she had met last year whoworked with at-risk youth.

"He had underlying conditions, but nothing particularly serious, and was starting to recover, then literally overnight took a turn for the worst. It was shocking to me," Lightfoot said. "That he lost his life in that way, its very painful."

Lightfoot said a note that she received from a boy in her neighborhood has been giving her the strength to work through the pain.

"It was a very short, sweet letter, and he basically said he was writing to thank me for what we were doing in the city," she said. "Ive been carrying that around because that meant so much to me."

The humor's helped, too, Lightfoot said. When the mayor closed down the city's Lakefront Trail at the end of March, a local graphic artist photoshopped an image of Lightfoot, hands clasped and stony-faced,into a picture ofthe fenced off trail.

"It really just kind of took off from there," Lightfoot said. "We just decided to take the moment of humor to really burn in the necessity to stay home and save lives. The level of ingenuity of people in this city really knows no limits. Its been very fun."

Memes of Lightfoot standing watch outside houses, perched atop traffic lights, glaring through rear-view mirrors, ordering Jesus back into the cave on Easterand more have circulated online.

An Instagram account called "whereslightfoot" has nearly 60,000 followers. The trend is so popular, it's become self-referential.

If she had to pick, two memes stand out as favorites, Lightfoot said.

"It was pretty early on, somebody did a Wheel of Fortune that said 'Stay the F*** Home' that I still think about and laugh every time.It just caught me and made me laugh," she said. "I think the one thats probably truly my favorite, there's one where you know the bat signal that beams up with my face? I kind of feel like that. I need to be and hope I am the guardian of this city."

Criticssay they're getting that message loud and clear. Last week, during a raucous City Council meetingover Zoom complete with shouting and expletives aldermen criticized a proposal to grant Lightfoot'sadministration emergency powers to make decisions about COVID-related spending. Critics called the move a "power grab" by the mayor, who campaigned on rooting out corruption in City Hall.

The ordinance passed, with 21of 50 aldermen votingagainst the measure, including several aldermen representing communities disproportionately affected by the virus.

Democratic Socialist Ald. Carlos Ramirez-Rosa voted against the ordinance, saying that it did not include oversight measures or guarantees that the emergency dollars would be prioritized for hardest hit communities.

"We have been told to trust this mayor,"Ramirez-Rosa said in the meeting. "Here in Chicago, weve seen the disastrous effect of when we trust the mayor to be Chicagos sole decision-maker and authority."

Echoing a critique of Lightfoot commonly heard amid last fall's 11-day teacher's strike, Ramirez-Rosa said that "when it comes to this mayor, you have got to put it in writing."

"We cannot go back to the times of one mayor overseeing everything and a rubber-stamp council," said Ald.Byron Sigcho Lopez.

As Lightfoot turns her focus toward a gradual reopening of the city, June 1 looms large in her mind. Last week, the mayor put together a team of local officials, business leaders and activists to advise her on plans for recovery.

"First of all, were going to be doing a change study. Were looking at uncovering the effect of COVID across a lot of sectors economic, but what I call the social fabric, how this has impacted individuals, neighborhoods, communities," Lightfoot said. "The goal is to have a final report by June 1. So its a sprint."

Lightfoot said that in addition to a focus on policy and economic recovery, the task force plans to have working groups focused on regional cooperation and mental and emotional health. The groups were developing a process to get public feedback, she said.

"We want to think very thoughtfully about what a staged reopening looks like," she said. "Because its not going to look the same as it did in February, pre-COVID. Its just not. Not until we get a vaccine thats viable. So its turning on the dimmer light and not flipping the switch."

When will US reach 100,000 deaths?After a horrific April, grim milestone could hit in May

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Coronavirus in Chicago: How the mayor of the nation's 3rd-largest city is waging her biggest fight - USA TODAY

On April 10, a pastor appeared on Carlsons show to accuse the city government of Greenville, Mississippi, of anti-Christian harassment because it did not allow drive-in church services.

Senator Rand Paul on April 10 tweeted an attack on Kentuckys warning that people who attended large services on Easter could face tickets and quarantine orders: Taking license plates at church? Quarantining someone for being Christian on Easter Sunday? Someone needs to take a step back here.

The Fox News host Jeanine Pirro on April 15 praised Michigan protesters who resisted an unnamed them who want to keep us away from churches and synagogues.

On April 18, Donald Trump retweeted this complaint about Easter restrictions:

Lets see if authorities enforce the social-distancing orders for mosques during Ramadan (April 23May 23) like they did churches during Easter.

At a press conference that day, Trump was invited to explain himself, and he did:

I am somebody that believes in faith. And it matters not what your faith is, but our politicians seem to treat different faiths very differently, and they seem to think, and I dont know what happened with our country, but the Christian faith is treated much differently than it was, and I think its treated very unfairly.

He added: They go after Christian churches, but they dont tend to go after mosques.

All of this might seem performative victimhood as usual, but on April 27, Attorney General William Barr issued a directive to the 93 U.S. attorneys and the civil-rights division of the Department of Justice to be on the lookout for state regulations that discriminate against religious institutions and religious believers.

The sense of persecution that pervades conservative talk has jumped to sway federal law enforcement.

It needs to be stressed at the outset that almost all faith groups in the United States have voluntarily and responsibly complied with public-health restrictions. Two dozen Muslim groups signed a statement on the eve of Ramadan urging Muslims to celebrate the holy month in rituals at home, not in mosques or Islamic centers. The Church of Jesus Christ of Latter-day Saints suspended all services worldwide on March 12. Catholic churches likewise suspended public Mass. Cellphone records confirm that the large majority of Christian worshippers marked Easter at home.

But human nature being what it is, people will predictably resist even sensible rules for their health. Hundreds of New Yorkers crowded together to watch a hospital ship dock, which would seem about the ultimate in self-defeating behavior. Police in many states have issued warnings and fines to enforce social distancing. People have been arrested for hanging out on Brooklyn street corners in too large numbers. People have been fined for gathering in large groups on Los Angeles beaches. (California Governor Gavin Newsom is warning of even stricter enforcement if rules are broken over this warm weekend.) And people have faced sanctions, including fines and arrest, for defying rules against religious assemblies.

The rest is here:

Trump Brings Religion Into the Coronavirus Culture War - The Atlantic

Reopening California has been complicated because the coronavirus outbreak is behaving differently in various parts of the state.

The San Francisco Bay Area has seen consecutive weekly declines in the number of new cases, while Southern California has seen the pace of new cases increase.

Los Angeles County has become the heart of the coronavirus crisis in California, recording more than 1,000 deaths. Even adjusted for its larger population, its rate of 9.9 deaths per 100,000 people is 68% higher than the next-hardest-hit urban county, Riverside, and 80% higher than the hotbed of the crisis in the Bay Area, Santa Clara County, according to a Times analysis of coronavirus data.

Hospitalizations also remain stubbornly high, helping to explain the reluctance to ease the stay-at-home order in California. Half of all hospitalized coronavirus patients in California are being treated in Los Angeles County, which is home to a quarter of the states population, the analysis found.

California has so far managed to avoid the death toll New York state has faced, with more than 22,000 dead. The Golden State has reported about 1,800 fatalities.

Yet the numbers of new coronavirus cases and deaths reported every week statewide although not increasing as fast as before are still rising on a weekly basis. The numbers have yet to begin a sustained downward trend.

Despite the recent increase, officials are expecting that L.A. County will start to see a decline in new cases around mid-May.

Heres a look at cases, hospitalizations and deaths:

Statewide

The number of confirmed cases of coronavirus infection can be a tricky indicator. The figure may be affected by backlogs in reported cases suddenly showing up in the public record.

And despite the stay-at-home order, more people continue to become infected, such as people in congregate care settings like nursing homes and people who continue to work as essential workers, as well as those who venture out for essential trips, such as picking up groceries.

Still, experts expect coronavirus case numbers to eventually decrease in areas including L.A. County, believing the stay-at-home order has been, and continues to be, effective.

Testing capacity continues to increase, and in L.A. County, once the testing sort of equilibrates out, I think youll start seeing declines, said Dr. George Rutherford, UC San Francisco epidemiologist and infectious diseases expert.

Los Angeles County has a higher vulnerability to health emergencies than the San Francisco area, the U.S. Centers for Disease Control and Prevention has said, due to differences in poverty, crowded housing and lack of access to transportation.

Deaths are a helpful indicator to track the progress of an outbreak, but will still be rising even as hospitalizations and new cases decrease.

Statewide

Health officials are particularly focused on the trend in the number of people hospitalized for COVID-19.

Dr. Grant Colfax, director of public health for San Francisco, said of hospitalization numbers, We need numbers to start dropping significantly and just stay down for several weeks.

Statewide

Read more here:

Coronavirus is advancing in L.A., retreating in Bay Area - Los Angeles Times

A new test for the coronavirus is so simple and straightforward, almost anyone could do it: Spit a glob of saliva into a cup, close the lid and hand it over.

While not as fast to process as the speediest swab tests, saliva tests could transform the diagnosis of Covid-19. If manufactured in enough numbers and processed by enough labs across the country, they could alleviate the diagnostic shortages that have hampered containment of the pandemic and offer a less onerous way for companies to see if workers are infected.

The first saliva-based test, already being offered in parts of New Jersey, detects genetic material from the virus, just as the existing tests do, but it avoids a long swab that reaches disturbingly far up a persons nose. For the saliva-based, health care workers do not need to wear and discard precious gowns and masks. And early evidence suggests it is just as sensitive, if not more so, than the swabs.

Because the saliva test relies on equipment that is widely available, it also offers the hope of a nationwide rollout without encountering the supply problems that have plagued the swabs.

Starting about two weeks ago, New Jersey has offered the saliva test at a walk-up site in New Brunswick; drive-through sites in Somerset and Edison; the states Department of Corrections; 30 long-term care facilities; and even the American Dream mall.

Experts not involved with the test praised it as a welcome solution to diagnostic shortages across the country.

If people are going back to work, and theyre going to be tested presumably on a regular basis, we really do need to have less invasive sampling methods than the swabs, said Angela Rasmussen, a virologist at Columbia University. To have to do nasopharyngeal swabs twice a week? No, thanks.

The next step would be an at-home saliva test kit that skirts even the need to go to a walk-in center, said Dr. Amesh Adalja, a senior scholar at the Johns Hopkins University Center for Health Security.

Dr. Adalja noted that LabCorp, one of the nations largest commercial laboratories, now offers an at-home test that people can use to swab their own nose. If we can do nasal swabs unsupervised, theres no reason why we cant do these tests unsupervised as well, he said.

On April 13, the Food and Drug Administration granted an emergency-use authorization, waiving some usual requirements, to a saliva test made by a Rutgers University lab, RUCDR Infinite Biologics.

The Rutgers lab has already processed close to 90,000 tests, according to its chief executive, Andrew Brooks, and expects to ramp up eventually to 30,000 tests per day. Results are available within 72 hours, although they could be sped up to just a few hours with enough infrastructure in place. By contrast, some rapid tests that rely on swabs deliver results in minutes.

Other states are expressing interest. Working with Rutgers, Oklahoma has begun validating a version of the test, and the Rutgers researchers have fielded questions from the White Houses coronavirus task force, from Indiana, Illinois, California and from several large companies. In New Jersey, the test is available for between $65 and $100.

After a disastrously slow start, the United States is starting to see an increase in testing types and capacity. The National Institutes of Health on Wednesday announced a new $1.5 billion shark tank style program aimed at encouraging swift innovation in coronavirus testing, with a goal of new tests by the end of summer. Also Wednesday, the testing manufacturer Hologic said that it had a new test that could allow labs to begin running up to 1 million additional tests per week.

The nasopharyngeal swabs that have mostly been used to test for the coronavirus are invasive and uncomfortable, and may be difficult for severely ill people to tolerate. They also put health care workers at high risk of infection and require them to wear gloves, gowns and masks.

The saliva test, by contrast, doesnt require any interaction with a health care worker. And its easy enough that New Jersey has also started using it at developmental centers with residents who have intellectual and developmental disabilities.

The saliva is immersed in a liquid that preserves it until it can be analyzed. This will be particularly important for developing tests that people can use at home and mail or drop off at a lab, or when dealing with large numbers of samples.

When youre testing 10,000 at a drive-through a day, when youre at a correctional facility collecting it from 1,500 people per day, the use of a preservation agent is really critical, Dr. Brooks said.

He said that the preservative in the Rutgers test is a secret sauce made by a Utah-based partner, Spectrum Solutions, but that the ingredients are easily available and unlikely to pose supply problems.

However, some of the PCR machines, which amplify viral genetic material, require labs to use the manufacturers own reagents. That could potentially be a supply issue, Dr. Rasmussen said.

The Rutgers test was validated in people who were severely ill, but the saliva test often yielded a stronger signal than the swab, suggesting that it is more sensitive yielding fewer false negatives than the swab. It also generated no false positives in all of the samples tested.

False negatives in particular have been a problem with the nasopharyngeal swabs. (A different type of test for antibodies, which can say whether a person was exposed to the virus and has recovered, is riddled with false positives.)

In separate research, a Yale University team reported that saliva may be able to detect the virus in people who are only mildly ill, while a nasopharyngeal swab cannot.

In their study, the team compared swabs and saliva samples from patients. They needed only a few drops of saliva for their test, an advantage for people who may have trouble producing more. Thinking about a favorite meal can often do the trick, said Anne Wyllie, the Yale teams leader.

The swabs are known to produce false negatives perhaps in part because of errors by health care workers under stress. The saliva test appeared to be more consistent and accurate over a longer period of time, detecting infections even after the amounts of the virus have waned, than the swab.

The nasopharyngeal swab is subject to so much more variability in how well its obtained, Dr. Wyllie said. A saliva test is definitely more reliable.

In one case, the team found a health care worker who twice tested negative using a nasopharyngeal swab before finally testing positive on a third day. But the workers saliva tested positive all three days, Dr. Wyllie said. She underlined the risks of asymptomatic health care workers getting a false negative and continuing to care for patients. You can imagine the implications, she said.

While the Yale team did not compare saliva tests with the shorter swabs used in some tests, Dr. Wyllie said she expected that saliva tests would prove superior there as well. Most people with Covid-19 do not have runny noses, which might influence how much virus a short swab can collect, she said.

Saliva tests would also be a preferred choice for at-home tests, Dr. Adalja added. A saliva test for H.I.V. is the only at-home test approved for an infectious disease, he said, but before the pandemic, the federal Biomedical Advanced Research and Development Authority had funded two companies to develop at-home nasal swab tests for influenza.

Its not a high bar to repurpose home testing for the coronavirus, he said. Its not something thats out of reach.

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New Coronavirus Test Offers Advantages: Just Spit and Wait - The New York Times