H5N1

COVID-19 in California: 5,307 new cases, 31 new deaths

Something has gone very badly wrong in California. A screenshot from the Department of Public Health: June29_CA_COVID-19_ByTheNumbers.png (2550×1908).

COVID-19 projection: 189,095 US deaths by October 1

A screenshot from COVID-19 Projections Using Machine Learning:

Dr. Tedros on COVID-19: 'This is not even close to being over'

A WHO transcript: WHO Director-General's opening remarks at the media briefing on COVID-19 - 29 June 2020. Excerpt:

WHO will continue to do everything in our power to serve countries with science, solidarity and solutions. The critical question that all countries will face in the coming months is how to live with this virus. That is the new normal.  

Many countries have implemented unprecedented measures to suppress transmission and save lives. These measures have been successful in slowing the spread of the virus. But they have not completely stopped it.

Some countries are now experiencing a resurgence of cases as they start to re-open their economies and societies. Most people remain susceptible. The virus still has a lot of room to move.

We all want this to be over. We all want to get on with our lives.  But the hard reality is: this is not even close to being over.  Although many countries have made some progress, globally the pandemic is actually speeding up.

We’re all in this together, and we’re all in this for the long haul. We will need even greater stores of resilience, patience, humility and generosity in the months ahead.  We have already lost so much – but we cannot lose hope.

This is a time for renewing our commitment to empowering communities, suppressing transmission, saving lives, accelerating research and political and moral leadership. 

But it’s also a time for all countries to renew their commitment to universal health coverage as the cornerstone of social and economic development – and to building the safer, fairer, greener, more inclusive world we all want. 

WHO: Countries complaining about contact tracing are 'lame'

Via an AP report in The New York Times, Dr. Tedros shows that even teddy bears have sharp teeth: WHO: Countries Complaining About Contact Tracing Are 'Lame'. Excerpt:

LONDON — The head of the World Health Organization on Monday dismissed complaints from countries complaining that contact tracing is too difficult to implement as a control strategy for the coronavirus pandemic as “lame.” 

The U.N. health agency has repeatedly advised countries that shutting down their COVID-19 outbreaks requires having a strong contact tracing program in place, a labor-intensive process of tracking down contacts of people with coronavirus to ensure those at risk isolate themselves.  

In recent months, countries with large outbreaks of COVID-19, including Britain and the U.S., have said there are simply too many contacts to trace for an effective system to be put into place.  

Britain had vowed to have a “world-class” contact tracing system in place earlier this month. But the U.K. ultimately ditched the digital app it developed for that purpose and politicians have acknowledged the program is not yet running at full strength despite recruiting thousands of workers. In recent weeks, British health officials have said their contact tracers are failing to reach about one quarter of people with the virus — leaving thousands of people free to pass on COVID-19.  

At a media briefing on Monday, WHO Director-General Tedros Adhanom Ghebreyesus pointed to his emergencies director Dr. Michael Ryan as an example of someone willing to go to extraordinary lengths to conduct contact tracing, citing Ryan’s work — while wearing a bulletproof helmet and vest — during an Ebola outbreak in a part of Congo where armed groups had attacked and killed health workers.  

“He believed he had to do everything to stop Ebola and to show that saving lives actually requires that level of commitment,” Tedros said. 

Tedros said it wasn't acceptable that some countries claimed there were too many contacts to trace and that the process itself was too difficult. He has previously lauded the contact tracing programs adopted by countries like South Korea, Singapore and China, which involved teams of health workers tracing tens of thousands of people and ensuring that those exposed to the virus were isolated. 

Tedros said that well-resourced countries that aren't fighting wars have little excuse for not carrying out good contact tracing.  

“If contact tracing helps you to win the fight, you do it, even (when) risking your life," he said. “If any country is saying contact tracing is difficult, it is a lame excuse.”

COVID-19: Total deaths for US, Canada, and Vietnam

Our World in Data has some very enlightening interactive graphs. Here's a screenshot from United States: Coronavirus Pandemic showing total COVID-19 deaths since January 22. I've added Canadian and Vietnamese numbers to those of the US:

The US total so far, as of today, is 125,804. While Canada has certainly managed to flatten the curve, we have still suffered 8,522 deaths. Vietnam has never had a curve to flatten. The Vietnamese have not lost a single life to COVID-19 so far.

COVID-19: What did people know, and when did they know it?

Thanks to James Fallows for providing the link in his excellent Atlantic article to a very helpful timeline in PDF on how COVID-19 came to the world's attention:

Download Covid19 and China.

In the same article, Fallows also links to the Obama administration's Pandemic Playbook, which the Trump administration dismissed and ignored:

Download Pandemic-Playbook.

 

Fauci doubts effectiveness of COVID-19 vaccine in US due to anti-vaxxers

Via The Guardian: Fauci doubts effectiveness of coronavirus vaccine in US due to anti-vaxxers.

The US is “unlikely” to achieve herd immunity to the coronavirus even with a vaccine, according to the country’s leading public health expert, who warned that a “general anti-science, anti-authority, anti-vaccine feeling” is likely to thwart vaccination efforts.  

In an interview with CNN, Dr Anthony Fauci also said people not wearing masks was “a recipe for disaster” and said of the Trump administration’s attempts at contact tracing: “I don’t think we’re doing very well.” 

The US reported a record number of new coronavirus cases in a single day on Friday, with 36 states reporting a rise in infections and Texas, Florida and Arizona particularly badly hit. With more than 2.5m coronavirus cases and more than 125,000 deaths, the US accounts for about 25% of all coronavirus cases and deaths worldwide. 

Countries including the US are scrambling to develop a vaccine, and Fauci has said one could be available by the end of 2020 or early 2021. But he suggested the vaccine would not be fully effective.  

“The best we’ve ever done is measles, which is 97% to 98% effective,” Fauci told CNN. “That would be wonderful if we get there. I don’t think we will. I would settle for [a] 70%, 75% effective vaccine.” 

Polls have shown that many Americans are skeptical of a vaccine. In May only half of Americans said they would get one if it becomes available, while a Washington Post survey showed 27% would likely refuse a vaccine.  

Fauci was asked if herd immunity could be achieved through two-thirds of the population taking a vaccine that was only 70% to 75% effective. 

“No – unlikely,” he said. 

“There is a general anti-science, anti-authority, anti-vaccine feeling among some people in this country – an alarmingly large percentage of people, relatively speaking,” Fauci said, adding that the government has “a lot of work to do” to educate people about vaccines.  

Contact tracing – the act of monitoring people who have come into contact with someone infected with the coronavirus – is seen as one of the most effective measures until a vaccine is developed. Asked how the US is performing on contact tracing, Fauci said: “I don’t think we’re doing very well.  

“If you go into the community and call up and say: ‘How’s the contact tracing going?’ The dots are not connected because a lot of it is done by phone. You make a contact, 50% of the people, because you’re coming from an authority don’t even want to talk to you.”  

Responding to people’s resistance to wearing masks, Fauci said it was “a recipe for disaster” and said some states had reopened too quickly.  

“There are some states in which the leadership and the decision [to open up] was a little too precipitous,” he said. “There are others when the leadership did it right, but the citizenry didn’t listen to them.”

The MIT Press and UC Berkeley launch Rapid Reviews: COVID-19

A news release from MIT Press: The MIT Press and UC Berkeley Launch Rapid Reviews: COVID-19. The link takes you to just this release, but I'm already signed up for more. Excerpt:

The MIT Press announced today the launch of Rapid Reviews: COVID-19 (RR:C19), an open access, rapid-review overlay journal that will accelerate peer review of COVID-19-related research and deliver real-time, verified scientific information that policymakers and health leaders can use.   

Scientists and researchers are working overtime to understand the SARS-CoV-2 virus and are producing an unprecedented amount of preprint scholarship that is publicly available online but has not been vetted yet by peer review for accuracy. Traditional peer review can take four or more weeks to complete, but RR:C19’s editorial team, led by editor-in-chief, Stefano M. Bertozzi, Professor of Health Policy and Management and Dean Emeritus of the School of Public Health at University of California Berkeley, will produce expert reviews in a matter of days.   

Using artificial intelligence tools, a global team will identify promising scholarship in preprint repositories, commission expert peer reviews, and publish the results on an open access platform in a completely transparent process. The journal will strive for disciplinary and geographic breadth, sourcing manuscripts from all regions and across a wide variety of fields, including medicine; public health; the physical, biological, and chemical sciences; the social sciences; and the humanities. RR:C19 will also provide a new publishing option for revised papers that are positively reviewed.   

Made possible by a $350,000 grant from the Patrick J. McGovern Foundation and hosted on PubPub, an open-source publishing platform from the Knowledge Futures Group for collaboratively editing and publishing journals, monographs, and other open access scholarly content, RR:C19 will limit the spread of misinformation about COVID-19, according to editor-in-chief Bertozzi.   

“There is an urgent need to validate—or debunk—the rapidly growing volume of COVID-19-related manuscripts on preprint servers,” explains Bertozzi. “I'm excited to be working with the MIT Press, the Patrick J. McGovern Foundation, and the Knowledge Futures Group to create a novel publishing model that has the potential to more efficiently translate important scientific results into action. We are also working with COVIDScholar, an initiative of UC Berkeley and Lawrence Berkeley National Lab, to create unique AI/machine learning tools to support the review of hundreds of preprints per week.”   

“This project signals a breakthrough in academic publishing, bringing together urgency and scientific rigor so the world’s researchers can rapidly disseminate new discoveries that we can trust,” says Vilas Dhar, trustee of the Patrick J. McGovern Foundation. “We are confident the RR:C19 journal will quickly become an invaluable resource for researchers, public health officials, and healthcare providers on the frontline of this pandemic. We’re also excited about the potential for a long-term transformation in how we evaluate and share research across all scientific disciplines.”

The COVID-19 coronavirus is mutating

I hesitate to pick up mutation stories; the term is too often used as a gimmick in science fiction to "explain" the inexplicable. But this report in The Washington Post may be onto something: The coronavirus is mutating. Excerpt:

When the first coronavirus cases in Chicago appeared in January, they bore the same genetic signatures as a germ that emerged in China weeks before. 

But as Egon Ozer, an infectious-disease specialist at the Northwestern University Feinberg School of Medicine, examined the genetic structure of virus samples from local patients, he noticed something different.  

A change in the virus was appearing again and again. This mutation, associated with outbreaks in Europe and New York, eventually took over the city. By May, it was found in 95 percent of all the genomes Ozer sequenced.  

At a glance, the mutation seemed trivial. About 1,300 amino acids serve as building blocks for a protein on the surface of the virus. In the mutant virus, the genetic instructions for just one of those amino acids — number 614 — switched in the new variant from a “D” (shorthand for aspartic acid) to a “G” (short for glycine).  

But the location was significant, because the switch occurred in the part of the genome that codes for the all-important “spike protein” — the protruding structure that gives the coronavirus its crownlike profile and allows it to enter human cells the way a burglar picks a lock.

And its ubiquity is undeniable. Of the approximately 50,000 genomes of the new virus that researchers worldwide have uploaded to a shared database, about 70 percent carry the mutation, officially designated D614G but known more familiarly to scientists as “G.”  

“G” hasn’t just dominated the outbreak in Chicago — it has taken over the world. Now scientists are racing to figure out what it means. 

At least four laboratory experiments suggest that the mutation makes the virus more infectious, although none of that work has been peer-reviewed. Another unpublished study led by scientists at Los Alamos National Laboratory asserts that patients with the G variant actually have more virus in their bodies, making them more likely to spread it to others.  

The mutation doesn’t appear to make people sicker, but a growing number of scientists worry that it has made the virus more contagious.

 “The epidemiological study and our data together really explain why the [G variant’s] spread in Europe and the U.S. was really fast,” said Hyeryun Choe, a virologist at Scripps Research and a lead author of an unpublished study on the G variant’s enhanced infectiousness in laboratory cell cultures. “This is not just accidental.” 

But there may be other explanations for the G variant’s dominance: biases in where genetic data are being collected, quirks of timing that gave the mutated virus an early foothold in susceptible populations. 

“The bottom line is, we haven’t seen anything definitive yet,” said Jeremy Luban, a virologist at the University of Massachusetts at Amherst.  

The scramble to unravel this mutation mystery embodies the challenges of science during the coronavirus pandemic. With millions of people infected and thousands dying every day around the world, researchers must strike a high-stakes balance between getting information out quickly and making sure that it’s right.

‘Feeling like death’: Inside a Houston hospital bracing for a COVID-19 peak

Via The New York Times: ‘Feeling Like Death’: Inside a Houston Hospital Bracing for a Virus Peak. Excerpt:

HOUSTON — Melissa Estrada had tried to be so careful about the coronavirus. For months she kept her three children at home, and she always wore a mask at the grocery store. She and her daughter even stitched face coverings for relatives and friends.  

But over the weekend Ms. Estrada, 37, was fighting the virus at Houston Methodist Hospital after a week of treatments that included an experimental drug, steroids, intensive care and high doses of oxygen. She probably contracted the virus while attending a dinner with relatives who had also been cautious, she said. Within days, all four adults and several children who had been at the gathering tested positive for the coronavirus.  

“It was really, really scary,” Ms. Estrada said of her illness. She worried constantly about leaving her children motherless. “You hear about it and you think it’s the older people or the people with underlying issues,” she said. “And I’m healthy. I don’t understand how I got this bad.” 

Coronavirus cases are rising quickly in Houston, as they are in other hot spots across the South and the West. Harris County, which includes most of Houston and is one of the largest counties in the nation, has been averaging more than 1,100 new cases each day, among the most of any American county. Just two weeks ago, Harris County was averaging about 313 new cases daily.  

Measures to cope with the surge and to plan for its peak were evident over the weekend at Methodist, which called nurses to work extra shifts, brought new laboratory instruments on line to test thousands more samples a day and placed extra hospital beds in an empty unit about to be reopened as patients filled new coronavirus wards.  

Gov. Greg Abbott, speaking in Dallas on Sunday, said that the virus had taken a “very swift and a very dangerous turn” in Texas, and that the increase in the rate of positive coronavirus tests, to over 13 percent in the past month from less than 4 percent, was an “alarm bell.” He made the grim assessment after meeting with Vice President Mike Pence and Dr. Deborah L. Birx, the coordinator of the White House’s coronavirus task force, who joined the governor in urging all Texans to wear masks and avoid close contact in crowds. 

Mr. Pence, appearing at a Dallas rally celebrating religious freedoms, threw his support behind Mr. Abbott and his efforts to reopen the state’s economy — even as the governor made an about-face on Friday in his phased plan by ordering bars closed and capacity at restaurants cut. Many young people had socialized in them, standing close together, not wearing masks, some expressing skepticism that they could become infected. 

During the virus’s first peak in April, the majority of patients testing positive in the Methodist hospital system were older than 50. Now the majority are, like Ms. Estrada, relatively young. Nearly one-third of intensive care patients are now under 50, much higher than in the initial coronavirus surge.

The stress on medical institutions burst into public view last week, when Texas Medical Center — a downtown cluster of Houston’s major public and private hospitals, including Methodist — announced that the baseline intensive care unit capacity across its hospitals was full, with 28 percent of beds occupied by virus patients. That was nearly twice a threshold established by the state, which called for I.C.U.s to have a maximum 15 percent of virus patients for hospitals to resume elective services.