The World vs. SARS-CoV-2

I’ve an eye on queer Behan and old Kate and the butter, trust me. She’ll do no jugglywuggly with her war souvenir postcards to help to build me murial, tippers! I’ll trip your traps!

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[A]bout half of patients report neurological symptoms, including headaches, confusion and delirium, suggesting the virus may also attack the brain.

A new study offers the first clear evidence that, in some people, the coronavirus invades brain cells, hijacking them to make copies of itself. The virus also seems to suck up all of the oxygen nearby, starving neighboring cells to death.

It’s unclear how the virus gets to the brain or how often it sets off this trail of destruction. Infection of the brain is likely to be rare, but some people may be susceptible because of their genetic backgrounds, a high viral load or other reasons.

Forty percent to 60 percent of hospitalized Covid-19 patients experience neurological and psychiatric symptoms, said Dr. Robert Stevens, a neurologist at Johns Hopkins University. But the symptoms may not all stem from the virus’s invasion of brain cells. They may be the result of pervasive inflammation throughout the body.

{ NY Times | Continue reading }

related { ‘Carnage’ in a lab dish shows how the coronavirus may damage the heart }

O, passmore that and oxus another! Don Dom Dombdomb and his wee follyo! Was his help inshored in the Stork and Pelican against bungelars, flu and third risk parties?

The World Health Organization has said it would prefer a vaccine to be at least 70% effective, but it has set its minimum threshold for a Covid-19 vaccine at 50%. […]

According to Shearing, figures from developers suggest 1 billion doses may be available this year, with another 7 billion ready for distribution in 2021. But those numbers assume multiple vaccines are approved, and supply could turn out to be significantly lower. Specialized needles and syringes will be needed to administer the vaccine, but countries including the United States don’t have enough on hand. There’s also a global shortage of glass vials to contend with. The WHO does not expect widespread vaccinations until the middle of next year, a spokesperson said Friday.

{ CNN | Continue reading }

An experimental submarine, the ‘Siren II,’ is sent to find out what happened to the missing ‘Siren I’

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Researchers in Hong Kong are reporting the first confirmed case of reinfection with the coronavirus.

“An apparently young and healthy patient had a second case of Covid-19 infection which was diagnosed 4.5 months after the first episode,” University of Hong Kong researchers said Monday in a statement.

The report is of concern because it suggests that immunity to the coronavirus may last only a few months.

The 33-year-old man had only mild symptoms the first time, and no symptoms this time around. The reinfection was discovered when he returned from a trip to Spain, the researchers said, and the virus they sequenced closely matched the strain circulating in Europe in July and August.

“Our results prove that his second infection is caused by a new virus that he acquired recently rather than prolonged viral shedding,” said Dr. Kelvin Kai-Wang To, a clinical microbiologist at the University of Hong Kong.

Doctors have reported several cases of presumed reinfection in the United States and elsewhere, but none of those cases have been confirmed with rigorous testing. Recovered people are known to shed viral fragments for weeks, which can cause tests to show a positive result in the absence of live virus.

But the Hong Kong researchers sequenced the virus from both rounds of infection and found significant differences in the two sets of virus, suggesting that the patient was infected a second time.

{ NY Times | Continue reading }

Some people can get the pandemic virus twice, a study suggests. That is no reason to panic. […]

Even if the finding settles the question of whether people can be reinfected with the pandemic virus, it raises many additional questions: How often does this happen? Do people have milder infections, or no symptoms at all, the second time around? Can they still infect others? If natural infection does not always confer solid protection, will that be true for vaccines as well?

{ Nature | Continue reading }

In type 1 immunity, pathogen clearance is mediated through effector cells including group 1 innate lymphocytes (ILC1), natural killer (NK) cells, cytotoxic T lymphocytes, and T helper 1 (TH1) cells

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It is clear from this and other studies that the immune response in hospitalized patients with severe COVID-19 is characterized by lymphopenia and the expression of molecules associated with ongoing inflammation8, whereas these same molecules are expressed at a lower level in people with mild or moderate disease. Differences in immune responses between the different categories of disease severity are even more evident when people with very mild or subclinical disease are included in the analyses.

A key next step will be to analyse samples from people with extremely early signs of COVID-19, and to compare longitudinal data in those who do and those who don’t require hospitalization. Some people who develop severe disease seem to have a suboptimal immune response initially, which might allow uncontrolled viral replication. Such high replication might, in turn, contribute to severe disease.

{ Nature | Continue reading }

related { Efforts are ongoing to find which human or viral factors underpin whether a person with COVID-19 will develop severe symptoms. Clinical evidence linked to two viral lineages now provides key insights into this enigma. | Nature }

quote { Longitudinal analyses reveal immunological misfiring in severe COVID-19 }

‘You act like mortals in all that you fear, and like immortals in all that you desire.’ –Seneca

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Amid all the fighting in your airways, messenger cells grab small fragments of virus and carry these to the lymph nodes, where highly specialized white blood cells—T-cells—are waiting. The T-cells are selective and preprogrammed defenders. Each is built a little differently, and comes ready-made to attack just a few of the zillion pathogens that could possibly exist. For any new virus, you probably have a T-cell somewhere that could theoretically fight it. Your body just has to find and mobilize that cell. Picture the lymph nodes as bars full of grizzled T-cell mercenaries, each of which has just one type of target they’re prepared to fight. The messenger cell bursts in with a grainy photo, showing it to each mercenary in turn, asking: Is this your guy? When a match is found, the relevant merc arms up and clones itself into an entire battalion, which marches off to the airways.

Some T-cells are killers, which blow up the infected respiratory cells in which viruses are hiding. Others are helpers, which boost the rest of the immune system. Among their beneficiaries, these helper T-cells activate the B-cells that produce antibodies—small molecules that can neutralize viruses by gumming up the structures they use to latch on to their hosts. Roughly speaking—and this will be important later—antibodies mop up the viruses that are floating around outside our cells, while T-cells kill the ones that have already worked their way inside. T-cells do demolition; antibodies do cleanup.

Both T-cells and antibodies are part of the adaptive immune system. This branch is more precise than the innate branch, but much slower: Finding and activating the right cells can take several days. It’s also long-lasting: Unlike the innate branch of the immune system, the adaptive one has memory.

After the virus is cleared, most of the mobilized T-cell and B-cell forces stand down and die off. But a small fraction remain on retainer—veterans of the COVID-19 war of 2020, bunkered within your organs and patrolling your bloodstream. This is the third and final phase of the immune response: Keep a few of the specialists on tap. If the same virus attacks again, these “memory cells” can spring into action and launch the adaptive branch of the immune system without the usual days-long delay. […]

Many infected people still clear the virus after a few weeks of nasty symptoms. But others don’t. Maybe they initially inhaled a large dose of virus. Maybe their innate immune systems were already weakened through old age or chronic disease. In some cases, the adaptive immune system also underperforms: T-cells mobilize, but their levels recede before the virus is vanquished, “almost causing an immunosuppressed state,” Iwasaki says. […]

There are also preliminary hints that some people might have a degree of preexisting immunity against the new coronavirus. Four independent groups of scientists—based in the U.S., Germany, the Netherlands, and Singapore—have now found that 20 to 50 percent of people who were never exposed to SARS-CoV-2 nonetheless have significant numbers of T-cells that can recognize it. These “cross-reactive” cells likely emerged when their owners were infected by other, related coronaviruses, including the four mild ones that cause a third of common colds, and the many that infect other animals.

But Farber cautions that having these cross-reactive T-cells “tells you absolutely nothing about protection.” It’s intuitive to think they would be protective, but immunology is where intuition goes to die. The T-cells might do nothing. There’s an outside chance that they could predispose people to more severe disease. We can’t know for sure without recruiting lots of volunteers, checking their T-cell levels, and following them over a long period of time to see who gets infected—and how badly.

Even if the cross-reactive cells are beneficial, remember that T-cells act by blowing up infected cells. As such, they’re unlikely to stop people from getting infected in the first place, but might reduce the severity of those infections.

{ The Atlantic | Continue reading }

deterioration in the forecasts of surface meteorology

51.jpgWeather forecasts play essential parts in daily life, agriculture and industrial activities, and have great economic value. Meteorological observations on commercial aircraft help improve the forecast. However, the global lockdown during the COVID‐19 pandemic chops off 50‐75% of aircraft observations. […] We see deterioration in the forecasts of surface meteorology and atmospheric stratification, and larger deterioration in longer‐term forecasts [AGU]

How the Porn Industry Is Changing During COVID-19

Why the porn industry has a lot to teach us about safety in the Covid-19 era

A new study finds that although musical instruments do generate airborne particles that could carry SARS-CoV-2, the risks for performers and audience may be manageable.

this month, a group of prominent scientists made the case that superspreading clusters suggest the virus is sometimes being transmitted over longer distances through the air in far smaller and more numerous particles. […] Why didn’t the infamous Lake of the Ozarks party spur lots of cases, while a much smaller gathering at a Michigan bar produced nearly 200? Part of the uneven spread of the coronavirus — and the phenomenon of superspreading — can be explained by extreme individual variation in infectivity, researchers say. Overall, researchers have estimated in recent studies that some 10 to 20 percent of the infected may be responsible for 80 percent of all cases. […] One proposal, from a Moscow State University professor, calls for shifting testing resources from the general public to efforts to identify potential “super emitters” with high viral loads by using randomized testing. Other proposals focus on limiting people’s more random interactions, such as on public transit, or at bars and restaurants, while loosening restrictions on their regular contacts, such as through work or school. [Washington Post]

Professional diver Emiliano Pescarolo contracted coronavirus in March and spent 17 days in hospital in the Italian port city of Genoa before being discharged on April 10. Now, three months later, the 42-year-old still experiences breathing difficulties. “Once back home, even after weeks I couldn’t see any progress: if I took a small walk, it was like climbing Mount Everest. I was out of breath also just for talking. I was very worried,” he said. Pescarolo is one of dozens of former Covid patients now receiving care at a rehabilitation clinic in Genoa — and says he is starting to see some progress. [CNN]

Despite how unnatural social distancing may feel to people, it is very much a part of the natural world, practiced by mammals, fishes, insects and birds. Social animals stay apart, changing behaviors such as grooming to stop the spread of diseases that could kill them.

And be sure of this: I am with you always, even to the end of the age

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We then showed that SARS-recovered patients still possess long-lasting memory T cells reactive to SARS-NP 17 years after the 2003 outbreak, which displayed robust cross-reactivity to SARS-CoV-2 NP. Surprisingly, we also frequently detected SARS-CoV-2 specific T cells in individuals with no history of SARS, COVID-19 or contact with SARS/COVID-19 patients.

{ Nature | Continue reading }

Perhaps there’s just little selection pressure on the virus as it races through millions of immunologically naïve people, scientists say. That could change with the advent of vaccines or new therapies, forcing the virus to evolve. But it could also indicate that the virus has been with people longer than we know, and was spreading before the first known cases in Wuhan, China, in December 2019. “The evolution of this virus to become a human pathogen may have already happened and we missed it,” Rasmussen says.

Wang thinks a version of the virus may have circulated earlier in humans in southern Asia, perhaps flying under the radar because it didn’t cause severe disease.

{ Science | Continue reading }

Every day, the same, again

76.jpgAre habits goal-free behaviours, or does every habit actually serve a purpose?

The “Pet Effect” is the idea that getting a pet will make you healthier and happier. This idea is highly promoted by the marketing departments of industry giants like Zoetis, the world’s largest veterinary products corporation. […] while some studies have found evidence linking pets and human health, most published research has not.

We recruited 29 participants to measure human prefrontal cortex activity, using functional near-infrared spectroscopy, during interactions with a cat.

Is there a growing class divide in happiness? Among U.S. adults ages 30 and over in the nationally representative General Social Survey (N = 44,198), the positive correlation between socioeconomic status (SES; including income, education, and occupational prestige) and happiness grew steadily stronger between the 1970s and 2010s. […] the happiness advantage favoring high-SES adults has expanded over the decades

In this essay, I show how difficult emotions, like aggression and murderous rage, are grappled with in horror movies. I discuss three patients who related to intense rage at the mother when viewing the films Joker and Jurassic Park.

The perception of facial attractiveness is not automatic (capacity-free) in general. Men show an automatic (capacity-free) processing of females’ facial attractiveness but not of males’ facial attractiveness. Women show no automatic (capacity-free) processing of males’ or females’ facial attractiveness.

On Aug 1, it will be against the law for adults to wear a face mask in North Carolina

To fully restart the U.S. economy by August, massive population testing for infections with the virus that causes COVID-19 is essential […] test 2 to 6% of the population per day, or between 5 and 20 million people per day […] The authors of the report estimate that this scheme for testing, tracing, and supported isolation (TTSI) would cost between $50 to $300 billion over two years. As they note this is extremely cheap compared to “the economic cost of continued collective quarantine of $100 to 350 billion a month.”

Why We Must Test Millions a Day

studies have suggested that many people who’ve never been infected with SARS-CoV-2, but who have semi-recently recovered from a common-cold coronavirus, may boast partial immunity to COVID-19. […] Chinese researchers monitored antibody levels in 74 COVID-19 patients — one half symptomatic, the other asymptomatic — for months after their recoveries. The scientists found that more than 90 percent of these patients displayed sharp drop-offs in antibody levels two-to-three months after their initial infections. […] The dominant strain of coronavirus in the U.S. may be more contagious than the initial variety. […] study found that the newer coronavirus strain has about five times more functional and intact spike proteins in each of its particles than its predecessor did. [NY mag]

Pool testing combines samples from several people and tests them for the coronavirus all at once, cutting down on the time and supplies required. […] “If everyone is negative, then you’re done” […] If the test detected the presence of the virus, then each person would have to be tested and the results individually analyzed to determine whose sample produced the positive result. […] How many samples are pooled? Researchers have generally suggested quantities between three and 50. The bigger the pool, the more likely a positive case with a low viral load will be too diluted to trigger detection of the virus. [Washington Post]

Norway, Denmark and Finland have closed their borders to Swedes, fearing that they would bring new coronavirus infections with them. […] In several countries, like the Netherlands and Cyprus, they are banned completely. Austria demands a health certificate. Greece makes Swedes quarantine for at least a week, even if they test negative for the coronavirus […] only France, Italy, Spain and Croatia are welcoming Swedes without restrictions.[SF Gate]

COVID-19 is associated with severe impairment of smell, taste, and chemesthesis

This upgraded robotic dolphin is being developed and tested for a series of attractions at a new Chinese aquarium where the government has put a stop to the wildlife trade as part of its efforts to slow and eventually stop the spread of Covid-19.

What if a single injection could lower blood levels of cholesterol and triglycerides — for a lifetime? In the first gene-editing experiment of its kind, scientists have disabled two genes in monkeys that raise the risk for heart disease. Humans carry the genes as well, and the experiment has raised hopes that a leading killer may one day be tamed. [NY Times]

The UK government’s plan to invest hundreds of millions of pounds in a satellite broadband company has been described as “nonsensical” by experts, who say the company doesn’t even make the right type of satellite the country needs after Brexit. […] “The fundamental starting point is, yes, we’ve bought the wrong satellites […] What’s happened is that the very talented lobbyists at OneWeb have convinced the government that we can completely redesign some of the satellites to piggyback a navigation payload on it.”

A growing list of companies say they’ll join an advertiser boycott on Facebook in protest of what they say are the site’s failures to stop the spread of hate.

The white iPhone with chipped paint that Moroccan journalist Omar Radi used to stay in contact with his sources also allowed his government to spy on him. They could read every email, text and website visited; listen to every phone call and watch every video conference; download calendar entries, monitor GPS coordinates, and even turn on the camera and microphone to see and hear where the phone was at any moment. Yet Radi was trained in encryption and cyber security. He hadn’t clicked on any suspicious links and didn’t have any missed calls on WhatsApp — both well-documented ways a cell phone can be hacked. Instead, a report published Monday by Amnesty International shows Radi was targeted by a new and frighteningly stealthy technique. All he had to do was visit one website. Any website. Radi’s phone shows that it was infected by “network injection,” a fully automated method where an attacker intercepts a cellular signal when it makes a request to visit a website. In milliseconds, the web browser is diverted to a malicious site and spyware code is downloaded that allows remote access to everything on the phone. [The Star]

All it took to compromise a smartphone was a single phone call over WhatsApp. The user didn’t even have to pick up the phone. [WIRED]

Milton Glaser, Co-founder of New York Magazine and Creator of ‘I❤NY,’ Dies at 91

How to make an SMS bot with Google Sheets + Twilio

If Great Britain was located next to Japan

Your sky is just a HOLE on the roof of my world, says the frog in the well

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It’s growing clearer that the coronavirus does not spread in an orderly way. Each infected person might infect two others on average but most people who get it infect no one.

On the diagram, where DeRisi’s cursor lingers, he highlights a person with a particular talent for spreading the disease. The genetic information shows you the urgency of getting that person into quarantine, but it does more than that: It has the potential to lead you more generally to the social activity that’s spreading the disease.

It works the other way, too. The approach DeRisi has developed can be used not just to shut things down but to open them up. Last week, in Northern California, a pair of workers at a fish-packing plant came down with symptoms of Covid-19. The Biohub processed their tests and found both workers had the virus. In an age not all that distant from ours, the fish-packing plant, which believed it had taken the measures to keep its workers safe, would have been forced to close, as it would have had to assume that one of the workers had infected the other on the job. But then Joe DeRisi’s Badass Virus Hunters sequenced the two viruses and showed they were genetically far apart: The two workers had contracted the virus independently and outside of work. The fish-packing plant was able to stay open — and its workers were able to stay on their jobs.

{ Bloomberg | Continue reading }

related { Social distancing and individual non-pharmaceutical interventions could potentially remove the need for lockdowns }

related { What do Covid-19, Ebola, Lyme and AIDS have in common? They jumped to humans from animals after we started destroying habitats and ruining ecosystems. | NY Times }

pollen and solar radiation

We hypothesize that pollen may explain the seasonality of flu-like epidemics including COVID-19. […] We conclude that pollen is a predictor for the inverse seasonality of flu-like epidemics including COVID-19, and solar radiation is a co-inhibitor. The observed seasonality of COVID-19 during Spring, suggests that COVID-19 may revive in The Netherlands after week 33 [mid-August].

dogs can detect a person infected by the SARS-CoV-2 virus

How readily can playing instruments transmit the virus?

It looks as if the low German fatality rate is not due to their superior testing capacity, but rather to the fact that the average German is less likely to get infected and die than the average Brit.

“Japan, I think a lot of people agree, kind of did everything wrong, with poor social distancing, karaoke bars still open and public transit packed near the zone where the worst outbreaks were happening. But the one thing that Japan did right was masks.” [NY Times]

Two-meter distancing might halve infection risk compared to one meter

Covid-19 can last for several months in some people

Nearly Half of Coronavirus Spread May Be Traced to People Without Any Symptoms — Another concern is that the virus may be damaging the bodies of asymptomatic in other, silent ways.

First Human Trial for COVID-19 Antibody Drug Begins — The antibody was discovered in a recovered patient’s blood using microfluidics, machine vision, and big-data tools

Nobody knows exactly what will happen as communities open up. The most likely scenario is that virus cases will continue to surge and fall around the globe for the foreseeable future. 5 Rules to Live By During a Pandemic

Every day, the same, again

32.jpgMen hired for sexual fantasy break into wrong house

The monkeys attacked the lab assistant and stole the sample box with three samples

A Security Flaw In Qatar’s Contact Tracing App Exposed Hundreds Of Thousands Of People’s Personal Data

In the past, national emergencies in the United States have resulted in increased gun preparation (ie, purchasing new guns or removing guns from storage); in turn, these gun actions have effected increases in firearm injuries and deaths. The aim of this paper was to assess the extent to which interest in gun preparation has increased amid the coronavirus disease (COVID-19) pandemic using data from Google searches related to purchasing and cleaning guns. […] Our results corroborate media reports that gun purchases are increasing amid the COVID-19. [JMIR]

Introductions and early spread of SARS-CoV-2 in the New York City area

Covid-19 has, so far it seems, three modes of transmission. One route is via surfaces, deposited on things like door handles or silverware that then picked up by someone who touches some entry point into the body—eyes, nose, mouth. […] A second route is through large droplets, like those someone might give off in a cough. […] the third, more complicated route. A vast number of the particles that come out of a person’s mouth are much smaller, under 5 microns. They dry out quickly in the air and become so light they can float around for hours. Even the slightly warm layer of air constantly wafting upward from every person—our “thermal plume”—can carry these particles up, up, and away. Random air flow makes their spread turbulent, bounced around by currents like sand in a tide pool. And we emit them all the time. […] “The overarching assumption is that the probability of transmission is proportional to the number of virus particles floating around in the air. The more that you inhale, the more likely you are to get it,” says William Ristenpart, a professor of chemical engineering at UC Davis who studies disease transmission. “The room you’re in right now has a roof. Turbulent diffusion goes up and can’t go through the roof. It reflects off. Outdoors, it can turbulently diffuse away.” [Wired]

The emerging long-term complications of Covid-19 — Somewhere between 5 and 80 percent of people who test positive for Covid-19 may be asymptomatic, or only develop symptoms days or even weeks after their test, and many of these people will have a mild form of the illness with no lasting symptoms. But the UK National Health Service assumes that of Covid-19 patients who have required hospitalization, 45 percent will need ongoing medical care, 4 percent will require inpatient rehabilitation, and 1 percent will permanently require acute care.

New Design Helps N95 Mask Wearers Breathe Easier (new device prevents oxygen deprivation)

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Healthy Selfishness and Pathological Altruism: Measuring Two Paradoxical Forms of Selfishness

How do children learn the typical features of objects in the world? For many objects, this information must come from the language they hear. However, people are more likely to talk about atypical features (e.g., “purple carrot”) than typical features (e.g., “orange carrot”). Does the speech children hear from their parents also overrepresent atypical features?

Octave Durham went to prison for stealing two van Gogh paintings. […] “I didn’t have a buyer before I did it,” he said. “I just thought I can either sell them, or if I have a problem I can negotiate with the paintings.” By “negotiate with the paintings,” Mr. Durham meant using the paintings as a bargaining chip with law enforcement officials, in case he got into trouble for something else. […] Mr. Brand said many thieves think they will be able to sell paintings on the open market, and then quickly find out that there aren’t legal buyers. “You have thieves who think there are buyers who would really like to have stolen art on their wall. That doesn’t exist.” […] That’s when they offer them to other criminals, often for much less than their real value. Mr. Brand estimates that a work of art in the criminal underworld is worth about 10 percent of its value in the legitimate art market — so if a painting might sell for $10 million at auction, it can be traded among criminals for a value of about $1 million. Mr. Durham said the value is even lower than that — about 2.5 to 5 percent of market value. [NY Times]

I can’t remember the last time I read a novel that feels so LA. Cooper’s rendering of the flat affect of Southern California is spot-on; in “Board,” the posters respond to vulgar depictions of violence with comments like “Here we go again” and “I don’t know whether to laugh or cry (LOL).” That’s what it’s like there — there’s no social space for reasoning or explanation, for genuine self-reflection. Sometimes you just shrug your shoulders and say, “Honey, it’s LA.” In a way, this L.A. affect prefigures the flat affect of the Internet, or even life in the 21st century. Sometimes you just shrug your shoulders and say, “Honey, it’s late capitalism.” [The New Inquiry]

One of the most important moments in the transition between the Eighties and Nineties, for live rock bands, was how much rock to leave behind.

Mullet Challenge

25.jpgYour face mask selfies could be training the next facial recognition tool

‘Tiger King’ Joe Exotic Asks America To Join ‘Mullet Challenge’ To Promote A Presidential Pardon

The Effects of Barefoot Running on Working Memory — working memory may be enhanced after at least 16 minutes of barefoot running if the individual has to focus attention on the ground

People in long term, committed relationships try to support their decisions to maintain their relationships with marriage illusions

Peru took strict measures. Covid-19 surged anyway.

“What’s crazy is, we’re three months in, and we’re still not able to calibrate our risk management. It’s a mess,” […] Scientists are still trying to understand the virus they call SARS-CoV-2, which causes the disease covid-19. Basic questions are not fully answered: How deadly is this virus? How contagious? Are there different strains with different clinical outcomes? Why does SARS-CoV-2 create a devastating disease in some people while leaving others without symptoms or even knowledge that they were infected? [Washington Post]

an 1/3 + 1/3 = 2/6? It seemed so!

Arthur Schopenhauer and Psychiatry

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