The World vs. SARS-CoV-2

The freaks of chance

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{ Seventy-seven cases of a new variant linked to a surge in Covid-19 cases in India have been found in the UK | FT | full story }

‘Film making is the process of turning money into light and then back into money again.’ –John Boorman

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Stanford scientists saved drops of the COVID-19 vaccine destined for the garbage can, reverse engineered them, and have posted the mRNA sequence that powers the vaccine on GitHub for all to see.

The GitHub post is four pages long. The first two are an explanation by the team of scientists about the work, the second two pages are the entire mRNA sequence for the Moderna COVID-19 vaccine.

{ Vice | Continue reading }

The triple Fates and unforgetting Furies

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The U.K.’s B.1.1.7 variant has spread to more than eighty countries and has been doubling every ten days in the U.S., where it is expected to soon become the dominant variant. […] new evidence also suggests that people infected with it have higher viral loads and remain infectious longer, which could have implications for quarantine guidelines. […]

“The fact that different variants have independently hit on the same mutations suggests we’re already seeing the limits of where the virus can go,” McLellan told me. “It has a finite number of options.”

Over time, SARS-CoV-2 is likely to become less lethal, not more. When people are exposed to a virus, they often develop “cross-reactive” immunity that protects them against future infection, not just for that virus, but also for related strains; with time, the virus also exhausts the mutational possibilities that might allow it to infect cells while eluding the immune system’s memory. “This is what we think happened to viruses that cause the common cold,” McLellan said. “It probably caused a major illness in the past. Then it evolved to a place where it’s less deadly. But, of course, it’s still with us.” It’s possible that a coronavirus that now causes the common cold, OC43, was responsible for the “Russian flu” of 1889, which killed a million people. But OC43, like other coronaviruses, became less dangerous with time. Today, most of us are exposed to OC43 and other endemic coronaviruses as children, and we experience only mild symptoms. For SARS-CoV-2, such a future could be years or decades away.

{ New Yorker | Continue reading }

‘Cannot wait to get the COVID vaccine so I can touch my face again.’ –Scott Shapiro

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Higher airborne pollen concentrations correlated with increased SARS-CoV-2 infection rates, as evidenced from 31 countries across the globe

[…]

We found that pollen, sometimes in synergy with humidity and temperature, explained, on average, 44% of the infection rate variability. Lockdown halved infection rates under similar pollen concentrations. […]

Pollen grains act on the very site of virus entry, the nasal epithelium, by inhibiting antiviral λ-IFN responses.

{ PNAS | Continue reading }

previously { We conclude that pollen is a predictor for the inverse seasonality of flu-like epidemics including COVID-19 }

wax crayon on paper { Jean-Michel Basquiat, Dog Shit in the Head of the Pope, 1981 }

A planet where apes evolved from men?

Veterinary techs distribute food every morning to more than 5,000 monkeys at the Tulane University National Primate Research Center outside New Orleans. […] Mr. Lewis, the chief executive of Bioqual, was responsible for providing lab monkeys to pharmaceutical companies like Moderna and Johnson & Johnson, which needed the animals to develop their Covid-19 vaccines.

Unable to furnish scientists with monkeys, which can cost more than $10,000 each, about a dozen companies were left scrambling for research animals at the height of the pandemic. […] The latest shortage has revived talk about creating a strategic monkey reserve in the United States, an emergency stockpile similar to those maintained by the government for oil and grain. […]

No country can make up for what China previously supplied. Before the pandemic, China provided over 60 percent of the 33,818 primates, mostly cynomolgus macaques, imported into the United States in 2019.

{ NY Times | Continue reading }

related { Drunk monkey sentenced to life behind bars after attacking 250 humans }

hey yayo, beep the air horn

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{ South Africa is back to its pre-B.1.351 baseline in covid cases. There’s no proof this variant is more infectious. Its immune evasion is enough to explain how it took off. And the descent occurred without vaccines. | Eric Topol }

If you see me in the club, nothin’ but Cris poppin’

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California Gov. Gavin Newsom on Friday revealed the most expensive budget in state history — a $227 billion spending plan highlighted by a $15 billion one-time surplus. How is it possible? […]

The Democratic governor and state lawmakers passed a budget last year with deep spending cuts to cover what they expected to be a $54.3 billion pandemic-induced shortfall. That estimate was wrong, as the recession was not as deep as they had anticipated […]

job losses have been concentrated among low-wage workers, who pay relatively little taxes […] wealthy residents have continued to make money and pay taxes, leading to much greater tax collections than officials predicted in early summer. 

{ AP | Cal Matters }

photo { Sheron Rupp, Mansfiled, OH, 2001-2002 }

Every day, the same, again

55.jpgrats, with holes in their knee joints drilled by the researchers to mimic cancer pain, who where exposed to Mozart K448 Sonata, consumed more food, gained more weight, and expressed lower amounts of p38a and p38b than the control group.

Many people may not have noticed yet but a few months ago, a kind of unassuming little pickup truck emoji appeared on most peoples’ electronic devices. The story behind that little truck is actually a window into the shadowy corporate cabal behind emoji and the big and sometimes dare we say DARK MONEY that companies are pushing around behind the scenes to shape our keyboards and influence how we communicate every day. [NPR]

What Is Rough Sex, Who Does It, and Who Likes It?

What makes a good question? What principles govern human information acquisition and how do people decide which query to conduct to achieve their goals?

This study uses the unprecedented changes in the sex ratio due to the losses of men during World War II to identify the impacts of the gender imbalance on marriage market and birth outcomes in Japan.

Bitcoin uses more electricity than Argentina

Jamaica faces marijuana shortage as farmers struggle and Louis Vuitton pulls “Jamaican Sweater” from online store after using wrong flag colors

Food sharing has become quite popular over the last decade, with companies offering food options specifically designed to be shared. As the popularity has grown, so too has concerns over the potential negative impact on consumer health. Despite companies’ explicit claims to the contrary, critics maintain that food sharing may be encouraging excessive caloric intake. The current article provides the first systematic exploration of why this may be happening. […] Our findings suggest that food sharing may be encouraging excessive caloric intake by leading consumers to underestimate the fattening potential brought on by shared food consumption.

We argue that Internet search reduces the likelihood of information being stored in memory.

Scientists are working on a shot that could protect against Covid-19, its variants, certain seasonal colds — and the next coronavirus pandemic. [NY Times]

In evolutionary terms, SARS-CoV-2 is an ‘evasion-light’ pathogen. It has not had to acquire an armamentarium of molecular features to outwit immune responses in general and neutralizing antibodies in particular. This is because it currently transmits from one person to another before immune responses have developed — and, in many cases, before disease symptoms are noted. Other pathogens are ‘evasion-strong’. The extreme example is HIV. It frequently co-exists with human immune systems, possibly for years, before onward transmission. […] The emergence of another pathogen with the evasion capabilities of HIV might be the worse-case scenario for a pandemic. […] A special class of protective antibodies called broadly neutralizing antibodies acts against many different strains of related virus — for example, of HIV, influenza or coronavirus. Such antibodies could be used as first-line drugs to prevent or treat viruses in a given family, including new lineages or strains that have not yet emerged. More importantly, they could be used to design vaccines against many members of a given family of viruses. [ Nature]

Israel’s swift vaccination rollout has made it the largest real-world study of Pfizer Inc’s COVID-19 vaccine. Results are trickling in. […] Among the first fully-vaccinated group there was a 53% reduction in new cases, a 39% decline in hospitalizations and a 31% drop in severe illnesses from mid-January until Feb. 6, said Eran Segal, data scientist at the Weizmann Institute of Science in Rehovot, Israel. In the same period, among people under age 60 who became eligible for shots later, new cases dropped 20% but hospitalizations and severe illness rose 15% and 29%, respectively. […] “We’ve so far identified the same 90% to 95% efficacy against the British strain […] It’s too early to say anything about the South African variant.” [Reuters]

The index case was a symptomatic patient in whom isolation was discontinued after 2 negative results on nasopharyngeal polymerase chain reaction testing. The patient subsequently infected multiple roommates and staff, who then infected others.

Susceptibility to infection such as SARS-CoV-2 may be influenced by host genotype. We found heritability of 49% (32−64%) for delirium; 34% (20−47%) for diarrhea; 31% (8−52%) for fatigue; 19% (0−38%) for anosmia; 46% (31−60%) for skipped meals and 31% (11−48%) for predicted COVID-19.

The idea was to provide medicines preventing or treating COVID-19 at a low cost or free of charge, the British university said. […] “We actually thought they were going to do that,” James Love, director of Knowledge Ecology International, a nonprofit that works to expand access to medical technology, said of Oxford’s pledge. […] A few weeks later, Oxford—urged on by the Bill & Melinda Gates Foundation —reversed course. It signed an exclusive vaccine deal with AstraZeneca that gave the pharmaceutical giant sole rights and no guarantee of low prices—with the less-publicized potential for Oxford to eventually make millions from the deal and win plenty of prestige.

Covid reinfections may be more common than realized. In Washington state, health officials are investigating nearly 700 cases that meet the criteria for possible reinfection. In Colorado, officials estimate that possible reinfections make up just 0.1 percent of positive coronavirus cases. In Minnesota, officials have investigated more than 150 cases of suspected reinfection.

During the second wave, in autumn 1918, cantonal authorities initially reacted hesitantly and delegated the responsibility to enact interventions to municipal authorities [..] A premature relaxation of restrictions on mass gatherings was associated with a resurgence of the epidemic. Strikingly similar patterns were found in the management of the COVID-19 outbreak in Switzerland.

Vitamin D supplementation to the older adult population in Germany has the cost-saving potential of preventing almost 30,000 cancer deaths per year

The rectal depth to which the thermistor is inserted affects measurement of rectal temperature. Clinicians should insert flexible rectal thermistors 15 cm (6 in) into the rectum.

McKinsey Settles for Nearly $600 Million Over Role in Opioid Crisis — The consulting firm has reached agreements with 49 states because of its sales advice to drugmakers, including Purdue Pharma, the manufacturer of OxyContin.

The Shocking Meltdown of Ample Hills — Brooklyn’s Hottest Ice Cream Company — They had $19 million, a deal with Disney, and dreams of becoming the next Ben & Jerry’s. Then everything fell apart.

Facing deficit (a potential shortfall of $150 million because of the pandemic), the Metropolitan Museum of Art has begun conversations with auction houses and its curators about selling some artworks to help pay for care of the collection. [NY Times]

People often use short timezone abbreviations like EST and PST to refer to timezones. If you’re doing this in a computer program, you are almost certainly making a huge mistake.

America’s Most Hated Office Jargon — Synergy, Teamwork, Thinking outside the box…

The Uni boxing Glove

almost a new virus

Ice cream tests positive for coronavirus in China

mutant strain in South Africa strongly resistant to past immunity. almost a new virus.

Smartwatches can help detect COVID-19 days before symptoms appear (subtle heartbeat changes)

Almost a third of recovered Covid patients return to hospital in five months and one in eight die — Research has found a devastating long-term toll on survivors, with people developing heart problems, diabetes and chronic conditions

Evidence is growing that self-attacking ‘autoantibodies’ could be the key to understanding some of the worst cases of SARS-CoV-2 infection.

That’s for us to know and you to find out

bulls.jpg A couple in Canada have been fined for breaking Covid curfew rules after the woman was caught “walking” her husband on a leash

We are currently faced with the question of how the CoV-2 severity may change in the years ahead. […] once the endemic phase is reached and primary exposure is in childhood, CoV-2 may be no more virulent than the common cold

First detection of SARS-CoV-2 spike protein N501 mutation [B.1.1.7/UK variant] in Italy in August, 2020

We have detected a new variant circulating in December in Manaus, Amazonas state, north Brazil

Japan has found a new Covid variant

How Dangerous Are New COVID-19 Strains?

These results provide evidence for the neuroinvasive capacity of SARS-CoV-2 and an unexpected consequence of direct infection of neurons by SARS-CoV-2

mRNA vaccines, what are in those injections and what happens once the shot is given

The Importance of Face Masks for COVID-19

The best masks remain N95s, which are designed with ultrahigh filtration efficiency. Layering two less specialized masks on top of each other can provide comparable protection.

N95 mask with RGB LEDs and voice projection. Each of the respirator-meets-amplifier rings can glow in the color of your choosing. Microphones and amplifiers embedded in the ventilators project your voice through the mask.

The virus will evolve fast enough to keep itself going

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UK scientists worry vaccines may not protect against South African coronavirus variant Vaccine makers are testing shots against new variants

In southeastern England, where the B.1.1.7 variant first caught scientists’ attention last month, it has quickly replaced other variants “One concern is that B.1.1.7 will now become the dominant global variant with its higher transmission and it will drive another very, very bad wave”

E484K (South African lineage) worrying for immune escape; RBD mutations in UK lineage less so (1/n).

In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing

“Even if we rolled out the best vaccine coverage program ever, we’re not going to vaccinate everybody. We can’t do it simultaneously. The virus will evolve fast enough to keep itself going. I think it’s endemic.”

Transmission Dynamics of Sars-CoV-2 Are More Complex Than Previously Believed

Breathing techniques from declassified CIA documents

‘What see’st thou else in the dark backward and abysm of time?’ –Shakespeare

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By mid-December, the Northern Hemisphere is usually well into the start of its annual cold and flu season — but so far this year, even as the COVID-19 pandemic surges in dozens of countries, the levels of many common seasonal infections remain extremely low. […] In the Southern Hemisphere — now past its winter — seasonal influenza hardly struck at all. That looks as though it might happen in the north, too.

Conversely, some common-cold viruses have thrived, and tantalizing evidence suggests that they might, in some cases, protect against COVID-19. One study of more than 800,000 people, for example, showed that adults who had had cold symptoms within the previous year were less likely to test positive for SARS-CoV-2 — although why this is so remains a mystery. […] One possible explanation is that previous infection with a coronavirus (another cause of the common cold) could confer some immunity to SARS-CoV-2. […] Previous coronavirus infections do seem to generate T cells and B cells — immune-system cells that help to attack and remember pathogens — that can recognize SARS-CoV-2. These pre-existing cells might provide some partial cross-protection against the new coronavirus. A few studies have shown that, because of other coronavirus infections, about one-quarter of people have antibodies that can bind to the SARS-CoV-2 virus. […]

Another way that seasonal colds might be contributing to COVID-19 immunity is that a current rhinovirus infection might interfere directly with SARS-CoV-2 — perhaps by kicking off interferon responses, part of the immune system that inhibits viral reproduction. A study6 by Ware and his colleagues, for example, shows that someone with a rhinovirus infection is 70% less likely to also get a common coronavirus infection, compared with someone who doesn’t have the sniffles.

{ Nature | Continue reading }