DAILY DOSE: The first unofficial official (aka pre-print) paper to incorporate the new Covid-origin data has dropped; Another scientist being shady is called out.


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The first unofficial official paper (also known as a pre-print) that includes and analyzes the new (and disappeared again) early Covid-19 data from Chinese scientists. It adds strength to the zoonotic origin theory. Per Reuters,

The sequences showed that raccoon dogs and other animals susceptible to the coronavirus were present in the market and may have been infected, providing a new clue in the chain of transmission that eventually reached humans, they said.

"This adds to the body of evidence identifying the Huanan market as the spillover location of Sars-CoV-2 and the epicentre of the COVID-19 pandemic," said the report.

It was written by authors including the University of Arizona's Michael Worobey, Kristian Andersen of Scripps Research in La Jolla, California, and Florence Débarre at the Sorbonne University in Paris, France, who accessed the data.

In comparison to the leaked information last week, the report adds more detail about other animals present at the market, as well as showing that some of the SARS-CoV-2 positive environmental samples had more animal than human genetic material in them, which the researchers said was consistent with the animals being infected.

More coming up… Keep reading… http://bit.ly/3JyQkbJ

Nature offered a more in-depth and technical look at the paper. Here’s a snippet,

The researchers were specifically interested in looking for evidence of mammals, which could have been intermediate hosts of the virus. They identified near-complete mitochondrial DNA sequences — some 16,000-base-pairs long — for five species of wildlife, including raccoon dog (Nyctereutes procyonoides), Malayan porcupine (Hystrix brachyura), Amur hedgehog (Erinaceus amurensis), masked palm civet (Paguma larvata) and hoary bamboo rat (Rhizomys pruinosus). “It’s remarkable to have a list,” says study co-author Alex Crits-Christoph, who is a computational biologist at a non-profit organization, and is based in Baltimore, Maryland.

Particularly notable was the raccoon dog mitochondrial DNA found in six samples from two stalls. Research has shown that raccoon dogs — small fox-like animals — are susceptible to SARS-CoV-2, and can spread the infection to other raccoon dogs without showing clear signs of sickness. Raccoon dogs and masked palm civets have also been found with infections of viruses that are almost identical to the one that causes severe acute respiratory syndrome (SARS), which is related to SARS-CoV-2 and caused an outbreak in people in 2003. And work in palm-civet cells indicates that the creatures could possibly become infected with SARS-CoV-2.

Studies suggest that a progenitor of SARS-CoV-2 probably originated in bats, but how it passed from bats to people is not clear. Scientists suspect an intermediate host was involved, but they have not found strong evidence, which has led to speculation that the virus could have instead leaked — deliberately or accidentally — from a laboratory in Wuhan.

The new study does not confirm whether the animals themselves were infected with the virus. But establishing that the animals were present at the market supports the hypothesis that the pandemic had an animal origin, say some researchers.

So there you have it. For now. Until something else comes to light. Probably from the people hiding all the data. https://bit.ly/3JTzUfk

Not to be outdone, the Associated Press ran an article taking a closer look at the damage done by Beijing’s snap decision to reopen and let Covid rip. According to the article,

When China suddenly scrapped onerous zero-COVID measures in December, the country wasn’t ready for a massive onslaught of cases. Hospitals turned away ambulances, crematoriums burned bodies around the clock, and relatives hauled dead loved ones to warehouses for lack of storage space.

Chinese state media claimed the decision to open up was based on “scientific analysis and shrewd calculation,” and “by no means impulsive.” But in reality, China’s ruling Communist Party ignored repeated efforts by top medical experts to kickstart exit plans until it was too late, The Associated Press found.

Instead, the reopening came suddenly at the onset of winter, when the virus spreads most easily. Many older people weren’t vaccinated, pharmacies lacked antivirals, and hospitals didn’t have adequate supplies or staff — leading to as many as hundreds of thousands of deaths that could have been avoided, according to academic modeling, more than 20 interviews with current and former Chinese Center for Disease Control and Prevention employees, experts and government advisors, and internal reports and directives obtained by the AP…

“It wasn’t a sound public health decision at all,” said a China CDC official, declining to be named to speak candidly on a sensitive matter. “It’s absolutely bad timing … this was not a prepared opening.”

Not that anyone will ever admit to, maybe, making a costly mistake. And this isn’t something particular to China. Politicians around the world are cut from the same, disingenuous cloth, it seems. http://bit.ly/3TznEDY

There are two events that seem to happen with amusing regularity: (1) evolutionary ideas about the nature of our human and non-human ancestors gets over-turned by some new discovery and (2) some well-known and respected scientist is forced to retract papers because they were fudging their data. So here we go, courtesy of Science

Steven Newmaster, a prominent University of Guelph (UG) botanist and entrepreneur who has faced allegations of scientific misconduct, has had another paper retracted without his consent. Last week the Canadian Journal of Forest Research pulled a study in which Newmaster and colleagues said they used a genetic identification system known as DNA barcoding to help determine the diet of woodland caribou. The retraction follows a misconduct complaint by one of the paper’s co-authors and others that cast doubt on the reliability of the data supplied by Newmaster, the lead author.

“Post-publication peer review found that study methods are not described in enough detail to enable reproducibility, nor were enough data provided in the article or public databases to verify the findings,” the journal said in its retraction notice. “Therefore, the Editors-in-Chief no longer have confidence in the validity of the DNA results.”

The journal noted that six co-authors agreed with the decision and one could not be reached. Only Newmaster disagreed, the journal added. (Science reached out to Newmaster and other authors on the caribou paper but none has so far responded.)

The website Retraction Watch makes for good reading if you are in to following this kind of stuff. https://bit.ly/3JB1xbt

Thanks for reading. Let’s be careful out there.

IMAGE CREDIT: Ken Ishigaki.

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