COVID-19 Origins & Research

[RTH10260]

Off Topic

to peek behind the WaPo paywall --> I still have a number of free 1-month subscriptions to give away - pm thru my profile if interested

[RTH10260]

I was looking up something else when I came accross this in https://en.wikipedia.org/wiki/Coronavirus

It's an old critter -

Origin

Origins of human coronaviruses with possible intermediate hosts

The most recent common ancestor (MRCA) of all coronaviruses is estimated to have existed as recently as 8000 BCE, although some models place the common ancestor as far back as 55 million years or more, implying long term coevolution with bat and avian species.[72] The most recent common ancestor of the alphacoronavirus line has been placed at about 2400 BCE, of the betacoronavirus line at 3300 BCE, of the gammacoronavirus line at 2800 BCE, and the deltacoronavirus line at about 3000 BCE. Bats and birds, as warm-blooded flying vertebrates, are an ideal natural reservoir for the coronavirus gene pool (with bats the reservoir for alphacoronaviruses and betacoronavirus – and birds the reservoir for gammacoronaviruses and deltacoronaviruses). The large number and global range of bat and avian species that host viruses have enabled extensive evolution and dissemination of coronaviruses.[73]

Many human coronaviruses have their origin in bats.[74] The human coronavirus NL63 shared a common ancestor with a bat coronavirus (ARCoV.2) between 1190 and 1449 CE.[75] The human coronavirus 229E shared a common ancestor with a bat coronavirus (GhanaGrp1 Bt CoV) between 1686 and 1800 CE.[76] More recently, alpaca coronavirus and human coronavirus 229E diverged sometime before 1960.[77] MERS-CoV emerged in humans from bats through the intermediate host of camels.[78] MERS-CoV, although related to several bat coronavirus species, appears to have diverged from these several centuries ago.[79] The most closely related bat coronavirus and SARS-CoV diverged in 1986.[80] The ancestors of SARS-CoV first infected leaf-nose bats of the genus Hipposideridae; subsequently, they spread to horseshoe bats in the species Rhinolophidae, then to Asian palm civets, and finally to humans.[81][82]

Unlike other betacoronaviruses, bovine coronavirus of the species Betacoronavirus 1 and subgenus Embecovirus is thought to have originated in rodents and not in bats.[74][83] In the 1790s, equine coronavirus diverged from the bovine coronavirus after a cross-species jump.[84] Later in the 1890s, human coronavirus OC43 diverged from bovine coronavirus after another cross-species spillover event.[85][84] It is speculated that the flu pandemic of 1890 may have been caused by this spillover event, and not by the influenza virus, because of the related timing, neurological symptoms, and unknown causative agent of the pandemic.[86] Besides causing respiratory infections, human coronavirus OC43 is also suspected of playing a role in neurological diseases.[87] In the 1950s, the human coronavirus OC43 began to diverge into its present genotypes.[88] Phylogenetically, mouse hepatitis virus (Murine coronavirus), which infects the mouse's liver and central nervous system,[89] is related to human coronavirus OC43 and bovine coronavirus. Human coronavirus HKU1, like the aforementioned viruses, also has its origins in rodents.[74]

[Phoenix520]

Fascinating…and complex. Thanks, Eurobot!

[tencats]

Viruses found in Laos bats are closest known relatives to SARS-CoV-2
By Rachael Rettner 1 day ago | https://www.livescience.com/closest-bat ... cov2-covid
Strengthening case for natural origin.

Researchers have discovered coronaviruses lurking in Laotian bats that appear to be the closest known relatives to SARS-CoV-2, the virus that causes COVID-19, found to date, according to news reports.

In a new study, researchers from the Pasteur Institute in France and the University of Laos captured 645 bats from limestone caves in northern Laos and screened them for viruses related to SARS-CoV-2. They found three viruses — which they dubbed BANAL-52, BANAL-103 and BANAL-236 — that infected horseshoe bats and shared more than 95% of their overall genome with SARS-CoV-2.

One of the viruses, BANAL-52, was 96.8% identical to SARS-CoV-2, according to Nature News. That makes BANAL-52 more genetically similar to SARS-CoV-2 than any other known virus. Previously, the closest known relative to SARS-CoV-2 was RaTG13, which was found in horseshoe bats in 2013 and shares 96.1% of its genome with SARS-CoV-2, Nature News reported.

What's more, all three of the newly discovered viruses are more similar to SARS-CoV-2 in a key part of their genome — called the receptor binding domain (RBD) — than other known viruses. The RBD is the part of the virus that allows it to bind to host cells. With SARS-CoV-2, the RBD binds to a receptor known as ACE2 on human cells, and the virus uses this receptor as a gateway into cells.

Critically, the new study found that BANAL-52, BANAL-103 and BANAL-236 can bind to ACE2 and use it to enter human cells. So far, other candidates proposed as ancestors of SARS-CoV-2 found in bats, including RaTG13, haven't been able to do this, the researchers said. The three viruses could bind to ACE2 about as well as early strains of SARS-CoV-2 found in Wuhan, they said.

"The receptor binding domain of SARS-CoV-2 looked unusual when it was first discovered because there were so few viruses to compare it to," Edward Holmes, an evolutionary biologist at the University of Sydney, who wasn't involved in the research, told Bloomberg. "Now that we are sampling more from nature, we are starting to find these closely related bits of gene sequence," Holmes said.

The authors say their findings support the hypothesis that SARS-CoV-2 resulted from a recombination of viral sequences existing in horseshoe bats.

Still, even though the newly discovered viruses are closely related to SARS-CoV-2, all three viruses lack a sequence for what is known as the "furin cleavage site," which is seen in SARS-CoV-2 and aids the virus's entry into cells, according to Nature News. This means that in order to better understand the origins of SARS-CoV-2 further research is needed to show how and when the furin site was introduced.

[Lani]

Interesting find. Thanks!

[RTH10260]

A note without a link (cause I did not keep it, may have been a German language source): a publication suggests that end of 2019 there were two strains of covid circulating (in China), which would make the claim of a labarotory escape less likely.

[RTH10260]

Covid ‘was spreading virulently in Wuhan’ as early as summer 2019, report suggests
Chinese government spent nearly twice the amount on PCR tests in 2019, compared to 2018, shows data compiled by Australian cyber security firm

Namita Singh

Labs in China’s Wuhan city dramatically increased the procurement of polymerase chain reaction (PCR) equipment in the second half of 2019, indicating that Covid-19 was “spreading virulently” months before the government reported the first case to the WHO in December 2019, according to a new report.

Data compiled by Internet 2.0, an Australian cyber security company, found that the Chinese government spent nearly twice the amount on PCR tests — used to detect certain viruses — in 2019, compared to the previous year. While China procured the PCR equipment for 36.7m yuan (£4.1mn) in 2018, it spent 67.7m yuan (£7.6m) in 2019.

The report also found that the total PCR procurement contracts rose from 89 in 2018 to 135 in 2019.

The “notable, significant and abnormal” increase in purchases was mainly from four institutions — the People’s Liberation Army Airborne Army Hospital, the Wuhan Institute of Virology, the Wuhan University of Science and Technology, and the Hubei Province Districts Centers for Disease Control and Prevention.

Robert Potter, chief executive and founder of Internet 2.0, told the Australian that some of the procurement data may be benign. “But taken together it gives us a trend that comprehensively challenged the official narrative that the pandemic started in December,” Mr Potter, also one of the authors of this study, said.



https://www.independent.co.uk/asia/chin ... 32574.html

[Lani]

I remember in the early days of the Covid Age that Italy dug up some graves and found that Covid was around in December 2019. In Washington where the earliest US cases were found, there was also some grave digging and proof of an earlier arrival. By 2020, it had spread around the world. In the US most of the early cases involved European travelers, not Chinese.

So far, the closest match to Covid in the wild is in Laos, not China.

[Sam the Centipede]

I don't remember anything about exhumations, but I remember hearing/reading about tests of stored blood samples that had been taken from patients who died during that period and some showed signs of the virus.

[Sam the Centipede]

The Guardian has a piece about another symptom or side effect of the virus: 'Covid toe' may be side-effect of immune response, says study. Covid Toe is red or purple lesions on the sole or sides of the feet, similar to chilblains.

As its headline indicates, this fits the pattern of most serious Covid problems being due to the body's immune response rather than direct action by the virus itself.

It's helpful (I think) when wondering about these phenomena to bear in mind that the immune system is essentially a destructive mechanism. It aims to eliminate unfamiliar organisms and to destroy the body's own cells if they are infected or have gone rogue. It kills. Some of the white blood cells (granulocytes) carry inside them little bags of nasty proteins, that they release to poison bacteria and other cells; indeed the short life time (hours, days at most) of these cells is probably due to them carrying around this payload of poison. When an immune response is active, it can disrupt normal functioning, as seems to happen with this Covid Toe effect.

[Suranis]

There was a particularly nasty cough going around that winter. I got it and I was seriously considering going to the doctor as I was having difficulty breathing. But the phlegm I got up was green, not the red that is typical of COVID.

[AndyinPA]

I remember hearing about Covid toe sometime last year.

Just anecdotally, we were supposed to go to China in October 2019, but canceled because of the death of one of our travel friends who was going with us. I was reading a lot of the feeds on my Facebook Viking groups in the months after our cancelation. Once it was known about Covid, and where it started, there were a lot of people talking about coming down really sick with a virus during and after the trips late that year. I'm sure not all of that was Covid, but I think there could have been some of that. It's not that unusual to pick up any virus while traveling, of course.

[Tiredretiredlawyer]

I have a friend who has been diagnosed with and received disability for rheumatoid arthritis and fibromyalgia. She had covid. She no longer has symptoms of rheumatoid arthritis or fibromyalgia. She is working full time and very active.

[AndyinPA]

https://thehill.com/policy/healthcare/5 ... earch?rl=1

Scientists from the University of Pittsburgh found that convalescent plasma treatment is "futile" to treat critically ill COVID-19 patients, according to findings from a study published Monday in the Journal of the American Medical Association.

Convalescent plasma treatment involves taking blood containing antibodies from recovered COVID-19 patients and infusing it into people who are currently fighting the virus.

The antibodies were thought to have some ability to help with the recovery process for active infections. Though the treatment style was successful for Ebola, it was deemed ineffective for most critically ill patients with COVID-19, according to the Pittsburgh Post-Gazette.

[RTH10260]

Note the wording "critically ill" - the treatment may still be of help for patients freshly admitted but in the early stages of the illness. Difficult to say as an outsider, but maybe the treatment window for this method may have already passed when patients are admitted to hospital. Means that there would be a need for MDs to filter out patients that would respond positive and have them get a hospital bed, the hospitals would need a separate section for lightly ill patients in this scenario.

[Sam the Centipede]

I have a friend who has been diagnosed with and received disability for rheumatoid arthritis and fibromyalgia. She had covid. She no longer has symptoms of rheumatoid arthritis or fibromyalgia. She is working full time and very active.

Rheumatoid arthritis is an autoimmune disease, fibromyalgia, I dunno, but could have autoimmune components.

Maybe the vicious kick to the immune system cause by the SARS-CoV-2 virus changed something?

It is well known that the measles virus causes "immune amnesia", where it destroys most of the victim's immune memory B-cells and T-cells in the lymph nodes by a sneaky mechanism. After measles, the victim loses immunity to other diseases and has to reacquire that via vaccines or infection. SARS-CoV-2 does NOT do that; measles is in a different family of viruses, they're different. (In fact, measles is irrelevant, I just think the immune amnesia thing and how measles sneaks into white blood cells using something called SLAM is interesting!)

It was reported early on that SARS-CoV-2 has a destructive impact on the germinal centers of the lymph nodes, which is where memory B- and T-cells hang out.

So here's some wild-assed ignorant guessing: maybe your friend's Covid trashed those germinal centers, knocking out all or most of the memory cells that were responsible for generating the autoimmune response, so she has developed some form of immune amnesia (full or partial), and now the root cause of her problems is gone because her immune system has forgotten how to attack her body?

[Tiredretiredlawyer]

Cool!!!!

[Lani]

I don't remember anything about exhumations, but I remember hearing/reading about tests of stored blood samples that had been taken from patients who died during that period and some showed signs of the virus.

2020 seems so long ago.... I forgot there was also water sampling. Some water departments kept samples of the waste water, which were later tested for covid. And there it was. I don't remember the dates other than finding it in 12/19 & 1/20 - which were earlier than the first diagnosis in those countries. I *think* Italy, Spain and Washington State reported the findings.

[Sam the Centipede]

I hadn't heard about the historic water samples, Lani, thanks for that. It's cool what can be done when clever people start looking and thinking.

[Lani]

Not good.

COVID-19 is linked to new diabetes cases—but long-term problems could be more severe
In addition to driving new cases of diabetes, the virus may be directly damaging the pancreas in ways that could lead to chronic inflammation and even cancer.
https://www.nationalgeographic.com/scie ... 48368741AA

In Italy, a COVID-19 epicenter in the earliest days of the pandemic, it became clear that the blood sugar levels of people who were hospitalized with COVID-19 were out of whack. Fiorina became interested in investigating these effects in April 2020. At the time, he was the chief of endocrinology at a hospital in Milan, which saw upwards of 20,000 new cases of COVID-19 on a daily basis—and held one funeral every hour.

One day, a pathologist remarked to Fiorina how strange it was that so many of the patients who had died were hyperglycemic, meaning that their blood sugar was too high—a sign that the pancreas wasn’t doing its job. “I know that people with diabetes are more prone to dying,” Fiorina recalls telling the pathologist at the time. “But there might be something else.”

Fiorina decided to investigate. In May 2021, he published a study of 551 patients with no prior history of diabetes showing that 46 percent were newly hyperglycemic. COVID-19 had completely disrupted the hormone profile of these patients—although their levels had been normal before their infection, now their glucose was dangerously high as their body had become less efficient at using insulin.

Around the same time, autopsies of people who died from COVID-19 also showed that the virus had infected the pancreas—which researchers confirmed in a set of studies published in the journal Cell Metabolism. Jackson, who was among those researchers, found that SARS-CoV-2 infects and kill the beta cells that produce insulin. It’s thought that these cells are not easily replenished—and losing them makes you more susceptible to diabetes.

[Lani]

If you want to read unbiased, science based information about the pandemic, you might appreciate this twice weekly John Hopkins newsletter. Sign up here for free: https://publichealth.jhu.edu/headlines/ ... newsletter

[keith]

I don't remember anything about exhumations, but I remember hearing/reading about tests of stored blood samples that had been taken from patients who died during that period and some showed signs of the virus.

2020 seems so long ago.... I forgot there was also water sampling. Some water departments kept samples of the waste water, which were later tested for covid. And there it was. I don't remember the dates other than finding it in 12/19 & 1/20 - which were earlier than the first diagnosis in those countries. I *think* Italy, Spain and Washington State reported the findings.

I don't know about 'historical' sampling, but every authority in Australia is testing waste water constantly and using it as a guide to focus testing surges. I have to assume that is happening all over the world.

[Lani]

I don't remember anything about exhumations, but I remember hearing/reading about tests of stored blood samples that had been taken from patients who died during that period and some showed signs of the virus.

2020 seems so long ago.... I forgot there was also water sampling. Some water departments kept samples of the waste water, which were later tested for covid. And there it was.

I don't know about 'historical' sampling, but every authority in Australia is testing waste water constantly and using it as a guide to focus testing surges. I have to assume that is happening all over the world.

It should be. Then we'd know when another covid surge is incoming.

[AndyinPA]

They do it in Boston. Another surge is coming.

[Lani]

I was surprised yesterday that the mahalo ceremony for the National Guard was canceled due to omicron. (posted elsewhere) The state knows that another crisis is incoming. Waste water has been tested for covid, but testing has been reduced due to the current military water pollution crisis.

I asked my kid what he wanted for Christmas. He asked for a water filtration system and water test kits. Being a good mom, I'm sending both to him.