The biology of coronavirus COVID-19 - including research and treatments

Virologist Vincent Rancaniello has an excellent podcast series (twiv microbe tv) about viruses and knows the chief Wuhan virologist. He points out that the Sars Co-vi-2 virus does not have what he terms a lab signature in its make-up. It is extremely unlikely if not impossible he said to have been messed with by the lab.

He says it took 10 years to trace the animal source of Sars 1 and it will take time to trace this one.

Points out that the CDC is located in Atlanta because of the history of malaria in the US---a lab was located close to the problem.

That same idea is why Wuhan is the site for study of bat viruses and Sars 1.

Rancaniello trusts the head of the Wuhan lab because he knows her and she is extremely dedicated to her work. Can you imagine the stress she is under with all this hype and false accusations by the entire globe?
 
shak8 said:
He says it took 10 years to trace the animal source of
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The SARS outbreak in Hong Kong started in February 2003 and they discovered a link to palm civets in May 2003, so claiming it took 10 years is very misleading.

Points out that the CDC is located in Atlanta because of the history of malaria in the US---a lab was located close to the problem.

That same idea is why Wuhan is the site for study of bat viruses and Sars 1.
Click to expand...

That is also false.
Wuhan is no where near any bat colonies. The Yunnan bat caves are around 1800 km away!

The "lab signature" idea is also based on the idea that parts of the virus were effectively designed and manipulated in a very specific way - but there are other ways of manipulation of viruses that lead to random selection (such as repeated passaging through cell cultures or animals) that won't leave such a "signature".
 
Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH's Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2's bat coronavirus relatives.
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https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1
 
(Can't find a link to the study in the article)

Stanford researchers find signs of inflammation in brains of people who died of COVID-19

A detailed molecular analysis of tissue from the brains of individuals who died of COVID-19 reveals extensive signs of inflammation and neurodegeneration, but no sign of the virus that causes the disease.

...

Activation levels of hundreds of genes in all major cell types in the brain differed in the COVID-19 patients’ brains versus the control group’s brains. Many of these genes are associated with inflammatory processes.

There also were signs of distress in neurons in the cerebral cortex, the brain region that plays a key role in decision-making, memory and mathematical reasoning. These neurons, which are mostly of two types — excitatory and inhibitory — form complex logic circuits that perform those higher brain functions.

The outermost layers of the cerebral cortex of patients who died of COVID-19 showed molecular changes suggesting suppressed signaling by excitatory neurons, along with heightened signaling by inhibitory neurons, which act like brakes on excitatory neurons. This kind of signaling imbalance has been associated with cognitive deficits and neurodegenerative conditions such as Alzheimer’s disease.

An additional finding was that peripheral immune cells called T cells, immune cells that prowl for pathogens, were significantly more abundant in brain tissue from dead COVID-19 patients. In healthy brains, these immune cells are few and far between.

“Viral infection appears to trigger inflammatory responses throughout the body that may cause inflammatory signaling across the blood-brain barrier, which in turn could trip off neuroinflammation in the brain,” Wyss-Coray said.​

https://med.stanford.edu/news/all-n...in-brains-of-people-who-died-of-covid-19.html
 
(Actually the paper was next in my list of news bookmarks so here it is)


Dysregulation of brain and choroid plexus cell types in severe COVID-19, Yang et al, 2021

(Added paragraph break)
Though SARS-CoV-2 primarily targets the respiratory system, patients and survivors can suffer neurological symptoms1–3. Yet, an unbiased understanding of the cellular and molecular processes affected in the brains of COVID-19 patients is still missing. Here, we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control (including 1 terminal influenza) and 8 COVID-19 patients. While a systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations which predict that choroid plexus barrier cells sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma.

We discover COVID-19 disease-associated microglia and astrocyte subpopulations that share features with pathological cell states reported in human neurodegenerative disease4–6. Synaptic signaling of upper-layer excitatory neurons—evolutionarily expanded in humans7 and linked to cognitive function8—are preferentially affected in COVID-19. Across cell types, COVID-19 perturbations overlap with those in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia, and depression. Our findings and public dataset provide a molecular framework to understand COVID-19 related neurological disease observed now and which may emerge later.​

https://www.nature.com/articles/s41586-021-03710-0
 
shak8 said:
Can you imagine the stress she is under with all this hype and false accusations by the entire globe?
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To be honest I do not see any hype here. If anything I see people protecting research interests.

Dr Racaniello may know the Wuhan lab director but that isn't relevant to the facts. We know that they were not using maximum security and I do not think it is necessary to suggest that Covid-19 was engineered. A coincidence would be a lot more remarkable than the analogy with Atlanta suggests.

Lab workers getting infected is commonplace. Smallpox escaped more than once. My mother was a microbiologist and she contracted at least one notifiable disease from her lab during her career.
 
Snow Leopard said:
The SARS outbreak in Hong Kong started in February 2003 and they discovered a link to palm civets in May 2003, so claiming it took 10 years is very misleading.



That is also false.
Wuhan is no where near any bat colonies. The Yunnan bat caves are around 1800 km away!

The "lab signature" idea is also based on the idea that parts of the virus were effectively designed and manipulated in a very specific way - but there are other ways of manipulation of viruses that lead to random selection (such as repeated passaging through cell cultures or animals) that won't leave such a "signature".
Click to expand...

I meant to relay that Rancaniello said that it took ten years to trace the lineage back to key sequences in a bat cave in Yunaan where necessary recombination took place (leading eventually to the finding in the civet). That was accomplished in 2013-16 (Wiki entry Sars-1).
 
Jonathan Edwards said:
To be honest I do not see any hype here. If anything I see people protecting research interests.

Dr Racaniello may know the Wuhan lab director but that isn't relevant to the facts. We know that they were not using maximum security and I do not think it is necessary to suggest that Covid-19 was engineered. A coincidence would be a lot more remarkable than the analogy with Atlanta suggests.

Lab workers getting infected is commonplace. Smallpox escaped more than once. My mother was a microbiologist and she contracted at least one notifiable disease from her lab during her career.
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Rancaniello thinks it's hype, and I am reporting his take on this because I listen to every podcast on TWIV. Some of my reported remarks of his are his off the cuff comments, which I know aren't quite scienc-y enough.

I certainly am not qualified to conjecture on origins matter. I hope we will be able to find out what exactly happened with SARS-2.

But more important are preventive measures and international cooperation in preventing animal spillover (or lab spillover). Politically that may be challenging.

Is lab security lax because China is still a second world country?
 
shak8 said:
Is lab security lax because China is still a second world country?
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My understandings that the level of security was part of a project with funding and collaboration by NIH. I don't think the finger is pointing at China here. It is much closer home.

Making bad mistakes with viruses seems to be a fairly widespread aspect of virology. The ongoing legal case over HIV and Hep C contamination of haemophiliac treatment, with thousands dead, is a simple reminder. People in high places knew there was disaster waiting to happen long before it was admitted.

I guess an honest account of this may be just too expensive. The NIH might be sued for about £1,000,000,000,000 dollars. And that would just be the USA case.
 
Jonathan Edwards said:
To be honest I do not see any hype here. If anything I see people protecting research interests.

Dr Racaniello may know the Wuhan lab director but that isn't relevant to the facts. We know that they were not using maximum security and I do not think it is necessary to suggest that Covid-19 was engineered. A coincidence would be a lot more remarkable than the analogy with Atlanta suggests.

Lab workers getting infected is commonplace. Smallpox escaped more than once. My mother was a microbiologist and she contracted at least one notifiable disease from her lab during her career.
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Agree e.g. friend works with common food pathogens (bacteria) and one of the students (working in the lab) was infected. So in reality accidents are a fact of life even in research laboratories.
 
I’m actually surprised infections happen so often in labs. I always imagined the precautions would be so good that it’s a super rare thing. Clearly my assumptions were wrong!
 
Jonathan Edwards said:
Making bad mistakes with viruses seems to be a fairly widespread aspect of virology. The ongoing legal case over HIV and Hep C contamination of haemophiliac treatment, with thousands dead, is a simple reminder. People in high places knew there was disaster waiting to happen long before it was admitted.
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I just want to say that microbiologists wanted the contamination with HIV and Hep C stopped but were overruled.

Lab precautions are a lot better now than they were, the days of mouth pipetting are long gone! My husband was in microbiology for over thirty five years without ever getting any infection not even diarrhoea.
 
Does anyone have a link to a recent article or study showing that fully vaccinated people can still spread the coronavirus?

I know that there are breakthrough infections (CDC has data on that for the USA, for example).

But can someone who is fully vaccinated, and then gets infected, transmit the coronavirus to someone else?

I've searched for this a of couple times, and I've found several "we still don't know" statements, but I can't find anything definitive.

And yet I keep seeing people stating this as a fact, saying that fully vaccinated people can definitely spread the virus. One person even called a fully vaccinated person who was not wearing a mask a "Superspreader." (even though this person was standing outside, and not in a crowd)

So I'm starting to wonder whether it's been proven or if it's still conjecture. Thanks!

PS. I'm still happy to wear my own mask after being vaccinated, I'm just curious.
 
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ahimsa said:
But can someone who is fully vaccinated, and then gets infected, transmit the coronavirus to someone else?
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Yes, the UK trial of household transmission of healthcare workers showed that although the risk was reduced, some healthcare workers who were vaccinated still contracted the disease and likely infected household members.

https://www.nejm.org/doi/full/10.1056/NEJMc2107717
 
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