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One interesting thing about Russia is its amazing support of its scientists. Russians invented the MRI machine, for example, and have many of them, which they're using for lung diagnostics right now. But more than that, Russians have real interest in PCR and CRISPR technology and large ability to test and research. I'm not sure that Russia has really tested as many as they claim, but I anticipate more scientific papers on the CoVid genome from Russia very soon. They're almost always published simultaneously in English.

That cladogram is fascinating.
 
NEXTSTRAIN

Many separate introductions to Delhi during March
Between March 1-April 15, 38 viral genomes from the Delhi area were sampled and sequenced (shown here).

In the middle of the tree, we see a sizable cluster of closely related cases. This is consistent with a single introduction, followed by local community spread.

However, it is crucial to consider the context of this cluster.
Scattered across the tree, we also see many other small clusters and isolated cases, representing separate introductions from all over the world. We don't have enough data to say what followed these other introductions -- if or how far they spread. But, we can say that the large cluster of cases is only part of the story.

auspice
 

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FRANCOIS BALLOUX

I've seen many alarmist and incorrect claims about mutations in #SARSCoV2 . In this thread I will address some of the major misconceptions. Parts of the material I cover can be found expressed more formally in an article we published recently. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 - ScienceDirect.
(1/11) Prof Francois Balloux on Twitter

Mutations are random errors arising during replication of the genetic material of an organism. A possible analogy would be mistakes made by Medieval copyist monks who were making copies of the bible over centuries.
(2/11) Prof Francois Balloux on Twitter

Most 'copying mistakes' both in texts and genomes are unlikely to alter the information, and can be considered as 'neutral typos'. Of those that change the meaning of a text/genome, few are expected to improve it. Those that do are likely to be retained in the future.
(3/11)

The mutation rate of #SARSCoV2 is largely unremarkable for an RNA virus and has been estimated to ~18 mutations/genome/year. A strain in circulation today is on average ~10 mutations away from its ancestor that jumped into humans in Oct/Nov 2019.
(4/11)

When #SARSCoV2 jumped into humans in late 2019. Its population was essentially invariant. Limited genetic diversity has since emerged. In a comparison of 7666 complete genomes (~30k base pairs), ~4k sites show some variation, the vast majority are 'irrelevant typos'.
(5/11)

As #SARSCoV2 is a recent human pathogen, it may not be perfectly adapted to its host and we may expect some mutations beneficial to the virus to increase in frequency. Virus don't 'benefit' from hurting their host but more transmissible lineages will increase in frequency.
(6/11)

It is plausible #SARSCoV2 will evolve to become more transmissible but there is no reason to expect its virulence will increase. Despite many claims to the contrary, there is no convincing evidence at this stage that the virus has become more/less transmissible/virulent.
(7/11)

Some positions in the #SARSCoV2 genome are candidates for adaptation to its novel human host. In particular, recurrently emerging mutations have been observed at some positions ('homoplasies'). None of these have been confirmed to affect transmission at this stage.
(8/11) Prof Francois Balloux on Twitter

There are no 'S', 'G', 'European', 'American' or whatnot #SARSCoV2 lineages. All such classifications are arbitrary and largely meaningless. Two random #SARSCoV2 genomes in circulation today are only ~10 mutations apart. This is a 'largely clonal population' at this stage.
(9/11)

Due to extensive international transmission, the whole diversity of #SARSCoV2 is recapitulated in most countries . Below, strains from Iceland are highlighted on the phylogenetic tree of strains from the whole world.
Everything is everywhere!
(10/11) Prof Francois Balloux on Twitter

mutations in #SARSCoV2 need to be closely monitored, in particular to ensure long-run potential of future vaccines. There's no reason the virus should become more virulent, but it may become more transmissible. At this stage, there's no strong evidence this has happened.
(11/11)

Prof Francois Balloux on Twitter

 

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Henry2326 said:
FRANCOIS BALLOUX

I've seen many alarmist and incorrect claims about mutations in #SARSCoV2 . In this thread I will address some of the major misconceptions. Parts of the material I cover can be found expressed more formally in an article we published recently. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 - ScienceDirect.
(1/11) Prof Francois Balloux on Twitter

Mutations are random errors arising during replication of the genetic material of an organism. A possible analogy would be mistakes made by Medieval copyist monks who were making copies of the bible over centuries.
(2/11) Prof Francois Balloux on Twitter

Most 'copying mistakes' both in texts and genomes are unlikely to alter the information, and can be considered as 'neutral typos'. Of those that change the meaning of a text/genome, few are expected to improve it. Those that do are likely to be retained in the future.
(3/11)

The mutation rate of #SARSCoV2 is largely unremarkable for an RNA virus and has been estimated to ~18 mutations/genome/year. A strain in circulation today is on average ~10 mutations away from its ancestor that jumped into humans in Oct/Nov 2019.
(4/11)

When #SARSCoV2 jumped into humans in late 2019. Its population was essentially invariant. Limited genetic diversity has since emerged. In a comparison of 7666 complete genomes (~30k base pairs), ~4k sites show some variation, the vast majority are 'irrelevant typos'.
(5/11)

As #SARSCoV2 is a recent human pathogen, it may not be perfectly adapted to its host and we may expect some mutations beneficial to the virus to increase in frequency. Virus don't 'benefit' from hurting their host but more transmissible lineages will increase in frequency.
(6/11)

It is plausible #SARSCoV2 will evolve to become more transmissible but there is no reason to expect its virulence will increase. Despite many claims to the contrary, there is no convincing evidence at this stage that the virus has become more/less transmissible/virulent.
(7/11)

Some positions in the #SARSCoV2 genome are candidates for adaptation to its novel human host. In particular, recurrently emerging mutations have been observed at some positions ('homoplasies'). None of these have been confirmed to affect transmission at this stage.
(8/11) Prof Francois Balloux on Twitter

There are no 'S', 'G', 'European', 'American' or whatnot #SARSCoV2 lineages. All such classifications are arbitrary and largely meaningless. Two random #SARSCoV2 genomes in circulation today are only ~10 mutations apart. This is a 'largely clonal population' at this stage.
(9/11)

Due to extensive international transmission, the whole diversity of #SARSCoV2 is recapitulated in most countries . Below, strains from Iceland are highlighted on the phylogenetic tree of strains from the whole world.
Everything is everywhere!
(10/11) Prof Francois Balloux on Twitter

mutations in #SARSCoV2 need to be closely monitored, in particular to ensure long-run potential of future vaccines. There's no reason the virus should become more virulent, but it may become more transmissible. At this stage, there's no strong evidence this has happened.
(11/11)

Prof Francois Balloux on Twitter
Click to expand...

Thanks for posting on the main thread how to read such phylogentic trees.

auspice
 
Abilene woman working on cure for COVID-19, part of research team


Dr. Lacy Galloway told me about her work on this treatment two years ago. She was inspired by the search for a treatment for Ebola. She worked with Dr. Rothstein, the former VP of John Hopkins, to use the UV light which she works with as a dentist to kill superbugs.

Rothstein describes it :

“Basically you put an IV in the patient, drain out approx. 3CC’sper kilogram of body weight, run it through a device over ultra violet light and then send it back into the body.”

I can’t believe this hasn’t received any national news coverage. It sounds to me like it would work much better and more quickly than the current drug therapy treatments we have now.
 
Apparently, Dr. Robert Rothstein, recently retired VP of Medicine at Johns Hopkins believes that it that it can.
Reference for Dr. Rothstein:
Robert Rothstein: Biographies

I made a mistake on Dr. Lacy Mankin’s last name. Galloway is her maiden name.
 
That is effectively dialysis which is expensive. Cells are constantly reproducing. It doesn’t sound like would accomplish much, if anything.

I was on a machine for 12 hours to remove all my blood and extract the bone marrow. It is not painful but it is exhausting. My insurance paid $90,000 just for that, not including all the treatment & supplies that go along with it.
 
"Ohio had six cases of the coronavirus in five counties in January, state Department of Health Director Dr. Amy Acton said Monday.

The state data shows cases began Jan. 7 and Jan. 26 in Miami County, Jan. 13 in Montgomery, Jan. 18 in Richland, Jan. 20 in Summit and Jan. 27 in Warren.

The state knows of the cases now only because of antibody testing."

Ohio had 6 coronavirus cases in 5 counties in January, says Health Director Dr. Amy Acton
 
Henry2326 said:
Nextstrain

159 sequences from MI, CA, and LA.

MI across the tree, while CA and LA in clusters.

Nextstrain on Twitter
Click to expand...

Wow. Intriguing. I'm so curious how it is that MI got so many different strains, while California's are all closely related. One would think it would be the opposite, given how many people go in and out of California.

And I'd have thought Louisiana would have more variation, due to tourism/Mardi Gras crowds.
 
Last time I checked Amazon, they were out of it - I'll go check.

It's backordered until June 2. But available, which is an improvement.

Or you can pay $40 a bottle from a third party vendor. :mad:
 
10ofRods said:
Last time I checked Amazon, they were out of it - I'll go check.

It's backordered until June 2. But available, which is an improvement.

Or you can pay $40 a bottle from a third party vendor. :mad:
Click to expand...
What's $40 if it can save your life?
 
jjenny said:
What's $40 if it can save your life?
Click to expand...

It's a bargain - and I do have it ordered. My experience with third party vendors is that they take just as long to get things to our house, so I prefer the Amazon delivery.

BTW, I so appreciate you, @jjenny. You always take the side of both personal responsibility AND personal safety.

In my case, it turns out I have a gene that makes me more susceptible to severe CoVid (yep, the gene studies are coming in and I've had to live with my knowledge of having this gene for quite a while - and now I have to live with the fact that I passed it on to one of my kids). It's not like a death sentence, it just means I should not be cavalier or optimistic in any way about this disease.

I also bought Glutathione and N Acetyl Cystine (NAC) because I think that's really promising (although whether supplementation works is still unknown).

I do think the relatively poor outcomes predicted for people with APOE-4 (the gene I have) is outweighed by the effects of Vitamin D, so I have that going for me. And I do not know exactly which variant of the gene I have - there are apparently a couple of them. One is worse than the other.
 
Do you have a source that isn't a hometown newspaper?

Here's an abstract:

Ultraviolet blood irradiation: Is it time to remember “the cure that time forgot”?

The damage to DNA is what makes it controversial. DNA damage is associated with many, many later issues.

OTOH, it does seem to help with the advanced and critical phase of cytokine storm - so if someone was on death's door, it could still be an option. I just wonder where they're going to test it (she is a dentist, she will need a hospital and a team of other specialists to test it). There are no publications about live patients being treated for the prior viruses listed in the newspaper. It would, of course, work in principle - but treating someone's entire blood supply (while the virus still lived on in organ tissue) would lower viral load for the very critically ill. I suppose if it were an elderly patient, the possible downsides of DNA mutation could be limited.

@PayrollNerd is right about the expense, and it is a treatment for multiple myeloma and life-saving. But I don't think the machine in that case uses UV. I think it's closer to a form of dialysis, as you say (filtering, not irradiating). It's apparently also used in several other diseases.

I'm sorry you had to go through that, Payroll.
 
jjenny said:
What's $40 if it can save your life?
Click to expand...

There are about 10-15 of these "can save your life" items out there. Pepcid is just one of them (and while it's promising, there are no big studies of it). If you're a family of 4, that's $160 per initial treatment - dosage in hospital use seems to be higher than stated for indigestion use. I suspect one box would last about 10 days. So you'd need 3X that per month. If a person has health insurance that pays for OTC meds (I don't, one daughter does, one doesn't), then that's fine. But for many families, $500 a month on a drug that probably needs to be taken alongside an antibiotic, zinc, NAC, glutamate and possibly vitamin C - each of those provides similar incremental aid in combating CoVid, it could get pricy.

Buy all of them? I don't think most people will. And for me, I can't buy just for myself - I will buy for my daughter and her family too (she is at risk for various reasons).

It should cost about $12. Price-gouging or whatever it is, is not good. BTW, I did buy some, but I'm sure I don't have enough and the first person in our family to get CoVid will get it. Hopefully, when local drugstores start functioning again, I can get more.

Right now, we're focusing on supplies of things (bioavailable vitamin D is first on the list) that strengthen immunity rather than combat covid. For people with the particular genetic situation that my daughter and I are in, it's likely that NAC and glutamate (and perhaps glysine) should be on the list - and melatonin is also promising, but at higher doses than on the label. My daughter is also severely anemic, and both of us have to work to get enough iron through our digestive systems.

It ends up being quite a bit of money, actually. Anyway, you need 9X the amount of Pepcid as you would use for indigestion. (Apparently, studies are still underway - but that's what the studies are using). So, I actually would need to 1) get CoVid, 2) need about 1 bottle every 5 days.

Thing is, if I get CoVid, I will be under a doctor's care and they can prescribe this drug (then my insurance will pay for it). If I decide I'm going to try and treat my own CoVid at home, for one month of treatment, I'd need about 6 bottles. Fortunately, at this exact moment, there's a generic version available on Amazon for much less. If we do have a second wave, some of us may be glad to have it.
 
10ofRods said:
There are about 10-15 of these "can save your life" items out there. Pepcid is just one of them (and while it's promising, there are no big studies of it). If you're a family of 4, that's $160 per initial treatment - dosage in hospital use seems to be higher than stated for indigestion use. I suspect one box would last about 10 days. So you'd need 3X that per month. If a person has health insurance that pays for OTC meds (I don't, one daughter does, one doesn't), then that's fine. But for many families, $500 a month on a drug that probably needs to be taken alongside an antibiotic, zinc, NAC, glutamate and possibly vitamin C - each of those provides similar incremental aid in combating CoVid, it could get pricy.

Buy all of them? I don't think most people will. And for me, I can't buy just for myself - I will buy for my daughter and her family too (she is at risk for various reasons).

It should cost about $12. Price-gouging or whatever it is, is not good. BTW, I did buy some, but I'm sure I don't have enough and the first person in our family to get CoVid will get it. Hopefully, when local drugstores start functioning again, I can get more.

Right now, we're focusing on supplies of things (bioavailable vitamin D is first on the list) that strengthen immunity rather than combat covid. For people with the particular genetic situation that my daughter and I are in, it's likely that NAC and glutamate (and perhaps glysine) should be on the list - and melatonin is also promising, but at higher doses than on the label. My daughter is also severely anemic, and both of us have to work to get enough iron through our digestive systems.

It ends up being quite a bit of money, actually. Anyway, you need 9X the amount of Pepcid as you would use for indigestion. (Apparently, studies are still underway - but that's what the studies are using). So, I actually would need to 1) get CoVid, 2) need about 1 bottle every 5 days.

Thing is, if I get CoVid, I will be under a doctor's care and they can prescribe this drug (then my insurance will pay for it). If I decide I'm going to try and treat my own CoVid at home, for one month of treatment, I'd need about 6 bottles. Fortunately, at this exact moment, there's a generic version available on Amazon for much less. If we do have a second wave, some of us may be glad to have it.
Click to expand...

Not sure if you are a member, but Costco has 250 20mg tables for $12.49.
 
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