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06 March 2020

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b

"Tests in China and perhaps elsewhere failed to identify the virus but the Australian lab had developed wide spectrum specialised tests and identified it as a Coronavirus. "

A nice Aussie hero story but contradicted by evidence.

This is from January 11:

China releases genetic data on new coronavirus, now deadly

In quickly moving developments last night, health officials from Wuhan, China, posted a novel coronavirus (nCoV) pneumonia outbreak update, which scaled back the number of cases to 41 and noted the first death, and researchers from China released the genetic sequence of the nCoV.

And this morning the World Health Organization (WHO) released several interim guidance documents, including advice on travel, lab testing, and medical evaluation.

Michael T. Osterholm, PhD, MPH, said he's pleased to see that health officials and scientists in China have released as much information as they have.

Chinese scientist were first to identify and sequence the virus.

29 of the 41 first cases were related to the wet market in Wuhan but the very first case had no relation at all to that market.

While the market was the first 'cluster' of cases it was not the source of the outbreak.

LondonBob

Any mention of the impact of weather? Outbreaks are happening in the northern hemisphere in places where we are emerging from winter but there have been very few cases in places like Australia, Thailand, HK, Singapore where you would expect there to be outbreaks first.

confusedponderer

Just to add some bad news about it ... (a bad habit, I know) ... yesterday I read that there has been a case with COVID-19 being transmitted from a human to a dog.

More entertaining is likely that Trump has declared that, because of COVID-19, he hasn't touched his face in three weeks. It is unknown whether rested his chin on his hand when saying that. He surely takes his unwanted hygiene advise to the rest of the world serious.

Trump has also declared that he will, sort of generous, donate a quarter of his annual presidential salary to research of the COVID-19 virus - that is, 100.000 $. Wow.

Now, it's not as if he isn't getting some of that back - after all there was that "golf club some person protection visit thing" with a the secret service bill demanding some 5000 $ just for the booze consumed during the weekend. It means just 20 visits there and he's "clean", strictly rhetorically

That said, just to put that in the right perspective: Trump says he is so rich that he cannot count all that money. Now, there is another man in the US who has a reputation of being really really rich, a more quiet person though.

That's this Mr. Bill Gates. He has iirc declared he'd donate 100 million $ for the research of the corona virus, 1000x as much as Trump, and, amusingly, likely what Gates earns in iirc ~ 4,5 days.

And even more amusing, there is an unspeakable Schlager singer here in Germany who yesterday shared his wisdom with the media, saying - sadly no joke - that of the real daft dumbies he is the most intelligent. Alas.

JJackson

Thanks Walrus
SST has wondered into an area I do know about and I would be happy to answer any questions or provide links to data you need.
A couple of minor points.
The first sequence (WH01) was created in China but up loaded to virologica by an Australian colleague who had an account there at their request, not that that matters.

Pangolins are unlikely to have been the intermediate host. Random genetic mutations occur at a reasonably steady rate and in RNA viruses (flu, COVID) this is very fast. The MRCA (most recent common ancestor) for covid can be calculated as being a few months old but the MRCA for SL betaCOV bat sequences, and the pangolins, is a few decades ago so there is likely to be a genetic reservoir we have not found yet that accounts for missing time period.

Re the 10 times as many unreported cases I would not put too much faith in the submerged portion bringing down the CFR substantially. As the Hubei cases have fallen from 2000+ per day to 1 or 2 hundred they have had capacity to widen their testing to contacts and very mild suspect cases. Sadly they are not seeing the hoped for asymptomatic population. Serology tests will give a more accurate answer, and are underway, but are not performed until a month or more post infection to allow time for antibody build up.

I wrote a much more detailed explanation of the Epidemiology, testing system, virology etc. here (posted 1st Jan) and two follow ups as the situation changed first to a downward trend in China and again, recently, as cases outside China moved into an exponential phase currently doubling once every 6 days (graph in current WHO update link below).
https://flutrackers.com/forum/forum/the-pandemic-discussion-forum/jjackson-s-workshop/826486-covid-ncov-preliminary-thoughts-jjackson-personal-opinion

This one is to the WHO daily situation reports with graphs & tables giving updates by country.
https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/

Ulenspiegel

"The researchers believe that the virus originated in Bats (notorious RNA Coronavirus carriers) and then infected Wuhan wet market produce - Pangolins, which then infected people. "

That is according to experts very likely not true. The Pangolin story is complete bogus, the original source still unclear.

Serge

Danan,

Worrying thing about one of the first Israeli cases is that he tested positive in Japan, was "fully recovered" and tested negative, then back in Israel became "reinfected" and tested positive again.

JJackson

Londonbob
As we do not have a full seasons data we do not know. The bat virus does seem to show some seasonality. As you say it seems to be doing fine in both hemispheres but his is not unusual in a novel pathogen as the advantage gained in no one having any immunity is out weighing the seasonal effect.

Charlotte
Epidemiological all the first cluster contact information points to the market being the common denominator but there is no smoking gun. WH01, the first sequence, is genetically distinct from all other sequences and had no decedents.

The virus in Italy has no significant genetic changes, are no Iranian sequences yet but several new ones are added daily (176 whole genomes at GISAID this morning). The exponential growth will due to poor containment leading to late treatment in an unprepared environment. The spike is covered in some detail in the virology section linked to in my first post.

Israel has reported 15 case 3 new yesterday.

J

Walrus,

COVID19 also can infect the victim through a person's eyes. The sphere you want to avoid is up to 6 feet away from a known victim or one you suspect has/is a carrier of COVID19.

The commercial masks that have been flying off store shelves worldwide are a waste of time and money, they're nothing more than expensive rags. Now if you've got the personal funds for a full up HAZMAT suit, go for it.

Cleanliness is one's best armor.

walrus

J Jackson, I saw an image of dead Pangolins, laid out for sale,together with the verbal comment that the place was swimming in virus. Liquids from dead animals were loaded with the virus. That is what we know.

I know not of virology, but I do know what I heard from an unimpeachable source regarding cases and CFR. I do know that there has been a concerted international effort since 31 Dec to get on top of this thing. This was laid out today although I may have not described it correctly.

Charlotte - don't worry. None of your concerns are real. The "HIV insertions" are a bad joke - like saying " my boat has a propeller, aircraft have propellers, therefore my boat is an aircraft", hundreds of virii have minute chunks in common.

London Bob - the weather effect is described as open warm airy piazzas versus pokey humid overheated rooms in winter. The infectivity isn't expected to change but in summer people spread out.

B, you are a malicious nationalistic, unhelpful, idiot. The press release you mention is dated 11 January. I told you the researchers made their discovery of the new virus on 10 January as a result of very fast work by a number of researchers including the dutch experts on SARS. The initial key to this was the Australian wide spectrum tests which are purposely designed to identify the TYPE of virus. They were brought in by WHO precisely to settle this matter. The rest of the existing coronavirus tests are specific to individual virii and showed nothing.

They also sequenced it and got it growing in culture by 29 Jan. The electron microscope images were shown. I don't have time to explain or reveal sources, or get into a length contest. Suffice to say, you are way out of your league and your comment is both wrong and unhelpful, I also told you my recollection isn't perfect.

walrus

There will be no further comments from me.

Calvin Keeler

Thank you Walrus. Well done. As a molecular virologist who studies avian coronaviruses, I too have been following this situation closely. One potentially positive finding is that there are two genetic forms of the virus (L and S). The early cases in China seem to have been caused by the L type, which appears to be more pathogenic. The S form (which actually predates the L form) is less aggressive and is the form is starting to be seen more frequently (30%). Also, encouraging to see clinical trials starting in China and Minnesota on a possible treatment, a nucleotide analogue that interferes with the virally encoded RNA dependent RNA polymerase. (Actually developed for Ebola and shown to have efficacy against SARS and MERS in animal models.)

English Outsider

Walrus, with reference to J's comment about masks - and in the best tradition of unsupported anecdotal evidence, so very much at the other end of the scale from your briefing - I'm told that pharmacists here in England are saying the masks are only useful if worn by an infected person in order to prevent transmission to others.

Except of course if someone knows they're infected they shouldn't be wandering around anyway. Maybe to avoid infecting carers etc. But from what you relate about the virus hanging about on surfaces, maybe gloves are more to the point.

Thank you for your account, and for taking the trouble to set it out. I don't expect your people had the time to look at broad trends, but in your view are we going to have to expect these world wide epidemics to occur regularly?

Kenneth Alonso, MD

The S spike in this virus is not found in any other coronavirus (thus, novel).

As reported from Scripps, it is possible this novelty did arrive from passage to another host not identified or that it arose from serial passage in many hosts in a short time frame and reflects an expected evolutionary thread.

However, the possibility of genetic engineering cannot be discarded based on the objective evidence presented to date.

The Beaver

Walrus,

Here is an article that reflects what you have reported:
https://www.statnews.com/2020/03/03/washington-state-risks-seeing-explosion-in-coronavirus-without-dramatic-action-new-analysis-says/

Check the graphs

d74

Charlotte Danan, I propose another explanation and a conclusion. They seem serious, though as speculative as your website.

Israel has a long experience in fighting a special virus: the Arab virus without crown.
It has therefore fought against the corona with the success that 70 years of experience gives.

If the good Israeli figures are confirmed, Israel will have added preventive explosives (shells, rockets, etc.) to a hitherto rather poor anti-corona arsenal.

Amir

Iranian government sent millions of masks & disinfectants to China when the Wuhan outbreak became public; leaving Iran with depleted stocks. That might have not contributed to the outbreak in Iran but surely is hindering the treatment: www.presstv.com/Detail/2020/02/03/617788/www.presstv.tv
For those who want a non-Iranian source:
https://financialtribune.com/articles/domestic-economy/102025/iran-to-ban-exports-of-face-masks

j. casey

Thank you for the report. One question: Isn't a three-species jump -- bats to pangolin to human -- in such short a time highly improbable, to put it mildly, perhaps unprecedented?

anon

Thanks for info.great advice.shortage of toilet paper and hand sanitizer in Australia.I am wearing rubber gloves coated with vaseline.Be prepared is my motto.

Brendan

Has anyone read this, and can comment on any possible relation to what is going on now? "A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence" - https://www.nature.com/articles/nm.3985

Walrus, that was a pretty micro-aggressive attack on b. He never used any ad hominem attacks on you, but just posted what he believes is contradictory evidence. Have you investigated the claims presented at that private meeting, or did you just accept it as gospel like most people did with the weapons of mass destruction that was presented by experts?

blue peacock

JJackson

Isn't there a national pandemic plan? It is not that this is not a possibility when even Netflix has a show about it.

It seems the CDC, NIH and the health care system in general is caught flat-footed as if they are surprised and didn't have a plan to execute. It looks like another Katrina moment highlighting an unprecedented level of incompetence.

This begs the question where the trillions of dollars in annual healthcare expenditures including funding of ever growing national institutions goes?

Deap

Update: ..."ADM Brett P. Giroir, M.D., a four-star admiral in the U.S. Public Health Service Commissioned Corps and Assistant Secretary for Health at the U.S. Department of Health and Human Services (HHS), reported today that the mortality rate of the coronavirus is likely between 0.1% and 1%.

That would put it somewhere between being comparable to the flu and up to six times more lethal, but nowhere near the mortality rate that’s been reported thus far.

The reason it is now believed by medical professionals who are examining the data that the mortality rate is lower than reported is because there are likely many more people infected than what’s publicly known.

The disease is turning out to be so mild in some that they do not display symptoms before their body beats it. Others get mildly ill and do not go to the doctor at all. ..."

fanto

My grandfather died in late 1917 of Spanish Flue, in prime of his life, early 40s, was healthy and robust. He died within 3 days of onset of symptoms. The story that it affected the young and healthy, robust male individuals I heard from my both parents, and other sources confirm this anecdotal observation that people between 20-40 years of age were the most victims.

https://de.wikipedia.org/wiki/Spanische_Grippe

the current COVID-19 pandemic has different "profile", seemingly.

Bobo

Walrus
You stimulated a good discussion and I learned a lot and Thanks to those with the technical expertise that chimed in, as usual SST brings in the best.
Now the 1,000th, 10,000th and 100,000th case in the USA is just around the corner. We all know our government agencies are slow to get going but the momentum is happening thus have faith and stay safe.

Terence Gore

https://twitter.com/NBCNews/status/1235786467420581888

mortality rate best estimates between .1 and 1%
as per Adm. Brett Giroir asst secretary at HHS


Terence Gore

Whatever you do don't touch your face!!!

https://twitter.com/FrankCaliendo/status/1235731480480845824

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