The UK government data website:
Dashboards:
https://www.arcgis.com/apps/opsdashboard/index.html#/f94c3c90da5b4e9f9a0b19484dd4bb14 (Desktop)
https://www.arcgis.com/apps/opsdashboard/index.html#/ae5dda8f86814ae99dde905d2a9070ae (Mobile)
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I’ll post this here so it does not get lost in the Covid bickering thread.
Anyone looking for something easy and useful, and low risk, they can do in Team Australia’s fight against Covid-19 should join up to this website. Deputy CMO Paul Kelly has mentioned it a few times in his press conference, so he sees it as important.
It is run from NSW but anyone in Australia or Tasmania East (NZ) can join.
I’ve joined, it is easy. You get regular weekly emails to remind you to log on and report if you have any flu symptoms, or not. It takes about 30 seconds. This information is used to map and track which post codes are developing as hot spots for flu symptoms (and therefore covid symptoms). You can zoom in to the map yourself to see how healthy your postcode is at the moment.
Link to actual map
https://denden.shinyapps.io/MapApp/
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Just want to expand a little on this. A clade is simply defined as a single common ancestor and all its descendents. This definition can be applied at any scale, e.g., all primates form a clade that is distinct from other mammals, but all mammals collectively form a clade of their own that is distinct from other tetrapods. Applying this definition to the trees above, any group of viruses that descend from a single branch are considered a clade. All human cases of SARS-CoV2 including the one involved in the original wildlife-to-human transmission event are considered a clade. Similarly, the virus carried by the idiot who goes to a party, together with the viruses subsequently carried by the 30 people he gave it to, are also considered a clade.
When it comes to defining a particular strain, or “subtype”, this is where it gets tricky. In general, there’s no clear and consistent definition for this. Sometimes, structural or functional distinctions can be used, such as in the case of influenza A, where different strains are defined according to the surface protein structure (e.g., H5N1, H1N1). Different strains can also be defined according to the native host. For instance, the bobcat strain of feline immunodeficiency virus is distinct from the mountain lion strain because the viruses are different enough that cross-species transmission is limited. In other cases, these distinctions can be relatively arbitrary, defined according to percentage of generic sequence similarity, or degree of phylogenetic divergence (the length of a branch on a phylogenetic tree). These cutoffs could be chosen as a function of variation among all the viruses being investigated (e.g., If the average genetic similarity among all pairs of viruses is 80%, then this might be used as a threshold for defining a strain or a subtype, such that all viruses sharing >80% similarity could be considered part of the same group) but not necessarily. However, as with the term “clade”, “strain” can also be applied at different hierarchical levels. For example, it would not be incorrect to refer (at least informally) to a virus isolated from me as a “strain”, and a virus isolated from you as another “strain”.
This is why people should not assume that different strains must have functional differences, such as one being more virulent than the other. This is possible, but the distinction between strains of SARS-CoV2 currently is based purely on degrees of phylogenetic divergence. No functional differences between strains are implied, nor, as far as I know, have any been discovered. A large proportion of genetic variation in a population, whether a population of animals or a population of viruses, does not have any direct physical (phenotypic) effect. This variation can tell you a lot about how closely related individuals/viruses are though, through which you can infer things like how the virus has spread over time and which countries it came from, or how often animals of a given species or population move between different locations.
Anyway, great thread, AT. I fell behind on the other threads ages ago and have been unable to catch up.
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Thanks @Kozza. I am a pragmatist. To me the concept of a “strain” is in the eye of the beholder. If you are interested in surface proteins of a virus, ie you are a virologist, you will look at lineages differently to a doctor, who is more interested in clinical matters. For the doctor, its all about whether a strain requires a different treatment. So a strain should be defined as the lineage in which individuals inherit the same characteristic of interest. The definition of degrees of divergence by mutation is arcane.
How much virus is needed to develop COVID-19? 1, or 1 million, or 10 million?
Does the severity of the disease depend on the number of viruses you pick up?
It turns out, experts don’t really agree, the ones sampled in this piece disagree quite a bit. So facts is a misnomer.
To summarise.
- The amount of virus you get is called the DOSE
- The amount an infected person sheds is called the LOAD. ( dates back to HIV blood analysis )
- In the case of influenza the size of the dose effects the severity. But there are a range of opinions on this for SARS-COV-19
- There are 2 types of immune response, immediate generalised response, which carries some of the symptoms with it. Then 2-3 weeks later, the newly created SARS-COV-19 antibodies swing into action. Many people die from a massive over-reaction by their own initial immune response, ( a “cytokine storm” ) before the antibodies have had a chance to kick in.
https://www.sciencemediacentre.org/expert-reaction-to-questions-about-covid-19-and-viral-load/
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Do you have a scientific background out of curiosity?
Physics.
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I don’t know where this came from but I think it is a canard.
It’s not surprising the experts don’t agree as they could not possibly know. No-one would have titrated the dosage in humans let alone correlate that with outcomes (though it may have been done by now in animal models).
Its not a carnard AT. The article quotes some very well qualified virologists. Are you suggesting the answers in the article are fake news?
The doses of influenza virus have been tested in mice, so it would make sense to do a comparative test in mice and as you say, it has probably already been done.
How much virus Joe Daniher kick?
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Yes it quotes some virologists. If you read what they say, they all skate around the question, except for the first one who agreed with what I said:
"It is unlikely that higher doses that would be acquired by being exposed to multiple infected sources would make much difference to the course of disease or the outcome. "
Another one mentioned load in SARS and MERS but a) we don’t know what the data is for these diseases (he did not provide a reference) and b) we do not know if SARS2 will behave in the same way that he said the others did.
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Here are your facts - the state response and advisory’s plus the commonwealth site are the one source of truth. Seriously fk the news off now if you want to feel sane.
I’ve left a link to the WhatsApp page which is really good.
Don’t spread info until you know it’s fact. Rumours are not helpful.
And yeah as DJR said good luck with this one.
https://www.dhhs.vic.gov.au/coronavirus-covid-19-daily-update
https://www.health.nsw.gov.au/Infectious/diseases/Pages/coronavirus.aspx
https://www.wa.gov.au/government/covid-19-coronavirus
Gov app;
This is the what’s app update;
Yes I know they are subject of criticism, but here is 30 minute WHO background from Mike Ryan in 2017.
Earlier Ryan said “go hard go early, do not wait for proof”!
Its a shame Tedros wasn’t listening to him early on.
It’s a duck??
That’s a Mallard you Goose. 
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Thought it was ‘duck’.
Checking -
yep, it’s duck in French!
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This a copy of the post I made on the main COVID-19 thread. Have copied here, and will update here, from this point forward following a suggestion from @Albert_Thurgood.
Lot of talk about the US - and of course Trump - so I thought I would try and piece together a rough timeline of what’s unfolded in the US, noting that I think no one individual is to blame (be it Trump or Cuomo or anyone else).
Note: I will continue update this as others bring facts I have missed. Thanks to all who do. I’ve expanded the timeline to the earliest possible point under the Trump administration.
- Reports emerge in early 2020 that Obama officials walked Trump aides through a hypothetical scenario in which a pandemic worse than the 1918 Spanish flu shut down cities like Seoul and London in early 2017, Politico reported. Of the Trump administration officials present during the meeting, about 66 percent no longer serve in the White House, according to Politico. Sean Spicer, who served as the administration’s first press secretary and was also present at the meeting, said the exercise was of limited use because the details of real pandemics are rarely as straightforward as such exercises.“There’s no briefing that can prepare you for a worldwide pandemic,” he told Politico. (My view is that a high staff turnover - constant under Trump due to his managerial style - is not conducive to long term planning and clearly the staff turn over did not help at all in making the administration better prepared for COVID-19. However, each pandemic is different from the last and the learnings would have been useful but no changed a whole lot as the facts unfolded e.g. China’s and the WHO’s behaviour would not have been different.
- China’s first confirmed Covid-19 case traced back to November 17 according to government data seen by The South China Morning Post on 13 March, 2020. Chinese authorities have so far identified at least 266 people who were infected last year, all of whom came under medical surveillance at some point. Some of the cases were likely backdated after health authorities had tested specimens taken from suspected patients. Interviews with whistle-blowers from the medical community suggest Chinese doctors only realised they were dealing with a new disease in late December.
(a) According to the World Health Organisation’s website, the first confirmed Covid-19 case in China was on December 8, but the global body does not track the disease itself but relies on nations to provide such information.
(b) A report published in medical journal The Lancet by Chinese doctors from Jinyintan Hospital in Wuhan, which treated some of the earliest patients, put the date of the first known infection at December 1. - Reports emerge, in early April 2020 and based on a report run by the US ABC News, that US intelligence agencies warned About Coronavirus In Wuhan In Late November, 2019. The White House’s National Security Council, the Pentagon’s Joint Staff and the Defense Intelligence Agency were all briefed on the impacts of the COVID-19 coronavirus outbreak in Wuhan, China, as early as late November, according to [ABC News].
The intelligence came in the form of communications intercepts and overhead images showing increased activity at health facilities, the officials said. The intelligence was distributed to some federal public health officials in the form of a “situation report” in late November, a former official briefed on the matter said. But there was no assessment that a lethal global outbreak was brewing at that time, a defense official said.(https://abcnews.go.com/Politics/intelligence-report-warned-coronavirus-crisis-early-november-sources/story?id=70031273), citing four unnamed sources familiar with a classified intelligence report. My view: intelligence sources knew something was up, bit no formal report was prepared and it seemed that COVID-19 itself wasn’t mentioned specifically in the report, noting the term itself did not not exist at the time.
(a) But the current and former officials told NBC News that while no formal assessment was produced in November — and hence no “intelligence product,” in the jargon of the spy agencies — there was intelligence that caught the attention of public health analysts and fueled formal assessments that were written in December. That material and other information, including some from news and social media reports, ultimately found its way into President Donald Trump’s intelligence briefing book in January. It is unknown whether he read the information.
(b) Air Force Gen. John Hyten, vice chairman of the Joint Chiefs of Staff, told reporters Thursday that he did not see intelligence reports on the coronavirus until January.
“We went back and looked at everything in November and December,” he said. “The first indication we have were the reports out of China in late December that were in the public forum. And the first intel reports I saw were in January.” - The Trump administration (but not Trump himself) first heard about the coronavirus outbreak in China on January 3 after Beijing rebuffed US efforts to send a CDC team into China.
- As late as January 14, China claimed publicly there was “no clear evidence of human-to-human transmission” of the virus.
- Trump was first briefed about the virus at Mar-a-Lago in Florida on January 18. There is therefore ~ 2 month delay between communications intercepts and overhead images showing increased activity at health facilities being picked up by US agencies and the information making it’s way into an actual intelligence report. Is this slow or fast given no specific threat is identified? I don’t know the answer to that question but it is one worth asking when the dust settles.
- On January 21 a Seattle man, who had returned from Wuhan, became the first American to test positive.
- On January 22, when Trump was asked his first question about the virus at a press conference, he said it was “totally under control … it’s one person coming in from China”.
- Some key things to note at this point:
(a) The White House began meeting CDC and other health officials but the early focus was on stopping infected people from travelling to the US from China.
(b) Little attention was given to the need for a way of testing for this new disease. No one involved in those early meetings predicted anything like the spread of the virus that has occurred. - Although Trump was still publicly dismissive of the virus, he acted early (ahead of the WHO) on January 31 to bar non-US citizens from travelling from China to the US.
(a) Problem was, more than 300,000 people had already come into the US from China in the previous month. The coronavirus, unseen, was already spreading throughout the US. - On 3 February, World Health Organization chief Tedros Adhanom Ghebreyesus said there was no need for measures that “unnecessarily interfere with international travel and trade” in trying to halt the spread of a coronavirus that had killed 361 people in China by that time.
- US Health authorities (presumably the FDA - Food and Drug Administration) then made a major error by entrusting the CDC — which had overseen the US response to Ebola, H1N1 and other outbreaks — to develop a coronavirus test rather than use tests developed by the World Health Organisation or allow private US companies to develop tests.
- In early February the CDC shipped out its first tests, only to discover a serious flaw meant they didn’t produce reliable results. It was not until four weeks later, on February 29, that the FDA ordered that private laboratories were allowed to try to develop their own tests. On the same day, the US had its first coronavirus fatality.
(a) So the US lost all of February when it came to producing a reliable test and then distributing test kits widely enough to get a picture of who was infected and how it was speeding across the country.
(b) This failing meant US authorities were largely flying blind in combating the pandemic, not knowing where to allocate scarce resources or the looming scale of the coming catastrophe. “It’s a failing, let’s admit it,” the country’s top infectious diseases expert, Anthony Fauci, declared last month (March).
(c ) On February 26, Trump appoint his VP, Mike Pence, to lead the COVID-19 response.
(d) On February 27, Pence announced that Deborah Birx, MD, U.S. global AIDS coordinator and U.S. special representative for global health, will act as the White House’s COVID-19 response coordinator. Birx’s 3-decade career includes work in HIV and AIDS immunology research, vaccine research and global health initiatives. She previously served as director of the CDC’s Division of Global HIV/AIDS. - Health authorities also realised the national stockpile of protective masks, gowns, gloves and ventilators was simply not enough to cover the likely need of the fast-spreading pandemic. The stockpile had been whittled down through years of budget cuts but, in fairness, no country had ever planned for a pandemic of such proportions. When Trump initially played down the virus in February, he was largely reflecting a low level of concern inside the White House and the administration. No American had yet died and the virus appeared to be centred in the one state, Washington.
- But by early last month (March), Trump’s continued dismissal of the virus flew in the face of mounting evidence that it was spreading fast and was dangerous. At this point, Trump’s opinion diverged from that of his health advisers. He adopted the mode of a salesman, playing down the virus as he became increasingly concerned that it might shut down the economy.
- On 12-March, the WHO declares (finally) a pandemic.
- It wasn’t until the middle of last month (March) that Trump accepted the true gravity of the pandemic.(a) “There was some coming to grips with the problem and the true nature of it — the 13th of March is when I saw him really turn the corner. It took a while to realise you are at war,” Republican senator and Trump ally Lindsey Graham said. “That’s when he took decisive action that set in motion some real payoffs.”
(b) At this point, fewer than 100 Americans had died but it was increasingly clear that the virus was spreading across the country in an uncontrolled manner. - On March 16, Trump finally urged Americans to practise social distancing. Since then, the US has been fighting the coronavirus from behind.
(a) In New York, the epicentre of the virus in the US where 6268 have died, Governor Andrew Cuomo admits his state gravely misjudged the threat and has been playing catch-up ever since. “We underestimated this virus,” he says. “It’s more powerful, it’s more dangerous than we expected.” - On 20 March, Trump signed an executive order invoking the Defence Production Act (DPA). The 1950s law allows the President to prioritise government manufacturing contracts and direct companies to produce certain goods in the name of national security. General Motors (GM) was tasked to produce ventilators.
- On 28 March, Trump publicly expresses frustration with GM over negotiations to produce ventilators and to stop wasting time.
- The pandemic has revealed the blurred lines in the US between the states and the federal government about which is primarily responsible for fighting a pandemic such as this (note: similar to what happened with the response of the bushfires here when the Fed Govt had to step in with the average person demanding it; yet state government’s not quite comfortable with it as bushfire response has traditionally been their responsibility).
In summary, Trump has made mis-steps without a doubt, but the refusal of China to let the US CDC visit on 3 January was the biggest mistake (exacerbated by continuing to insist there was no evidence of human - human transmission) as it would certainly have led to an earlier ban on travel from China to the US. That would have greatly reduced how many infected people brought it into the US.
Second is the WHO’s blatant supporting of China and all its decisions, in the face of mounting facts. The WHO president became nothing but a propaganda mouthpiece for the Chinese government. They didn’t declare a pandemic until 12 March when it was clear at least 2 weeks earlier to other countries which is why they banned flights from China. Morrison was quite open about treating the situation as a pandemic when he banned flights on 1 February.
Thirdly, the US Health Bureaucrats - FDA - who decided not to use proven/approved test kits from overseas but task the CDC to produce them, banning even private companies from producing them. This cost the US a month in lost testing, over February, as it would have uncovered a bigger rate of infection than was realised. Note that the US didn’t even have its first death from COVID-19 until 29 February which one suspects lulled the FDA into thinking the situation was under control.
Then, I think, comes Trump. His managerial style leads to high staff turnover; so the benefit of any hand over on pandemic planning from the Obama administration is basically lost, as limited as it might have been given the uniqueness of each pandemic - every little bit of forward planning helps. He acted ahead of the WHO in banning travel from China on 31 January, having received intelligence reports during January. He started giving out mixed messages for a period of 1- 2 weeks from early-mid March. Since then he has stayed to the script of his health advisors. He has made good, decisive decisions like invoking a war time act. Problem is, his tweeting and talking don’t align with the serious acts he has actually taken, hence he created confusion about how seriously people should take the situation. US Governors are not better or worse than Trump. Health is primarily a state responsibility in the US like it is in Australia. The FDA might approve new drugs, biological products and medical devices but it is actually up to each state to order what it thinks it needs. Trump appointing Spence at the end of February to lead the effort against COVID-19 seems like a slap to the FDA/CDC after they got the test kit manufacture wrong.
I’ve tried to be as objective as I can be with pulling all this together from different sources and then offered my opinion as I see the facts.
WHO chief says widespread travel bans not needed to beat China virus
World Health Organization chief Tedros Adhanom Ghebreyesus said on Monday there was no need for measures that “unnecessarily interfere with international travel and trade” in trying to halt the spread of a coronavirus that has killed 361 people in…
Donald Trump has invoked powers of war to battle coronavirus. Here’s what…
Calling himself a wartime president, Donald Trump is shifting his tone in the COVID-19 fight. But will new measures be enough?
Trump tells GM: Stop ‘wasting time’, build ventilators to address coronavirus
U.S. President Donald Trump on Friday invoked emergency powers to require General Motors Co to build much-needed ventilators for coronavirus patients after he accused the largest U.S. automaker of “wasting time” during negotiations.
Trump appoints Pence to lead US response to COVID-19
President Donald J. Trump announced Wednesday that Vice President Mike Pence will lead the United States COVID-19 response.“Mike will be working with the professionals, doctors and everybody else that’s working,” Trump said at a White House press…
C.D.C. and W.H.O. Offers to Help China Have Been Ignored for Weeks
Privately, Chinese doctors say they need outside expertise. But Beijing, without saying why, has shown no interest so far.
Report: U.S. Intelligence Officials Warned About Coronavirus In Wuhan In Late…
It adds to mounting reports that the U.S. government could have acted much sooner to contain the virus.
U.S. spies had raw intel hinting at health crisis in China in November
Current and former officials say there was no formal assessment in November but that there was raw intelligence that fueled formal assessments written in December.
Obama officials walked Trump aides through global pandemic exercise in 2017:…
The Obama administration walked incoming Trump administration officials through a hypothetical scenario in which a pandemic worse than the 1918 Spanish flu shut down cities like Seoul and London in early 2017,
China’s first confirmed Covid-19 case traced back to November 17
Government records suggest first person infected with new disease may have been a Hubei resident aged 55, but ‘patient zero’ has yet to be confirmed.
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It’s worth saving this here.
As of two weeks ago, Covid19 is now the leading cause of deaths of all the top 15 causes in the USA:
and here is where they were a month earlier:
I couldn’t embed the video of the movie showing the day by day increase, but it’s very instructive and can be see here:
(To be clear, the covid deaths are real, as reported whereas the others are the expected averaged daily deaths from annual figures).
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Are any of those Trump aides briefed by Obama still engaged as Trump aides.?