COVID COVID-19 Coronavirus Containment Efforts

[mfb]

We know it’s not going to hurt because we now know that the vaccine is completely safe.

Their phase 2 trials will have 400-500 people, presumably the phase 1 trials had fewer, and all of them healthy. They don't know if it is "completely safe". Anyway, good to see more progress.

 

[bhobba]

The Australian numbers in a global context are still quite low. Perhaps bad is relative. South Africa has over 10,000 new cases per day. I'd say that's very bad.

Bad is definitely relative. But we all know basic math on this forum, and the consequences of an r0 of about 2.5 compared to the flu's r0 of about 1.2. The Spanish flu with an r0 of 2.2 was virtually eliminated here when one case quickly sparked a second wave much worse than the first. We must clamp down on this early and hard or we will end up like South Africa. The question is it now time to take a risk and deploy the vaccine? India is very aggressive and will deploy one of their vaccines by at the latest August 16. I think, because Australia is relatively still in a good place, we do not need to be that aggressive, but IMHO the end of the year is realistic, and we can use it now to dampen hotspots in say nursing homes as they emerge,

Thanks
Bill

 

[OCR]

Lol. . . thanks Bill. .

End of Article

For a time there, I thought I was locked into a. . . .

.

 

[bhobba]

Their phase 2 trials will have 400-500 people, presumably the phase 1 trials had fewer, and all of them healthy. They don't know if it is "completely safe". Anyway, good to see more progress.

Yes - there is risk involved. For the UQ vaccine we had thousands of volunteers for the 120 they are using in phase 1 trials. I think we will get thousands of volunteers for challenge phase 2 trials where volunteers are deliberately infected, as well as using it to inoculate known hot spots like nursing homes. If we then deploy the vaccine or wait until phase 3 trials with 50.000 people will depend on the situation at the time. We may even get enough people here in Australia to volunteer to do a challenge phase 3 trial. Do we have the courage and 'true grit'. We will see.

Thanks
Bill

 

[Ygggdrasil]

The Australian numbers in a global context are still quite low. Perhaps bad is relative. South Africa has over 10,000 new cases per day. I'd say that's very bad.

Here's the plot of the 7-day rolling averages of daily new cases for the USA, UK, Australia, Spain, and South Africa:

Indeed, the Australian cases per million are still quite small and the increase is also small compared to the increases seen in the US, South Africa, and Spain. The numbers in South Africa are indeed bad, approaching similar per capita levels of new infections as the US.

The US and South Africa are among the worst large countries (pop > 5M) in terms of cumulative per capita cases over the past two weeks along with Brazil, Israel and Colombia (Kyrgzstan tops this list but this is due to basically one day reporting >10,000 cases, with the rest showing more than an order of magnitude fewer cases):

Note that because testing rates and availability are not the same across all countries, comparing case counts across countries is not a fair apples-to-apples comparison.

 

[StevieTNZ]

Herman Cain died from the "china virus" on 30 July (US).

The president paid tribute to Mr Cain on Thursday at the White House, saying: "He was a very special person... and unfortunately he passed away from a thing called the China virus."

-- https://www.bbc.com/news/world-us-canada-53600376

 

[BillTre]

Updates on Efforts to Have Sports Leagues Play:
(Sports as a Model for Society)

This NY Times article (‘Bubbles’ Are Working. But How Long Can Sports Stay Inside?') reviews how different leagues, using different approaches, are doing wrt controlling infections and continuing to be able to play.

This news article from Science goes into detail about how organization running The Basketball Tournament (TBT) worked with Tara Kirk Sell, who specializes in trying to reduce the health impacts of large-scale events such as disasters and terrorism, so they could run their 24 team tournament with minimal problems.
This is a really nice article with lots of details about planning out lots of contingencies ahead of time, a great testing scheme, and continual procedural improvement, all of which seem necessary for success to me.

Sell's interests in the job:

From Sell’s standpoint, TBT could be in some respects described as a natural culmination of her professional life. She has always been “intrigued” by the emotional power sports hold to advance the public health. For members of certain minority communities, star athletes from similar backgrounds in MLB or NBA can be seen as both advocates and role models for the community’s safety. When NBA basketball star Steph Curry speaks on Instagram to Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases and a leader of the U.S. COVID-19 response, those who admire and trust the player might pay heed to the scientist more than they would in other circumstances.

Sports, in this way, must be considered as much a part of a national public health strategy as funding for vaccines, says Sell, whose doctoral thesis evaluated the “media and policy responses to … dreaded communicable diseases” such as Ebola. She feels a particular urgency to this end—because the “loss of trust, increased division, and outright confusion” surrounding COVID-19 has meant doubt in U.S. health authorities has been mounting since April.

Description of their methods:

In late April, through a series of teleconferences with the TBT staff, Sell “pounded into our heads that the devil was in every last detail,” Mugar says. The goal, he notes, was “to leave no stone unturned to derisk every touchpoint.”

The foundation of the TBT plan was built on saliva tests meant to detect proteins associated with active infection of SARV-CoV-2: Players would take six over the course of the 11-day tournament. To ensure results would be accessible within 18 hours, TBT enlisted a Rutgers University–associated lab within driving distance, should inclement weather prevent flights. (Such saliva “antigen” tests are not as sensitive and accurate as tests looking for viral genes—but they are cheaper, faster, and if used regularly enough, some scientists say, they can still stop an outbreak quickly. TBT used viral genome assays on nasal swabs only to confirm positive saliva tests, and MLB is adopting a similar strategy.)

In turn, clear hygiene protocols, including disinfecting objects such as benches, room keys, gym equipment, and water bottles, would reduce the risk of transmission from anyone individual to another. Laundry would be handled centrally, signage defined how players should reduce the risk of transmission in shared spaces such as elevators and dining halls, and text message reminders to maintain precautions for hand washing and mask wearing would be constant.

Sell and Mugar also designed a health monitoring questionnaire that players could complete on their smartphones twice daily, in the hopes of catching COVID-19 symptoms that developed in between saliva tests—or in case of false negative tests (which could inappropriately lead a player who was sick to be cleared). An incomplete questionnaire—or one that noted worrisome symptoms such as fever or shortness of breath—would constitute criteria for isolating a player. Finally, in the near-inevitability that players tested positive, the formation of self-contained cohorts within teams for transportation to and from playing facilities—as well as dining and other group activities—would facilitate contact tracing if and when required.

This worked out for the tournament, and provides a possible guide for bringing back the economy in general, if people were to consider it.

She hopes the procedures adopted by TBT can help beyond sports, too. Symptom self-monitoring, hygiene procedures, routine testing, and strategies for cohort contact tracing have all been applied in countries such as Taiwan, Singapore, and Japan that have, for now, safely reopened their economies. “Things are not going to be 100% normal for a [while],” Sell says, “I don’t think we can afford overlooking … the tiniest details.”

Probably asking too much of some people.

 

[bhobba]

Melbourne to be in stage 4 lockdown soon. Personally I would not call it a total stage 4 lockdown (eg you can still go out for fresh air and exercise), but a stronger stage 3 and some stage 4 measures:
https://www.9news.com.au/national/v...hey-mean/2e508cdb-6cfe-4a6f-ad80-52af9601435a

Personally I think the whole state of Victoria should be put in a total stage 4 lockdown immediately (a real one) - experience has shown the sooner you go as hard as you can the better. And they must deploy the vaccine I mentioned previously to protect those in nursing homes and front line medical workers (since it is part of a stage 2 trial volunteers of course). IMHO a real leader would - but most politicians seem to prefer spin to actual action when making really tough decisions.

Thanks
Bill

 

[bhobba]

Now I am getting dejected and very disappointed. The latest on the Flinders University vaccine from todays Courier Mail:

'The US, UK and Korean governments are supporting the trials of the vaccine but Professor Petrovsky said neither Australia’s government nor our vaccine manufacturer CSL will deal with him. “They don’t return our phone calls,” he said. “It’s politics, but I would argue in the middle of a pandemic you should put politics aside”.

A funding application from the government’s Medical Research Future Fund was recently knocked back, he said. Professor Petrovsky has reached out to the Victorian Government and wants to move the next stage of his clinical trials into aged care homes in Victoria where hundreds of people have been infected with coronavirus. “They’ve got nothing to lose,” he said. “It’s frustrating to watch people dying and we have a vaccine that could stop those deaths,” he said.

The Governor of Norfolk Island which has an elderly population has asked whether his entire population can be injected with the vaccine as part of the next phase of the trial.“We’re open to looking at that but we would have to get the right ethics approvals before that could go ahead,” he told News Corp.'

I have mentioned before we have politicians and associated bureaucrats coming out of our ears - but real leaders, people with actual vision and what I call 'true grit', are few and far between. Norfolk Island, an Australian Territory, is showing some actual leadership. But as to the rest of Australia - well let's just say slogans like Australia Is The Smart Country - is looking like it has no actual substance.

I have never done this before, but I am going to ring our local member who is a MD and holds a Masters in Public Administration from Harvard. He spent time working in remote Aboriginal communities and so would know it would be a disaster if it got into those. If it will make a difference I do not know - but I feel I need to do something.

Thanks
Bill

 

[atyy]

Now I am getting dejected and very disappointed. The latest on the Flinders University vaccine from todays Courier Mail:

'The US, UK and Korean governments are supporting the trials of the vaccine but Professor Petrovsky said neither Australia’s government nor our vaccine manufacturer CSL will deal with him. “They don’t return our phone calls,” he said. “It’s politics, but I would argue in the middle of a pandemic you should put politics aside”.

Could it be that the Australian government is betting on the Queensland vaccine (ie. maybe it is not politics)?

What is the Flinders vaccine strategy?

 

[bhobba]

Could it be that the Australian government is betting on the Queensland vaccine (ie. maybe it is not politics)? What is the Flinders vaccine strategy?

That's it according to Professor Petrovsky - I only gave an extract from the entire news story. I would call that politics - but I suppose it's what you mean by politics. To be a bit more positive the UQ vaccine is only a few weeks behind the Flinders vaccine, and works in a similar way, so as far as getting Australia and other countries vaccinated it will not make much difference I think. But the situation in Victoria is now getting a lot worse, and especially bad in nursing homes where most of the deaths are occurring.

The vaccine is called Covax-19 and has collaborated with South Korean biopharma firm Medytox for its development and commercialisation.

It uses the Advax adjuvant technology, developed by Dr Peter Cooper at the ANU and Professor Petrovsky, in combination with a recombinant SARS-CoV-2 spike protein. Medytox signed a memorandum of understanding on 12 May. They will jointly carry out product and process development, clinical trial programme and commercial scale-up for the Australian and Asian markets, including Korea. It is not part of CEPI so that is a possible issue.

The more I think about it, the more I believe talking to our local federal member about it is the way to go. He has the right background to look into this issue:
https://www.aph.gov.au/Senators_and_Members/Parliamentarian?MPID=E0H

If he can't get anything done, then I do not think much more is possible.

It's just so frustrating, especially as I write this and listening to the local news you hear a doctor saying we need a vaccine ASAP to get out of this mess - and that was just the issue of deferral of surgery due the need to keep beds free. Trials are not complete, but we can make emergency use of a vaccine for critical front line medical staff and patients at high risk.

Thanks
Bill

 

[Vanadium 50]

we now know that the vaccine is completely safe

He should not say such things.

If he has 400 subjects (and that seems questionable) he is reasonably sure than the rate of serious adverse reactions is under 1%. That's a pretty big number. It's even above the CDC fatality rate of 0.26%. He needs a larger study to even show it's safer than the disease, much less "completely safe".

 

[bhobba]

He should not say such things.

If he has 400 subjects (and that seems questionable) he is reasonably sure than the rate of serious adverse reactions is under 1%. That's a pretty big number. It's even above the CDC fatality rate of 0.26%. He needs a larger study to even show it's safer than the disease, much less "completely safe".

Valid point. But he is only proposing to use it as part of a stage 2 trial which is voluntary. Actually I think the stage 1 trials would have been less than 400 - more like the 120 UQ is using which only makes it worse. But the death rate in the nursing homes is scary - 33.7%:
https://pubmed.ncbi.nlm.nih.gov/32220208/

It would need analysis by a biostatistician and could be valid reason to reject it. But at least consider it and give a rational reason.

Thanks
Bill

 

[StatGuy2000]

Current story in USA Today:

https://www.usatoday.com/story/news...t-region-second-coronavirus-spike/5526854002/

I think this is a swing and a miss on the premise (but they need something to write about...).

Starting in mid-April, New York's test positivity rate dropped smoothly and exponentially to the 1-2% range by the beginning of June and hasn't budged since. New Jersey's curve wasn't smooth due to awful early testing rates, but it also dropped below 2% by the second week of June and also hasn't budged.

Both states have largely re-opened (NYC just went to "phase 4" on July 20, which isn't quite normal), but I don't believe that New York and New Jersey have uniquely excelled at personal mitigation efforts since April while other states such as PA have experienced a resurgence as they re-opened. Whether it's 25% or nearly everyone who has been exposed, it seems pretty clear to me that NY and NJ have achieved herd immunity, and COVID is basically finished with them.

The implications of this are that we get to see what it looks like to let COVID run wild and then get back to normal quickly, and compare that to, say, Pennsylvania, which I expect will be in a state of partial shutdown for the next 6 months.

From a number of sources I have read (including the following article from John Hopkins University), for herd immunity to take into effect, approximately 70% of a given population needs immunity (whether from direct exposure to the pathogen, or from vaccines) from a particular pathogen to achieve herd immunity, depending on how contagious an infection is.

https://www.jhsph.edu/covid-19/articles/achieving-herd-immunity-with-covid19.html

I find it highly doubtful that 70% of the population of New York or New Jersey are actually immune to the SARS-CoV-2 virus (there are estimates that somewhere around 19-25% of New York City's population have already been exposed, which is orders of magnitude less than 70%). So I'm dubious about any claims that these states have achieved herd immunity. After all, even countries like China (the first country to be severely impacted by COVID-19) are seeing a resurgence of cases (although with the caveat that it appears that the new cases are based primarily around Beijing and surrounding areas, not Hubei province or its largest city, Wuhan).

https://www.ctvnews.ca/world/china-...d-19-after-lockdown-measures-lifted-1.4985866

 

[Vanadium 50]

But the death rate in the nursing homes is scary - 33.7%:

Yes it is, although that is a single home. However, the fatality rates in NJ, MA and NY are consistent with at or near 100% of the patients infected. Which is why the exhortations to the other governors to be more like Gov. Kodos Cuomo frightens me. However, you're making the implicit assumption that any vaccinne side effects are distributed uniformly, but the Covid risk is not. That is unlikely to be the way it turns out. Usually vulnerable populations are, well, vulnerable. To pretty much everything.

 

[Ygggdrasil]

He should not say such things.

If he has 400 subjects (and that seems questionable) he is reasonably sure than the rate of serious adverse reactions is under 1%. That's a pretty big number. It's even above the CDC fatality rate of 0.26%. He needs a larger study to even show it's safer than the disease, much less "completely safe".

It is worse than that. The phase I trial had 40 participants, and 30 received the vaccine (these are typical numbers for a phase I trial). The Phase II trial aims to have ~ 400 participants. Although I have found news reports of the trial, I have not seen the data underlying the claims of safety or the ability to generate an immune response, so it is difficult to assess how well these claims match the evidence (especially compared to other vaccine candidates).

The phase II trails for the Flinders University vaccine is not scheduled to begin until Sept (perhaps suggesting time needed to manufacture the necessary doses), which could suggest that it could be difficult to scale production of the vaccine (especially given some of the quotes from the team cited above regarding trouble accessing funding and manufacturing partners).

 

[atyy]

To be a bit more positive the UQ vaccine is only a few weeks behind the Flinders vaccine, and works in a similar way, so as far as getting Australia and other countries vaccinated it will not make much difference I think.

I haven't seen the details, but one issue with just using the protein is that the protein configuration will not be the same as when it is part of a virus, and this difference in configuration may lead to a less effective vaccine. It seems the Queensland vaccine has some method that is intended to hold the protein in the right configuration. I suppose if the government has enough money then both can be supported, but another possibility is that supporting both would dilute resources so that neither will succeed.
https://advance.qld.gov.au/vaccine
https://en.wikipedia.org/wiki/Molecular_clamp

 

[berkeman]

This is amazing dedication to patient care. Respect.

https://www.cnn.com/interactive/2020/07/health/coronavirus-houston-hospital/index.html

 

[mfb]

I haven't heard of a vaccine that either kills you or leaves you with no negative effects at all. If none of the 40 patients had any side effects then this vaccine is unlikely to kill 1 in 20 (something you can't rule out from death statistics alone) - but as I mentioned before, saying it's known to be completely safe is wrong.

I find it highly doubtful that 70% of the population of New York or New Jersey are actually immune to the SARS-CoV-2 virus (there are estimates that somewhere around 19-25% of New York City's population have already been exposed, which is orders of magnitude less than 70%).

A factor 3 is half an order of magnitude.
It makes it easier to keep the reproduction rate at or below 1, especially as people more likely to infect others are more likely to be immune now.

 

[Vanadium 50]

PA's positivity rate bottomed-out on June 18 and started rising again. Why? Because between May 29 and June 26, all but one county entered the "green" phase of re-opening (in groups, roughly weekly). So this tells us that at some point we reached a threshold of social interaction where R went above 1 again.

I'm not sure I would describe it that way. Here is data from The Covid Tracking Project:

To me, this tells me that pre- and post- June 15 cases are fundamentally different. In the later data, the number of new cases is proportional to the number of new tests, while the number of hospitalizations is much flatter, and the number of deaths seems unaffected - maybe there's an inflection point.

 

[mfb]

New cases per day more than doubled since the minimum June 15, new tests increased by 60% or so. That means the fraction of positive tests rises. Rising test rate and rising rate of positive tests means more people get infected. It seems to affect more healthier people now, and of course hospitals got better at keeping people alive.

 

[bhobba]

New story in the Courier Mail today about the Covax-19 vaccine making less wild claims about its safety, but otherwise basically the same. He wants to use it to dampen outbreaks in nursing homes in the second wave of outbreaks in Victoria as part of stage 2 trials. Will give our local member of parliament a ring about it just to make sure the government is on top of this.

Added Later:
Rang the MP and the staff will definitely pass the issue onto our local MP Dr Laming.

Thanks
Bill

 

[Vanadium 50]

It seems to affect more healthier people now, and of course hospitals got better at keeping people alive.

In the limit where 100% have the disease but there are zero hospitalizations and zero deaths, how much should we spend on mitigation? And if your answer is "not very much", surely PA is closer to that limit than it was in April or May.

That said, I think "new cases" is a fairly meaningless metric, as it covers someone who is asymptomatic but tests positive but also someone who died and was discovered to have Covid. And if you go to that site, you will find huge disparities between the shape of the "new cases", "new hospitalizations" and "new deaths" curves. You'd think if you knew one, you'd at least know the major features of the others. Nope - pretty much every combination imaginable is represented somewhere in the US.

 

[mfb]

In the limit where 100% have the disease but there are zero hospitalizations and zero deaths, how much should we spend on mitigation?

Depends on what other effects are there, but probably not much.

And if your answer is "not very much", surely PA is closer to that limit than it was in April or May.

And what do we conclude from that? Let everyone get infected now because hospitalization and death rate are not as bad as in April? I guess not.

 

[Ygggdrasil]

That said, I think "new cases" is a fairly meaningless metric, as it covers someone who is asymptomatic but tests positive but also someone who died and was discovered to have Covid. And if you go to that site, you will find huge disparities between the shape of the "new cases", "new hospitalizations" and "new deaths" curves. You'd think if you knew one, you'd at least know the major features of the others. Nope - pretty much every combination imaginable is represented somewhere in the US.

Mild and asymptomatic cases are not meaningless because, while the usually don't pose risk of death, they are still infectious and could pass the disease to people who could be vulnerable to suffer more severe outcomes from infection by the virus. Case counts are useful tools to tell us the extent to which transmission is occurring in the community and the relative risk of acquiring the disease from the community.

 

[Vanadium 50]

Let everyone get infected now because hospitalization and death rate are not as bad as in April? I guess not.

Did I say that, Mr. Mentor? Don't stick words in my mouth. It is the cheapest form of debate and beneath you and your office.

 

[mfb]

I didn't claim you would have said that. But my question stands: What do we conclude from that? Is there anything we can learn from it, or any action we should take based on a mathematically shorter distance to a purely hypothetical situation?

 

[Vanadium 50]

I think the conclusion is that the expenditures should match the risk.

 

[Ygggdrasil]

And if you go to that site, you will find huge disparities between the shape of the "new cases", "new hospitalizations" and "new deaths" curves. You'd think if you knew one, you'd at least know the major features of the others. Nope - pretty much every combination imaginable is represented somewhere in the US.

An important note on hospitalization data in the US: In July, the Trump administration ordered changes to the ways hospitals report hospitalization data, which has caused problems in recent hospitalization data.

Since the beginning of the pandemic, hospitals have been reporting bed capacity and other key data to CDC through its National Healthcare Safety Network COVID-19 module. No hospital staff interviewed by NPR described problems with this system. They said that it had been used by hospitals for 15 years to monitor the impact of other illnesses and that staff are comfortable with it.

The established system was disrupted by a memo dated July 10, issued to hospitals by HHS. In the memo, HHS took the unusual step of instructing hospitals to stop reporting the capacity data to CDC and to instead use a reporting platform developed recently by private contractor TeleTracking. As NPR has reported, the details of how the contract was awarded to TeleTracking are unclear.

Hospitals received only a few days notice of the change and scrambled to adapt.

The sudden reporting switch to HHS, bypassing CDC, prompted an immediate outcry.

https://www.npr.org/sections/health...t-bypasses-cdc-plagued-by-delays-inaccuracies

The NPR article notes many problems with the new reporting system including inaccuracies and delays. For example:

When HHS took over the collection and reporting of this hospital capacity data, it promised to update "multiple times each day." Later, the agency walked that back to say it would be updated daily.

Those daily updates have yet to materialize. On Thursday, an HHS spokesperson told NPR via email, "We will be updating the site to make it clear that the estimates are only updated weekly."

The HHS Protect Public Data Hub, the public-facing website set up by HHS, offers three items as a "Hospital Utilization Snapshot," all of which have data that is over a week old.

Furthermore, the Covid Tracking Project, whose charts and data @Vanadium 50 cited above, said in a recent post on their site:

But two weeks after the rules began, it’s clear that technical requirements associated with the new guidelines have caused major problems. Some of the states facing the largest COVID-19 outbreaks—such as California, Texas, and South Carolina—have warned that they are not reporting accurate hospital information due to the switchover.

These problems mean that our hospitalization data—a crucial metric of the COVID-19 pandemic—is, for now, unreliable, and likely an undercount. We do not think that either the state-level hospitalization data or the new federal data is reliable in isolation. (As we describe below, the new federal hospitalization figures are substantially higher than the same data as reported by most states.)

(emphasis their's)
https://covidtracking.com/blog/whats-going-on-with-covid-19-hospitalization-data

 

[Vanadium 50]

In July, the Trump administration ordered changes to the ways hospitals report hospitalization data, which has caused problems in recent hospitalization data.

There was also a change around then, maybe earlier, that alters the way hospitals are reimbursed. "Admitted for X but also has Covid" is different for "Admitted for Covid but also has X".

(PS How does one decide if an action is by "The Trump Administration", or some executive branch health organization (like the CDC)?")