Mutating Corona Virus

[BazzaS]

a) BCG isn’t 100% effective against TB. I’d still rather have it than not, though.

TB never quite went away.....

b) Measles is a horrible disease, and highly infectious. The anti-vaxx’ers who say “natural immunity is best”  seem to forget measles KILLS, (not always, but enough to be a concern)

Either early, or late as the patients brain turns to mush (SSPE : subacute sclerosing panencephalitis). Avoidable, through vaccination.
Still, the anti-vaxxers are right in a way (about ‘natural infection boosts your immunity’)  : if you catch measles and die, you certainly won’t catch another disease, ever again .......

 

c) There isn’t a vaccine against the coronaviruses. SARS, MERS, and the new one (2019-nCoV). Whilst lots of people who get it “will just get a cold”, some will get very ill (and go to hospital, which is why it is a risk for outbreaks in hospitals,  as SARS was), and some will die. Nobody yet knows in what numbers and what proportions.

Time will tell : including just how well it can spread person-to-person. Wuhan is certainly seeing cases in people who haven’t visited the “wet market” where the initial cases had been (and where it is suggested the virus first ‘jumped’ from animals - now felt likely snakes -to humans).
 

d) There isn’t a reliable antiviral against coronaviruses. Some viruses have antivirals active against them, many don’t.

[BazzaS]

8 hours ago, tobyjugg2 said:

 

One new case of rubella re-infection in a pregnant woman was also reported.

 

https://www.gov.uk/government/news/mmr-vaccination-call-following-high-numbers-of-measles-cases

 

I thought that must be a typo, as conventional wisdom is once you are immune to rubella you are immune.

 

I’ve checked the original source:

https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/853589/hpr4119_mmr.pdf
 

and that is indeed (p.6) what is says.

I’ll have a dig around, and see if I can find out what the experts are saying about it.

 

(So, if the first rubella report for her was a false positive, or if she’s had her previous immunity “wiped out” : such as having needed a stem cell transplant, some immunological treatments, or even having had measles, which is now believed can ‘reset’ immune systems.... another good reason to be vaccinated!)

[BazzaS]

Accurate ethos, but inaccurate factually.

 

not “All viruses mutate”, and not “viruses succeed if they don’t kill their host”.

 

Smallpox didn’t mutate. Smallpox killed many of those it infected. It was incredibly ‘successful’, but was eradicated (made possible by it having a fixed target for vaccine, no carrier state, and a massive international co-operation)

 

Polio : similar, though for a few countries that it remains endemic in, efforts to eradicate it are hindered by attitudes to vaccination and local politics.

 

Influenza “mutates”, both by “drift” and “shift”. Kills some it infects, but still incredibly successful. Even where it kills more (e.g. 1918 Spanish Flu, where it was recognised for killing young fit people), still very ‘successful’

 

Ebola: it isn’t “unsuccessful”. It remains a massive risk. The last outbreaks were only curtailed by a gigantic international response.

To describe Ebola as ‘unsuccessful’ doesn’t pay tribute to the healthcare workers (civilian and military!) who went and set up Ebola Treatment Centres, at great personal risk. Some were infected despite all the precautions they took, not all survived. Those that weren’t infected still worked in awful conditions (doing their work wearing full protective equipment, in searing heat, is very demanding).

The UK health worker who got infected has suffered some longer term effects of the illness (and also had the emotional challenge of facing a disciplinary around the circumstances of her return! Though was cleared by that tribunal)

 

WHO have declared (in the past) Ebola outbreaks as a Public Health Emergency of International Concern (PHEIC).

2019-nCoV hasn’t (yet) been declared a PHEIC (but watch this space!).

 

Part of the issue there is that PHEIC is binary : (“is or isn’t”). This may yet change in future to a more graded response, so that e.g. 2019-nCoV gets a classification of “not quite, but almost, a PHEIC”, allowing WHO (politically) to do more before it gets to be a PHEIC.

 

 

Edited January 24, 2020 by BazzaS

[BazzaS]

I can’t reply fully ATM, but as a quick response:

 

a) Smallpox is a virus. HIV is a virus. Yersinia pestis (cause of bubonic plague) is a bacterium.

hardly surprising then that “HIV is more phylogenetically related to Smallpox than Yersinia pestis”. That proves nothing.

 

b) Science blog : “Smallpox eradicated 1978”

Factually incorrect. Last naturally occurring case 1977. (Subsequent “lab release case” where a University photographer, Janet Parker, died). WHO declared smallpox eradicated in 1980. If they can’t get their dates right, can you trust the peer review of their paper (was it peer reviewed?)

 

c) “The poxviruses” : they are talking about the family of 60+ viruses (including smallpox, cowpox, and orf), of which smallpox is just one.

OK then, to clarify : minor attributes of smallpox would mutate (the reason that countries interested in biowarfare would try to gain samples of the most virulent). The vaccine target was stable, giving one strain to target, no mutations in vaccine target. None. Zero.

 

I agree that the lockdowns in China aren’t guaranteed to work. Absolutely better than no lockdown, but the genie may already be out of the bottle.

[BazzaS]

Wrong (again!)

 

it isn’t a 14 day incubation period.

it is less but no-one yet knows for sure.

 

(I’ll explain more when have more time, but if A appears to infect C is this A -> C or A-> B -> C)

 

So the UK’s case definition to qualify for investigation  is:

a) appropriate symptoms with

b) Exposure to Wuhan (expect this to be expanded geographically) or to a confirmed case (outside of Wuhan), within the previous 14 days

 

That isn’t the same as “incubation period is 14 days “

 

[BazzaS]

If they felt the incubation period was 14 days, the case definition period would be longer, to account for natural variability

[BazzaS]

Eradication date ‘arbitrary’.

Ahh well, if you know better than WHO, little chance I’ll have to persuade you!

[BazzaS]

Why 2 dates? Read my post

One “last naturally occurring case”

One date WHO declared eradication

2 different dates for 2 different events!

 

Janet Parker wasn’t infected by a “mutated smallpox”. There was an accidental release of a lab stock being held for research. As a result lab stocks have been destroyed (except for 2 high security labs, and even now debate continues : destroy those or keep them?)

[BazzaS]

2 hours ago, tobyjugg2 said:

So which is it Bazzas?

* The date that the last sample will be destroyed (Three labs still reportedly keep samples)?

* Whenever all even close variants are eradicated?

 

Arbitrarily chose one as an 'eradication' date

 

remind me, which 3 labs?

 

(it is 2, “Vektor” in what was the Soviet Union, and CDC in the USA. Both under BSL-4 conditions)

 

which is the 3rd you know of, and should you be letting WHO know?

 

Which “close variants”? Orf and cowpox don’t need destroying ; they don’t cause variola major.

Edited January 24, 2020 by BazzaS

[BazzaS]

That Time page says:

“The bioweapons facility, located in Koltosvo, in the Novosibirsk region of Siberia, is known for being one of two centers in the world housing samples of smallpox”

That is Vector/Vektor, which I mentioned.

 

So, which is the 3rd?

if it is so easy to find : go ahead, and show me up.

Monkeypox: no point in destroying lab stocks, as it is still out in the wild.

[BazzaS]

1 hour ago, tobyjugg2 said:

 

You're doing all right yourself.

Show us your source for the false claim that smallpox virus/virus generally - don't mutate ... if you aren't the source

 

 

I’ve clarified above: the smallpox vaccine target didn’t mutate. That is what was key to the eradication (along with what I said before : no carrier state, massive international effort)

 

My proof : that there was one single vaccine, and it worked.

 

I’ve never said “viruses don’t mutate”.

I’ve highlighted flu A’s “shift” and “drift”

I can talk about which circulating strains are at higher risk of Oseltamivir resistance if you like.

 

If you are concerned I don’t know what I’m talking about : search my previous ‘flu posts, and where I highlighted the likely change in UK vaccination recommendations...... which were confirmed 3 months later........

Edited January 24, 2020 by BazzaS

[BazzaS]

1 hour ago, tobyjugg2 said:

Oh and here's the official advice

 

" Individuals should seek medical attention if they develop respiratory symptoms within 14 days of visiting Wuhan, either in China or on their return to the UK.

 

https://publichealthmatters.blog.gov.uk/2020/01/23/wuhan-novel-coronavirus-what-you-need-to-know/

See above. That is the “case definition for testing”. It means that the incubation period is less than 14 days, but for abundance of caution they use 14 days, to rule out who shouldn’t be tested (for “don’t even bother testing if more than 14 days”)

 

The problem seems to be that you don’t understand the difference between the screening algorithm and the actual incubation period.

my sources: previous sources replaced by a new update today.

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/news--wuhan-coronavirus/

 

The bit where they say “This estimate is based on the following assumptions“

(So, it is all still assumption. Expert’s “best guess”, but even the experts aren’t sure yet, as I’ve previously highlighted!)

 

“There is a mean 10-day delay between infection and detection, comprising a 5-6 day incubation period and a 4-5 day delay from symptom onset to detection/hospitalisation of a case”

 

incubation period 5-6 days, not 14. (Incubation period is time from exposure to symptoms)

 

even if you take “time from exposure/ infection, to detection/hospitalisation” (in case you now claim that is what you meant by “incubation period”)

still 10 days mean, with a range of 9-11 days (and they haven’t given us the distribution which will presumably be a normal distribution, nor given us the standard deviation).

 

Not 14 days.

Edited January 24, 2020 by BazzaS

[BazzaS]

2 hours ago, tobyjugg2 said:

What you seem to be missing is that the smallpox virus was cleared as a result of a worldwide program of vaccination which didn't give its slower rate of mutation chance to mutate and gain a fresh foothold. They of course used the variola vaccination program which replaced the

Claiming that it DOESN'T mutate is incorrect, foolish and dangerous.

 

 

 

 

 

“They of course used the variola vaccination program which replaced the

Claiming that....”

 

looks like you are missing some text there after “replaced the” !

 

As for “slower rate of mutation a chance to mutate” : smallpox is believed to have been around since 3rd Century BC, and maybe even 7 centuries before that. Apologies : I don’t have formal evidence for 10th Century BC (why I’m saying “maybe”). Good quality peer reviewed studies for 22 centuries (plus) ago are rare

 

There is no reason to believe that dairymaids (back then) who had had cowpox didn’t develop the immunity Jenner later characterised : so there would have been some selective pressure for smallpox to mutate its vaccine target even then.

Variolation was used in the Far East (1549) even before it started to be used in the West in the 1720’s : that is some 428 years of further increased selective pressure to mutate the vaccine target, (250 years if you want to say “both East & West”)

 

Jenner started using vaccinia around 1796, but only published his paper on cowpox / vaccinia (from which the term vaccination is derived) in 1798. At least 179 years of even greater selective pressure yet still no mutation of the vaccine target.....

 

“Ahh, but those aren’t modern vaccines!” I hear you cry.... Well there was gradual improvement in the vaccines but there was a major step (freeze dried, heat-stable vaccine) in the 1950’s (25 years of yet further increased selective pressure)

 

So, with 22 centuries in which to mutate the vaccine target, 300 million deaths in the 20th century, and 15 million cases a year as late as 1967. Not a shred of evidence that there was a single mutation of the vaccine target...... that isn’t “slow”.

that is zero.

 

 

 

[BazzaS]

2 hours ago, tobyjugg2 said:

 

 

and as I said - the 14 days is the outside of the possible period. ie 14 days too late.

 

 

.Maalin was a hospital cook in Merca, Somalia. On October 12, 1977, he accompanied two smallpox patients in a vehicle from the hospital to the local smallpox office. On October 22, he developed a fever.

 

https://www.who.int/csr/disease/smallpox/vaccines/en/

“and as I said - the 14 days is the outside of the possible period. ie 14 days too late.”

 

 

I fear you have confused yourself again. You were claiming a 14 day incubation period for 2019-nCoV, and now you bring up 14 days in a nonsensical statement (14 days too late for what?) while talking about smallpox .....

 

incubation period for smallpox is 7-17 days, BTW, so that spans 14 days, but isn’t “14 days”

 

October 10th (exposure)  to October 22nd (first symptoms). Even the case you cite was 12 days incubation, not 14 !

 

Great work cut n pasting the WHO info page: not only does it show the 10 day incubation period of the last naturally occurring case of smallpox, but nothing in there is in contradiction to my posts .... confirming I’m correct.

Edited January 24, 2020 by BazzaS

[BazzaS]

As for:

1.

“Smallpox is just one thing,“ I don’t know what you mean by “just one thing” (especially when you are trying to put words in my mouth / create a “straw man”) - so it’s hard to answer.

If you mean “one vaccine target not mutating over many centuries“ - yes.
 

“we have a 'cure'” : I never said we have a cure, yet another attempt to put words in my mouth.

As for “treatment” rather than “cure” : Work on Cidofovir and its analogue brinCidofovir started, though they never got FDA approval.

Tecovirimat: FDA approved.

 

“and its gone forever (apart from 2 declared labs (and maybe one alleged other lab at most))“

 

Never said that either. Official stocks are held in 2 labs (hey! You haven’t named the 3rd lab you said held stocks, and now your position has changed to “(and maybe one alleged other lab at most))“ - strange that!

 

A single case of smallpox anywhere in the world would be a global health  There might be stocks not found / not destroyed (though I’d hope not!)

There might be “rogue actors”

There might be “rogue nations”

exhumed victims are a concern.

None if that is in contradiction to what I’ve posted .....

 

”Even if it isn't gone forever, we have the cure for the one virus which doesn't change/mutate”

more trying to get me to say that which I haven’t said. We have treatments, we have vaccine.

There are experts to rapidly identify any case, and (no doubt!) plans to isolate cases and contacts and ring-fence vaccinate. Some people can’t be vaccinated. There isn’t (currently!) enough vaccine to vaccinate the whole world. There are treatments.

That is what I’m happy to say, but never have I claimed “there is a cure”

 

If smallpox re-emerges, if it isn’t contained rapidly I’d expect a massive death toll, followed by a renewed eradication program, then a period of post-eradication surveillance.....

[BazzaS]

3 hours ago, tobyjugg2 said:

anyway

Cutting through

 

please confirm your stance is:

 

2.

People haven't got Coronavirus if they are clear of symptoms for 6 days?

 

 

Again, you seem resistant to explanation, and unclear in what you are asking.

 

”Coronavirus” you ask. Any Coronavirus? Just 2019-nCoV ??

 

”haven’t got ..... if they are clear of symptoms for 6 days”?

 

You might mean “if they have had 2019n-CoV and have been clear of symptoms : are they still infectious” : your question isn’t clear.

 

If your question actually is “if they were exposed to 2019n-CoV and have been clear of any symptoms by (say, 12 days)

AND they haven’t had a subsequent exposure AND they give an accurate exposure history : will they NOT develop 2019n-CoV” my position is definately. This is “incubation period”, not “case finding definition period”..... see below

 

Do they then use 14 days for case finding / testing: (Case finding relies on symptoms sufficient to require testing and detection) Definately.

10 days for time to symptoms bad enough to come to attention for testing, and detectable levels. Further 4 days for “wiggle room / patients don’t report accurately”

House was a fictional character who said “everybody lies”. Some patients lie (“have you had a temperature ? They won’t let me board that plane if I say yes, so I’ll say no”)

Others don’t deliberately lie, but may not give an accurate travel history (“Which state in China was I in?” “Which day did I leave”

 
Still : 10 days incubation period. Might it be 11 days? Possibly.

12 days. I’m happy until further info comes out.

14 days? Nothing currently to suggest that is even close.

Edited January 24, 2020 by BazzaS

[BazzaS]

22 minutes ago, BazzaS said:

 

 

A single case of smallpox anywhere in the world would be a global health  There might be stocks not found / not destroyed (though I’d hope not!)

 

“Would be a global health  There”

should read “would be a global health emergency. There”

[BazzaS]

I’ve tried (patiently and repeatedly) answering your questions.

 

Your turn:

A) where is the 3rd lab holding smallpox stocks? (the one you said was easily findable)

B) what is the incubation period of 2019-nCoV (and I mean the generally accepted definition of incubation period, time from exposure to development of first sign / symptom) any current peer reviewed analysis will suffice

C) When would smallpox have mutated its vaccine target if it hadn’t have been eradicated (any high quality statistical analysis will do!)

Edited January 24, 2020 by BazzaS

[BazzaS]

20 hours ago, BazzaS said:

Further 4 days for “wiggle room / patients don’t report accurately”

House was a fictional character who said “everybody lies”. Some patients lie (“have you had a temperature ? They won’t let me board that plane if I say yes, so I’ll say no”)

Others don’t deliberately lie, but may not give an accurate travel history (“Which state in China was I in?” “Which day did I leave”

 

https://www.telegraph.co.uk/news/2020/01/24/ire-chinese-woman-cheated-coronavirus-checks-fly-france-michelin/

wow! It is almost like I predicted such......

 

[BazzaS]

My point, HB, is that I predicted that “people lie, so the case finding definition factors this (and other human factors) in”.

 

”Case finding definition” (14 days) should always be longer than both “currently known incubation period” (5-6 days), and “current predicted time to detection” (10 days), so:

 

saying that the “case finding 14 days” means that the incubation period must be 14 days is wrong.

 

To do so, and to keep doing so even after explanation of the difference shows a lack of understanding. 

That flyer, she was indeed very selfish, but that is human behaviour for you. You can’t stop such (people lying during screening) any more than you can stop people deliberately trying to game the system (taking anti-pyretics before flight boarding screening, and prior to destination screening) or innocently and inadvertently  answering screening questions incorrectly (The “what state was I in?” What day did I leave?” that I mentioned above)

 

 

 

 

 

Edited January 25, 2020 by BazzaS

[BazzaS]

“There is the science, and then the art”.

 

The science gives you verifiable facts and figures. The art is applying the science in the real world, taking human factors into account.

 

If I had been in Wuhan, I’d hope I’d apply the principles of Bentham utilitarianism, taking all measures I could to protect myself but without risking others (so, no lying to evade movement controls). Yet, until actually placed in that situation: would I?

I don’t know what I’d actually do until I’m in the situation.

 

What then if (early on in the Wuhan outbreak, before the travel embargo) I am already booked on a pre-planned flight out?

Do I cancel it? Not if I don't have a temperature....

 

What if I have a temperature? I should ‘not travel’, but what would you (or I) actually do?

Public opinion (looking at the case of the ‘Michelin traveller’) says to travel would be selfish.

 

What if I had a temperature, but my flight (booked before the outbreak) was to visit a terminally ill relative, who had only a very short time remaining?. Things are rarely cut and dried.

 

What would you (anyone, not just me and HB) do? Do you believe that what you think you’d do (when considering the issues) is going to always be the same as what you do when actually in that situation?

 

Human factors.

Eyam plague: The village of the damned http://www.bbc.co.uk/news/uk-england-35064071

 

Would people do the same, today?

Edited January 25, 2020 by BazzaS

[BazzaS]

On 23/01/2020 at 22:53, BazzaS said:

Wuhan is certainly seeing cases in people who haven’t visited the “wet market” where the initial cases had been (and where it is suggested the virus first ‘jumped’ from animals - now felt likely snakes -to humans).
.

it is now believed the original animal reservoir is bats. 

https://www.nejm.org/doi/full/10.1056/NEJMe2001126?query=recirc_curatedRelated_article

 

Unless there were bats in the market, and with the original suggestions that snakes in the market were the “animal to human” vector, I wouldn’t be surprised if it turns out it was

“bats -> snakes -> humans”.

 

 However “bats -> humans” directly, with an index human case at the market, is also possible, given that human to human transmission has now been confirmed.

[BazzaS]

The key determinant to UB’s scenario is : at what point in relation to when they develop symptoms are those people infectious.

 

Chickenpox, for example, is infectious (by airborne droplet spread) 2 days before the rash appears. So, the patient might feel a “bit unwell / virally ill” without any specific signs, and not have sufficient symptoms / signs to allow action to be taken.

 

There isn’t enough data (yet!) to know when 2019-nCoV becomes infectious.

 

https://www.cdc.gov/coronavirus/2019-ncov/about/transmission.html

 

“Best guess” is when they start having symptoms of coughing and sneezing, at least that will be peak infectivity.
 

If they are soon to become symptomatic, how infectious is a single cough or sneeze? Nobody yet knows.

Edit: hot off the press:

China coronavirus 'spreads before symptoms show' https://www.bbc.co.uk/news/world-asia-china-51254523

 

As for “Do the Government/NHS have sufficient contingency measures in place to deal with any such crisis ?“

 

The Agency leading (at least for England, each of the other 3 nations of the UK has a similar body) is Public Health England. It isn’t part of the NHS per se, (but works with the NHS).

It is “government”, but quasi-autonomous.

 It describes itself as “We are an executive agency of the Department of Health and Social Care, and a distinct organisation with operational autonomy”.

 

PHE has issued guidance, both for primary care and secondary care, for (amongst other things):

a) who gets tested,

b) case management, and

c) infection prevention measures.

 

Whilst more information specific to 2019-nCoV is being learnt, these are pretty much based on what we know from SARS and MERS, but I’d expect them to get “fine-tuned” as we know more.

 

So, there are plans.

 

2 factors spring to mind immediately, though.

 

A) Can the plans be fully implemented? Hospitals are already facing bed pressures.

If demand for resources (such as FFP3 masks) soars: will supplies match demand? (Both for “total number of units available overall, over the total period of demand”, but equally importantly  “supplies deliverable on demand: what would be the equivalent of ‘cashflow’ for a bank“)

 

B) Availability of testing. With a small number of cases meeting the case definition, each can be tested.

If 2019-nCoV becomes widespread, will the availability of testing match demand? What will the turnaround time for testing be?

 

Will testing matter if it becomes widespread?

At the moment, there is widespread availability of testing for Flu and the most common respiratory viruses. This is useful so that they can prioritise the isolation of Flu A patients in hospital, and offer them treatment for FluA, and Mrs Bloggs who looks like they might have flu, but actually has picornavirus on a background of chronic bronchitis doesn’t get isolated and doesn’t get flu treatment once her results are back.

 

Will testing matter as much for 2019-nCoV? Not for treatment (as there is no specific antiviral at the moment). How about for decision on isolation? That’ll depend on how many cases there are (there may not be enough side rooms), and if testing supply can match demand.

 

(not quite “worst case” but “not great case”) scenario is :
A) Hospital wards: not enough side rooms. “Cohort nursing” in bays (or even “cohort wards”), so Mrs Bloggs with her rhinovirus and chronic bronchitis gets put in the bed next door to Mrs Bull who has 2019-nCoV (or, even: next door to Mr Bull, if things get bad enough the ‘same sex’ rules get suspended).

B) Split Emergency Departments. Non “?flu, ?2019-nCoV” go to one side, those with compatible respiratory symptoms go to another waiting area. All the respiratory symptom patients lumped in, waiting, together.

I’d expect once people realised where they would be waiting they would only go if they really had no other choice ......

On the plus side, much was learnt from the SARS outbreak, so they are better informed than when they first faced SARS

Edited January 26, 2020 by BazzaS

[BazzaS]

I wouldn’t want to live under a repressive government that had a centrally controlled economy and actively suppressed dissent.

Yet such an economy could bring massive resources (financial and manpower) into play.

 

Coronavirus: How can China build a hospital so quickly? https://www.bbc.co.uk/news/world-asia-china-51245156

 

It isn’t just that it is being built so quickly, but also that it is being built with infection control in mind, and means other healthcare facilities can transfer suspected cases there, retaining their capacity to treat non-respiratory illness patients.

Edited January 26, 2020 by BazzaS

[BazzaS]

Citing random resources without stating how they support your argument is easy to do, but doesn’t demonstrate understanding.

 

you still haven’t answered my three questions.

 

you still are resistant to understanding the difference between “incubation period” and “period used for case finding”, which is probably why you aren’t answering that question.

 

You are still resistant to addressing that the smallpox vaccine target didn’t mutate across centuries... which is probably why you aren’t answering that question.

 

The third question was “which is the 3rd lab that holds stocks of smallpox virus? (which you even claimed was “easily found”) ... if it is so easy, why not let us know?