2019-nCoV / Corona virus Pt 2

[The Atheist]

Going back to the two types of disease, that all makes perfect sense, and I raised the possibility way back in the very early pages of the thread.

The theory was that viruses are more likely to mutate into less-deadly forms, because people who aren't too sick are more likely to spread it than those desperately ill.

It looks to me like most of the evidence points to that having happened, and the milder version is the one spreading fastest around the world. CNN shows this report: https://www.cnbc.com/2020/03/04/coronavirus-chinese-scientists-identify-two-types-covid-19.html

If it's all correct, China should be given a huge thanks from all of the rest of the world, because if the more dangerous one circulated at the fatality rate shown up Hubei/Wuhan, we'd be looking at 100 million deaths, and the evidence is building strongly that it's going to end up somewhere between 1/5 & 1/10th the 3.4% rate in Wuhan.

 

[theprestige]

OK. If a "long time" turns out to be a couple weeks or a month I'd agree that's within current evidence.

We already know:
a) China reported the first official cases in mid-January
b) The virus has likely been around since at least early November.
That's two months right there, according to the current evidence.

Bad use of parentheses if he meant what you are claiming. He can clarify how many of those offices he expects to detect the virus. As written he implies he's expecting his clinic/office/whatever would be detecting it.

I think you're looking for objections where none reasonably exist.

Why do you object to the idea that it may have been spreading for longer than we know, and may have spread farther than we think? Given that it was out there for about two months before the Chinese government even announced it?

 

[RecoveringYuppy]

We already know:
a) China reported the first official cases in mid-January
b) The virus has likely been around since at least early November.
That's two months right there, according to the current evidence.

Right. Those are the dates supported by evidence.

Why do you object to the idea that it may have been spreading for longer than we know, and may have spread farther than we think? Given that it was out there for about two months before the Chinese government even announced it?

First, simply because it's wrong. Second, being wrong this way is being used to say this disease is possibly less dangerous than we can reasonably know. The suggestion is that we've been living with this disease without knowing about it for a "long time".

Read the link I cited. We have good reason to believe the first human infection was November, October at the earliest. We even have evidence regarding when the virus came in to existence in an animal reservoir.

 

[dudalb]

The Governor just declared a state of emergency in California. It is starting to hit the fan.

 

[Trebuchet]

In Washington State, the apparent death rate is about 25%, with 11 dead out of 45 diagnosed cases. That's an anomaly, of course, because of the nursing home and lack of availability of testing, but still scary.

 

[Planigale]

Going back to the two types of disease, that all makes perfect sense, and I raised the possibility way back in the very early pages of the thread.

The theory was that viruses are more likely to mutate into less-deadly forms, because people who aren't too sick are more likely to spread it than those desperately ill.

It looks to me like most of the evidence points to that having happened, and the milder version is the one spreading fastest around the world. CNN shows this report: https://www.cnbc.com/2020/03/04/coronavirus-chinese-scientists-identify-two-types-covid-19.html

If it's all correct, China should be given a huge thanks from all of the rest of the world, because if the more dangerous one circulated at the fatality rate shown up Hubei/Wuhan, we'd be looking at 100 million deaths, and the evidence is building strongly that it's going to end up somewhere between 1/5 & 1/10th the 3.4% rate in Wuhan.

Apart from the fact you have that the wrong way round. The milder form (allegedly) is the 'original' form the more deadly form is what it has mutated into.
https://www.telegraph.co.uk/science...as-mutated-aggressive-disease-say-scientists/
Which is what the modelling I referenced earlier predicted; a novel emerging virus is most likely to mutate into a more virulent form. Since this was based on only 103 cases there is considerable doubt about the reliability of the data.
https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463

To depress you the UK is moving to a view that 1:8 infected will have clinically significant illness (ie requiring hospital care) previously the view was only 1:20 would require hospital care; and 25% of those will require high level care (previously only 10%). So if a variant is circulating in Europe the UK thinks it is the more virulent form. As previously posted WHO are officially going for a 3% mortality.

 

[xjx388]

OK. If a "long time" turns out to be a couple weeks or a month I'd agree that's within current evidence.

Could be that or even 2-3 months before China clamped down. I'm not suggesting that it's been here for years.

A person in China contracts it in October, spreads it a bit locally. Some of those people travel and spread it elsewhere. Extend that out for a month or two before we ever heard of coronavirus. I'm suggesting that it's very possible that this thing was out of the gate long before they tried to shut it.

Bad use of parentheses if he meant what you are claiming. He can clarify how many of those offices he expects to detect the virus. As written he implies he's expecting his clinic/office/whatever would be detecting it.

If it had indeed been spreading for a month or two before China reported it in January, then I don't see how it wouldn't pretty much be everywhere by now. Look at the spread since January. Look at the cases popping up with no suspicious contact. Look at the cases presenting with only mild illness. We (in the US, anyway) aren't testing everyone with normal cold symptoms, only the cases with suspicious contact.

Indeed, in Washington they are discovering that it had been circulating for at least several weeks before the first cases had been identified:

Researchers who have examined the genomes of two coronavirus infections in Washington State say the similarities between the cases suggest that the virus may have been spreading in the state for weeks.

Washington had the United States’ first confirmed case of coronavirus, announced by the Centers for Disease Control and Prevention on Jan. 20. Based on an analysis of the virus’s genetic sequence, another case that surfaced in the state and was announced on Friday probably was descended from that first case.

The two people live in the same county, but are not known to have had contact with one another, and the second case occurred well after the first would no longer be expected to be contagious. So the genetic findings suggest that the virus has been spreading through other people in the community for close to six weeks, according to one of the scientists who compared the sequences, Trevor Bedford, an associate professor at the Fred Hutchinson Cancer Research Center and the University of Washington.

Yes indeedilee-do, if it were possible for me to test every URI that walked in my office today, I would say it's likely that at least one would test positive for the new bug. If I could bet at 1:5 odds on that possibility, I would do it. I don't know that I would if the odds were 1:10, if that gives any indication as to how sure I am (not completely, but somewhat).

 

[The Atheist]

Apart from the fact you have that the wrong way round.

Ok, the age might be the wrong way around, but the strains aren't.

The article states:

The more aggressive type of virus was found to be prevalent in the early stages of the outbreak in Wuhan — the Chinese city where COVID-19 was first detected late last year.

But the frequency of this type of virus has since decreased from early January.

It wouldn't be unheard of for the Torygraph to be wrong, and I note their link leads to the actual research page, which states:

Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

The less-deadly form is circulating.

The fact that community-spread infections are arising everywhere supports the idea the less-aggressive version is the main driver, because we're not seeing the severe cases until much later in the outbreak. The data from both Diamond Princess and South Korea also supports a less-deadly form of the disease. even USA's six weeks of undiscovered spread supports it.

All the rest of China is clearly getting the milder version, so I reiterate that China may have taken a bullet for the rest of the world by locking down Hubei.

 

[xjx388]

Right. Those are the dates supported by evidence.

Good. Then we agree that it could have left China in November?

First, simply because it's wrong.

I don't see how you can say that with any confidence.

Second, being wrong this way is being used to say this disease is possibly less dangerous than we can reasonably know. The suggestion is that we've been living with this disease without knowing about it for a "long time".

Sure, if a "long time" is 2-3 months, which I would argue is a long time considering how easily it has spread. If there are around 100 confirmed cases in the US right now with 10 deaths . . . what if there are actually 500 cases or more in the wild that no one can currently detect? That might indicate that perhaps the bug isn't as deadly as it appears with those confirmed numbers.

Read the link I cited. We have good reason to believe the first human infection was November, October at the earliest. We even have evidence regarding when the virus came in to existence in an animal reservoir.

Right. So how can you say the evidence doesn't support it being spread further than we currently can measure?

 

[Skeptic Ginger]

I did read your wikipedia link. I even used the citiations to go deeper. For example:

https://www.sciencemag.org/news/202...-not-be-source-novel-virus-spreading-globally

So there is currently no certainty at all regarding exactly when the first infections occurred. It could have been October; it would be impossible to know for sure, especially if for a lot of (most?) people the symptoms are no different to the common cold.

If that's true, then there should be no question about the good possibility that this thing was out in the wild before the "first cases" were reported in China, January 11.

Now, if you have something specific that indicates what I'm saying is way off, I welcome it.

As early as Oct is nothing close to what you said about circulating for a long time and there's no evidence from that of any widespread circulation.

Rather it is just what I said, they believe it began somewhere before it spread from the animal market. And we know it wasn't widespread from the genome epidemiology.

 

[Skeptic Ginger]

Here is the original post from xjx388 that I am disputing.


Nothing supports the idea that this virus has been in the population for a long time or that every doctor's office would be detecting this now if they tested for it.

This ^

 

[theprestige]

As early as Oct is nothing close to what you said about circulating for a long time and there's no evidence from that of any widespread circulation.

Three and a half months seems like a pretty long time.

If it started in October, and didn't get detected by Chinese authorities until January, and attempts to mitigate the spread didn't start until around that time, then how could there not be widespread circulation by now?

As I understand it, there isn't even widespread testing yet, to rule out widespread circulation.

 

[RecoveringYuppy]

OK. So at least you aren't suggesting the virus was spreading before it existed.

If it had indeed been spreading for a month or two before China reported it in January, then I don't see how it wouldn't pretty much be everywhere by now. Look at the spread since January.

This is simply not supported by the data. Your opinion is simply not convincing.

 

[novaphile]

Meanwhile, back in Oz, our count is now at 61.

State by state

• NSW 25 cases
• QLD 13 cases
• Victoria 10 cases
• SA 8 cases
• WA 3 cases
• TAS, NT 1 case each

Source

A woman and her eight-month-old baby are being treated in South Australia, where they are the state's seventh and eighth cases.

 

[xjx388]

As early as Oct is nothing close to what you said about circulating for a long time and there's no evidence from that of any widespread circulation.

Rather it is just what I said, they believe it began somewhere before it spread from the animal market. And we know it wasn't widespread from the genome epidemiology.

“A long time,” for a virus like this could be 2-3 months.

It was in Washington State more or less six weeks, based on the genome epidemiology, before the first cases were identified on January 20th. China didn’t lock down until January 23.

So it was likely already in Washington in late December, a month before we ever heard of it. Why couldn’t it have been elsewhere, looking like the common cold? That’s the part I’m not getting.

 

[theprestige]

OK. So at least you aren't suggesting the virus was spreading before it existed.

Nobody was ever suggesting that.

This is simply not supported by the data. Your opinion is simply not convincing.

If it's been around since October, then it's probably spread a lot further than we realize, and the data won't catch up until we have widespread testing of all flu-like cases.

 

[Planigale]

Ok, the age might be the wrong way around, but the strains aren't.

The article states:



It wouldn't be unheard of for the Torygraph to be wrong, and I note their link leads to the actual research page, which states:



The less-deadly form is circulating.

The fact that community-spread infections are arising everywhere supports the idea the less-aggressive version is the main driver, because we're not seeing the severe cases until much later in the outbreak. The data from both Diamond Princess and South Korea also supports a less-deadly form of the disease. even USA's six weeks of undiscovered spread supports it.

All the rest of China is clearly getting the milder version, so I reiterate that China may have taken a bullet for the rest of the world by locking down Hubei.

The problem with this study is that the 107 isolates they studied are not representative, but opportunistic. The definition of aggressive is based on assumptions about the mutations not clinical outcomes.

To be specific they identified 29 'S' strains and 72 'L' strains.

Hence, although the L type (~70%) was more prevalent than the S type (~30%) in the SARS-CoV-2 viruses we examined, the S type is actually the ancestral version of SARS-CoV-2.

the L type is derived from the S type, L (~70%) is more prevalent than S (~30%) among the sequenced SARS-CoV-2 genomes we examined. This pattern suggests that L has a higher transmission rate than the S type... the L type had accumulated a significantly higher number of derived mutations than S type (P < 0.0001, Wilcoxon rank-sum test; Fig. S5). We propose that, although the L type newly evolved from the ancient S type, it transmits faster or replicates faster in human populations, causing it to accumulate more mutations than the S type. Thus, our results suggest the L might be more aggressive than the S type due to the potentially higher transmission and/or replication rates.

Among the 27 viruses isolated from Wuhan, 26 (96.3%) were L type, and only 1 (3.7%) was S type. However, among the other 73 viruses isolated outside Wuhan, 45 (61.6%) were L type, and 28 (38.4%) were S type. This comparison suggests that the L type is significantly more prevalent in Wuhan than in other places (P = 0.0004, Fisher’s exact test, Fig. 6 and Table S3). All of the 26 samples isolated before January 7, 2020, were from Wuhan, and among the 74 samples collected from January 7, 2020, only one was from Wuhan, 33 were from other places in China, and 40 were from patients outside China. Thus, it is not surprising that the L type was significantly more prevalent before January 7, 2020 (96.2%, 25 L and 1 S) than after January 7, 2020 (62.2%, 46 L and 28 S) (P = 0.0008, Fisher’s exact test, Fig. 6 and Table S3).

If the L type is more aggressive than the S type, why did the relative frequency of the L type decrease compared to the S type in other places after the initial breakout in Wuhan? One possible explanation is that, since January 2020, the Chinese central and local governments have taken rapid and comprehensive prevention and control measures. These human intervention efforts might have caused severe selective pressure against the L type, which might be more aggressive and spread more quickly. The S type, on the other hand, might have experienced weaker selective pressure by human intervention, leading to an increase in its relative abundance among the SARS-CoV-2 viruses. Thus, we hypothesized that the two types of SARS-CoV-2 viruses might have experienced different selective pressures due to different epidemiological features. Of note, the above analyses were based on very patchy SARS-CoV-2 genomes that were collected from different locations and time points.

The dominant circulating strain 2:1 outside of China is still the more 'aggressive' and better transmitting L type. Which unless there are the selective pressures it is hypothesised were present in Wuhan one can expect the L type to become more dominant as it is hypothesised to be more highly transmissible.

ETA it may also be hypothesised that the greater prevalence of the more aggressive L type in Wuhan simply reflects that it is later in the epidemic so the more aggressive strain has come to dominate and the same will be found later elsewhere.

 

[xjx388]

OK. So at least you aren't suggesting the virus was spreading before it existed.

Uh no. I’m suggesting it existed before we knew it existed.

This is simply not supported by the data. Your opinion is simply not convincing.

It was in Washington about six weeks before the first cases there were identified, which means mid to late December. Would you agree that the data supports at least that much?

Assuming so, why couldn’t it have been other places that early or even earlier?

 

[RecoveringYuppy]

Uh no. I’m suggesting it existed before we knew it existed.

OK. But you understand we have good reason to know when it first existed now, right?

 

[xjx388]

OK. But you understand we have good reason to know when it first existed now, right?

Yes, in October-November 2019. I have made it pretty clear this is what I’m working from.