Posted on 03/03/2020 8:29:53 AM PST by ProtectOurFreedom
The field of genomic epidemiology focuses on using the genetic sequences of pathogens to understand patterns of transmission and spread. Viruses mutate very quickly and accumulate changes during the process of transmission from one infected individual to another. The novel coronavirus SARS-CoV-2 which is responsible for the emerging COVID-19 pandemic mutates at an average of about two mutations per month. After someone is exposed they will generally incubate the virus for ~5 days before symptoms develop and transmission occurs. Other research has shown that the "serial interval" of SARS-CoV-2 is ~7 days. You can think of a transmission chain as looking something like:
where, on average, we have 7 days from one infection to the next. As the virus transmits, it will mutate at this rate of two mutations per month. This means, that on average every other step in the transmission chain will have a mutation and so would look something like:
The first case in the USA was called "USA/WA1/2020". This was from a traveller directly returning from Wuhan to Snohomish County on Jan 15, with a swab collected on Jan 19. This virus was rapidly sequenced by the US CDC Division of Viral Diseases and shared publicly on Jan 24 (huge props to the CDC for this):
Our best guess of a scenario looks something like:
(Excerpt) Read more at bedford.io ...
We know that Wuhan went from an index case in ~Nov-Dec 2019 to several thousand cases by mid-Jan 2020, thus going from initial seeding event to widespread local transmission in the span of ~9-10 weeks. We now believe that the Seattle area seeding event was ~Jan 15 and we're now ~7 weeks later. I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia.
We are currently estimating ~600 infections in Seattle, this matches my phylodynamic estimate of the number of infections in Wuhan on Jan 1. Three weeks later, Wuhan had thousands of infections and was put on large-scale lock-down. However, these large-scale non-pharmaceutical interventions to create social distancing had a huge impact on the resulting epidemic. China averted many millions of infections through these intervention measures and cases there have declined substantially.
This is where his article gets odd and seems to go off the rails. He says the severe and harsh steps the Chinese took got their spread under control (which I personally doubt). But then he ignores their seeming success using draconian public health methods (possible in a communist country) and goes on to say we can control this with the easy steps of frequent hand washing, avoiding crowds, cough into your sleeve, don't touch your face, disinfect surfaces, etc.
It seems like the author is assuming facts not in evidence.
Pinging the original FReepers who posted links to this. Thanks for making this available via links in other threads!
This us stilled inferred.
If true (certainly possible, it’s a logical inference) it shows how benign the virus is.
There’s nothing cryptic about epidemics.
“I expect Seattle now to look like Wuhan around ~1 Jan, when they were reporting the first clusters of patients with unexplained viral pneumonia.”
This may be the stupidest statement here since back in January when the one guy said there’d be 100 million cases by March 1st.
I’m not so sure; the jury is still out.
China —
Cons: very poor public hygiene. No culture of hand-washing. Public defecation. Open wildlife game markets with butchering in stalls. Lots of air pollution. Lots of male smokers. Government covering up the epidemic and providing bad data or maybe intentional misinformation.
Pros (in a way): draconian measures to quarantine people (unfortunately, after the horse left the barn).
US —
Cons: cannot lock down an entire city, metro area, or state like the Chinese can
Pros: excellent public hygiene, better culture of hygiene, better health care, more open data and sharing of data
Which will win?
“China —
Cons: very poor public hygiene. No culture of hand-washing. Public defecation. Open wildlife game markets with butchering in stalls. Lots of air pollution. Lots of male smokers. Government covering up the epidemic and providing bad data or maybe intentional misinformation.
Pros (in a way): draconian measures to quarantine people (unfortunately, after the horse left the barn).”
Yes. And note that in the second most infected province the death rate is about ten-fold less than in Hubei. This is in Guangdong, the most advanced and modern region in the PRC.
Many thanks for posting this info!!
Ping!
Interesting article.
Thanks for posting.
We do not have good public hygiene on the West Coast! San Francisco is downright awful. When I was there a few months ago, I saw people shooting up on the streets. I’ve heard the homeless situation in Seattle is as bad as San Francisco. What happens when it gets into those groups?
I’m in the process of getting my house up for sale in San Jose. Unfortunately, I don’t think it will be quick enough.
The later of course!
Thanks for the info about Guangdong. I hadn’t thought about that. I’m surprised at how concentrated the cases are in Hubei and how they rapidly diminish in adjacent provinces.
We are up the road from you near Mountain View. I worry that house prices are going to start dropping like a rock very soon now. We are wondering if we should put ours up for sale, too.
Of course, one theory is that there are many more Chinese wanting to get their money OUT of China right now and they like to invest in property in the US.
Houses are still spending only a few days or a week or two on the market...so far.
The tell will be how it moves through the homeless camps in Seattle. Loony, non-hygienic, mobile people sound like the ideal core of infection.
I have one question: I was in the Seattle Pike Place Market over the weekend. Should I self quarantine for 9 to 10 weeks?
Are you asking in jest? Or in all seriousness? Do you live nearby? Or were you visiting Seattle from a another Puget Sound town? Or from another state? That's a tough call.
Lastly, would you like me to come by and weld your door shut from the outside? Or do you have a wood door and should I bring a hammer and nails. We don't want to lose any good FReepers, so I'd be happy to build a slot into your wall where we can shove in plates of food.
“Thanks for the info about Guangdong. I hadn’t thought about that. I’m surprised at how concentrated the cases are in Hubei and how they rapidly diminish in adjacent provinces.”
Yes.
It’s incredibly concentrated there.
I don’t buy in to conspiracy theories.
In this case I am beginning to think this was due to an accidental release or contamination from the Wuhan virus lab.
Not a bio weapon, just a strain they’d collected that somehow contaminated the city. I can think of a number of scenarios. Scenarios more likely to happen in China such as a janitor in a hurry not following protocol and not incinerating waste because he’s in a hurry, and tossing it out on the side of the road because he wanted to leave early.
This is why it is and has been so focused in that area.
I don’t know, but this seems supported by data.
“The tell will be how it moves through the homeless camps in Seattle. Loony, non-hygienic, mobile people sound like the ideal core of infection.”
Almost literally a Petrie dish.
Of course if it happens it will be Trump’s fault.
Fascinating information, thanks for posting.
There’s the culture of unscrupulous people selling used lab animals for meat, too. One guy went to jail for 12 years in Beijing for selling government property (used animals).
Plus, the Chinese have been criticized for a long time for lax security and safeguards at their BSL-4 facility.
My question was a bit hyperbolic, but I think most people would like to know if they are in a hotspot for a short period and then travel back home across the country, could they be a carrier? I guess only time will let us know where the guardrails are.
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