> All the viral genome sequences from affected individuals are very very close to each other. Several are identical and none has more than 5 differences (99.983% similarity). This strongly suggests that transmission into humans came from a single pointed source and happened very recently, between Sep-Dec 2019.
> Given what we are learning from viral genome sequencing above, and given all the emergency measures being put in place in China in particular and around the world in general, there is every reason to believe that the epidemic will be controlled shortly.
I'm not sure what the latter is based on. Up to 5m people may have left Wuhan before the city was locked down.
What's more is that Hong Kong has still not restricted travel, while offering free medical care to anyone. As a HKer, that makes me especially nervous.
Well, they could take a leaf from India and just rename the city? Although, politically motivated in India, it works. Eventually Bombay became Mumbai, Bangalore is Bengaluru, Madras is now Chennai and what was known as Allahabad is now Prayagraj.
Those are the original names of those cities... The British Raj changed the names when they took control, and the residents of those cities wanted to go back to their original names.
If that were true, the people would have renamed them back 70 years ago when India took back control, just as a symbol of regaining control. They didn't.
Failing that, local culture would refer to those cities by those reticent names somewhere. Local newspapers, pamphlets, propaganda material. No evidence of that.
Apparently the effort to reestablish native Indian community names began in 1947 and has been going on for several decades[0], you're not correct about this.
It used to be a joke in the UK that after a nuclear incident 'they' would change the name of the facility so that people wouldn't make the connection. I remember hearing this in the context of the Windscale Fire [0], after which the site was referred to as Sellafield. In fact Sellafield is a multi-function nuclear site [0] of which Windscale was just one facility of many.
Even today, experts aren’t certain where the outbreak originated. Some say China, some say the American Midwest, and others suggest France. But one thing’s for certain—it wasn’t Spain.
“Nobody calls it [the Spanish flu],” says Albert Bosch, president of the Spanish Society for Virology. “It just happened to be the place where it was reported, and that’s it.” Arnold says the Spaniards themselves had different names for the virus—sometimes “the French flu” for their historic rival, sometimes “Naples Soldier” after a popular musical—but it was the name in the Times that would stick.
The singular of species is species, not specie. The only person who gets a pass on that is Vincent Price during his monologue at the beginning of the Alice Cooper song "Black Widow", and that's only because he's Vincent Price.
I'm fairly sure the name "Wuhan coronavirus" is a colloquial name and the proper name is actually 2019-nCoV. It was first found in 2019, and it is a novel (n) Corona Virus (CoV).
There is not yet a proper name for this virus, thus the proliferation of variations on "2019 novel coronavirus". The WHO subcommittee that names things has promised they will choose a name soon, and that it will not include the term "Wuhan".
In addition to naming the virus, there is also the resulting disease to be named. It will be named by the International Classification of Diseases (ICD). The virus will be named by the International Committee on the Taxonomy of Viruses. [1]
Officially, sure, but unofficially people will remember it like that for some time. In Dutch we have "Mexicaanse Griep" (Mexican Flu) which is H1N1: https://nl.wikipedia.org/wiki/Mexicaanse_griep
In English I think it's more commonly referred to as "swine flu" though.
Swine flu did not originate from swine/pigs though. So the term unfairly and unnecessary alienates pigs and pig farmers. This while "bird flu" is accurate.
My erm… favourite example of naming is: "Syphilis had a variety of names, usually people naming it after an enemy or a country they thought responsible for it. The French called it the ‘Neapolitan disease’, the ‘disease of Naples’ or the ‘Spanish disease’, and later grande verole or grosse verole, the ‘ great pox’, the English and Italians called it the ‘French disease’, the ‘Gallic disease’, the ‘morbus Gallicus’, or the ‘French pox’, the Germans called it the ‘French evil’, the Scottish called it the ‘grandgore‘, the Russians called it the ‘Polish disease’, the Polish and the Persians called it the ‘Turkish disease’, the Turkish called it the ‘Christian disease’, the Tahitians called it the ‘British disease’, in India it was called the ‘Portuguese disease’, in Japan it was called the ‘Chinese pox’, and there are some references to it being called the ‘Persian fire’." — https://jmvh.org/article/syphilis-its-early-history-and-trea...
In Polish it's called "franca" which comes from "French disease". I never heard it referred as "Turkish" and there's 0 google results for "turecka choroba"
I find genome sequences fascinating, life's binary code has only 4 opcodes, a, c, g and t. I wonder if any computer VM will ever be able to actually fully run it. Still, the massively parallel capacity needed to run it "realtime" is not quite here just yet.
There's also lots of information at other layers, e.g. epigenetics, that is difficult to capture and adds additional complexity to interpreting a genome, in addition to elaborate post-processing and other aspects of the 'compiler'.
The 'compiler' is also built from DNA. The amount of epigenetics inheritance is subject to debate AFAIK. In the end look at what's being passed on to carry the information through generations. It's (almost) just the DNA !
The genomic machinery is incredible complex and messy. Imagine some code, that is interpreted by little machines not created by that code, that then create other machines, that read that code in a different way, to create other machines, that copy that code, which is then read by other machines, etc, etc. These "machines" are chunks of molecules that require quantum mechanics to fully understand, and also tend to have a lot of issues with them. As an example of the weirdness, look at motor proteins: https://www.youtube.com/watch?v=9RUHJhskW00
It's amazing how utterly mad it all is, and yet not only does it work, our simple models of how it works have actually been helpful even though they were wrong. I mean, it's not like there's actually a single value in your DNA that is looked up by some "eyeball creation" machine when it determines the color of your eyes. Rather, there's a whole slew of genes that, when used as a map to build proteins and then, over a cascade of complex reactions, ends up with an eyeball that is also blue (and, additionally, probably more light sensitive, more tolerant to alcohol, and also more likely to have alcohol use disorder)
Source: work for genomenon.com which is like a search engine for genetic research papers)
(1) If we have a rock, can we expect slowly by small modifications to make it into a hammer?
(2) If we have a horse, can we expect slowly by small modifications to make it into a Model T?
(3) ... a mechanical adding machine into an iPhone?
(4) ... a log cabin into the Empire State Building?
(5) ... a pocket knife into a computer numerically controlled milling machine?
(6) ... any software from the earliest operating system or simplest application into to all the software we have now?
Especially for software, we believe that lots of little modifications will lead to technical debt, need for refactoring, to throwing out and starting over with a clean sheet of paper, to "plan to throw one away because you will anyway". In software, often it seems that there is no reasonable way to get from here to there and, instead, have to start over.
Well, with DNA, on this planet apparently the first version of life
able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA.
So, maybe the point is, DNA is not really life but just a design for a life, not a species but just a design for one. And we do believe that easily enough we could go to an architect and building engineer with standard tools for generating blue prints and doing the engineering for buildings, and they could use the same tools for a log cabin or a floating city.
Okay, but for life there hasn't been any design means, hasn't been any alternatives, other than just DNA.
Moreover, the simplest design tools for life have also been sufficient for the life to understand the design tools, life, the earth, and the universe.
Moreover, we are about the first, one of the first graduating classes of life that understands DNA, life, ..., and the universe: It's been about 14 billion years since the big bang, and our solar system was made about 5 billion years ago from the results of exploding stars that grew and exploded in the first 9 billion years which is not much longer than it took for the first stars to form and explode. So, apparently to get life able to understand the universe had to take about 14 billion years from the big bang and we are among the first instances of such life.
> Well, with DNA, on this planet apparently the first version of life able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA.
Are you sure? I remember that life started as RNA not DNA.
>Moreover we got here by small modifications of the DNA.
That's not true, at least not if you start from the beginning.
There were a lot of "freak events", large scale mutations like whole genome duplication, integration of other organisms e.g. mitochondria, transposons etc...
In no way can this explain any of the complexity of life, but, I found the DNA walk graphs very fascinating to look at anyway. You assign a direction to each letter (a=up, c=down, g=left, t=right) and plot pixels in a sequence.
Gene sequences are easy. Methylation, expression, and protein folding are hard. You can sequence a human genome with a single computer in a day or two; sequencing generates about 30G of data. By contrast, protein folding has its own distributed crowdsourcing project (Folding@Home), with collected computational power of 98.7 petaflops, and it still has barely scratched the surface of our understanding for how specific proteins generate their biological effects.
There isn't a vaccine for either SARS or MERS, in part because they don't happen very often. In the case of SARS, that one outbreak was it so far, while in MERS we've seen a grand total of about 1500 people infected worldwide, although the disease is still circulating.
From the scattered information I have read, the infection has a very long dormant period (2 weeks), during which it may be contagious, and a high R_0 value of at least about 2.0. The R_0 value states how many people will catch the virus from an existing infected person.
These two factors together are scary. I am extremely interested in seeing better data though.
"The mean estimate of R0 for the 2019-nCoV ranges from 3.30 (95%CI: 2.73-3.96) to 5.47 (95%CI: 4.16-7.10), and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks."
But what happens if the virus mutates? Wasn't this the case with the Spanish flu? The first wave, then the mutation from which causes the second wave. Could that potentially occur?
Yes. Although it's important to note that mutation doesn't necessarily imply increased virulence. A blog post from This Week in Virology from a few days ago noted that the SARS epidemic may have actually been blunted due to a mutation it undertook.
68 comments
[ 2.9 ms ] story [ 117 ms ] thread> Given what we are learning from viral genome sequencing above, and given all the emergency measures being put in place in China in particular and around the world in general, there is every reason to believe that the epidemic will be controlled shortly.
What's more is that Hong Kong has still not restricted travel, while offering free medical care to anyone. As a HKer, that makes me especially nervous.
That’s a very different context than a virus originating from a particular area.
Also, in India the colonial reference was the official excuse. In my view, it was purely a show of political power.
Failing that, local culture would refer to those cities by those reticent names somewhere. Local newspapers, pamphlets, propaganda material. No evidence of that.
0: https://en.wikipedia.org/wiki/Renaming_of_cities_in_India
[0] https://en.wikipedia.org/wiki/Windscale_fire
[1] https://en.wikipedia.org/wiki/Sellafield
Even today, experts aren’t certain where the outbreak originated. Some say China, some say the American Midwest, and others suggest France. But one thing’s for certain—it wasn’t Spain.
“Nobody calls it [the Spanish flu],” says Albert Bosch, president of the Spanish Society for Virology. “It just happened to be the place where it was reported, and that’s it.” Arnold says the Spaniards themselves had different names for the virus—sometimes “the French flu” for their historic rival, sometimes “Naples Soldier” after a popular musical—but it was the name in the Times that would stick.
[1] https://www.sciencefriday.com/articles/the-origin-of-the-spa...
https://www.history.com/news/why-was-it-called-the-spanish-f...
It sounds like they have a chicken and egg problem if they're still called "The WHO subcommittee that names things"
https://www.who.int/docs/default-source/coronaviruse/situati...
In English I think it's more commonly referred to as "swine flu" though.
[1] https://en.wikipedia.org/wiki/Middle_East_respiratory_syndro...
There are other 'opcodes' such as the initiation factor, but codons are the main ones.
It's amazing how utterly mad it all is, and yet not only does it work, our simple models of how it works have actually been helpful even though they were wrong. I mean, it's not like there's actually a single value in your DNA that is looked up by some "eyeball creation" machine when it determines the color of your eyes. Rather, there's a whole slew of genes that, when used as a map to build proteins and then, over a cascade of complex reactions, ends up with an eyeball that is also blue (and, additionally, probably more light sensitive, more tolerant to alcohol, and also more likely to have alcohol use disorder)
Source: work for genomenon.com which is like a search engine for genetic research papers)
(1) If we have a rock, can we expect slowly by small modifications to make it into a hammer?
(2) If we have a horse, can we expect slowly by small modifications to make it into a Model T?
(3) ... a mechanical adding machine into an iPhone?
(4) ... a log cabin into the Empire State Building?
(5) ... a pocket knife into a computer numerically controlled milling machine?
(6) ... any software from the earliest operating system or simplest application into to all the software we have now?
Especially for software, we believe that lots of little modifications will lead to technical debt, need for refactoring, to throwing out and starting over with a clean sheet of paper, to "plan to throw one away because you will anyway". In software, often it seems that there is no reasonable way to get from here to there and, instead, have to start over.
Well, with DNA, on this planet apparently the first version of life able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA.
So, maybe the point is, DNA is not really life but just a design for a life, not a species but just a design for one. And we do believe that easily enough we could go to an architect and building engineer with standard tools for generating blue prints and doing the engineering for buildings, and they could use the same tools for a log cabin or a floating city.
Okay, but for life there hasn't been any design means, hasn't been any alternatives, other than just DNA.
Moreover, the simplest design tools for life have also been sufficient for the life to understand the design tools, life, the earth, and the universe.
Moreover, we are about the first, one of the first graduating classes of life that understands DNA, life, ..., and the universe: It's been about 14 billion years since the big bang, and our solar system was made about 5 billion years ago from the results of exploding stars that grew and exploded in the first 9 billion years which is not much longer than it took for the first stars to form and explode. So, apparently to get life able to understand the universe had to take about 14 billion years from the big bang and we are among the first instances of such life.
YMMV, but looks amazing to me!
Hmm ....
Are you sure? I remember that life started as RNA not DNA.
That's not true, at least not if you start from the beginning.
There were a lot of "freak events", large scale mutations like whole genome duplication, integration of other organisms e.g. mitochondria, transposons etc...
For example: https://academic.oup.com/view-large/figure/139941708/bty1021...
There was also a partly functioning interactive at http://www.g-language.org/g3/ (click on DNA walk tab) and zoom in.
These two factors together are scary. I am extremely interested in seeing better data though.
"The mean estimate of R0 for the 2019-nCoV ranges from 3.30 (95%CI: 2.73-3.96) to 5.47 (95%CI: 4.16-7.10), and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks."
https://www.biorxiv.org/content/10.1101/2020.01.23.916395v1
https://www.who.int/news-room/detail/23-01-2020-statement-on...
https://www.academia.edu/41743064/Systemic_Risk_of_Pandemic_...
https://gizmodo.com/deadly-wuhan-virus-in-china-may-have-com...