
Genomic epidemiology of novel coronavirus (HCoV-19) - 2a0c40
https://nextstrain.org/ncov
======
julienchastang
Has anyone tried to play the "movie" in the map. As I understand it, there has
already been back-propagation of the virus from North America back to Asia.
Can anyone confirm this is actually the case?

Edit: On a separate note, this tool is one of the best "web meets science"
websites I've ever seen. Really nice work for those involved in its creation.

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mmmrtl
That backprop is most likely an artifact of a sample on a lineage being
sequenced in North America, but the lineage also continues in Asia, where that
lineage had not been sequenced yet. As in, someone in Asia spread COVID-19 to
two people, one of whom traveled to North American and had their virus
sequenced. The lineage also continued in Asia and was eventually sequenced
days/weeks later, so the inferred tree includes a North American sample
seeming to give rise to more Asian infections.

~~~
borkt
My father in law is a pilot (currently not showing any systems virus) has been
back and forth between China, Korea, HK (Guangzou most recently) at least 3
times since January. His last trip he was one of only 30 people in the hotel,
being monitored every 30 minutes or so for fever while on a layover. His
company is still scheduling him trips there, so I have no doubt with companies
still requiring similar travel that it could have easily gotten back to China
from someone who has been in the US over the past few months, now that we know
it has been in the wild here for at LEAST 6 weeks.

~~~
wahern
mmmrtl's explanation seems more parsimonious.

~~~
RL_Quine
That’s a really good word.

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kire2345
So am I reading this correctly that for example the strain in Lombardy
Italy/CDG1/2020 (GISAID EPI ISL 412973) from 20.02.2020, has its origin in the
strain collected in Bavaria Germany/BavPat1/2020 (GISAID EPI ISL 406862) from
28.01.2020.

So the outbreak in Bavaria that was thought be contained somehow made its way
to Italy? Or do these kind of interpretations not make any sense?

~~~
cstejerean
That seems like the right interpretation. The second case in Washington State
appears to be a descendant of the first case on January 19, so we’ve also had
about 6 weeks of undetected spread here from a case that was believed to be
contained. It goes to show that “contained” doesn’t mean much when you only
test people with symptoms but you know that the virus can spread
asymptomatically.

Early on the official guidance was that asymptomatic spread while possible is
not playing a major role in global transmissions. Now we’re seeing the results
of that position.

~~~
consp
Or people having just a mild variant which does not cause fever and airway
problems. If they think it is something else, or don't care, it is just as
well a transfer risk as asymptomatic individuals and in my opinion at least as
likely.

~~~
core-questions
Well, what are you supposed to do?

If you have the snuffles, are you supposed to react like it's COVID, or react
like it's just one of the million other colds and such going around every
winter until things get bad enough that your symptoms concern you?

If you react like it's COVID, then what - go to a hospital or otherwise burden
the health system? All they can tell you is to quarantine yourself,
unless/until it gets bad enough that it's worth testing you.

~~~
shados
> If you have the snuffles

If you just have the sniffles you probably shouldn't panic and go to the ER,
but you should stay the hell away from big conventions and not go to work, at
least within reason.

I work for a company that has unmetered sick leave (that you can take without
people judging you), great VPN/work from home policy, and will actively shun
people who come to work sick (that is, no one is even remotely close to being
pressured to come for butt in seat time).

And people still come to work sniffling and coughing. I keep having to kick
them back home day after day. Like, wtf, seriously.

~~~
core-questions
I agree 100% for myself - I always self quarantine and work remote when I have
a cold. However, you gotta remember that the vast majority of people still
need to be physically present and can't work remote; and most of them have far
more limited sick leave policies, sometimes including only partial pay, etc.

~~~
shados
For sure. I did add clarification that even some people with very generous
sick leave policies and who can work from home still go to the office for no
good reason.

Actually, as I'm typing this Im hearing someone coughing and sneezing a few
rows from me, and yet again Ill have to talk to them and maybe even their
manager, because here we're super privileged and there's exactly zero reason
to come in sick.

I agree not everyone has that privilege, but if those who DO actually
exercised it, it would at least have SOME impact on the spread.

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jmartrican
Could it be the case that the least symptomatic variants of the virus will be
the winning ones in the long run? I suspect that variants that do the most
damage will be the ones quarantined and the ones that do least amount of harm
(least symptoms) will spread faster.

If so, will this virus just domesticate itself (or rather domesticated by
humans filtering out those more deadly versions)? By domesticate I mean that
it lives with us just like the common cold without causing a 10% dip in the
stock market.

~~~
Symmetry
That's normal. Diseases act as parasites on their hosts and its not in the
best interest of a parasite to kill its host, or at least not quickly. That's
what tends to make zoonotic diseases so dangerous, they've calibrated
themselves to exist in an equilibrium with a host animal population but when
they transfer to humans that balance is out of whack and they either are
immediately wiped out by the immune system or they tend to overdo it and kill
the host. COVID-19 seems to have "gotten lucky" in that it found itself with,
from its perspective, a thankfully low lethality allowing it to spread widely.

This can apply to bacteria even more than viruses, see
[https://aeon.co/essays/when-bacteria-kill-us-it-s-more-
accid...](https://aeon.co/essays/when-bacteria-kill-us-it-s-more-accident-
than-assassination)

EDIT: I should say, though, that you shouldn't expect that to happen
_quickly_. The selective pressure for COVID-19 to become less lethal is far
less than it was for, say, MERS.

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redcalx
Iran is ominously missing any cases according to this data. I guess you could
say Iran is a known unknown.

~~~
throwanem
Iran isn't represented in this dataset. Neither is Africa or New Zealand. I'm
not sure what's meant to be ominous about any of this.

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rjtavares
We know the virus is widespread in Iran. We don't know if it is widespread in
Africa or New Zealand.

~~~
throwanem
No more so in Africa or in New Zealand [1] than in Finland, which _is_
represented in this dataset. I'm not really seeing the basis for whatever
conspiracy theory the original parent comment seems like it wants to point
toward, is what I'm getting at here.

These are the early stages of what looks to be a pandemic of a disease at
least an order of magnitude, possibly several orders of magnitude [2], more
lethal than seasonal flu, which is no picnic already. Isn't that enough to be
worrying about, all on its own?

[1] [https://coronavirus.zone](https://coronavirus.zone)

[2] CDC headline numbers for the 2019-2020 flu season, vs. the commonly given
2% lethality guesstimate.

~~~
nostromo
Estimates are dropping down from 2% as we discover lots of cases that were
mild or asymptomatic.

The New England Journal of Medicine says it may likely be considerably less
than 1%:

[https://www.nejm.org/doi/full/10.1056/NEJMe2002387](https://www.nejm.org/doi/full/10.1056/NEJMe2002387)

People should remember the context of a respiratory disease in China. 2/3rds
of men smoke, and air pollution is common. Things also spread faster there as
it’s densely populated with lower hygiene standards than developed countries
(for example: spitting is still common in some areas).

~~~
jfoster
Suppose you're right about reasons why it spreads fast & lethally in China.
How do you explain the fast spread and lethality outside China?

~~~
Enginerrrd
The two "fast"'s are relative. Epidemic dynamics are likely to differ in
different countries for a bunch of reasons.

And, it does appear to be less lethal outside of China. That may be because
healthcare systems are not yet overwhelmed, or it may be because of the
smoking and pollution exposure in the different demographics. It is probably
even both of those things.

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inciampati
Am I reading the documentation correctly, that you have to register at GISAID
to download the sequences, and that you can't publish any part of the
sequences in subsequent papers? Would it be problematic in any way to just
release them under a CC-BY-SA-NC license?

~~~
bionhoward
you can download a bunch of sequences here (i filtered for lung and
'oronasopharynx'):

[https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType...](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&Isolation_csv=lung&Isolation_csv=oronasopharynx)

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united893
Had no idea that we could trace tiny differences so elaborately, this is
amazing and gives me hope.

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psim1
China always wants to be seen as a global influencer. Now they certainly are,
to their great shame.

~~~
dang
Please do not post nationalistic flamebait, or any flamebait, to Hacker News.

[https://news.ycombinator.com/newsguidelines.html](https://news.ycombinator.com/newsguidelines.html)

