Genomic epidemiology of novel coronavirus (HCoV-19)

[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.

[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.

[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.

[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...

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.

[emiliobumachar]

The common cold definitely destroys vast amounts of wealth day after day, we just don't see a dip because it's regular and predictable, that is, already priced in stock prices.

As to the question, yes, that can well happen.

Note that we could also argue that the common cold virus has domesticated us. We're its cattle.

[rolph]

i wish i could say yes, but i cant.

in the short term, if a virus can replicate itself and pass on to another host , that will in turn transmit the virus,,, that means a success.

if debilitating symptoms occur after transmission occurs then those symptoms dont influence selection, this is what happens with asymptomatic incubation and infectious states.

this type of virus uses RNA to carry its code, and a property of RNA is that it is much more error prone than DNA so accidental variations in the code occur quite frequently. A lot of these variants fizzle out but some of them will chance across an advantageous change in the code.

so we see a virus that passes through populations and shifts its codeing by being error prone. this can result in dynamic swings between dominance of strains over time, and lead to innovations such as high communicability, or asymptomatic transmission.

[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.

[DyslexicAtheist]

seems the Iranian government can't be trusted with the information they put out there in any circumstance:

https://twitter.com/aliostad/status/1233668766124400640

https://news.ycombinator.com/item?id=22457840

[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...

[united893]

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

[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