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Genomic epidemiology of novel coronavirus (HCoV-19)

nextstrain.org

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Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#21

Post by core-questions »

consp wrote: post #17
cstejerean wrote: post #16

Earlier quoted context omitted.

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 guidanc…

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.

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.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#22

Post by Enginerrrd »

jfoster wrote: post #13
nostromo wrote: post #11

Earlier quoted context omitted.

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 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 lowe…

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

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.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#23

Post by icegreentea2 »

rjtavares wrote: post #6
throwanem wrote: post #3

Earlier quoted context omitted.

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.

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

Yes, but this dataset is essentially manually populated. Someone has to isolate coronavirus from a patient, sequence it, and then upload it to GISAID.

So the question is why is it ominous that no one in Iran has isolated and uploaded a sequence?

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#24

Post by icegreentea2 »

cstejerean wrote: post #16
kire2345 wrote: post #15

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?

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 guidanc…

I think it's important to understand that while it's definitely not good that asymptomatic spread is a thing, it's worth considering what the real alternatives where.

For example in the USA, by only testing the highest risk categories, the positive rate is still only ~3%. Increases in the population screened will eventually lead to decreasing the positive rate. In that sense, broadening the criteria by which we do testing will lead to dilution of utility of resources. That's not to say that the choices we made were optimal, but rather to say that scaling our testing to the point where we are catching a significant portion of asymptomatic carriers may not have been the best choice.

Remember that both test consumables and testing capability are not unlimited.

You can model this out at home with different asymptomatic carrier rates and different transmission rates and find the optimal resource allocation for each case.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#25

Post by prox »

core-questions wrote: post #21
consp wrote: post #17

Earlier quoted context omitted.

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.

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 get…

Home quarantine is one of the best things right now, so you don’t infect others. Right now a lot of countries ask you to call your doctor, he will come do a swab.

Another one is risk factor, like any ties with people who are infected or people who came from high risk areas.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#26

Post by 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.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#27

Post by emiliobumachar »

jmartrican wrote: post #26

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 i…

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.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#28

Post by skrtskrt »

icegreentea2 wrote: post #23
rjtavares wrote: post #6

Earlier quoted context omitted.

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

Yes, but this dataset is essentially manually populated. Someone has to isolate coronavirus from a patient, sequence it, and then upload it to GISAID. So the question is why is it ominous that no one in Iran has isolated and uploaded a sequence?

I believe they meant that it's scary that we don't have data in here from a place where we have heard the virus is both spreading quickly and having a high mortality rate.

Not ominous as in any way indicative of a conspiracy or otherwise.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#29

Post by rolph »

jmartrican wrote: post #26

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 i…

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.

Re: Genomic epidemiology of novel coronavirus (HCoV-19)

#30

Post by Symmetry »

jmartrican wrote: post #26

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 i…

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.

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