
Welcome to the Virosphere - vo2maxer
https://www.nytimes.com/2020/03/24/science/viruses-coranavirus-biology.html
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dsign
I think that "only 250 virus infect humans" means something like "so far, we
only know of 250 viruses in record that cause notable diseases".

In an ideal world, we should be sequencing viruses for each single patient,
just like we measure blood pressure.

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alexpotato
Along these lines, I wonder if we will eventually see charts like this for ALL
human viruses with a person by person trace:
[https://nextstrain.org/ncov](https://nextstrain.org/ncov)

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sjg007
Yes we will

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Ericson2314
Why so confident? We have the technical skills, but this also takes
institutional cooperation we suck at. We don't even have a standard format for
conventional medical records in the US!

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sjg007
I expect legislation that will require CDC and DHHS to establish surveillance
programs. We will be sequencing. This will be academic labs and clinic labs
most likely. There might be a national sequencing center established. If we
work together with China we might leverage their massive sequencing capacity.

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aasasd
It generally seems like evolution is better described by continuums, not
discrete entities: if one gene is changed among thousands, is the result
worthy of a new name? Just like with languages vs dialects—those are the same
thing, but on different scale.

Edit: to clarify, I'm aware of the criterion of sexual incompatibility, and
that genes don't usually work one-by-one, but still—slapping an arbitrary
Latin-ish name on each of the millions of, say, fly species seems of dubious
use, at least to an outsider.

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blauditore
First, it's important to distinguish between genotype and phenotype. Most
genetic mutations don't cause any change in behavior or appearance, so the two
individuals are phenotypically equal.

With sexual reproduction, individuals can differ genetically but still be
compatible, so there is some notion of a pool with a clear boundary. For
viruses, this is of course a bit trickier because they "reproduce
asexually"[0] and quite rapidly, so mutations happen at a high rate. But one
useful property to distinguish them is which receptors (and thus which cells)
they bind to, generally affecting what symptoms and diseases they cause.

[0]: Viruses are not considered living things, so the concept of reproduction
is already quite a stretch.

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dragontamer
> With sexual reproduction, individuals can differ genetically but still be
> compatible, so there is some notion of a pool with a clear boundary.

The boundary isn't very clear.

[https://en.wikipedia.org/wiki/Ring_species](https://en.wikipedia.org/wiki/Ring_species)

A can breed with B, B can breed with C, C can breed with D, and D can breed
with A.

But A cannot breed with C.

Are A and C part of the same species, or not? These "ring species" occur
around geographic rings, such as the Arctic Circle, so each population remains
genetically compatible with its neighbors... but not "across the ring".

[https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ri...](https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ring_species_seagull.svg/800px-
Ring_species_seagull.svg.png)

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throwaway5466
Yeah. Basically the concept of _species_ is bust taxonomically and largely a
social construct at this point. (That is to say, what is a species is what the
community agrees to be a species for the sake of convenience)

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merricksb
[http://archive.is/VbTDd](http://archive.is/VbTDd)

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globular-toast
I studied viruses for a job a few years ago. I looked at RNA viruses mostly
and specifically influenza. The way they work is truly astonishing but you
quickly realise it's an unfortunate inevitability given the way our genetics
works.

One interesting thing I remember is that virtually every human over a year old
or so is "infected" with at least a handful of viruses for life. The scare
quotes are because we really don't know what effect these viruses have on us.
They could be beneficial for all we know.

To add further complexity consider that bacteria get infected by viruses
(called bacteriophages). All those bacteria inside you are in turn "infected"
by viruses. Phages are so numerous that a drop of seawater contains about ten
million of them. Also they are literally like microscopic genome injection
machines. Look up some pictures and electron microscope images.

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packetlost
Could you expand on the statement:

> virtually every human over a year old or so is "infected" with at least a
> handful of viruses for life

That sounds like a very interesting concept, and it's one that I haven't heard
of before. If you don't want to write yourself, linking me to some reputable
sources would be awesome too.

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DoingIsLearning
I simple example of this is chicken pox (Varicella Zoster).

A large proportion of adults have had it as kids. The immune system fights it
off but virus particles can still 'hide' from it and lay dormant inside
pheripheral nerve tissue.

A proof of this is 'shingles' in adults. i.e. a virus which probably infected
the host +50 years ago and went dormant in their nerves finds the host immune
system weak enough to come out again and start replicating.

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ajnin
How is a virus species defined ? As I understand it a species is a group of
organisms that can reproduce viably with each other. But a virus doesn't
reproduce like that, they clone themselves by hijacking a cell's machinery, so
there is no notion of compatibility between viruses. The article says that
Covid-19 is "similar" to SARS so it was put in the same species, but that
seems a rather soft definition. Especially if there are trillions of different
viruses like the article says, some objective criterion is needed. Not to
mention viruses mutate all the time, at what point does it become a new
species?

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nvrspyx
The International Committee on Taxonomy of Viruses (ICTV) is responsible for
classifying viruses and they use a bunch of different criteria, such as
chemical characteristics, structure (e.g. look at Covid-19 vs a
bacteriophage), type of nucleic acid, mode of replication, host organisms, and
the types of diseases they cause. They also group them based on common
ancestors.

In other words, it becomes a new species when there's a change to the
phenotypic traits above.

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ppod
Will the media ever understand the difference between "we underestimate tail
risks all the time" and "we have been underestimating this specific tail
risk"?

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nisa
That something like this would happen was clear for at least the last ten
years. It was only not clear _when_ it would happen.

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cactus2093
Why 10? Why not the last 50 years, or last 100?

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neonate
[https://archive.md/V7wvl](https://archive.md/V7wvl)

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romanovcode
Why link paywalled article?

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drivers99
Why don’t you just buy a subscription?

