[gewa]

I don't think the article addresses the point right. Yes, there is only one strain of Sars-CoV-2 as the definition of a strain is a strict scientific term. Nevertheless, there are different clades [1] of Sars-CoV-2, which are characterised as organisms with a common ancestor [2]. This doesn't has to imply a changed property, like infectivity or mortality, but it implies common heritage which is of course of interest. You can see it nicely in the the phylogenetic tree of the sequenced genomes [3].

[1] https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25902

[2] https://en.wikipedia.org/wiki/Clade

[3] https://nextstrain.org/ncov/global

[kurthr]

Indeed, and you can see on nexstrain (The green RNA region labeled S) that there has been a very prolific functional mutation to the Spike Protein RNA. It is possible that the rapid growth of that strain (in Europe and NY) is due to either a founders effect or higher transmissibility (researchers do not see higher mortality, but may see higher viral load). There are possibilities that it changes the effectiveness of immune response, but it’s all under active research. The outcomes are very significant and unknown. Making broad fairly pedantic statements as the OP has, is unhelpful to understanding.

https://blogs.sciencemag.org/pipeline/archives/2020/05/07/mu...

[oehtXRwMkIs]

Nitpick, but viruses are not organisms and so they don't have clades. That's why the paper you linked used the term "viral clades". Like how quasispecies is used rather than species for viruses.

[ravenstine]

I respectfully disagree. Viruses contain RNA, have reproduction dependent on DNA, and are subject to evolution, which is why they're still categorized in their own tree of "life" with kingdoms, phyla, families, genuses, species, strains, etc. There's no reason why you can't categorize a virus under a clade.

Someone reading this might be wondering how speciation can be measured with viruses, since viruses don't reproduce sexually. Well, we don't test whether different species of animals can reproduce with each other. There's no way to conduct such experiments at any meaningful scale. The vast majority of defined species are educated guesses, and in reality has very little to do with whether two groups of organisms can reproduce with each other. In a lot of cases, species are simply determined by the appearance or behavior of one group of organisms over another group of closely related organisms. The term "species" didn't even originally have anything specifically to do with reproduction; the word effectively meant "looks like", which is why the words "species" and "spectacle" share the first 4 letters.

[gewa]

Yes viruses are not alive and speaking strictly there are no clades or specieses. But I stopped beeing to strict with terminology like this on HN. Most people are not from this field and don't have broad prior knowledge and so it would just complicate and confuse unnecessarily.

[foobarbecue]

Do they not use OTUs like for bacteria? (operational taxonomic units)

[koheripbal]

This is all correct, but the importance here is to combat the misinformed titles everywhere talking about multiple different "strains" going around, as well as that one damn Chinese paper (now retracted) claiming two different strains with different mortality rates.

Put more simply, two samples of virus can be of the same "strain" even if they aren't _exactly_ the same sequence. This is because replication can sometimes make errors on segments of the genome that do not impact functionality - moreover these same irrelevant loop segments are not error-corrected either, so mutations are common - despite not modifying the properties of the virus. These irrelevant mutations are actually very useful for tracking the virus spread.

A virus mutation becomes a different "strain" when the change is meaningful for the viruses interaction with the host or the environment.

SARS-COV2-2 is a type of virus that does error correction (unlike flu), so the rates of mutation are extremely low. This is good news because if means a vaccine will work, and we won't need a yearly one - like the flu.

[dragonwriter]

> A virus mutation becomes a different "strain" when the change is meaningful for the viruses interaction with the host or the environment.

Of course, that also means that detecting different strains is dependent on understanding those interactions and where they differ. If the post-infection cluster of pediatric multisystem inflammatory syndrome in NYC isn't just NYC being better at identifying that effect, it could well be a sign of a different strain with meaningfully different interactions with hosts. (It could still be a variety of other things, too.)

[lowwave]

For sure. But I think the point the @gewa trying to make is that yes in the strict academic/technical sense it is correct, however in every day English people probably use "strain" to mean Clad. But not everyone is a evolutionary biologist of some sort.

[tialaramex]

> This is good news because if means a vaccine will work, and we won't need a yearly one - like the flu.

That's way ahead of the facts. It means we're more likely to be able to develop a vaccine that works and it's more likely we won't need frequent vaccination to be effective.

Vaccine success involves a certain amount of finger crossing, because it's a natural system rather than an engineered one that we're trying to tamper with. If you've ever boggled at a large spaghetti program, the human immune system makes that look like two dozen lines of clearly documented Java by comparison. None of it has to make sense because Mother Nature doesn't care why she only does results, and in the most brutal way possible.

This is why we've got a bunch of different vaccine programmes in different centres. Some of them might work, hopefully at least one does, and hopefully it produces an immunity that lasts a useful amount of time, has minimal side effects and is cheap to produce in bulk. But there aren't any promises without us having way more advanced biotechnology than exists anywhere today.

[newhouseb]

> SARS-COV2-2 is a type of virus that does error correction

What is the biological process that does this? I'd love to learn more.

[ianai]

And apparently that mutation already happened

https://www.santafenewmexican.com/news/coronavirus/lanl-find...

[coldtea]

>This doesn't has to imply a changed property, like infectivity or mortality

What about the reports of different strains that focus on having found them having different properties (such as "much more infective")? Are they bogus?

[koheripbal]

That report was from a Chinese hospital (then repeated millions of times by the media) - they were never confirmed with any sequencing, and the paper was never published due to lack of evidence.

[numpad0]

Probably bogus but hyper convenient and comforting so people keeps spreading it

[sradman]

TLDR; use “isolate” not “strain” to describe genomic differences in viruses

Strain implies functional differences. SARS-CoV-2, like it’s Coronavirus cousins, is quite stable. The genomic sequences found on NextStrain.org are a powerful tool to track the spread of this virus but it is wrong to assume that the difference in each “isolate” carries with it a functional difference; it does not.

The blog post comes from the same scientists that create the TWiV (This Week I’m Virology) podcast which continues to be a tremendous source of quality information for me.

[pbhjpbhj]

>it is wrong to assume that the difference in each “isolate” carries with it a functional difference; it does not. //

Is that what people are assuming?

It's not that every mutation causes a [medically relevant] functional change, it's that a mutation could have. And, AFAIK, we don't have the ability to sequence _and_ relate sequences to differences in symptoms in the general case at present.

Maybe in 10 years someone will have developed an AI to relate RNA sequences, medical history, and functional changes in real time??

[pbhjpbhj]

NextStrain is an amazing resource, it shows all sorts of viruses, not just Covid19. Really incredible.