19 ms·

There is one, and only one strain of SARS-CoV-2

368 points by aberoham 6y ago

skybrian 6y ago
...as far as we know, because it's difficult to prove otherwise and would take months. Why the impulse to round off uncertainty to certainty? Ed Yong explained it better: https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/ https://www.theatlantic.com/health/archive/2020/05/coronavir...
- ilitirit 6y ago
  So a more more accurate description seems to be "there is no evidence that thinking of the viruses in terms of multiple strains is scientifically helpful".
  - AmericanChopper 6y ago
    Thinking of things that aren’t proven to exist is scientifically unhelpful?...
    - jraph 6y ago
      You, you are going to be crucified by scientists. :-) More seriously, I get your point but many discoveries are done by finally observing something which existence has been anticipated, hypothesized but still unproven. A planet that had an effect on nearby objects because of its gravity for instance. Or the Higgs boson. So, yes, thinking of things that are not proven to exist (yet) is often scientifically helpful. You still want to apply Occam's razor of course.
    - pbhjpbhj 6y ago
      You've cut the context, was that on purpose? The context is a discussion of improving medical interventions during the current pandemic, in that context, at present the argument is that 'considering Covid19 to be separate "strains" (isolates) will not help to treat patients'. Is that clearer?
      - AmericanChopper 6y ago
        It’s not clearer, it’s a completely different statement. The idea of the answer to a question being “medically unhelpful” doesn’t seem at all related to “scientifically unhelpful”.
  - inopinatus 6y ago
    I’d refine that further to clinically relevant
- colmvp 6y ago
  I feel like that's an important distinction. In Canada, our officials said in January that asymptomatic individuals were not main drivers of epidemics. And while that may have been true with something like influenza, a more accurate statement would've been we don't have evidence _yet_ that suggests asymptomatic individuals could effectively spread the virus. We proceeded to operate on that assumption by not forcing incoming travelers from infected regions to isolate, unless they contacted health officials with symptoms associated to the virus. We didn't change this stance until late March, well after the virus had infected thousands of people across the country. In contrast, Taiwan implemented mandatory 14-day self-isolations for incoming travelers from specific regions as early as late January. In Ontario, we've had cases of airport taxi drivers pass away from Covid-19. Whereas Taiwan recognized that there'd likely be a large number of people coming home with the virus, so they created special airport quarantine taxis equipped with mandatory masks for passengers and isopropyl alcohol for the driver.
  - pbhjpbhj 6y ago
    Worth noting how some people, including mainstream press, have vilified WHO for saying there was "no evidence yet of human-human transmission" (at the point there was no evidence yet), and for saying (paraphrasing) "it's not a pandemic yet, not until there's community spread across global regions" when it wasn't yet a pandemic. So, yes, I'd agree with your 3rd para, but press can spin such statements to create reputational damage which is really underserved.
pfortuny 6y ago
Ouch! I feel exactly like when the WHO stated once and again “NOT A PANDEMIC!!” And then, just because a silly observational threshold was passed “PANDEMIC!!!!!”. Same as “not recession/recession” just because of a silly totally arbitrary threshold...
- FooBarWidget 6y ago
  What exactly do you expect? If we can predict a recession, the world wouldn't have recessions. There's a reason why the label "pandemic" is purely an observational threshold and not a warning for what's to come.
- Gwypaas 6y ago
  Because they in the next breath said it had potential to become a pandemic if no intervention is done? At the same time declaring it an emergency outbreak of a novel virus? Words have meaning, and pandemic a very specific one. Would you have declared SARS a pandemic when the first cases started to show up simply because it's a scary virus?
  - AmericanChopper 6y ago
    A pandemic actually had an incredibly vague meaning. It’s been the topic of heated debate amongst epidemiologists for quite a while. You can read this [0] to get a hint of vague it all is, and if you look, you’ll find plenty of different highly qualified perspectives on the topic. The WHO waited until it spread to over 100 countries before it called it a pandemic. This wasn’t because it had crossed a very specific threshold to become classified as one. It was an opinionated decision. It wasn’t supported by a strict technical definition, or academic concensus. Because those things don’t exist. The definition of a pandemic is very simple: > an epidemic occurring worldwide, or over a very wide area, crossing international boundaries and usually affecting a large number of people Laymen are perfectly capable of understanding this, and forming their own perfectly reasonable opinions about it themselves. It is perfectly reasonable to criticize the WHO’s decision making around this, and they absolutely don’t have a technical definition to hide behind. [0]: http://www9.who.int/bulletin/volumes/89/7/11-088815/en/ http://www9.who.int/bulletin/volumes/89/7/11-088815/en/
eru 6y ago
I guess the important thing is not so much if two viruses differ in any base pairs or in any 'biological property'; but whether immunity to one is also immunity to the other? If they were two strains of SARS-CoV-2 but your body fights them the same, that's as good as only one strain for most people. But still very interesting for scientists. Equivalently, if we see lots of differences in base pairs but no differences in biological properties yet, that might still alert us to the possibility of new strains rapidly emerging in the future.
- H8crilA 6y ago
  That is certainly a "biological property". Immune response depends on the "outer form" of the pathogen - what does its protein structure look like from the outside?
akg_67 6y ago
Based on the difference in virulence of the virus in Western Europe and US versus Asia, it is hard to believe there is only one strain of SARS-CoV-2. My hypothesis is that while Asia was originally infected by Wuhan originated strain, the Western Europe and US may have been infected by a mutated strain. The differences in impact in different countries is very difficult to explain without the hypothesis of multiple strains. Edit: There was a decent article recently (I am unable to find now, most probably from NYT, WSJ) that addressed several factors mentioned in replies and showed none of those could explain the discrepancy in cases across countries. For example, high temperature and warm weather don’t explain differences in cases between Singapore, Thailand, Indonesia, Malaysia, and Amazon region of Brazil. The closest article, I could find using google search is from Brookings. https://www.brookings.edu/blog/future-development/2020/05/05/the-unreal-dichotomy-in-covid-19-mortality-between-high-income-and-developing-countries/ https://www.brookings.edu/blog/future-development/2020/05/05...
- solarkraft 6y ago
  Could you elaborate on this? How do the effects differ and couldn't a lot of it be explained by the vastly different pandemic reactions (lock-down vs doing almost nothing)?
  - CamperBob2 6y ago
    Because there are too many wildly differing reactions in similar populations. More than 700 passengers on the Diamond Princess were infected, leading to a total of eight deaths. This would have been an older-than-usual cohort, simply by dint of demographics on cruise ships. Meanwhile, in New York, deaths in long-term care homes have approached 5,000. Obviously nursing home residents are a more vulnerable population, but with this kind of disparity in outcomes, I'm not buying it. Nursing homes may have an older clientele, but then, cruise ships aren't staffed by medical professionals. IMHO it's been obvious that there are multiple strains in circulation for a long time. Otherwise, the medical community needs to explain exactly why outcomes vary so dramatically, not only from one individual to the next, but between populations with similar demographics. When they explain that, then I'll be more interested in their opinions regarding how many strains are out there. If they think the bugs are all the same, they aren't looking closely enough.
brigandish 6y ago
For anyone else reading and wondering what the founder effect is: > In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. https://en.wikipedia.org/wiki/Founder_effect https://en.wikipedia.org/wiki/Founder_effect
- franciscop 6y ago
  Yes, I searched the exact same thing. For how clear the article was in general, I was surprised that this bit was surprisingly confusing in the way it was explained.
- roosterdawn 6y ago
  Did anyone else read this and, experiences colored by startups, immediately begin thinking about an analogous effect in startup organizational developmental dynamics? Anyways, to be more on topic, I read this quote from the article: "Because of the founder effect, showing that a particular mutation increases viral transmission in humans is very difficult." Does the author here mean that it is hard to determine whether a mutation increases viral transmission in humans or not because that mutation's survival may not necessarily be the result of genetic fitness but founder effect?
narrator 6y ago
That sure looks like more than 1 strain to me: https://nextstrain.org/ncov/ https://nextstrain.org/ncov/
- Zanni 6y ago
  Yes, it looks like that, but it isn't. All those distinct lineages are functionally equivalent. That's the point. A detectable difference isn't the same as a functional difference in transmissibility, virulence, etc.
  - SomeoneFromCA 6y ago
    Well you cannot claim either way. There is still circumstantial evidence for a significant difference in virulence and mortality across the globe, so there might be indeed multiple strains, we just do know about it.
    - Symmetry 6y ago
      You can definitely claim it if, say, a CUA codon is replaced by a CUG codon because both of those code for Leucine and the resulting proteins will be absolutely identical.
      - SomeoneFromCA 6y ago
        That is not what I said. If there is observable difference between two populations, then indeed there might be two different strains at work. If you want to be super pedantic, not all RNAs are mRNAs, and there might be difference between CUA and CUG in tRNA's behavior.
  - jansan 6y ago
    How is it known that they are "functionally equivalent"? Is that common knowledge among virologists, has it been tested or simulated?
gewa 6y ago
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 https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25902 [2] https://en.wikipedia.org/wiki/Clade https://en.wikipedia.org/wiki/Clade [3] https://nextstrain.org/ncov/global https://nextstrain.org/ncov/global
- sradman 6y ago
  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 6y ago
    >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??
- coldtea 6y ago
  >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?
hyperpallium 6y ago
Cases and deaths in Asia (N & S hemispheres, 1st & 3rd world) are significantly lower than elsewhere. > So far no one has shown that any of these virus isolates differ in any fundamental property. A different sequence is prevalent elsewhere. Not proof, but suggestive of a property difference.
- dmos62 6y ago
  I'm shooting in the dark here, but isn't it equally suggestive of a property difference among races (if that's the proper term)?
  - lexicality 6y ago
    Tbh the most likely explanation is the very strong prevalence of mask wearing in asian cultures which dramatically reduces (but doesn't eliminate) transmission rates.
- 9nGQluzmnq3M 6y ago
  The jury is still very much out for many Asian countries (India, Indonesia, etc), and there are a plethora of other factors that can explain the difference: demographics, genetics, comorbidities, sunlight (UV-B), heat/humidity, access to testing etc. Also, the virus originated from one point (Wuhan) and was spread more or less simultaneously across the world. It would be quite odd if one strain hopped on all the west/east-bound planes, while another strain found its way only to the south-bound planes. Not to mention that the 'second wave' of infections in APAC originated largely from Europe.
  - hyperpallium 6y ago
    The hypothesis is the mutation occurred outside of Asia, and countries in Asia closed ports after the initial infections, but before the mutation. > sunlight (UV-B), heat/humidity Much of Asia is in the northern hemisphere (e.g. China and Japan); same season as Europe and USA. Australia is in Asia too, close to China with much travel between. I agree there are many factors and it's early. But the low cases and deaths over all countries in Asia has a peculiar uniformity - in contrast to elsewhere.
jepcommenter 6y ago
The author is Vincent Racaniello Ph.D., Professor of Microbiology & Immunology in the College of Physicians and Surgeons of Columbia University(https://www.virology.ws/about/ https://www.virology.ws/about/) I absolutely recommend his virology lectures https://youtu.be/lj3NhPgOoX4 https://youtu.be/lj3NhPgOoX4
- micburks 6y ago
  In addition, he is possibly the most prolific podcaster of our time. He's started no less than 6 different podcasts over the last decade or so, collectively known as the TWIx podcasts (This Week in Virology/Microbiology/Parasitology/etc. I'm a huge fan of TWIV, but they're all top-notch. https://www.microbe.tv/ https://www.microbe.tv/
Jaruzel 6y ago
As a layperson, the question that springs to my mind is: If there's only one 'strain' then that means one 'vaccine' will work on all patients, correct? So it's unlike the Flu where the vaccine only works half the time and they keep having to update it ?
- Scarblac 6y ago
  Yes.
- FriendlyNormie 6y ago
  Good job, you fell for the scam. Hell is too good of a destination for useful idiots like you.
CapriciousCptl 6y ago
The crux of the argument is showing different strains requires showing different phenotypes, and that that hasn't been supported with enough evidence. D614S is taken as an example, which purportedly increases transmissibility (thus would be a different strain), but most-likely doesn't. Apparently the data in support of D615S is just based on it being found in a lot of isolates-- but that would also be seen in the case of founder effect.
userbinator 6y ago
Did anyone else notice the ".ws" domain of the site and, not being familiar with the site, immediately think "that looks a bit shady"? That's been the long-time association of that TLD for me, probably because a lot of cracks/warez/virus (the computer type) sites used it, along with SEO spam and such.
- everybodyknows 6y ago
  In this case, looks to have been a tactic to gain some "virology.*" for the domain name: https://www.samoanic.ws/ https://www.samoanic.ws/
ianai 6y ago
Wrong. A national lab has identified enough variance in “strains” in the population to negate a singular vaccine. Source: https://www.santafenewmexican.com/news/coronavirus/lanl-finds-more-contagious-coronavirus-strain-has-emerged/article_cf549a5a-8ef3-11ea-abca-8fa643b35e8c.html https://www.santafenewmexican.com/news/coronavirus/lanl-find...
standardUser 6y ago
There are several downvoted comments here attempting to express the common idea that this virus has impacted different regions in very different ways. That observation alone is not an argument against there being only a single strain of this virus, but it is a valid observation in its own right. There are plenty of half-explanations that rely on cultural differences (hand shaking, masks), climate (heat, humidity), and various other factors, but so far no one has proven precisely what factors make the biggest differences. That piece of information is one of the most valuable things in the world right now and we do not have it. The other big factor is the different government responses, but these are all over the map. Specifically, the lack of a lockdown does not always equal a high rate of transmission, and the presence of a lockdown does not always result in a low enough rate of transmission to avoid a crisis. This is something we should all be curious about.
- ekianjo 6y ago
  > lockdown does not always result in a low enough rate of transmission to avoid a crisis. On that topic, Cuomo just declared that among the last batch of infected people in NY, more than 80% were apparently respecting the lockdown and staying at home and we have no idea how they were even contaminated. Puzzling.
  - usaar333 6y ago
    That's a bit of a stretch of what he said (https://www.cnbc.com/2020/05/06/ny-gov-cuomo-says-its-shocking-most-new-coronavirus-hospitalizations-are-people-staying-home.html https://www.cnbc.com/2020/05/06/ny-gov-cuomo-says-its-shocki...). * Hospitalizations, not cases and not infections. That skews old/out of the workforce. * The stat is that 66% live at home and 84% not working. * That doesn't mean they are 100% to the letter respecting social distancing. Nor does it mean they don't have housemates that aren't working. (That could be the case, but there's no data).
  - aeyes 6y ago
    Do you have a link? With incubation periods of up to two weeks and cases without symptoms everything is possible.
Oricle 6y ago
And.... Over 98% recover from it, it's been around for over 12 months and it's no more dangerous than any other cold or flu virus. The question is when as any government (puppet shows for the "chosen ones") ever told the truth? Not when has it told a lie?! What do people with power and control want? Always more!
zbjornson 6y ago
The authors of the D614G paper do attempt to rule out a founder effect. I'm not saying their analysis is bullet proof, but the OP doesn't address its merits. To differentiate between founder effects and a selective advantage driving the increasing frequency of the G clade in the GISAID data, we applied the suite of tools that we had been developing for the SARS-CoV-2 analysis pipeline (Fig. 2, Fig. 3, Fig. S2 and Fig. S3). A clear and consistent pattern was observed in almost every place where adequate sampling was available. In most countries and states where the COVID-19 epidemic was initiated and where sequences were sampled prior to March 1, the D614 form was the dominant local form early in the epidemic (orange in Figs. 2 and 3). Wherever G614 entered a population, a rapid rise in its frequency followed, and in many cases G614 became the dominant local form in a matter of only a few weeks (Fig. 3 and S3).
xutopia 6y ago
Can someone explain to me like I'm 5yo why a virus is not considered alive?
- drdec 6y ago
  People like to classify things. They like having neat buckets to place things in, give them a name, make them feel like they have a handle on it. The world is not easily classified. But people persist. So we end up with situations like "is Pluto a planet?" and "is a virus alive?" Then people start focusing on their classifications and definitions when in fact they don't actually matter to the reality of the situation. I need to dumb this down more if the audience is a 5 year old. People like to give things names. Like the colors: red, orange, yellow, green, blue and purple. But sometimes a color can't be easily named. For example the shirt I'm wearing might look blue to me and green to you. Then we start arguing about what color the shirt is when what we really should talk about is if it matches my pants.
- jcranmer 6y ago
  5 is a very difficult age to target, but let me try. Viruses lack several things that are often deemed necessary for life. The most important (in descending order): * They lack the internal structure all other life has [this is the cell]. * They lack the ability to "eat" to "live" [metabolism]. * They lack the ability to make more of themselves without "borrowing" others' abilities.
- downerending 6y ago
  Because by themselves, they don't have most of the properties of living things. They have no metabolism, and they do not reproduce, for example. They're kind of like (physical) books. They can affect living things (people), and some books cause living things to reproduce the books, sometimes in large numbers. But few people would regard books as alive in the way that a dog or tree is.
- CamperBob2 6y ago
  Can someone explain to me like I'm 5yo why a virus is not considered alive? Because the scientific community carefully picked certain completely-arbitrary attributes with the intent of drawing a bright line of division between viruses and cell-based organisms. This doesn't make the slightest bit of sense to Mother Nature, of course, but it makes sense to the scientists. A much better definition of "Alive" would simply be, "Subject to the rules of evolution by natural selection." Viruses certainly quality under that rubric.
kerkeslager 6y ago
I'm not an expert in this field or any related fields. I am, however, in a field where I have to frequently communicate on technical topics to a nontechnical audience. The following is a critique of the technical communication in this article, not of the science. There are some more nuanced claims which are made or hinted at: 1. There's not adequate evidence to prove a difference in mortality between the L and S variations of the virus. 2. There's not adequate evidence to prove increased viral transmission over time of the virus. And if your definition of the word "strain" is "reserved only for special changes that confer a new property to the virus", then both of those would be arguments that there's not adequate evidence to prove the existence of different strains of the virus. However, is the definition of the word "strain" really the important point you want to communicate? Either point 1 or 2 could have been made without talking about the word "strain" (note how I sidestepped the whole strain/isolate issue by using the word "variation"). I would argue that either of those two points are much more important than the meaning of the word "strain". Sure, using the proper jargon is a strong indicator of expertise in a field. But jargon arises from expertise, not the other way around. Correcting people's jargon before they have the adequate mental framework to differentiate between the terms just creates conflict and is counterproductive.
- micburks 6y ago
  Yes, science can be pedantic at times, but I do believe that it's necessary to describe terms before you discuss why they're important. For me, this article reads exactly as I was taught to write technical papers. It builds upon the definition of "species" to make an argument against the reoccurring claims that this virus is mutating to become more transmissible. Of course, I did study microbiology at university, so I can see how others might find it too focused on the jargon. What this pandemic has taught me over anything else is that wielding scientific terms without proper understanding is damaging to progress of science itself. It becomes difficult to tease apart legend from fact, especially for those not trained to do so. I go crazy every day listening to half-baked hypotheses and conspiracies that don't understand the foundations for the things they're claiming. All this said, Dr. Racaniello is very gracious and humble. He has dedicated his life to teaching, both in the classroom and through his podcasts. I highly suggest sending him your concerns about his discourse and subscribing to his podacast TWIV [0]. He and his colleagues respond to every email at the end of each podcast. [0] http://www.microbe.tv/twiv/ http://www.microbe.tv/twiv/
FriendlyNormie 6y ago
Not reading this obvious bullshit whose sole goal based on the title alone is to shape the narrative to convince everyone that a faulty vaccine that has already been ready to go for years should be globally mandatory as was always part of the plan before this manmade virus was intentionally released. You gullible assholes can all go fuck yourselves.
devy 6y ago
This echoed what Peter Kolchinsky (Harvard-trained Virologist turned VC in Life Science)[1] had said why the initial wave of vaccines for SARS-CoV-2 will arrive and will be mostly effective[2] [1]: https://peterkolchinsky.com/bio https://peterkolchinsky.com/bio [2]: https://news.ycombinator.com/item?id=22900397 https://news.ycombinator.com/item?id=22900397
teh_klev 6y ago
Vincent Racaniello's[0] YouTube channel[1] is well worth a visit. He publishes his lectures on virology on the channel, updated each year to reflect latest research etc. His website Microbe.tv[2] also hosts various regular podcasts (which are also published as audio to YouTube) about virology and microbiology, they're very interesting. I can thoroughly recommend. [0]: https://en.wikipedia.org/wiki/Vincent_Racaniello https://en.wikipedia.org/wiki/Vincent_Racaniello [1]: https://www.youtube.com/user/profvrr/videos https://www.youtube.com/user/profvrr/videos [2]: https://www.microbe.tv/ https://www.microbe.tv/
gregwebs 6y ago
It is ironic that this blog post is published just a little after a preprint was posted making a case that the D614G mutation has biologically significant differences. There is an explanation of the paper here: https://chrismasterjohnphd.com/covid-19/why-the-mutated-virus-spreads-faster-in-america-and-europe-than-east-asia https://chrismasterjohnphd.com/covid-19/why-the-mutated-viru...
darkerside 6y ago
The tone of this content seemed a bit off to me. It converted a high degree of certainty, when the purpose was to decry that we are placing a high degree of certainty on a fact that is unproven and likely unprovable, if not totally untrue. Seems ironic. Anyway, this was the money line to me: "For an amino acid change such as D614S to be positively selected, as opposed to being maintained as a consequence of the founder effect, requires selective pressure. For such an already highly transmissible virus, the nature of such selection pressure is difficult to discern." QED
- godelski 6y ago
  This is backwards of what science does. Science doesn't really rule things in, rather it rules things out till there is nothing left. For example, take the discussion about D614S here. The original claim was that D614S makes the virus more transmittable, and the author claims this is wrong. Who has the burden of proof? It is the researchers that claimed D614S made Cov2 more transmissible. The author here points out that there is no selection pressure here and that there is a more reasonable solution to the results. Occam's razor is in play. So not all arguments need a burden of proof. It is the one that is making the claim that has the burden.
  - alexandercrohde 6y ago
    Right, and this article is titled "There is one, and only one strain" which is an affirmative statement, and calls for a burden of proof. What this piece should be titled is "We don't have any evidence yet of multiple strains."
    - darkerside 6y ago
      I'd even be happy with "We don't have any evidence yet of multiple strains, and we probably never will"
    - godelski 6y ago
      Except the claim was that there are more than one strain and the author is responding to that. The burden of proof lies in the one making the claim that there are multiple strains. The author has no burden of proof. This would be akin to one person making the claim: "Unicorns are not only real, but are causing a global pandemic" and then someone writing an article titled "Unicorns aren't real, STFU". The second title doesn't have the burden of proof and we wouldn't be having this conversation if these were the titles of the respective articles. Why is the unicorns title an accurate analogy? Because the science doesn't expect there to be multiple strains in the same way the science doesn't expect unicorns to exist. I'm using the same vernacular here that we use in science. I didn't say "unicorns don't exist" but "we don't expect unicorns to exist". This is how we say things.

368 points by aberoham 6y ago

...as far as we know, because it's difficult to prove otherwise and would take months. Why the impulse to round off uncertainty to certainty? Ed Yong explained it better: https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/ https://www.theatlantic.com/health/archive/2020/05/coronavir...

ilitirit 6y ago
So a more more accurate description seems to be "there is no evidence that thinking of the viruses in terms of multiple strains is scientifically helpful".
- AmericanChopper 6y ago
  Thinking of things that aren’t proven to exist is scientifically unhelpful?...
  - jraph 6y ago
    You, you are going to be crucified by scientists. :-) More seriously, I get your point but many discoveries are done by finally observing something which existence has been anticipated, hypothesized but still unproven. A planet that had an effect on nearby objects because of its gravity for instance. Or the Higgs boson. So, yes, thinking of things that are not proven to exist (yet) is often scientifically helpful. You still want to apply Occam's razor of course.
  - pbhjpbhj 6y ago
    You've cut the context, was that on purpose? The context is a discussion of improving medical interventions during the current pandemic, in that context, at present the argument is that 'considering Covid19 to be separate "strains" (isolates) will not help to treat patients'. Is that clearer?
    - AmericanChopper 6y ago
      It’s not clearer, it’s a completely different statement. The idea of the answer to a question being “medically unhelpful” doesn’t seem at all related to “scientifically unhelpful”.
- inopinatus 6y ago
  I’d refine that further to clinically relevant
colmvp 6y ago
I feel like that's an important distinction. In Canada, our officials said in January that asymptomatic individuals were not main drivers of epidemics. And while that may have been true with something like influenza, a more accurate statement would've been we don't have evidence _yet_ that suggests asymptomatic individuals could effectively spread the virus. We proceeded to operate on that assumption by not forcing incoming travelers from infected regions to isolate, unless they contacted health officials with symptoms associated to the virus. We didn't change this stance until late March, well after the virus had infected thousands of people across the country. In contrast, Taiwan implemented mandatory 14-day self-isolations for incoming travelers from specific regions as early as late January. In Ontario, we've had cases of airport taxi drivers pass away from Covid-19. Whereas Taiwan recognized that there'd likely be a large number of people coming home with the virus, so they created special airport quarantine taxis equipped with mandatory masks for passengers and isopropyl alcohol for the driver.
- pbhjpbhj 6y ago
  Worth noting how some people, including mainstream press, have vilified WHO for saying there was "no evidence yet of human-human transmission" (at the point there was no evidence yet), and for saying (paraphrasing) "it's not a pandemic yet, not until there's community spread across global regions" when it wasn't yet a pandemic. So, yes, I'd agree with your 3rd para, but press can spin such statements to create reputational damage which is really underserved.

pfortuny 6y ago

Ouch! I feel exactly like when the WHO stated once and again “NOT A PANDEMIC!!” And then, just because a silly observational threshold was passed “PANDEMIC!!!!!”. Same as “not recession/recession” just because of a silly totally arbitrary threshold...

FooBarWidget 6y ago
What exactly do you expect? If we can predict a recession, the world wouldn't have recessions. There's a reason why the label "pandemic" is purely an observational threshold and not a warning for what's to come.
Gwypaas 6y ago
Because they in the next breath said it had potential to become a pandemic if no intervention is done? At the same time declaring it an emergency outbreak of a novel virus? Words have meaning, and pandemic a very specific one. Would you have declared SARS a pandemic when the first cases started to show up simply because it's a scary virus?
- AmericanChopper 6y ago
  A pandemic actually had an incredibly vague meaning. It’s been the topic of heated debate amongst epidemiologists for quite a while. You can read this [0] to get a hint of vague it all is, and if you look, you’ll find plenty of different highly qualified perspectives on the topic. The WHO waited until it spread to over 100 countries before it called it a pandemic. This wasn’t because it had crossed a very specific threshold to become classified as one. It was an opinionated decision. It wasn’t supported by a strict technical definition, or academic concensus. Because those things don’t exist. The definition of a pandemic is very simple: > an epidemic occurring worldwide, or over a very wide area, crossing international boundaries and usually affecting a large number of people Laymen are perfectly capable of understanding this, and forming their own perfectly reasonable opinions about it themselves. It is perfectly reasonable to criticize the WHO’s decision making around this, and they absolutely don’t have a technical definition to hide behind. [0]: http://www9.who.int/bulletin/volumes/89/7/11-088815/en/ http://www9.who.int/bulletin/volumes/89/7/11-088815/en/

eru 6y ago

I guess the important thing is not so much if two viruses differ in any base pairs or in any 'biological property'; but whether immunity to one is also immunity to the other? If they were two strains of SARS-CoV-2 but your body fights them the same, that's as good as only one strain for most people. But still very interesting for scientists. Equivalently, if we see lots of differences in base pairs but no differences in biological properties yet, that might still alert us to the possibility of new strains rapidly emerging in the future.

H8crilA 6y ago
That is certainly a "biological property". Immune response depends on the "outer form" of the pathogen - what does its protein structure look like from the outside?

akg_67 6y ago

Based on the difference in virulence of the virus in Western Europe and US versus Asia, it is hard to believe there is only one strain of SARS-CoV-2. My hypothesis is that while Asia was originally infected by Wuhan originated strain, the Western Europe and US may have been infected by a mutated strain. The differences in impact in different countries is very difficult to explain without the hypothesis of multiple strains. Edit: There was a decent article recently (I am unable to find now, most probably from NYT, WSJ) that addressed several factors mentioned in replies and showed none of those could explain the discrepancy in cases across countries. For example, high temperature and warm weather don’t explain differences in cases between Singapore, Thailand, Indonesia, Malaysia, and Amazon region of Brazil. The closest article, I could find using google search is from Brookings. https://www.brookings.edu/blog/future-development/2020/05/05/the-unreal-dichotomy-in-covid-19-mortality-between-high-income-and-developing-countries/ https://www.brookings.edu/blog/future-development/2020/05/05...

solarkraft 6y ago
Could you elaborate on this? How do the effects differ and couldn't a lot of it be explained by the vastly different pandemic reactions (lock-down vs doing almost nothing)?
- CamperBob2 6y ago
  Because there are too many wildly differing reactions in similar populations. More than 700 passengers on the Diamond Princess were infected, leading to a total of eight deaths. This would have been an older-than-usual cohort, simply by dint of demographics on cruise ships. Meanwhile, in New York, deaths in long-term care homes have approached 5,000. Obviously nursing home residents are a more vulnerable population, but with this kind of disparity in outcomes, I'm not buying it. Nursing homes may have an older clientele, but then, cruise ships aren't staffed by medical professionals. IMHO it's been obvious that there are multiple strains in circulation for a long time. Otherwise, the medical community needs to explain exactly why outcomes vary so dramatically, not only from one individual to the next, but between populations with similar demographics. When they explain that, then I'll be more interested in their opinions regarding how many strains are out there. If they think the bugs are all the same, they aren't looking closely enough.

brigandish 6y ago

For anyone else reading and wondering what the founder effect is: > In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. https://en.wikipedia.org/wiki/Founder_effect https://en.wikipedia.org/wiki/Founder_effect

franciscop 6y ago
Yes, I searched the exact same thing. For how clear the article was in general, I was surprised that this bit was surprisingly confusing in the way it was explained.
roosterdawn 6y ago
Did anyone else read this and, experiences colored by startups, immediately begin thinking about an analogous effect in startup organizational developmental dynamics? Anyways, to be more on topic, I read this quote from the article: "Because of the founder effect, showing that a particular mutation increases viral transmission in humans is very difficult." Does the author here mean that it is hard to determine whether a mutation increases viral transmission in humans or not because that mutation's survival may not necessarily be the result of genetic fitness but founder effect?

narrator 6y ago

That sure looks like more than 1 strain to me: https://nextstrain.org/ncov/ https://nextstrain.org/ncov/

Zanni 6y ago
Yes, it looks like that, but it isn't. All those distinct lineages are functionally equivalent. That's the point. A detectable difference isn't the same as a functional difference in transmissibility, virulence, etc.
- SomeoneFromCA 6y ago
  Well you cannot claim either way. There is still circumstantial evidence for a significant difference in virulence and mortality across the globe, so there might be indeed multiple strains, we just do know about it.
  - Symmetry 6y ago
    You can definitely claim it if, say, a CUA codon is replaced by a CUG codon because both of those code for Leucine and the resulting proteins will be absolutely identical.
    - SomeoneFromCA 6y ago
      That is not what I said. If there is observable difference between two populations, then indeed there might be two different strains at work. If you want to be super pedantic, not all RNAs are mRNAs, and there might be difference between CUA and CUG in tRNA's behavior.
- jansan 6y ago
  How is it known that they are "functionally equivalent"? Is that common knowledge among virologists, has it been tested or simulated?

gewa 6y ago

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 https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25902 [2] https://en.wikipedia.org/wiki/Clade https://en.wikipedia.org/wiki/Clade [3] https://nextstrain.org/ncov/global https://nextstrain.org/ncov/global

sradman 6y ago
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 6y ago
  >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??
coldtea 6y ago
>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?

hyperpallium 6y ago

Cases and deaths in Asia (N & S hemispheres, 1st & 3rd world) are significantly lower than elsewhere. > So far no one has shown that any of these virus isolates differ in any fundamental property. A different sequence is prevalent elsewhere. Not proof, but suggestive of a property difference.

dmos62 6y ago
I'm shooting in the dark here, but isn't it equally suggestive of a property difference among races (if that's the proper term)?
- lexicality 6y ago
  Tbh the most likely explanation is the very strong prevalence of mask wearing in asian cultures which dramatically reduces (but doesn't eliminate) transmission rates.
9nGQluzmnq3M 6y ago
The jury is still very much out for many Asian countries (India, Indonesia, etc), and there are a plethora of other factors that can explain the difference: demographics, genetics, comorbidities, sunlight (UV-B), heat/humidity, access to testing etc. Also, the virus originated from one point (Wuhan) and was spread more or less simultaneously across the world. It would be quite odd if one strain hopped on all the west/east-bound planes, while another strain found its way only to the south-bound planes. Not to mention that the 'second wave' of infections in APAC originated largely from Europe.
- hyperpallium 6y ago
  The hypothesis is the mutation occurred outside of Asia, and countries in Asia closed ports after the initial infections, but before the mutation. > sunlight (UV-B), heat/humidity Much of Asia is in the northern hemisphere (e.g. China and Japan); same season as Europe and USA. Australia is in Asia too, close to China with much travel between. I agree there are many factors and it's early. But the low cases and deaths over all countries in Asia has a peculiar uniformity - in contrast to elsewhere.

jepcommenter 6y ago

The author is Vincent Racaniello Ph.D., Professor of Microbiology & Immunology in the College of Physicians and Surgeons of Columbia University(https://www.virology.ws/about/ https://www.virology.ws/about/) I absolutely recommend his virology lectures https://youtu.be/lj3NhPgOoX4 https://youtu.be/lj3NhPgOoX4

micburks 6y ago
In addition, he is possibly the most prolific podcaster of our time. He's started no less than 6 different podcasts over the last decade or so, collectively known as the TWIx podcasts (This Week in Virology/Microbiology/Parasitology/etc. I'm a huge fan of TWIV, but they're all top-notch. https://www.microbe.tv/ https://www.microbe.tv/

Jaruzel 6y ago

As a layperson, the question that springs to my mind is: If there's only one 'strain' then that means one 'vaccine' will work on all patients, correct? So it's unlike the Flu where the vaccine only works half the time and they keep having to update it ?

Scarblac 6y ago
Yes.
FriendlyNormie 6y ago
Good job, you fell for the scam. Hell is too good of a destination for useful idiots like you.

CapriciousCptl 6y ago

The crux of the argument is showing different strains requires showing different phenotypes, and that that hasn't been supported with enough evidence. D614S is taken as an example, which purportedly increases transmissibility (thus would be a different strain), but most-likely doesn't. Apparently the data in support of D615S is just based on it being found in a lot of isolates-- but that would also be seen in the case of founder effect.

userbinator 6y ago

Did anyone else notice the ".ws" domain of the site and, not being familiar with the site, immediately think "that looks a bit shady"? That's been the long-time association of that TLD for me, probably because a lot of cracks/warez/virus (the computer type) sites used it, along with SEO spam and such.

everybodyknows 6y ago
In this case, looks to have been a tactic to gain some "virology.*" for the domain name: https://www.samoanic.ws/ https://www.samoanic.ws/

ianai 6y ago

Wrong. A national lab has identified enough variance in “strains” in the population to negate a singular vaccine. Source: https://www.santafenewmexican.com/news/coronavirus/lanl-finds-more-contagious-coronavirus-strain-has-emerged/article_cf549a5a-8ef3-11ea-abca-8fa643b35e8c.html https://www.santafenewmexican.com/news/coronavirus/lanl-find...

standardUser 6y ago

There are several downvoted comments here attempting to express the common idea that this virus has impacted different regions in very different ways. That observation alone is not an argument against there being only a single strain of this virus, but it is a valid observation in its own right. There are plenty of half-explanations that rely on cultural differences (hand shaking, masks), climate (heat, humidity), and various other factors, but so far no one has proven precisely what factors make the biggest differences. That piece of information is one of the most valuable things in the world right now and we do not have it. The other big factor is the different government responses, but these are all over the map. Specifically, the lack of a lockdown does not always equal a high rate of transmission, and the presence of a lockdown does not always result in a low enough rate of transmission to avoid a crisis. This is something we should all be curious about.

ekianjo 6y ago
> lockdown does not always result in a low enough rate of transmission to avoid a crisis. On that topic, Cuomo just declared that among the last batch of infected people in NY, more than 80% were apparently respecting the lockdown and staying at home and we have no idea how they were even contaminated. Puzzling.
- usaar333 6y ago
  That's a bit of a stretch of what he said (https://www.cnbc.com/2020/05/06/ny-gov-cuomo-says-its-shocking-most-new-coronavirus-hospitalizations-are-people-staying-home.html https://www.cnbc.com/2020/05/06/ny-gov-cuomo-says-its-shocki...). * Hospitalizations, not cases and not infections. That skews old/out of the workforce. * The stat is that 66% live at home and 84% not working. * That doesn't mean they are 100% to the letter respecting social distancing. Nor does it mean they don't have housemates that aren't working. (That could be the case, but there's no data).
- aeyes 6y ago
  Do you have a link? With incubation periods of up to two weeks and cases without symptoms everything is possible.

Oricle 6y ago

And.... Over 98% recover from it, it's been around for over 12 months and it's no more dangerous than any other cold or flu virus. The question is when as any government (puppet shows for the "chosen ones") ever told the truth? Not when has it told a lie?! What do people with power and control want? Always more!

zbjornson 6y ago

The authors of the D614G paper do attempt to rule out a founder effect. I'm not saying their analysis is bullet proof, but the OP doesn't address its merits. To differentiate between founder effects and a selective advantage driving the increasing frequency of the G clade in the GISAID data, we applied the suite of tools that we had been developing for the SARS-CoV-2 analysis pipeline (Fig. 2, Fig. 3, Fig. S2 and Fig. S3). A clear and consistent pattern was observed in almost every place where adequate sampling was available. In most countries and states where the COVID-19 epidemic was initiated and where sequences were sampled prior to March 1, the D614 form was the dominant local form early in the epidemic (orange in Figs. 2 and 3). Wherever G614 entered a population, a rapid rise in its frequency followed, and in many cases G614 became the dominant local form in a matter of only a few weeks (Fig. 3 and S3).

xutopia 6y ago

Can someone explain to me like I'm 5yo why a virus is not considered alive?

drdec 6y ago
People like to classify things. They like having neat buckets to place things in, give them a name, make them feel like they have a handle on it. The world is not easily classified. But people persist. So we end up with situations like "is Pluto a planet?" and "is a virus alive?" Then people start focusing on their classifications and definitions when in fact they don't actually matter to the reality of the situation. I need to dumb this down more if the audience is a 5 year old. People like to give things names. Like the colors: red, orange, yellow, green, blue and purple. But sometimes a color can't be easily named. For example the shirt I'm wearing might look blue to me and green to you. Then we start arguing about what color the shirt is when what we really should talk about is if it matches my pants.
jcranmer 6y ago
5 is a very difficult age to target, but let me try. Viruses lack several things that are often deemed necessary for life. The most important (in descending order): * They lack the internal structure all other life has [this is the cell]. * They lack the ability to "eat" to "live" [metabolism]. * They lack the ability to make more of themselves without "borrowing" others' abilities.
downerending 6y ago
Because by themselves, they don't have most of the properties of living things. They have no metabolism, and they do not reproduce, for example. They're kind of like (physical) books. They can affect living things (people), and some books cause living things to reproduce the books, sometimes in large numbers. But few people would regard books as alive in the way that a dog or tree is.
CamperBob2 6y ago
Can someone explain to me like I'm 5yo why a virus is not considered alive? Because the scientific community carefully picked certain completely-arbitrary attributes with the intent of drawing a bright line of division between viruses and cell-based organisms. This doesn't make the slightest bit of sense to Mother Nature, of course, but it makes sense to the scientists. A much better definition of "Alive" would simply be, "Subject to the rules of evolution by natural selection." Viruses certainly quality under that rubric.

kerkeslager 6y ago

I'm not an expert in this field or any related fields. I am, however, in a field where I have to frequently communicate on technical topics to a nontechnical audience. The following is a critique of the technical communication in this article, not of the science. There are some more nuanced claims which are made or hinted at: 1. There's not adequate evidence to prove a difference in mortality between the L and S variations of the virus. 2. There's not adequate evidence to prove increased viral transmission over time of the virus. And if your definition of the word "strain" is "reserved only for special changes that confer a new property to the virus", then both of those would be arguments that there's not adequate evidence to prove the existence of different strains of the virus. However, is the definition of the word "strain" really the important point you want to communicate? Either point 1 or 2 could have been made without talking about the word "strain" (note how I sidestepped the whole strain/isolate issue by using the word "variation"). I would argue that either of those two points are much more important than the meaning of the word "strain". Sure, using the proper jargon is a strong indicator of expertise in a field. But jargon arises from expertise, not the other way around. Correcting people's jargon before they have the adequate mental framework to differentiate between the terms just creates conflict and is counterproductive.

micburks 6y ago
Yes, science can be pedantic at times, but I do believe that it's necessary to describe terms before you discuss why they're important. For me, this article reads exactly as I was taught to write technical papers. It builds upon the definition of "species" to make an argument against the reoccurring claims that this virus is mutating to become more transmissible. Of course, I did study microbiology at university, so I can see how others might find it too focused on the jargon. What this pandemic has taught me over anything else is that wielding scientific terms without proper understanding is damaging to progress of science itself. It becomes difficult to tease apart legend from fact, especially for those not trained to do so. I go crazy every day listening to half-baked hypotheses and conspiracies that don't understand the foundations for the things they're claiming. All this said, Dr. Racaniello is very gracious and humble. He has dedicated his life to teaching, both in the classroom and through his podcasts. I highly suggest sending him your concerns about his discourse and subscribing to his podacast TWIV [0]. He and his colleagues respond to every email at the end of each podcast. [0] http://www.microbe.tv/twiv/ http://www.microbe.tv/twiv/

FriendlyNormie 6y ago

Not reading this obvious bullshit whose sole goal based on the title alone is to shape the narrative to convince everyone that a faulty vaccine that has already been ready to go for years should be globally mandatory as was always part of the plan before this manmade virus was intentionally released. You gullible assholes can all go fuck yourselves.

devy 6y ago

This echoed what Peter Kolchinsky (Harvard-trained Virologist turned VC in Life Science)[1] had said why the initial wave of vaccines for SARS-CoV-2 will arrive and will be mostly effective[2] [1]: https://peterkolchinsky.com/bio https://peterkolchinsky.com/bio [2]: https://news.ycombinator.com/item?id=22900397 https://news.ycombinator.com/item?id=22900397

teh_klev 6y ago

Vincent Racaniello's[0] YouTube channel[1] is well worth a visit. He publishes his lectures on virology on the channel, updated each year to reflect latest research etc. His website Microbe.tv[2] also hosts various regular podcasts (which are also published as audio to YouTube) about virology and microbiology, they're very interesting. I can thoroughly recommend. [0]: https://en.wikipedia.org/wiki/Vincent_Racaniello https://en.wikipedia.org/wiki/Vincent_Racaniello [1]: https://www.youtube.com/user/profvrr/videos https://www.youtube.com/user/profvrr/videos [2]: https://www.microbe.tv/ https://www.microbe.tv/

gregwebs 6y ago

It is ironic that this blog post is published just a little after a preprint was posted making a case that the D614G mutation has biologically significant differences. There is an explanation of the paper here: https://chrismasterjohnphd.com/covid-19/why-the-mutated-virus-spreads-faster-in-america-and-europe-than-east-asia https://chrismasterjohnphd.com/covid-19/why-the-mutated-viru...

darkerside 6y ago

The tone of this content seemed a bit off to me. It converted a high degree of certainty, when the purpose was to decry that we are placing a high degree of certainty on a fact that is unproven and likely unprovable, if not totally untrue. Seems ironic. Anyway, this was the money line to me: "For an amino acid change such as D614S to be positively selected, as opposed to being maintained as a consequence of the founder effect, requires selective pressure. For such an already highly transmissible virus, the nature of such selection pressure is difficult to discern." QED

godelski 6y ago
This is backwards of what science does. Science doesn't really rule things in, rather it rules things out till there is nothing left. For example, take the discussion about D614S here. The original claim was that D614S makes the virus more transmittable, and the author claims this is wrong. Who has the burden of proof? It is the researchers that claimed D614S made Cov2 more transmissible. The author here points out that there is no selection pressure here and that there is a more reasonable solution to the results. Occam's razor is in play. So not all arguments need a burden of proof. It is the one that is making the claim that has the burden.
- alexandercrohde 6y ago
  Right, and this article is titled "There is one, and only one strain" which is an affirmative statement, and calls for a burden of proof. What this piece should be titled is "We don't have any evidence yet of multiple strains."
  - darkerside 6y ago
    I'd even be happy with "We don't have any evidence yet of multiple strains, and we probably never will"
  - godelski 6y ago
    Except the claim was that there are more than one strain and the author is responding to that. The burden of proof lies in the one making the claim that there are multiple strains. The author has no burden of proof. This would be akin to one person making the claim: "Unicorns are not only real, but are causing a global pandemic" and then someone writing an article titled "Unicorns aren't real, STFU". The second title doesn't have the burden of proof and we wouldn't be having this conversation if these were the titles of the respective articles. Why is the unicorns title an accurate analogy? Because the science doesn't expect there to be multiple strains in the same way the science doesn't expect unicorns to exist. I'm using the same vernacular here that we use in science. I didn't say "unicorns don't exist" but "we don't expect unicorns to exist". This is how we say things.