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

368 点作者 aberoham大约 5 年前

21 条评论

gewa大约 5 年前
I don&#x27;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&#x27;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].<p>[1] <a href="https:&#x2F;&#x2F;onlinelibrary.wiley.com&#x2F;doi&#x2F;abs&#x2F;10.1002&#x2F;jmv.25902" rel="nofollow">https:&#x2F;&#x2F;onlinelibrary.wiley.com&#x2F;doi&#x2F;abs&#x2F;10.1002&#x2F;jmv.25902</a><p>[2] <a href="https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Clade" rel="nofollow">https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Clade</a><p>[3] <a href="https:&#x2F;&#x2F;nextstrain.org&#x2F;ncov&#x2F;global" rel="nofollow">https:&#x2F;&#x2F;nextstrain.org&#x2F;ncov&#x2F;global</a>
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kerkeslager大约 5 年前
I&#x27;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.<p>There are some more nuanced claims which are made or hinted at:<p>1. There&#x27;s not adequate evidence to prove a difference in mortality between the L and S variations of the virus.<p>2. There&#x27;s not adequate evidence to prove increased viral transmission over time of the virus.<p>And if your definition of the word &quot;strain&quot; is &quot;reserved only for special changes that confer a new property to the virus&quot;, then both of those would be arguments that there&#x27;s not adequate evidence to prove the existence of different strains of the virus.<p>However, is the definition of the word &quot;strain&quot; really the important point you want to communicate? Either point 1 or 2 could have been made without talking about the word &quot;strain&quot; (note how I sidestepped the whole strain&#x2F;isolate issue by using the word &quot;variation&quot;). I would argue that either of those two points are much more important than the meaning of the word &quot;strain&quot;.<p>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&#x27;s jargon before they have the adequate mental framework to differentiate between the terms just creates conflict and is counterproductive.
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standardUser大约 5 年前
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 <i>precisely</i> 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.<p>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.
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jepcommenter大约 5 年前
The author is Vincent Racaniello Ph.D., Professor of Microbiology &amp; Immunology in the College of Physicians and Surgeons of Columbia University(<a href="https:&#x2F;&#x2F;www.virology.ws&#x2F;about&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.virology.ws&#x2F;about&#x2F;</a>)<p>I absolutely recommend his virology lectures <a href="https:&#x2F;&#x2F;youtu.be&#x2F;lj3NhPgOoX4" rel="nofollow">https:&#x2F;&#x2F;youtu.be&#x2F;lj3NhPgOoX4</a>
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brigandish大约 5 年前
For anyone else reading and wondering what the <i>founder effect</i> is:<p>&gt; 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.<p><a href="https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Founder_effect" rel="nofollow">https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Founder_effect</a>
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skybrian大约 5 年前
...as far as we know, because it&#x27;s difficult to prove otherwise and would take months.<p>Why the impulse to round off uncertainty to certainty? Ed Yong explained it better:<p><a href="https:&#x2F;&#x2F;www.theatlantic.com&#x2F;health&#x2F;archive&#x2F;2020&#x2F;05&#x2F;coronavirus-strains-transmissible&#x2F;611239&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.theatlantic.com&#x2F;health&#x2F;archive&#x2F;2020&#x2F;05&#x2F;coronavir...</a>
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zbjornson大约 5 年前
The authors of the D614G paper do attempt to rule out a founder effect. I&#x27;m not saying their analysis is bullet proof, but the OP doesn&#x27;t address its merits.<p><i>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).</i>
teh_klev大约 5 年前
Vincent Racaniello&#x27;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.<p>His website Microbe.tv[2] also hosts various regular podcasts (which are also published as audio to YouTube) about virology and microbiology, they&#x27;re very interesting.<p>I can thoroughly recommend.<p>[0]: <a href="https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Vincent_Racaniello" rel="nofollow">https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;Vincent_Racaniello</a><p>[1]: <a href="https:&#x2F;&#x2F;www.youtube.com&#x2F;user&#x2F;profvrr&#x2F;videos" rel="nofollow">https:&#x2F;&#x2F;www.youtube.com&#x2F;user&#x2F;profvrr&#x2F;videos</a><p>[2]: <a href="https:&#x2F;&#x2F;www.microbe.tv&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.microbe.tv&#x2F;</a>
CapriciousCptl大约 5 年前
The crux of the argument is showing different strains requires showing different phenotypes, and that that hasn&#x27;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&#x27;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.
darkerside大约 5 年前
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.<p>Anyway, this was the money line to me: &quot;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.&quot;<p>QED
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eru大约 5 年前
I guess the important thing is not so much if two viruses differ in any base pairs or in any &#x27;biological property&#x27;; but whether immunity to one is also immunity to the other?<p>If they were two strains of SARS-CoV-2 but your body fights them the same, that&#x27;s as good as only one strain for most people. But still very interesting for scientists.<p>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.
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userbinator大约 5 年前
Did anyone else notice the &quot;.ws&quot; domain of the site and, not being familiar with the site, immediately think &quot;that looks a bit shady&quot;? That&#x27;s been the long-time association of that TLD for me, probably because a lot of cracks&#x2F;warez&#x2F;virus (the computer type) sites used it, along with SEO spam and such.
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Jaruzel大约 5 年前
As a layperson, the question that springs to my mind is:<p>If there&#x27;s only one &#x27;strain&#x27; then that means one &#x27;vaccine&#x27; will work on all patients, correct?<p>So it&#x27;s unlike the Flu where the vaccine only works half the time and they keep having to update it ?
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gregwebs大约 5 年前
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: <a href="https:&#x2F;&#x2F;chrismasterjohnphd.com&#x2F;covid-19&#x2F;why-the-mutated-virus-spreads-faster-in-america-and-europe-than-east-asia" rel="nofollow">https:&#x2F;&#x2F;chrismasterjohnphd.com&#x2F;covid-19&#x2F;why-the-mutated-viru...</a>
xutopia大约 5 年前
Can someone explain to me like I&#x27;m 5yo why a virus is not considered alive?
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devy大约 5 年前
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]<p>[1]: <a href="https:&#x2F;&#x2F;peterkolchinsky.com&#x2F;bio" rel="nofollow">https:&#x2F;&#x2F;peterkolchinsky.com&#x2F;bio</a><p>[2]: <a href="https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=22900397" rel="nofollow">https:&#x2F;&#x2F;news.ycombinator.com&#x2F;item?id=22900397</a>
ianai大约 5 年前
Wrong. A national lab has identified enough variance in “strains” in the population to negate a singular vaccine.<p>Source: <a href="https:&#x2F;&#x2F;www.santafenewmexican.com&#x2F;news&#x2F;coronavirus&#x2F;lanl-finds-more-contagious-coronavirus-strain-has-emerged&#x2F;article_cf549a5a-8ef3-11ea-abca-8fa643b35e8c.html" rel="nofollow">https:&#x2F;&#x2F;www.santafenewmexican.com&#x2F;news&#x2F;coronavirus&#x2F;lanl-find...</a>
narrator大约 5 年前
That sure looks like more than 1 strain to me: <a href="https:&#x2F;&#x2F;nextstrain.org&#x2F;ncov&#x2F;" rel="nofollow">https:&#x2F;&#x2F;nextstrain.org&#x2F;ncov&#x2F;</a>
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hyperpallium大约 5 年前
Cases and deaths in Asia (N &amp; S hemispheres, 1st &amp; 3rd world) are significantly lower than elsewhere.<p>&gt; So far no one has shown that any of these virus isolates differ in any fundamental property.<p>A different sequence is prevalent elsewhere. Not proof, but suggestive of a property difference.
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pfortuny大约 5 年前
Ouch! I feel exactly like when the WHO stated once and again “NOT A PANDEMIC!!”<p>And then, just because a silly observational threshold was passed “PANDEMIC!!!!!”.<p>Same as “not recession&#x2F;recession” just because of a silly totally arbitrary threshold...
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akg_67大约 5 年前
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.<p>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.<p>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.<p>The closest article, I could find using google search is from Brookings.<p><a href="https:&#x2F;&#x2F;www.brookings.edu&#x2F;blog&#x2F;future-development&#x2F;2020&#x2F;05&#x2F;05&#x2F;the-unreal-dichotomy-in-covid-19-mortality-between-high-income-and-developing-countries&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.brookings.edu&#x2F;blog&#x2F;future-development&#x2F;2020&#x2F;05&#x2F;05...</a>
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