Note: This thread is related to #Coronavirus #COVID19

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Carl T. Bergstrom+ Your Authors @CT_Bergstrom #BlackLivesMatter Prof. Biol. @UW. Info flow in bio, society, & science. I love crows and ravens. he/him Book *Calling Bullshit* Aug 4th: tinyurl.com/y7ekfkhx Jun. 29, 2020 5 min read + Your Authors

So various media are reporting a new pandemic flu virus discovered in China.

What does this actually mean?

Let's look at the original paper. Actually, that's not so easy to do because—unconscionably in my opinion—@PNAS has put it behind a paywall.

 https://www.pnas.org/content/early/2020/06/23/1921186117 

The paper reports on a surveillance project looking at flu strains in pigs in China from 2011-2018. Pigs are an important reservoir for influenza, which can jump from this species to humans wholesale or by genomic recombination with a human strain.

The main finding is that a new genotype of H1N1 flu, known as G4, emerged and by 2016 became the dominant strain in pigs.

So that's the first thing to notice. This is not a *new* new virus; it's been very common in pigs since 2016.

I should caution that it became the dominant strain *in the sample population*, which did not include all of China. Below, details from the supplementary information associated with the paper:

The study also finds that the virus is different enough from previous H1N1 strains that human populations would not currently be immune, should it start to spread. Moreover it has a number of characteristics that *could* make it well suited to spreading in humans.

It was formed by recombination between a previous dominant strain in swine, and the human 2009 H1N1 virus, and other sources.

The virus is capable of infecting humans, with two zoonotic cases briefly mentioned in the paper. Neither resulted in human-to-human transmission.

Swine-to-human transmission is probably far more common, however. About 10% of those working with pigs have antibodies to G4, whereas antibodies are rare in humans elsewhere.

So are we facing the start of a double pandemic, COVID + influenza?

Not immanently.

There's no evidence that G4 is circulating in humans, despite five years of extensive exposure. That's the key context to keep in mind.

The paper is not describing an immediate threat to the general public, despite news outlets running headlines that suggest otherwise.

The problem with the click-based advertising model is that there are strong incentives to get you to click.

What the paper does do is something important for the epidemiological community: it points to a virus that we need to be keeping a careful eye on.

That's something we can do. Screening will be important, particularly if clusters of illness emerge in swine workers.

But every indication is that the G4 virus would have to undergo some evolutionary change to spread readily in people, and it may never do that.

If it does? We know how to make vaccines for influenza viruses. It could be included in the seasonal vaccine; the only issue is timing.

So that's the G4/H1N1 story.

Worth watching for people in the field.

No immediate threat to public health.

For the time being, we can all get back to figuring out what we're going to do about the picture below.

That was fast:

 https://www.nytimes.com/reuters/2020/06/29/world/asia/29reuters-health-coronavirus-china-pigs.html 

.@angie_rasmussen goes into further depth about the paper:

Followup: this is probably a minor quibble, but I'm not thrilled with the alarmist tone of this @nytimes piece.

Not that there's anything technically wrong with the headline, but most readers wouldn't think "new" means "extremely common since 2016"

 https://www.nytimes.com/2020/06/30/world/asia/h1n1-swine-flu-virus-china-pig.html?smtyp=cur&smid=tw-nytimes 

Nor is it completely obvious that "urgent control" refers to control in swine.

Nor will readers necessarily pick up at a glance the distinction between spreading *to* humans and spreading *in* humans.

And in fact the lead paragraph reinforces that latter confusion.

For me, "silently spreading *in* workers" can't really mean anything other than human-to-human transmission (which could be happening, but for which there is no evidence.)

The next bit is straight-up untrue. It may be a subtle untruth, but this is a distinction that matters.

We do not know if the virus replicates efficiently in human airways, and the study does not show this.

What the study shows is that the virus replicates efficiently *in cell culture*, using epithelial cells from the human airway.

Here's a really subtle issue. Typically when reporting on a scientific study, a reporter will consult with outside researchers for their views. Such is the case here; the reporter consulted with Li-Min Huang and Ian Brown, and notes Brown was a reviewer for the paper.

Normally a reviewer would be a good arm's-length choice for getting outside perspective. But this is a *contributed* paper. The NAS member who authors and submits the paper also chooses the reviewers, and thus may be inclined to choose scientists who are sympathetic to the study.

I want to stress that I am not alleging any kind of bias on the part of author George Gao or reviewer Ian Brown in this particular instance.

It's just interesting to think about what it takes to find an arm's-length perspective on a contributed PNAS study.

Finally, the story is brought back to earth, but it happens far too late. Compare the language at the start: "spreading silently in workers", talk of "urgency", "replicates efficiently" with the summary from Tony Fauci buried toward the end of the article.

Obviously we don't know whether G4/H1N1 will evolve the ability for sustained human-to-human transmission and it could indeed trigger a pandemic if the dice come up snake eyes. But I would have preferred to see Fauci's perspective elevated and the alarmism eliminated.

Here's an alternative way of presenting the story that I really like. @dctrjack published the following with @CNET. First of all, note the very different tone to the headline.

 https://www.cnet.com/news/why-you-shouldnt-panic-about-the-swine-flu-strain-with-pandemic-potential/ 

Better yet @dctrjack takes a few paragraphs to teach us something about how stories get from the lab to the limelight, and he raises that issue of press releases designed to get attention for papers hidden behind paywalls.

Here's the start of that section. Read the whole thing.


You can follow @CT_Bergstrom.



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