This influenza lineage may have become extinct | Hacker News Reader

This influenza lineage may have become extinct

nature.com

44 pointsperihelions47 comments

Worth reading the actual article, but for those who won't: The article is referring to the B/Yamagata lineage of influenza becoming extinct, which is only one of the four main lineages of influenza. The other lineages circulate in animals thus will be a bit harder to eradicate. Also, this lineage was also already on the way out, lacking the genetic diversity of the other lineages.

Still, interesting news!

I'm reading about the history of smallpox and it seems like it takes a herculean effort to actually eradicate an infectious virus from the planet. Obviously smallpox is far more virulent than influenza, but still....it seems premature to declare extinction just because we haven't found any in awhile.

I can imagine lots of ways old viruses can be reintroduced.

Blood banks, dead bodies, mosquito bites, experiments in secret underground laboratories...

Why go underground when rent next to the wetmarket is so cheap?

Don’t forget the melting Siberian permafrost.

It actually appears that influenza is very close to extinct in Australia for now. It will be interesting to see if influenza returns with the opening of borders this summer.

>There has not been a death certified due to influenza in the first six months of 2021. The last death certified as being due to influenza occurred in July 2020.

0. https://www.abs.gov.au/statistics/health/causes-death/provis...

I would say in case of influenza, close to extinction is not close enough and is probably even nothing to cheer about.

What I mean is as soon as restrictions are lifted we are going to see a huge correction for influenza cases with population that has not been exposed to it for the duration of pandemic.

It is inevitable because it only takes couple cases in some corner of the world to ensure it comes back.

Absolutely. I do note we have had a pretty big uptake on influenza vaccines through the pandemic so that should blunt the impact a little.

You'd have to keep the borders closed if you want to keep influenza out.

I thought these viruses had reservoirs in common farm animals and that's why they were so hard to eradicate. Is there reason to believe they've disappeared from those populations as well?

The article mentions that the influenza B virus has no known animal reservoir.

Not this strain. From the article: "With circulation of IBV only in humans and no established animal reservoir... The considerable reductions of influenza circulation globally due to COVID-19 may have already precipitated the extinction of the B/Yamagata lineage."

No animal reservoirs that we know of. Big difference.

What else did you think what the origin comment meant? You thought that person is an omniscient god that can inspect the entirety of the animal kingdom at a moments notice and verify there are no animal reservoirs?

This is not surprising at all. I haven't had anything that feels like a cold or a flu, since COVID started. I think this can be mostly attributed to the sudden increase of mask usage and hand-washing.

I believe influenza was very vulnerable to this change of behavior given its seasonal nature, shorter incubation period and generally weaker virality.

same, I have not had a cold/flu in 2 years now which is a record for me, usually I am getting sick 4-5 times a year.

I haven't had a cold or flu since Covid, either. This is probably the longest I've ever gone without one, usually I'd get one every couple of years or so.

I don't know if I'll ever take public transit / fly without a mask on again. Same.

I'm not sure how effective that will be if the sick person isn't also masked.

N95s are designed to protect the wearer from situations like that, even for 8 hours of contact. Cloth masks will not work in that situation though if the sick person isn’t masked.

In NZ we had a period of lockdown during which colds and flus were non-existant and then we went completely back to normal life for a while.

In that winter after the lockdown we had an absolutely ferocious amount of colds and flus all of a sudden.

I had 6 back-to-back. It was 12 weeks of hell. Every other person I know had at least 2. Parents (such as myself) all had 4+ colds/flus in a 3 month period.

There was a lot of speculation that the spread was significantly worse because it got into a population entirely made of people who had not been sick for a while.

So you might have that to look forward to.

I traveled from NYC to Albania and experienced this... and many people I know here got some type of cold recently.

They all got this cold/flu that was pretty bad, but thankfully it was not covid. (associated with coughing, and upper congestion, but nothing serious, and it cleared within a week).

New Zealand's rates of flu were extremely low this year; what you had was probably some sort of cold.

Nobody likes a flukeeper.

They literally said "flus and colds" why do you have to suggest this person's experience isn't what they say it is.

Have you had the flu before? Do you know what it is?

Do you know how absolutely fucking annoying it is to be gaslit when you know you've had the flu and no it wasn't just a bad fucking cold?

> Do you know how absolutely fucking annoying it is to be gaslit when you know you've had the flu and no it wasn't just a bad fucking cold?

This actually keeps me up at night...shutter

Yeah I’m experiencing this atm in the US. No sickness in 2020, but this year I’ve had RSV, hand foot and mouth disease, numerous colds. It’s horrific lol

Also the topic of today's xkcd: https://xkcd.com/2523/

I use this dashboard to see influenza spread in my state, scroll down to the state by state activity monitor to see how your state is doing.

https://www.cdc.gov/flu/weekly/index.htm

I read a speculation somewhere that coronaviruses may have occupied the niche flu took over for a while with the 1918 pandemic and we're just going back to the norm.

(No sources will be provided.)

I've seen similar, and don't doubt it. I just keep wondering: how does that work, mechanistically? A coronavirus infection doesn't protect me from influenza: it should be perfectly possible to be infected by both. How do they compete?

Influenza and coronavirus 'compete' by forcing people to alter their behavior, thus removing potential carriers from the general population before the other virus can reach them. The more infectious virus wins this competition.

The flu isn't very infectious compared to even ancestral covid; its R number is normally reckoned at well below 1.5, so covid suppression techniques (which pushed covid's below 1 in many places last year) would have been pretty hard on it.

Just because this is the top comment right now, I'd like to point out that the conventional explanation works fine too. The interventions taken against covid worked even better against the flu and because diseases are exponential you only have to get the reproduction rate a bit below 1 to see huge impacts. Oh and also covid is currently a more dangerous disease so it would still be pretty bad if flu was replaced by it

Yeah, right, why do we still have a bunch of common cold viruses then? Any argument referring the interventions has to also explain why _only_ flu disappeared out of huge variety of respiratory viruses.

We're talking about a flu, not the flu. There are still plenty of influenza viruses out there, alive, well, and waiting. The difference with this particular lineage is that it seems to be human-only, with no known animal reservoir.

Some of the cold viruses are extremely infectious, certainly moreso than boring ol' Original Covid or Alpha, and some possibly more than Delta.

R number for influenza is normally reckoned at well under 1.5; it's really not that infectious.

> why _only_ flu disappeared out of huge variety of respiratory viruses.

Some of the viruses which cause the common cold may well have become rare or outright disappeared; we probably wouldn't notice.

But if you assume that measures are equally effective against flu, cold and covid, you'd probably expect flu to be suppressed first, then ancestral and alpha covid, then most colds, then delta.

Case in point: This summer my family all came down with Norovirus, aka the "winter" vomitting bug. This is much more infectious than COVID, each year infecting roughly 685 million people.

What role does the "this" at the beginning of the title play? I actually thought it said "the" at first scan.

The word "this" is used to identify a specific person or thing close at hand or being referred to (in this case, a specific influenza lineage).

If the word "the" were used instead, the headline wouldn't make sense.

Personally i think using "An" would be better than "this" or nothing at all, but i also think this entire thread is very nitpicky.

Good point, the title of the article is: "Influenza lineage extinction during the COVID-19 pandemic?", I don't know how the HN headline came to be ("This influenza lineage may have become extinct"), but it does seem like a very very light form of clickbait.

It's a quote from the abstract. I found "influenza lineage extinction" difficult to parse, but the abstract expands it into clear English.

>"In particular, the B/Yamagata lineage has not been isolated from April 2020 to August 2021, suggesting that this influenza lineage may have become extinct,"

So I'm not the only one who notices this.

The unnecessary this prefix strikes me as a sort of clickbait-adjacent red flag. I'm fairly sure it wasn't anywhere near this common 10 years ago.

Often with a short follow-on sentence in the format:

This article is clickbait. Here's why.

Sharp decrease in influenza alongside a sharp increase in covid all across the world at the same time?

No.

The PCR tests are equally sensitive to influenza A and B, common cold coronaviruses, adenoviruses and rhinoviruses.

THAT'S how "influenza disappeared" - i.e. it didn't at all. It's that the "COVID PCR" tests positive for influenza so all flu was counted as COVID!

This not accurate. The PCR test was designed to be extremely specific to SARS-CoV-2. The CDC's PCR test was physically tested against human coronavirus (strains 229E, OC43, NL63, and HKU1), MERS-coronavirus, SARS-coronavirus, bocavirus, Mycoplasma pneumoniae Streptococcus Influenza A(H1N1) Influenza A(H3N2) Influenza B Human adenovirus, type 1 Human metapneumovirus respiratory syncytial virus (strain Long A), rhinovirus, parainfluenza 1 (strain C35), parainfluenza 2 (strain Greer), parainfluenza 3 (strain C-43), and parainfluenza 4 (strain M-25). All of these tested negative.

In addition, on computer it was "evaluated against 831,910 recent high-quality genome sequences available in Global Initiative on Sharing All Influenza Data (GISAID, https://www.gisaid.org) as of June 6, 2021 to demonstrate the predicted inclusivity of the 2019-nCoV real-time RT-PCR Diagnostic panel." This all somes from the instructions for use (PDF)[1] for the test.

The PCR test detects SARS-CoV-2 and only SARS-CoV-2.

Besides, regular flu tests continued to be done using the same technologies as used in previous years. More than 1.2 million flu tests were performed in the U.S. and 99.8% of the specimens tested negative.[2]

[1] https://www.fda.gov/media/134922/download#page=41

[2] https://i.imgur.com/noBw6zV.png

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