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PHealthy t1_j7ghm2e wrote

During the pandemic, yes, SARS-CoV-2 had much higher incidence:

https://coronavirus.jhu.edu/testing/individual-states

But the normally circulating coronaviruses as we call them are definitely still around and currently making their annual peak right now:

https://www.cdc.gov/surveillance/nrevss/coronavirus/natl-trends.html

The usual disclaimer of course that many viruses make up the "common cold".

In case anyone likes infectious disease news: r/ID_News

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NotAnotherEmpire t1_j7gwfqv wrote

Makes sense because the universal mitigation measures used on SARS-CoV-2 impair all respiratory viruses. Everything from masks to absolute bans on going to work / school / day care with respiratory illness.

The others aren't as contagious so while the pandemic is extremely hard to drive transmission down below 1, the others are temporarily removed.

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PHealthy t1_j7h52pz wrote

It's also good to remember that coronaviruses aren't just some singular static thing. SARS-CoV-2, for instance, is highly mutable. So a better question would be variant competition because as far as viral species go, you can definitely be co-infected.

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atred t1_j7haedb wrote

I seem to remember that people were saying that SARS-CoV-2 was not highly mutable and a potential vaccine (at the time they were saying that) would solve the problem. Why did they think that and what changed?

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Asterose t1_j7i1byq wrote

One mark of good, real science at work is when a prediction, based on evidence, is shown to be incorrect and scientists update the predictions with the new data.

Complaints about scientists "not being 100% certain" and "they keep changing what they're saying" are red flags revealing people who do not understand how science works and why the scientific method is so important to everything we have today.

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Fight_the_bastards t1_j7i9h4x wrote

Yeah, it’s like people who complain about how the rules for masking “changed constantly.” Well, when you’re learning new things about a disease, countermeasures are going to change, and also it didn’t help that a substantial percentage of people (including in state and federal government leaders), actively ignored the guidance for idiotic reasons.

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Asterose t1_j7iacdj wrote

Seriously. They might as well be saying "last week the weatherman said it would be sunny but NOW they're saying I'll need an umbrella tomorrow?! Those idiots who study weather are obviously useless and don't know what they're talking about!" Except instead of just risking getting soaked, they're playing games with a goddamn virus.

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birdstork t1_j7jicz0 wrote

People do say that about the weatherman - I hear it all the time. Meteorologists take time & explain how the pattern could shift but people don’t listen.

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Endogamy t1_j7jjuav wrote

Yeah complaining about inaccurate forecasts is so widespread and almost always wrong. It’s almost always someone who didn’t pay attention to the details of the forecast or misheard/misunderstood/misremembered it, or heard a forecast for another place but assumed it applied to them etc.

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Asterose t1_j7kifq2 wrote

And also doesn't understand that weather is just really damn difficult to predict. That humans have figured out the level of accuracy we do get now is genuinely impressive.

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Asterose t1_j7kip5x wrote

Slightly different, I'm well aware of that which is why I specified it being sunny last week, as in people thinking last week's sunny weather should mean it couldn't possibly be rainy tomorrow ;)

I might not have worded it quite clearly enough and gave the impression I meant people complaining about current forecasts being wrong. Weather is actually really difficult to predict in quite a few cases, so the level off accuracy we currently have is genuinely impressive, and I wish more people could appreciate that.

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jsgui OP t1_j7kgdd1 wrote

It would be like the weatherman playing the game of pretending the weather will be dry so when he goes to the shop there are still umbrellas in stock for him and the various other weathermen to buy. Then as soon as supply of umbrellas is not the pressing issue the weatherman admits it’s actually raining.

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jsgui OP t1_j7kg4sl wrote

At some point early on the guidance itself was untruthful. The public were being told that masks were not effective while various hospitals were buying and using them.

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CySU t1_j7klonm wrote

Those same people rely on monochromatic thinking to get through their daily lives. A lot less energy is spent weighing pros and cons so if someone else appears to be making conflicting statements overtime it’s a lot easier to dismiss as “hacks who can’t even get their story straight”.

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BeatlesTypeBeat t1_j7i2i8j wrote

This has been my biggest takeaway as well. We've always adjusted as new data became available.

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zeeke42 t1_j7ibt0x wrote

I didn't read the question that way at all. I took it as "why did they think that at the time, and what have we learned since then about why they were wrong?"

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atred t1_j7ik52g wrote

yeah, it wasn't a complain about scientists, it was more why it was considered unlikely to mutate and what changed that now is considered "highly mutable" as OP put it.

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Lumpy-Dingo-947 t1_j7iko3k wrote

I mostly heard “if they were wrong before, how can you be sure inconveniencing me is right????”

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pablofs t1_j7kqzt6 wrote

Scientists are portrayed in movies and media as “knowing” everything, no wonder people is confused. Basically they take a mystic cultist character and call it a scientist.

But true scientists would be difficult to film, always having more questions than answers, null hypothesis and margins of error.

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cynric42 t1_j7jsxu1 wrote

Also represented in how scientists talk when asked about how something is going to play out in the future. There are often qualifiers involved or limitations like "if it behaves like similar viruses, we can expect", or "from what we've seen so far, it is likely ..." etc. Sadly those often get left out for headlines or in short excerpts from media about what someone said.

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bmyst70 t1_j7lwuyk wrote

I think it was during the pandemic that many people saw real science unfolding almost in real time. Until then most people only had the orderly, bite sized chunks in school. Which give the illusion that science is always an orderly process.

But real science is messy, with an educated best guess proven or disproven. Lather, rinse, repeat. It does amazing things but orderly, it is not.

And these many people got very upset and decided it's not a good thing because it's not crisp, black and white and unchanging.

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Asterose t1_j7m223c wrote

Excellent insight! Thank you for pointing these out :)

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DrQuailMan t1_j7lljwo wrote

However, a red flag for fake science at work is if when asked to explain its predictions, or changes in its predictions, no details are provided.

Of course this is not the case for covid-19 science. But the person asked a legitimate question about the state of the research. You don't have to give conspiracy theorists ammo by responding with a non-answer like that. Just say which early studies indicated low mutability, and which later studies or observations indicated high mutability.

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Asterose t1_j7m114f wrote

>You don't have to give conspiracy theorists ammo by responding with a non-answer like that.

Well, I literally said: "One mark of good, real science at work is when a prediction, based on evidence, is shown to be incorrect and scientists update the predictions with the new data."

Please specify where and how exactly I "give conspiracy theorists ammo by responding with a non-answer like that" then. I did not read the person's comment as needing detailed links and explanations on Scientific Method 101, but you are welcome to provide those if you feel the person needs the basics.

>Just say which early studies indicated low mutability, and which later studies or observations indicated high mutability.

You are welcome to do so, because I personally didn't and don't have the time to go hunting for those specifics just to repeat all the searching and link-sourcing dozens to hundreds of other commenters have already been doing across the replies to both that person and OP. Since you are concerned they didn't get answers out of the many other comments doing exactly that, you can provide the answers you feel they still need.

Because I was solely focusing on and responding with some reassurance that changing statements and predictions with new evidence are part of how the Scientific Method works.

In fact, a few people replying to the same initial comment as me are also talking about the scientific method and public reactions, so I think several of us found it relevant for a few people to discuss and reassure about that since sources and info on the COVID-related questions are already in so many other comments.

I've had a really hard day at work so I am potentially coming across here as angry or passive-aggressive, this is the best I can do to explain right now.

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DrQuailMan t1_j7mc1um wrote

>I did not read the person's comment as needing detailed links and explanations on Scientific Method 101

Youre missing the point. Bringing up "scientific method 101" is a step backwards, as this person's actual request was to see the scientific method in action, not to have the concept of it described to them.

>just to repeat all the searching and link-sourcing dozens to hundreds of other commenters have already been doing across the replies to both that person and OP.

No one has replied with a link / reference to this person yet, as of an hour ago.

>Since you are concerned they didn't get answers out of the many other comments doing exactly that, you can provide the answers you feel they still need.

I don't have the expertise to do that. Is that supposed to be a gotcha? If anything you're slightly gotcha-ing yourself by saying it would take you a long time to find appropriate sources, and exposing your own overconfidence. Not every scientific misprediction gets analyzed scientifically, so without already being familiar with the appropriate sources, you can't know whether there are appropriate sources.

You'd think that on r/askscience, people would accept the idea of answering questions with actual scientific data, or an explanation that the data doesn't exist, and would understand the non-triviality of providing the correct answer.

>In fact, a few people replying to the same initial comment as me are also talking about the scientific method and public reactions

Virologists are rare on the internet. Clueless know-it-alls are common. An abundance of replies from the common type of person doesn't indicate that such replies were particularly warranted, compared to the uncommon type. People act within their capabilities. Sometimes that drowns out other people, to ill effect.

>I am potentially coming across here as angry or passive-aggressive

I am just explaining how your comment was indirectly harmful. Save your back-to-basics warning for suspicious questions about science, not all questions about science.

"Why does science say X" is a normal question. "Why did science say X, but now says Y" is also a normal question.

"Why did science say <thing it obviously didn't>, but now says Y" is a suspicious question. "Why did science say <thing that is obviously compatible with Y>, but now says Y" is a suspicious question.

Like, post this all day on questions about mask or vaccine efficacy, where trolls try to pretend masks were supposed to 100% prevent transmission, or vaccines were supposed to prevent all sickness for everyone. But this guy, he's just asking about mutation research, not saying anything about that research being untrustworthy or tainted.

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Straight-Plankton-15 t1_j7o2vau wrote

>Complaints about scientists "not being 100% certain" and "they keep changing what they're saying" are red flags revealing people who do not understand how science works

It's not that deep. If you're averse to non-personal questions, this isn't the correct sub.

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NotAnotherEmpire t1_j7hccp7 wrote

Confidence in how it would behave in humans was too high.

It was mostly stable. The problem is that it also seems likely the virus can chronically infect people with a compromised immune system, producing evolution that wouldn't occur going from host to host. That's very likely how Alpha and Omicron came out of nowhere.

Original Omicron isn't competitive evolution gradually picking up changes to evade immunity to the others. It was isolated from the rest of the pandemic and then appeared with a very different spike.

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Seicair t1_j7hp047 wrote

Alpha came from an immunocompromised individual? I thought alpha and beta were pretty close to the original strain?

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PHealthy t1_j7hqjrj wrote

It's thought Delta evolved within an immunocompromised person(s) and Omicron was likely a spillover from humans to mice and back to humans.

https://www.nejm.org/doi/full/10.1056/NEJMsb2104756

https://www.sciencedirect.com/science/article/pii/S1673852721003738

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Seicair t1_j7i6fy4 wrote

Both of those links were fascinating, I hadn’t heard that omicron probably jumped species!

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NotAnotherEmpire t1_j7hzrjv wrote

If Alpha had evolved gradually the UK or Denmark would have seen it with their massive surveillance programs. No one's reported an Alpha-in-progress.

Alpha had far more than the expected number of mutations and was materially different in behavior. Fortunately it didn't matter for vaccine targeting.

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Seicair t1_j7i4yh9 wrote

I somehow never heard that. I remember hearing Omicron came out of left field and it was thought to have evolved in an immunocompromised patient due to the sheer number of mutations. I thought Alpha and Beta were two notable strains that were more successful than other small mutations. Now that I look though, I see AB both have a significant number of mutations, just the spike was mostly unchanged.

Fascinating. I studied some microbiology/immunology in school, I would’ve liked to have delved deeper.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8714679/#:~:text=delta)%2C%20B.-,1.1.,of%20these%20variants%20%5B1%5D.

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jayhillcpa t1_j7ix4s8 wrote

How are the mutations identified when testing? Wouldn’t the mechanisms need to change every time a new variant popped up?

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gengengis t1_j7jjmf6 wrote

Genetic testing. The viral genome is sequenced and edits between specimens are catalogued.

There are a shitload of mutations between most specimens. Many of these might be single amino acid flips which might not do anything at all. But the viral genome has certain core regions essential to its function. For instance, with Covid, one of these regions codes for the spike protein necessary for infecting host cells.

We can then count up the major core mutations and get an idea of how different one specimen is from another. And indeed, because this science has advanced so much, we can even make predictions about how certain mutations will affect the viral proteins, and how those changes might affect transmissibility and immune evasion.

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jayhillcpa t1_j7jtuap wrote

So if I drive through one of the mobile testing sites, sequencing and editing occurs all within minutes whilst I’m waiting in my car? Wouldn’t it behoove the individuals by specifying the variant they tested positive for? How does the (what sounds like splicing) categorization occur with the home testing kits - the testing kits that clearly state it cannot and does not differentiate between SARS-COV-1 and COV-2?

As far as predictions go, the “science” apparently isn’t that advanced. It’s as if I were to propose the following, because I can count to 100, I can predict the winning power ball numbers.

By the way thank you for the response.

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sirgog t1_j7jussa wrote

A small percentage of people who are tested have their sample sequenced as well.

If a lab performs 250000 PCR tests a week and gets 20000 positives, it will likely sequence 100 of the positives.

This then shows trends across the population in which variants are dominating.

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GaitAtaxia t1_j7jso9t wrote

It was actually always known to halve a relatively high point mutation rate, giving it a higher rate of genetic drift. It does NOT have the same mechanism as influenza for allowing genetic SHIFT.

We focussed on talking about its low rate of genetic shift and ignored the high rate of genetic drift when making claims of low mutability, but it was really only a half truth at best.

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zeiandren t1_j7ipcnf wrote

It’s not highly mutable. The fact we give the strains names shows how few there are. Some viruses every single one of the millions of copies a single cell makes will have major mutations. Like we talk about flu viruses by what proteins they have in a mad libs format because every virus is so different than it’s parent that species don’t even make sense.

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GreggAlan t1_j7jqhpf wrote

That's why making a universal vaccine for influenza, or for all the rhinoviruses and coronaviruses hasn't been figured out. There's so many variants that play hokey-pokey-mixmaster with their components that a vaccine for one may only work on it and a few closely related mutations.

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Straight-Plankton-15 t1_j7o3xrx wrote

The caveat is that virtually every new variant since 2022 has simply been placed under the Omicron umbrella label, when some of them are more different from one another than the previous variants of concern were from the original variant.

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czyivn t1_j7k8ph0 wrote

I think part of the reason it seemed unusually stable was that it was operating in basically a vacuum for immune evasion pressure. Every host was a naiive one without prior covid exposure. There was therefore not as strong of a selection pressure as the other coronaviruses were under to evolve new variants that could evade prior immunity. Once you get that selection pressure, the number of apparent new variants ratchets up quickly, because anything that isn't new can't spread effectively in our high-immunity environment.

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NohPhD t1_j7n9wmw wrote

One interesting factor that might be exacerbating the situation is there exists an anti-COVID medicine that works by promoting mutations in the virus RNA during replication. While this tactic may help the intended recipient it now appears that the medication may be contributing to the unexpectedly high overall mutation rate of the COVID virus.

Who thought this was a good idea in the long run?

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Straight-Plankton-15 t1_j7o2e0x wrote

I think this comparison was probably because the viral polymerases encoded by coronaviruses are less prone per cycle to replication errors that cause mutations than some other viruses, such as influenza viruses. So for each instance at a molecular level of a polymerase replicating an mRNA sequence, a mutation is more likely for influenza viruses than for coronaviruses.

At the same time, an extremely infective virus like SARS-CoV-2 (especially with newer variants) will produce so much viral load that there becomes more opportunity for mutations per infection. Combine that with far more individuals being infected with SARS-CoV-2 each year than influenza, and you have SARS-CoV-2 mutating at a much faster rate.

Stopping the spread of the virus would be the most effective strategy to stop the continued development of new mutations.

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TearsFallWithoutTain t1_j7k9535 wrote

Was that the prediction though? Seems like a virus that's just jumped a species gap has a lot of easy optimisation available. What I was seeing in my academic circles was the expectation that the first version would be replaced fairly quickly

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JAK2222 t1_j7lu7j9 wrote

Because in a sense it is true. SARS CoV 2 is I still a virus that mutates relatively slowly ( actually has proofreading machinery) compared to many other viruses.

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atred t1_j7lx0bm wrote

I was responding to this:

> SARS-CoV-2, for instance, is highly mutable.

To be charitable to the OP, the comparison base they used was probably different. Thanks for clarification.

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notchoosingone t1_j7jn8du wrote

I was picking up a prescription in August 2020, the middle of some very strict lockdowns in Australia, and I asked the lady at the pharmacy about the cold and flu season. She said it basically hadn't happened that year; she had drug company reps calling her like "do you need supplies? ...please?".

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TearsFallWithoutTain t1_j7k9atl wrote

> "do you need supplies? ...please?".

That is very funny, while also an indication that things along the lines of "yearly vaccination that a country needs" probably should be nationalised lol

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coachrx t1_j7jxolx wrote

I think this is the most revealing thing about the covid lockdown. I am a hospital pharmacist and we noticed that the traditional flu season did not take place to any appreciable degree. It is not realistic to adopt these extreme measures moving forward, I just hope at the very least people gained a little more insight into the pathology and transmission of communicable disease.

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MCPhssthpok t1_j7jpbmp wrote

The winters of 2020 and 2021 were the only ones I can remember where I didn't catch some cold or other. This winter I didn't even get to the end of October before someone coughed all over me without even bothering to cover their mouth and gave me RSV.

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Livesies t1_j7haplq wrote

To add:

The quarantine measures taken to combat covid were so effective that the incidence, and particularly mortality, of the various common cold viruses tanked dramatically, I saw figures saying <1% compared to typical. Some variants were reportedly wiped out due to these same measures.

That being said, many of the viruses labeled as the common cold also have the ability to infect animals which makes it highly unlikely that those would be eradicated.

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humanophile t1_j7hc0b9 wrote

This story was the moment I knew that COVID probably would never go away. I think the first infected deer they found were on Staten Island.

https://www.nature.com/articles/d41586-021-02110-8

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SocialWinker t1_j7hkvkc wrote

I feel like I remember seeing a few sporadic articles about household pets testing positive for COVID during 2020, though it may have been later. I know the first time I had to quarantine, the telehealth nurse on the phone told me to avoid my pets, if possible, to prevent spreading it to them. Seemed sort of weird at the time, even though I was aware that it’s possible for a virus to jump species easily enough.

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Gisschace t1_j7hqt4o wrote

If I recall; dogs and cats can carry it but it doesn’t really effect dogs that badly whereas Cats can have similar symptoms to us

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SocialWinker t1_j7hse94 wrote

I could see that. I never heard anything about them actually getting "sick", just little things like the CDC site.

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Gisschace t1_j7ht4cf wrote

This is a shitty site but explains it, dogs have a mutation in their ACE2 which means they have a natural resistance to it, which cats don’t. So they can catch it but the virus replicates poorly and so it doesn’t really spread to us or other dogs.

https://www.aaha.org/publications/newstat/articles/2020-08/the-reason-cats-get-covid-and-dogs-dont/

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xoriatis71 t1_j7jpiha wrote

It's not just about the severity of COVID when it comes to pets. Like a previous commenter stated, COVID can jump ship, infecting animals as well as humans. While infected, animals can help COVID mutate, and due to the fact that it can then jump back to humans, we risk contracting a completely new COVID variant at worst.

Edit: A reply right below this one said that due to a mutation in their ACE2, dogs are resistant to COVID, as that mutation doesn't allow COVID to multiply efficiently, thus reducing transmissibility between humans and other dogs. As a result, my reply doesn't really apply to dogs.

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PainfulJoke t1_j7hobw2 wrote

I also heard that same advice being mentioned to avoid animals being uninfected carriers of the disease (as in on their fur, saliva, etc).

I'd be interested to learn if it's currently known to be transmittable to common housepets or if that advice was out of an abundance of caution.

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SocialWinker t1_j7hori9 wrote

The CDC site says it has been transmitted to household pets. >Pets worldwide, including cats and dogs, have been infected with the virus that causes COVID-19, mostly after close contact with people with COVID-19.

Sounds like it's a realistic concern. Not that there's a ton of information on there.

Source: https://www.cdc.gov/healthypets/covid-19/pets.html

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birdstork t1_j7jhsvh wrote

In NYC we were concerned about cats after a Lion and a few tigers at the Bronx Zoo caught covid. The zoo had been closed to the public but caretakers were coming to work as usual. This was a rough week; we’d already been hearing sirens nonstop (ambulances) and then it was like “oh come ON now cats too???”

https://newsroom.wcs.org/News-Releases/articleType/ArticleView/articleId/14084/Update-Bronx-Zoo-Tigers-and-Lions-Recovering-from-COVID-19.aspx

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samanthasgramma t1_j7i6wew wrote

For me, I knew it was never going away when they said it was a coronavirus. I had recently done some reading on the Spanish Flu that took me into that rabbit hole I call "hyperlinks" (can get lost for hours). When they said "coronavirus", I said "And those would be part of our seasonal colds and flus, and they just keep mutating but don't actually die off."

I told that to someone and they said "Oh, big lady with the crystal ball!". Yeah. Dude. It's a coronavirus. I didn't need one.

I never bought into "It's going to be OVER". I was just resigned to it from the get go. I haven't decided if that's a good thing or a bad thing.

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Lumpy-Dingo-947 t1_j7ilbxe wrote

We managed to slow it down enough to keep the hospitals from getting completely overrun in the US at least.

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lafigatatia t1_j7kj1lu wrote

SARS (the original not the remake) was a coronavirus and it did go away, after appropriate contention measures. But it didn't have asymptomatic carriers, which made those measures much easier. The moment this one spread out of Wuhan it was already too late.

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PRSArchon t1_j7lx0aw wrote

While it is true the virus will never be gone, it is over in many countries. I have not noticed a single thing about covid in the past ~10 months where I live. That’s mostly due to very good vaccination rates. Sure there will be seasonal vaccinations for some demographics but that is no different than the flu.

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binary101 t1_j7i5qng wrote

I do wonder, in a perfect world if everyone adhered to a three-week quarantine, just how many different strains of viruses or bacterial diseases we could have eliminated.

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androgenoide t1_j7ipyam wrote

As opposed to living in a world where workers have to go in and prepare our food when they're sick because they don't get paid sick days?

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binary101 t1_j7ivssg wrote

I know it's unrealistic, asking as a hypothetical because there will always be an exception.

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androgenoide t1_j7j3213 wrote

I know. It bothers me because it seems like it should be such an easy fix to keep food workers home but it turns out to be almost impossible.

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binary101 t1_j7j5tfe wrote

I think there are several issues, it can be done but it would require massive amount of planning, which like you said would make it almost impossible.

If we look at the COVID response and past pandemics, its very sudden and catches people out and causes mass panic (everyone going out to buy toilet paper). As no one knows/knew how long the lock downs would be.

However, if we announced it beforehand, informing the public of the duration of the quarantine. Set up supply drop offs, re-assure the public that there won't be supply issues, account for basic contingencies, it could be done, but it would require an almost militaristic amount of planning and logistics.

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ThisUsernameIsTook t1_j7j7whe wrote

Isn’t that sort of what China tried to do? Human nature makes it a really hard problem to solve out in the imperfect world.

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binary101 t1_j7j8aic wrote

Not really, China just had unexpected quarantines with no info on end dates and letting the public figure out how they were going to get supplies to keep alive for the duration.

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p-terydatctyl t1_j7jk5pe wrote

If you'd like to know look at new zealand. They managed to eradicate covid and while we were in full swing they were playing rugby in full stadiums w/ no masks. Shame the rest of the world couldn't follow suit

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crispy48867 t1_j7iqjok wrote

If the world were to mask up for maybe 5 weeks, most airborne diseases would be wiped out, at least for a few years if not longer.

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Octavia9 t1_j7ksjfs wrote

It’s pretty impossible for everyone to quarantine. We need safety services, health care, food, agriculture can’t just stop especially caring for livestock. Utilities have to keep running. It’s a long list and reminds me how interdependent we really are on each other.

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