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Medicine Science

'We Study Virus Evolution. Here's Where We Think the Coronavirus Is Going.' (nytimes.com) 130

Posted by msmash from the closer-look dept.
Sarah Cobey, who studies the interaction of immunity, virus evolution and transmission at the University of Chicago, Jesse Bloom and Tyler Starr, both of whom study virus evolution at Fred Hutchinson Cancer Research Center in Seattle, writing for The New York Times: It's impossible to say whether future variants will have more big Omicron-like jumps or more typical stepwise changes, but we are confident SARS-CoV-2 will continue to evolve to escape immunity. While transmissibility of viruses does plateau at a certain point, other human viruses that escape immunity keep doing so. The influenza vaccine has been updated annually for decades to chase viral evolution, and some influenza viruses show no sign of slowing down. Immune escape is an endless evolutionary arms race, because the immune system can always make new antibodies and the virus has a vast set of mutations to explore in response. For instance, Omicron has just a tiny fraction of the many mutations that have been observed in SARS-CoV-2 or related bat viruses, which are in turn just a small fraction of what lab experiments suggest the virus could potentially explore.

Taking all this together, we expect SARS-CoV-2 will continue to cause new epidemics, but they will increasingly be driven by the ability to skirt the immune system. In this sense, the future may look something like the seasonal flu, where new variants cause waves of cases each year. If this happens, which we expect it will, vaccines may need to be updated regularly similar to the flu vaccines unless we develop broader variant-proof vaccines. And of course, how much all this matters for public health depends on how sick the virus makes us. That is the hardest prediction to make, because evolution selects for viruses that spread well, and whether that makes disease severity go up or down is mostly a matter of luck. But we do know that immunity reduces disease severity even when it doesn't fully block infections and spread, and immunity gained from vaccination and prior infections has helped blunt the impact of the Omicron wave in many countries. Updated or improved vaccines and other measures that slow transmission remain our best strategies for handling an uncertain evolutionary future.
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'We Study Virus Evolution. Here's Where We Think the Coronavirus Is Going.' More

'We Study Virus Evolution. Here's Where We Think the Coronavirus Is Going.'

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  • Long term effects (Score:4, Insightful)

    by sTERNKERN ( 1290626 ) on Wednesday March 30, 2022 @04:35PM (#62403877)
    While the flu can be dangerous to the elderly and sick it generally generally one can get through it without sideeffects. This can not be said about Covid, so if it stays with us the way flu does it may have considerable long term issues with the general public.
    • The US clearly needs set precedence now, in order prevent undue weight on our beleaguered medical insurance companies by declaring Covid as a pre-existing condition. We were fortunate that our legislative bodies pushed so hard to protect . . . healthcare workers . . . from law suits by making sure you can't sue anyone over covid. We narrowly avoided a 'pandemic of law suits" . . . you know, in the US.

      I know. I'm a bad man . . . but they set the bar so low for wiseacres these days.

      Get off my lawn.

    • Re: (Score:2)

      by AmiMoJo ( 196126 )

      Long COVID seems to be very similar to, possibly the same thing as CFS/ME. I have the latter, and it's hell. It really is no joke, even if the death rate is lower now the long term effects can be devastating.

      There are also big economic ramifications of large numbers of people being removed from the workforce, or going part-time because of Long COVID.

    • According to https://www.npr.org/sections/g... [npr.org]

      The % of infected people who suffer from long covid is from 5 to 60%, depending on how it's defined.

      Even if only 5% get long covid, and only a million people are infected yearly, out of which 5% will need ongoing long term care, that's an additional 50,000 people who will need some form of long term care - and keep adding another 50,000 every year. In 10 years that will be an additional 500,000 people.

      If the numbers are worst, expect more people to need long te

    • There are cases of "long flu" as well, though in terms of numbers a lot less than COVID.

    • Re: (Score:2)

      by Xenna ( 37238 )

      We could be looking at multiple Covid infections every year if we go back to our old life styles (I haven't). This is not what we're used to with influenza. I can't remember the last time I had a flu. This alone makes Covid a lot more dangerous. You roll the dice for long term effects every infection and with every new variant. Each infection shields you from reinfection for a few months tops.

  • March 2020 called (Score:1)

    by Anonymous Coward

    Seriously, we knew all this 2 years ago. It was also known when they started pushing the vaccines as hard as they were.

    Which makes all the restrictions and vax mandates as galling as they are. It's as if they're still aiming for zero-covid.

    Speaking of the annual flu vaccine; 30% efficacy is considered a "good" year. Normally it's lower. That's what we can look forward to with the c19 vaccine...which is mandated, remember. This, too, was known in March of 2020.

    • Re: (Score:2)

      by dgatwood ( 11270 )

      Speaking of the annual flu vaccine; 30% efficacy is considered a "good" year. Normally it's lower. That's what we can look forward to with the c19 vaccine...which is mandated, remember. This, too, was known in March of 2020.

      You don't know what you're talking about. The typical range for flu VE is 40 to 60%. Anything as low as 30% would be a spectacularly BAD year, though there are occasionally years where it is lower than that.

      And one reason that flu effectiveness is so low is because flu is thoroughly endemic, with a ridiculous number of strains. Another reason is because flu vaccines are produced by infecting actual living cells with an attenuated virus, and that virus sometimes mutates [science.org], resulting in a vaccine that doesn'

  • Influenza (Score:3)

    by phantomfive ( 622387 ) on Wednesday March 30, 2022 @05:16PM (#62403923) Journal

    I really wish people would stop using influenza as the benchmark for how quickly viruses mutate. Some viruses hardly mutate at all, like polio. Others mutate very quickly.

    Influenza is one of the fastest mutating viruses out there. Coronavirus is somewhere between polio and influenza. If you want to understand how it will behave, then both polio and influenza will mislead you. It's somewhere inbetween.

    • Thanks for mentioning that.

      It occurs to me that flu is the ONLY virus (family) for which we need new vaccines every year.

      Most of us got vaccinated against about fourteen different things when we were kids, and those vaccinations still protect us.

      • tdap vaccine is boosted every 10 years in adulthood, plus more frequently when you have a kid or work with babies because the pertussis vaccine wanes rather quickly and the virus is deadly to infants.

      • Re: (Score:2)

        by edwdig ( 47888 )

        It occurs to me that flu is the ONLY virus (family) for which we need new vaccines every year.

        I'm not sure what point you're trying to make.

        HIV mutates way faster, and it's been a huge barrier to creating a vaccine.

        Cold viruses mutate very fast as well, but there are tons of them, and they aren't very severe, so it hasn't been worth the effort to try to develop vaccines.

        Flu hits a sweet spot where the mutation rate is still somewhat manageable for vaccine development, and the disease is severe enough to be worth the effort to develop the vaccine.

        I'm sure there are more relevant examples, but those a

  • that keeps on giving! Year after year. This is why gain-of-function research should be strictly regulated if not banned. If you don't deliberately teach a virus how to infect humans it will have a much harder time doing so. But since COVID-19 was likely a "tweaked" escapee it was already fully adept at human transmission.

    • Re: (Score:2)

      by DRJlaw ( 946416 )

      If you don't deliberately teach a virus how to infect humans it will have a much harder time doing so.

      Were the Chinese deliberately teaching the virus how to infect North American white-tailed deer too [pbs.org]?

      Or maybe, just maybe, SARS-COV-2 managed to jump species barriers into humans, mink, deer, and the like all on its own. *gasp*

      • Yeah, it's way more likely that it teleported to Wuhan market from some bat cave 1000 km from there (*if* it even exists in the wild there, which still hasn't been proven, despite the Chinese putting lot of effort into it), than got there from a lab across the street, doing GOF research on it.

        • So why are you so desperate to believe it?

        • Re: (Score:2)

          by DRJlaw ( 946416 )

          Yeah, it's way more likely that it teleported to Wuhan market from some bat cave 1000 km from there (*if* it even exists in the wild there, which still hasn't been proven, despite the Chinese putting lot of effort into it), than got there from a lab across the street, doing GOF research on it.

          No teleportation necessary [npr.org]. The wet market vendors bring the animal to you. You know, the very purpose of a market.

          • So a wild bat from 1000km away infected a raccoon dog which was then transported to Wuhan where it sneezed on someone and thus the virus started there.... already extremely well-adapted to human transmission. OR the virus came from a nearby lab that was collecting bats from remote areas and experimenting with gain-of-function research. A low-security lab that had a history of control issues, so much so that the State Department sent an urgent telegram about it.

          • Yeah, it's way more likely that it teleported to Wuhan market from some bat cave 1000 km from there (*if* it even exists in the wild there, which still hasn't been proven, despite the Chinese putting lot of effort into it), than got there from a lab across the street, doing GOF research on it.

            No teleportation necessary [npr.org]. The wet market vendors bring the animal to you. You know, the very purpose of a market.

            Except, it's not a "wetmarket", it's a seafood market, there is precisely zero evidence it ever traded in bats, despite lists of stock traded there being available, bats are not commonly eaten in the region and you'd be as likely to find one there as in supermarket in US. Yeah, definitely much more likely than a lab worker getting infected at work, and visiting the market across the street after work to get some stuff for dinner and coughing at stuff. And Chinks ran a frantic coverup at the lab just for teh

            • Re: (Score:2)

              by DRJlaw ( 946416 )

              Except, it's not a "wetmarket", it's a seafood market,

              Raccoon dogs and red foxes are seafood? [npr.org] News to me...

              there is precisely zero evidence it ever traded in bats, despite lists of stock traded there being available, bats are not commonly eaten in the region and you'd be as likely to find one there as in supermarket in US.

              Because the source could only be a bat [usnews.com], eh?

              Yeah, definitely much more likely than a lab worker getting infected at work, and visiting the market across the street after work to get some s

              • The market did trade in a few Racoon Dogs. None of them tested positive for SARS-2, only things touched by people.

                We know that the market did not trade bats, via other authoritative surveys.

                We know the market was a super spreader. Crowded and damp. But there is no evidence it was a source.

                For details see
                https://www.originofcovid.org/ [originofcovid.org]

              • Hmm. Progress. Went from "tinfoil hat conspiracy theory" to "equally likely". For now that'll suffice.

                • Re: (Score:2)

                  by DRJlaw ( 946416 )

                  Hmm. Progress. Went from "tinfoil hat conspiracy theory" to "equally likely". For now that'll suffice.

                  No, stayed in the exact same position. Quote where I wrote anything like "tinfoil hat conspiracy theory."

                  Meanwhile, you won't even acknowledge the possibility of a natural interspecies-jumping origin, will you?

    • gain-of-function research

      Did you even know what that was before Fox started throwing the phrase around?

    • The fact that just two years of evolution in human hosts has made the virus an order of magnitude more infectious is pretty much proof that the original strain was in no way optimized to infect people.

      • A pile of BS.. earlier SARS virus outbreaks were short lived because the virus was not adept at human transmission. COVID *exploded* onto the human world stage. It genome did not need to evolve at all. And "just two year of evolution" is a long time for a global viral pandemic.
  • I thought we weren't supposed to say that

  • It's impossible to say whether future variants will have more big Omicron-like jumps or more typical stepwise changes, but we are confident SARS-CoV-2 will continue to evolve to escape immunity.

    Immune escape is an endless evolutionary arms race, because the immune system can always make new antibodies and the virus has a vast set of mutations to explore in response.

    There has thus far not been sufficient changes to meaningfully interfere with polyclonal immune response. This is the reason the original vaccines are still effective at preventing severe disease and death while being nearly worthless at preventing infection.

    Antibodies are very specific and therefore easily affected by viral changes which will cause people to become infected yet infections are not the relevant metric. People don't care and don't get vaccinated over whether they get infected or not they ca

    • Why would we want to slow transmission when natural infection is most likely to improve immunity against both reinfection and unknowable future variants above and beyond current vaccines?

      Why would you think that is the actual case? Neither vaccination nor previous infection seem effective against infection with Omicron. No reason to think infection with Omicron will be durable either (which is true of coronaviruses in general). Too soon to even know so you are speculating based on nothing, and certainly not historic experience.

      • Why would you think that is the actual case?

        Infection has been shown to provide superior immunity.
        https://www.cdc.gov/mmwr/volum... [cdc.gov]
        https://www.biorxiv.org/conten... [biorxiv.org]

        Infection is likely superior against unknown future changes because it is able to produce an immune response to more of the virus than just the single s-protein analogue.

        Neither vaccination nor previous infection seem effective against infection with Omicron.

        Prevention of infection is irrelevant. What matters is health outcomes not infections.

        No reason to think infection with Omicron will be durable either (which is true of coronaviruses in general).

        Again irrelevant. What matters is durability against severe outcomes not infection.

        Too soon to even know so you are speculating based on nothing, and certainly not historic experience.

        Which historic experience would this be? Since whe

        • Prevention of infection is irrelevant. What matters is health outcomes not infections.

          The risk of adverse health outcomes as a result of acquiring immunity through infection is much higher than through vaccination. That is why we have vaccines in the first place.

          What matters is durability against severe outcomes not infection.

          And when immunity starts to wane, you can just get infected again to give it a boost. I'll just get a booster shot thanks.

          • The risk of adverse health outcomes as a result of acquiring immunity through infection is much higher than through vaccination. That is why we have vaccines in the first place.

            My original question: "Why would we want more vaccines when natural infection AFTER vaccination does a better job?"

            Clearly NOT about choosing between vaccination and infection.

            The issue at hand is not a contest between vaccination and natural infection but rather leveraging natural infection post vaccination to maximize immunity.

            Current vaccines are not offering useful sterilizing immunity and so everyone can expect to be exposed regardless of whether or not they are vaccinated. All hiding from infection d

            • All hiding from infection does post vaccination is reduce your immunity to covid when (not if) you catch it.

              Not catching it is the goal to aspire to, but by all means you do you.

              • Not catching it is the goal to aspire to, but by all means you do you.

                Not catching it is not an option for most everyone living on planet earth.

    • Your comment title "Evidence free assertions" is perfect for your comment, especially the end:

      Why would we want more vaccines when natural infection after vaccination does a better job?

      You assert that natural infection after vaccination does a better job of prepping the immune system to react, but in fact you are safer if vaccinated whether you have had covid or not [hopkinsmedicine.org].

      • Your comment title "Evidence free assertions" is perfect for your comment, especially the end:

        You assert that natural infection after vaccination does a better job of prepping the immune system to react, but in fact you are safer if vaccinated whether you have had covid or not.

        Did you read what you wrote before clicking submit? How can one catch covid after vaccination and not be vaccinated while catching covid? What is it about "after vaccination" you do not understand?

        • How can one catch covid after vaccination and not be vaccinated while catching covid?

          What I said was that vaccination improves resistance even if you have resistance from catching covid, and not whatever you imagined I said in your fever dream.

          • What I said was that vaccination improves resistance even if you have resistance from catching covid, and not whatever you imagined I said in your fever dream.

            Are you able to answer my question? If you've already been vaccinated prior to catching covid how can you catch covid without being vaccinated? If this is not possible then it stands to reason that you would have already been vaccinated when catching covid...e.g. you would have both.

            If you can't answer it then what is the purpose of "Your comment title "Evidence free assertions" is perfect for your comment" and what is the basis of your disagreement? What are you disagreeing with?

            • What you said, and I quote, is "Why would we want more vaccines when natural infection after vaccination does a better job?" And in fact the evidence runs contrary to that. It doesn't matter whether you get Covid before or after you get a vaccine, either way you get better outcomes with two shots than you do with one shot and one infection.

              • What you said, and I quote, is "Why would we want more vaccines when natural infection after vaccination does a better job?" And in fact the evidence runs contrary to that. It doesn't matter whether you get Covid before or after you get a vaccine,

                I've have not claimed sequencing matters WRT immunity. The reason for sequencing vaccination prior to infection is obviously preventing illness not maximizing immunity.

                either way you get better outcomes with two shots than you do with one shot and one infection.

                Why are you talking about shots? Why do you think vaccination means getting "one shot"? Who said anything about getting one shot? It sure as heck was not me.

  • I've always taken covid seriously, it's killed a lot of people and the long covid stuff sucks (though there will be a lot of psychogenic "long covid" like there is "lyme's diseases"). I got vaccinated and boosted.

    But the Very Online Left is getting real weird about this shit. I don't even understand a lot of the dumb shit I see on twitter from self-proclaimed "disability advocates". It seems they expect everyone to basically mask up forever? Weird take - it's not going to happen. Once risk for 90% of the c

    • It seems they expect everyone to basically mask up forever?

      Yeah. Obviously. Have you only just realised that?

      Weird take - it's not going to happen.

      I was mildly disparaging of the habit that high proportions of the population of Asian cities acquired after the MERS/ SARS worries about a decade ago : wear a medical mask everywhere that there are a lot of people. Well, I was wrong ; they were right.

      Compared to the grudging, slow, inconsistent take up of masks in the West in general, the East knew why, and wh

    • Weird take - it's not going to happen. Once risk for 90% of the country gets to reasonable levels the masks are off. Sorry not sorry.

      What's reasonable? Out of the top five things that kill us, writing in a new #1 with a whopping 30% additional deaths per week, is that reasonable?
      https://www.cdc.gov/nchs/nvss/... [cdc.gov]

      • Re: (Score:2)

        by jvkjvk ( 102057 )

        >>Weird take - it's not going to happen. Once risk for 90% of the country gets to reasonable levels the masks are off. Sorry not sorry.

        >What's reasonable? Out of the top five things that kill us, writing in a new #1 with a whopping 30% additional deaths per week, is that reasonable?

        Reasonable is when it becomes endemic instead of a pandemic. And we are getting there. I just don't see wearing masks either becoming a societal issue or a legal issue in the US.

    • The real interesting thing about what you're describing is how this mask thing really has nothing to do with right or left in actuality. In my country (Israel) it's the exact opposite, we had a "right-wing" pro-trump leader, however, unlike Trump, he was very strongly pro-masks and pro-vaccination. In response to this, many people in our extreme left started believing in US right wing conspiracy theories, insisting that masks are meant to oppress our personal freedom, and that our government has some secret

  • It's a virus. It's not intelligent. It has no motives. It mutates, 'evolves', and some variants are so unsuccessful they are never noticed. Others maybe linger but never are able to spread much and fail within a small population. Some, yes, they are wildly more communicable, resistant to immune response, and spread rapidly. Some even inspire serious disease symptoms, and cause a lot of trouble

    'Escape'? 'Evolve'? Romantic language, but many of us hardly understand this stuff at all, and we cling to understa

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