10 ms·

Omicron Time

47 points by hprotagonist 5y ago

h2odragon 5y ago
Refreshingly hype and agenda free reporting, as usual from Derek Lowe. And still "[vaccination] is better than a naive immune system" with the conspicuous gap of where "already infected / recovered / might not have had symptoms even" might go. "effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet.
- jaywalk 5y ago
  > "effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet. And yet you call this simple, scientific fact that wouldn't have been remotely controversial two years ago an "antivaxer argument"
  - Retric 5y ago
    Why is that supposed to be an antivaxer argument? It doesn’t mean an effective vaccine eliminates variant formation.
    - jaywalk 5y ago
      I have no idea, I'm not the one who said it was. Even though the Covid vaccines don't prevent infection and transmission, by helping the body fight off the virus they absolutely do help prevent variant formation.
      - landemva 5y ago
        Variants are developing in animals like cats and deer, and spreading back to humans. The sooner we get to variants that are highly transmissible with only cold-like effects, the sooner we can stop the nonsense about trying to prevent variants.
        deleted 5y ago
        [deleted]
      - metamet 5y ago
        They also do reduce infection and transmission, just not completely prevent it all the time.
        jaywalk 5y ago
        They definitely do not reduce transmission, at least not with the currently circulating variants: https://www.ucdavis.edu/health/covid-19/news/viral-loads-similar-between-vaccinated-and-unvaccinated-people https://www.ucdavis.edu/health/covid-19/news/viral-loads-sim...
        Retric 5y ago
        That doesn’t support your argument. Although vaccinated people with a breakthrough infection are much less likely to become severely ill than unvaccinated, the new study shows that they can be carrying similar amounts of virus and could potentially spread the virus to other people Could potentially spread is not the same as saying their equally likely to spread. Fewer infections and less severe cases both reduce transmission to the general population at least in the short term. Long term it may be that effectively everyone gets either COVID and or the vaccine.
        jaywalk 5y ago
        When I say they don't reduce transmission, I mean (and the article backs up) that an infected vaccinated person transmits the virus just as much as an infected unvaccinated person. Probability of infection between the two groups is a different subject.
        Retric 5y ago
        They specifically say: “Our study does not provide information on infectiousness.” That said, if people are equally infections while sick, but their sick for a shorter period then their less likely to infect others.
  - kgwgk 5y ago
    I don't think it's an antivaxer argument but if you develop the reasoning it really becomes somewhat controversial. The problem is that vaccines are not completely effective (efficacy goes down with time, is lower against new variants, there are breakthrough infections, etc.) so variant formation is not completely supressed. Everything being equal (given one exposed or even one infected person) you may have less variant formation with vaccines. But when you have more infections you will end up having more variants. That the number of infections would increase as people's behaviour adapted to the lower fatality rate was not unexpected: people take more risks because the prognosis of an infection is not so bad anyway, once infected they may have a mild, undiagnosed evolution and still contribution propagation... And it's no longer an hypothetical scenario. In many European countries there are more infections now than ever before.
- sv123 5y ago
  I don't keep up with antivaxer arguments, and maybe I'm daft, but doesn't that mean if everybody were vaccinated then fewer variants would show up?
  - neuronexmachina 5y ago
    Yeah, I'm not sure how what the other commenter is saying follows from what Lowe wrote.
- Barrin92 5y ago
  you gotta explain to me how that's an antivaxer argument because suppressing variant formation is a good thing. As he explains in the very next sentence strengthening the immune response lowers the risk of prolonged battles and chances for mutation which is what we want
  - sigg3 5y ago
    Anti-antivaxer, i think.
- rafale 5y ago
  Is he saying the current vaccines are not efficient? I still don't get what makes covid different from the flu. Yes, covid is a little bit more deadly, but other than, why don't we just accept it as part of our lives like we did with the flu?
  - landemva 5y ago
    Fear sells.
  - Retric 5y ago
    Over 700,000 (edit it’s now 800,000) dead Americans is about 20x as bad as the flu even with all of these measures, that’s huge. But even that understates the difference when you measure years of life lost. The flu typically kills the extreme elderly or people with extremely compromised immune systems. Aka they might die at 94 vs 95. COVID on the other kills people who are relatively much healthier, someone that dies at 75 vs 95 lost 20 years not 1. This is also why people 70+ are almost fully vaccinated in the US. For that age range it’s an extremely serious disease with a high chance of killing them after infection.
    - dev_tty01 5y ago
      >This is also why people 70+ are almost fully vaccinated in the US. For that age range it’s an extremely serious disease with a high chance of killing them after infection. Older people certainly dominate the vulnerable groups, but there are many other people living with various forms of immune system dysfunction. This is why the rest of us need to mask, vaccinate, and get boosters to minimize our chance of propagating the disease to the more vulnerable parts of our population. Not doing so is basically saying you don't care about other people.
      - stolenmerch 5y ago
        Very honest and good faith question. Until when? What are the specific metrics for when we don't need masks or non-tweaked vaccines tailored to yearly variants like normal flu shots? At some point we need to say "if you are immunocompromised you need to take special precautions like you always did before covid". Just wondering out loud when that should be because for some of us it's sooner rather than later.
- nobody9999 5y ago
  >"effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet. Are you implying that since variants exist, then the vaccines aren't effective? That's not what the data shows[1]. I'd point out that South Africa, where the Omicron variant was first characterized, vaccines have only ~30% penetration in the population[0], making it a good reservoir for mutated variants to spread. [0] https://ourworldindata.org/covid-vaccinations https://ourworldindata.org/covid-vaccinations [1] https://www.news-medical.net/news/20211123/Systematic-review-finds-COVID-19-vaccine-efficacy-remains-high-for-at-least-six-months.aspx https://www.news-medical.net/news/20211123/Systematic-review...
  - nradov 5y ago
    The current thinking is that new variants are most likely to evolve in immunocompromised patients who experience prolonged infections. While I encourage everyone eligible to get vaccinated, the vaccines aren't very effective in people with malfunctioning immune systems. https://www.scientificamerican.com/article/covid-variants-may-arise-in-people-with-compromised-immune-systems/ https://www.scientificamerican.com/article/covid-variants-ma...
    - mlyle 5y ago
      No, but increased vaccination rates and resultant lower case rates mean the conditions that are ideal for the formation of variants arise less often. (Yes, I know the vaccine isn't completely sterilizing, but it still has significantly tamped down the degree of spread).
    - metamet 5y ago
      > While I encourage everyone eligible to get vaccinated, the vaccines aren't very effective in people with malfunctioning immune systems. Isn't the fact that folks with malfunctioning immune systems are surviving rather than dying evidence that the vaccine is working? Granted, their survival has the side effect of a prolonged infection, but immunocompromised folks don't fare well against COVID.
    - nobody9999 5y ago
deleted 5y ago
[deleted]
pattrn 5y ago
My naive understanding of why it's so difficult to stop coronaviruses in general from spreading is due to the virus moving between humans and animals. If that's true, and if that causes virus mutation, then is it possible to stop the mutations even with a theoretical 100% global vaccination?
- fooey 5y ago
  I would say the goal of vaccinations is to minimize death and to prevent medical systems from being overwhelmed. I don't think COVID-19 is a disease that can be eradicated. The fewer hosts out there though, the fewer opportunities it has to mutate.
  - pwned1 5y ago
    Since every household that has a pet has additional hosts, there is no way to meaningfully reduce the number of hosts.
- technobabbler 5y ago
  It may have been possible to contain it early on. Way too late now. It's here to stay forever, with new strains constantly evolving.
jl6 5y ago
I seem to recall one of the original arguments for the “artificial origin” hypothesis last year was that the virus was too different from other known viruses and therefore it was implausible that it had developed naturally. But if we see here an apparently-sudden jump to a significantly different variant, does that make it less surprising that the original strain was novel?
- vadfa 5y ago
  What if that new variant is also engineered?
  - technobabbler 5y ago
    What if new variants inevitably emerge given global mutations and lackluster vaccinations?
  - grlass 5y ago
    most "artificial origin" hypotheses centre around a lab-leak. The number of scenarios where the new variant is engineered are vastly reduced, since it's less likely that this variant is a lab leak. Other scenarios can still be within the realm of plausibility, but there are fewer of them.
- JamesBarney 5y ago
  I think there are few differences. 1) Covid-19 was more dissimilar from previous coronaviruses than Omicron is from current ones. 2) There is a lot more covid-19 in the world now so rare occurrences are more common. 3) There was other evidence for the lab leak hypothesis. A cover up from China, a viral research lab in the city with the outbreak, etc...
  - waynecochran 5y ago
    Just to be pedantic. Covid-19 is the disease, not the virus. SARS-COV-2 is the virus.
- manojlds 5y ago
mfer 5y ago
One thing I don't see being talked about is how virulent (rapid onset of severe illness) omicron is. The rate of spread isn't the only element. The viruses that are the common cold spread wildly but don't cause major issues for most people. Why don't we talk about this more?
- nradov 5y ago
  There are several other endemic human coronaviruses like HCoV-OC43 which cause common cold symptoms. Most of us catch them as youths and the resulting natural immunity protects us from severe symptoms during later reinfections. However they can still be deadly to frail and immunocompromised patients. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252012/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252012/
- JamesBarney 5y ago
  I see discussions of this all the time around Omicron, the problem is we have no idea how virulent Omicron is. The attributes we care about are immune evasion, transmissibility, severity. We know the most about immune evasion, we have a little data on transmissibility, but we know didly squat about severity. People aren't talking about it much because we don't even have a bad guess about severity, much less a good guess. It'll takes a while to figure out severity. Deaths happen 2-8 weeks after symptoms. Which means we're still probably several weeks before we have any good data on severity. And this data is still really hard to parse out especially with immune evasion which makes the average case more mild, even if the disease is more virulent.
  - onlyrealcuzzo 5y ago
    Median time to death from onset of symptoms ~18.5 days: https://www.drugs.com/medical-answers/covid-19-symptoms-progress-death-3536264/ https://www.drugs.com/medical-answers/covid-19-symptoms-prog... Median time for first symptoms is ~4.5 days: https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guidance-management-patients.html https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guida... Within a week, we should start to have a decent picture WRT severity. Obviously, as time goes by, that picture will only get clearer.
dragontamer 5y ago
Its been a week to decompress from the hyperbolic headlines of last week, but this is still not enough time to answer the important questions. * How transmissible is Omicron? * Are Omicron infections milder, or more severe? * Can Omicron become dominant in this Delta environment? * How much can Omicron evade the vaccine-immunity and/or natural-immunity? These are the only questions people should care about, and it seems like none of these questions have an answer yet. ------- So I guess... lets wait another week and see if people have good answers to these questions. And if we don't have answers on Dec. 9th, then we will wait another week for Dec. 16th.
- Enginerrrd 5y ago
  I'll venture some guesses here: * How transmissible is Omicron? Very. But how much? Based on current data, there's a sort of invariant involving a tradeoff between greater escape of post-infection/post-vaccination immunity and greater transmissibility where anything along that invariant line can explain it's aggressive rise. Either way, it doesn't really matter. If it continues to behave as it has, we'll see a lot more of omicron. ~60% confidence * Are Omicron infections milder, or more severe? That's the BIG question right now. I've seen one MD describe patients that they've seen with omicron as being mild. On the other hand, there's also been a significant rise in hospitalizations in affected areas, however, if there's simply more infected, that would be expected. I don't have a good guess here. We haven't had enough time to find out. * Can Omicron become dominant in this Delta environment? Given it's very rapid rise to dominance in the small subset of testing data I've seen, I'll put money on it out-competing delta. ~60% confidence * How much can Omicron evade the vaccine-immunity and/or natural-immunity? Another good question. Despite the fact it has a lot of spike-protein mutations, and many experts believe that immune escape is likely here: I'm not convinced that's the best metric, and I've only 20-30% confidence in my agreement with it. I'll revise this according to the following pieces of evidence I expect to see, in increasing order of how much confidence I'll gain in that assessment for each piece: I'll gain more after I hear a lot of anecdotes about vaccinated getting sick, more if I see lab results confirm lower antibody affinity, and more still after actual numbers to high statistical significance confirm that previously infected or people 2-6 months post-vaccination have a high rate of infection en par with the rest of the population.
waynecochran 5y ago
That is by far the best science article I have read on SARS-COV-2 yet. The summary is concise and relevent and the linked graphics are incredible and tell the story well: https://covariants.org/variants/21K.Omicron https://covariants.org/variants/21K.Omicron https://nextstrain.org/groups/neherlab/ncov/21K.Omicron https://nextstrain.org/groups/neherlab/ncov/21K.Omicron
clircle 5y ago
Does anyone know if this blog still has an RSS feed? I think it has moved to a new domain.
- joshyeager 5y ago
  Yes, but I can only find the link on the main page of the blog, not in individual posts. Here it is: https://blogs.sciencemag.org/pipeline/feed https://blogs.sciencemag.org/pipeline/feed
cwkoss 5y ago
I don't know much about virology. Is it possible for variants to 'blend'? It sounds like Omicron has a number of variations vs Delta and other major variants. Is it possible that someone who is simultaneously infected with both Delta and Omicron to generate virus particles that utilize proteins from both variants in the same viral particle? If this can occur, would the genome of those viral particles get blended together, or would it just carry the genome of one or the other variants? i.e. would co-infection of multiple variants simultaneously increase mutation rate, or could hybrid variants appear?

47 points by hprotagonist 5y ago

Refreshingly hype and agenda free reporting, as usual from Derek Lowe. And still "[vaccination] is better than a naive immune system" with the conspicuous gap of where "already infected / recovered / might not have had symptoms even" might go. "effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet.

jaywalk 5y ago
> "effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet. And yet you call this simple, scientific fact that wouldn't have been remotely controversial two years ago an "antivaxer argument"
- Retric 5y ago
  Why is that supposed to be an antivaxer argument? It doesn’t mean an effective vaccine eliminates variant formation.
  - jaywalk 5y ago
    I have no idea, I'm not the one who said it was. Even though the Covid vaccines don't prevent infection and transmission, by helping the body fight off the virus they absolutely do help prevent variant formation.
    - landemva 5y ago
      Variants are developing in animals like cats and deer, and spreading back to humans. The sooner we get to variants that are highly transmissible with only cold-like effects, the sooner we can stop the nonsense about trying to prevent variants.
      - deleted 5y ago
        [deleted]
    - metamet 5y ago
      They also do reduce infection and transmission, just not completely prevent it all the time.
      - jaywalk 5y ago
        They definitely do not reduce transmission, at least not with the currently circulating variants: https://www.ucdavis.edu/health/covid-19/news/viral-loads-similar-between-vaccinated-and-unvaccinated-people https://www.ucdavis.edu/health/covid-19/news/viral-loads-sim...
        Retric 5y ago
        That doesn’t support your argument. Although vaccinated people with a breakthrough infection are much less likely to become severely ill than unvaccinated, the new study shows that they can be carrying similar amounts of virus and could potentially spread the virus to other people Could potentially spread is not the same as saying their equally likely to spread. Fewer infections and less severe cases both reduce transmission to the general population at least in the short term. Long term it may be that effectively everyone gets either COVID and or the vaccine.
        jaywalk 5y ago
        When I say they don't reduce transmission, I mean (and the article backs up) that an infected vaccinated person transmits the virus just as much as an infected unvaccinated person. Probability of infection between the two groups is a different subject.
        Retric 5y ago
        They specifically say: “Our study does not provide information on infectiousness.” That said, if people are equally infections while sick, but their sick for a shorter period then their less likely to infect others.
- kgwgk 5y ago
  I don't think it's an antivaxer argument but if you develop the reasoning it really becomes somewhat controversial. The problem is that vaccines are not completely effective (efficacy goes down with time, is lower against new variants, there are breakthrough infections, etc.) so variant formation is not completely supressed. Everything being equal (given one exposed or even one infected person) you may have less variant formation with vaccines. But when you have more infections you will end up having more variants. That the number of infections would increase as people's behaviour adapted to the lower fatality rate was not unexpected: people take more risks because the prognosis of an infection is not so bad anyway, once infected they may have a mild, undiagnosed evolution and still contribution propagation... And it's no longer an hypothetical scenario. In many European countries there are more infections now than ever before.
sv123 5y ago
I don't keep up with antivaxer arguments, and maybe I'm daft, but doesn't that mean if everybody were vaccinated then fewer variants would show up?
- neuronexmachina 5y ago
  Yeah, I'm not sure how what the other commenter is saying follows from what Lowe wrote.
Barrin92 5y ago
you gotta explain to me how that's an antivaxer argument because suppressing variant formation is a good thing. As he explains in the very next sentence strengthening the immune response lowers the risk of prolonged battles and chances for mutation which is what we want
- sigg3 5y ago
  Anti-antivaxer, i think.
rafale 5y ago
Is he saying the current vaccines are not efficient? I still don't get what makes covid different from the flu. Yes, covid is a little bit more deadly, but other than, why don't we just accept it as part of our lives like we did with the flu?
- landemva 5y ago
  Fear sells.
- Retric 5y ago
  Over 700,000 (edit it’s now 800,000) dead Americans is about 20x as bad as the flu even with all of these measures, that’s huge. But even that understates the difference when you measure years of life lost. The flu typically kills the extreme elderly or people with extremely compromised immune systems. Aka they might die at 94 vs 95. COVID on the other kills people who are relatively much healthier, someone that dies at 75 vs 95 lost 20 years not 1. This is also why people 70+ are almost fully vaccinated in the US. For that age range it’s an extremely serious disease with a high chance of killing them after infection.
  - dev_tty01 5y ago
    >This is also why people 70+ are almost fully vaccinated in the US. For that age range it’s an extremely serious disease with a high chance of killing them after infection. Older people certainly dominate the vulnerable groups, but there are many other people living with various forms of immune system dysfunction. This is why the rest of us need to mask, vaccinate, and get boosters to minimize our chance of propagating the disease to the more vulnerable parts of our population. Not doing so is basically saying you don't care about other people.
    - stolenmerch 5y ago
      Very honest and good faith question. Until when? What are the specific metrics for when we don't need masks or non-tweaked vaccines tailored to yearly variants like normal flu shots? At some point we need to say "if you are immunocompromised you need to take special precautions like you always did before covid". Just wondering out loud when that should be because for some of us it's sooner rather than later.
nobody9999 5y ago
>"effective vaccines actually suppress variant formation" is going to get him yelled at for supporting antivaxer arguments, I bet. Are you implying that since variants exist, then the vaccines aren't effective? That's not what the data shows[1]. I'd point out that South Africa, where the Omicron variant was first characterized, vaccines have only ~30% penetration in the population[0], making it a good reservoir for mutated variants to spread. [0] https://ourworldindata.org/covid-vaccinations https://ourworldindata.org/covid-vaccinations [1] https://www.news-medical.net/news/20211123/Systematic-review-finds-COVID-19-vaccine-efficacy-remains-high-for-at-least-six-months.aspx https://www.news-medical.net/news/20211123/Systematic-review...
- nradov 5y ago
  The current thinking is that new variants are most likely to evolve in immunocompromised patients who experience prolonged infections. While I encourage everyone eligible to get vaccinated, the vaccines aren't very effective in people with malfunctioning immune systems. https://www.scientificamerican.com/article/covid-variants-may-arise-in-people-with-compromised-immune-systems/ https://www.scientificamerican.com/article/covid-variants-ma...
  - mlyle 5y ago
    No, but increased vaccination rates and resultant lower case rates mean the conditions that are ideal for the formation of variants arise less often. (Yes, I know the vaccine isn't completely sterilizing, but it still has significantly tamped down the degree of spread).
  - metamet 5y ago
    > While I encourage everyone eligible to get vaccinated, the vaccines aren't very effective in people with malfunctioning immune systems. Isn't the fact that folks with malfunctioning immune systems are surviving rather than dying evidence that the vaccine is working? Granted, their survival has the side effect of a prolonged infection, but immunocompromised folks don't fare well against COVID.
  - nobody9999 5y ago

deleted 5y ago

[deleted]

pattrn 5y ago

My naive understanding of why it's so difficult to stop coronaviruses in general from spreading is due to the virus moving between humans and animals. If that's true, and if that causes virus mutation, then is it possible to stop the mutations even with a theoretical 100% global vaccination?

fooey 5y ago
I would say the goal of vaccinations is to minimize death and to prevent medical systems from being overwhelmed. I don't think COVID-19 is a disease that can be eradicated. The fewer hosts out there though, the fewer opportunities it has to mutate.
- pwned1 5y ago
  Since every household that has a pet has additional hosts, there is no way to meaningfully reduce the number of hosts.
technobabbler 5y ago
It may have been possible to contain it early on. Way too late now. It's here to stay forever, with new strains constantly evolving.

jl6 5y ago

I seem to recall one of the original arguments for the “artificial origin” hypothesis last year was that the virus was too different from other known viruses and therefore it was implausible that it had developed naturally. But if we see here an apparently-sudden jump to a significantly different variant, does that make it less surprising that the original strain was novel?

vadfa 5y ago
What if that new variant is also engineered?
- technobabbler 5y ago
  What if new variants inevitably emerge given global mutations and lackluster vaccinations?
- grlass 5y ago
  most "artificial origin" hypotheses centre around a lab-leak. The number of scenarios where the new variant is engineered are vastly reduced, since it's less likely that this variant is a lab leak. Other scenarios can still be within the realm of plausibility, but there are fewer of them.
JamesBarney 5y ago
I think there are few differences. 1) Covid-19 was more dissimilar from previous coronaviruses than Omicron is from current ones. 2) There is a lot more covid-19 in the world now so rare occurrences are more common. 3) There was other evidence for the lab leak hypothesis. A cover up from China, a viral research lab in the city with the outbreak, etc...
- waynecochran 5y ago
  Just to be pedantic. Covid-19 is the disease, not the virus. SARS-COV-2 is the virus.
manojlds 5y ago

mfer 5y ago

One thing I don't see being talked about is how virulent (rapid onset of severe illness) omicron is. The rate of spread isn't the only element. The viruses that are the common cold spread wildly but don't cause major issues for most people. Why don't we talk about this more?

nradov 5y ago
There are several other endemic human coronaviruses like HCoV-OC43 which cause common cold symptoms. Most of us catch them as youths and the resulting natural immunity protects us from severe symptoms during later reinfections. However they can still be deadly to frail and immunocompromised patients. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252012/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7252012/
JamesBarney 5y ago
I see discussions of this all the time around Omicron, the problem is we have no idea how virulent Omicron is. The attributes we care about are immune evasion, transmissibility, severity. We know the most about immune evasion, we have a little data on transmissibility, but we know didly squat about severity. People aren't talking about it much because we don't even have a bad guess about severity, much less a good guess. It'll takes a while to figure out severity. Deaths happen 2-8 weeks after symptoms. Which means we're still probably several weeks before we have any good data on severity. And this data is still really hard to parse out especially with immune evasion which makes the average case more mild, even if the disease is more virulent.
- onlyrealcuzzo 5y ago
  Median time to death from onset of symptoms ~18.5 days: https://www.drugs.com/medical-answers/covid-19-symptoms-progress-death-3536264/ https://www.drugs.com/medical-answers/covid-19-symptoms-prog... Median time for first symptoms is ~4.5 days: https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guidance-management-patients.html https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guida... Within a week, we should start to have a decent picture WRT severity. Obviously, as time goes by, that picture will only get clearer.

dragontamer 5y ago

Its been a week to decompress from the hyperbolic headlines of last week, but this is still not enough time to answer the important questions. * How transmissible is Omicron? * Are Omicron infections milder, or more severe? * Can Omicron become dominant in this Delta environment? * How much can Omicron evade the vaccine-immunity and/or natural-immunity? These are the only questions people should care about, and it seems like none of these questions have an answer yet. ------- So I guess... lets wait another week and see if people have good answers to these questions. And if we don't have answers on Dec. 9th, then we will wait another week for Dec. 16th.

Enginerrrd 5y ago
I'll venture some guesses here: * How transmissible is Omicron? Very. But how much? Based on current data, there's a sort of invariant involving a tradeoff between greater escape of post-infection/post-vaccination immunity and greater transmissibility where anything along that invariant line can explain it's aggressive rise. Either way, it doesn't really matter. If it continues to behave as it has, we'll see a lot more of omicron. ~60% confidence * Are Omicron infections milder, or more severe? That's the BIG question right now. I've seen one MD describe patients that they've seen with omicron as being mild. On the other hand, there's also been a significant rise in hospitalizations in affected areas, however, if there's simply more infected, that would be expected. I don't have a good guess here. We haven't had enough time to find out. * Can Omicron become dominant in this Delta environment? Given it's very rapid rise to dominance in the small subset of testing data I've seen, I'll put money on it out-competing delta. ~60% confidence * How much can Omicron evade the vaccine-immunity and/or natural-immunity? Another good question. Despite the fact it has a lot of spike-protein mutations, and many experts believe that immune escape is likely here: I'm not convinced that's the best metric, and I've only 20-30% confidence in my agreement with it. I'll revise this according to the following pieces of evidence I expect to see, in increasing order of how much confidence I'll gain in that assessment for each piece: I'll gain more after I hear a lot of anecdotes about vaccinated getting sick, more if I see lab results confirm lower antibody affinity, and more still after actual numbers to high statistical significance confirm that previously infected or people 2-6 months post-vaccination have a high rate of infection en par with the rest of the population.

waynecochran 5y ago

That is by far the best science article I have read on SARS-COV-2 yet. The summary is concise and relevent and the linked graphics are incredible and tell the story well: https://covariants.org/variants/21K.Omicron https://covariants.org/variants/21K.Omicron https://nextstrain.org/groups/neherlab/ncov/21K.Omicron https://nextstrain.org/groups/neherlab/ncov/21K.Omicron

clircle 5y ago

Does anyone know if this blog still has an RSS feed? I think it has moved to a new domain.

joshyeager 5y ago
Yes, but I can only find the link on the main page of the blog, not in individual posts. Here it is: https://blogs.sciencemag.org/pipeline/feed https://blogs.sciencemag.org/pipeline/feed

cwkoss 5y ago

I don't know much about virology. Is it possible for variants to 'blend'? It sounds like Omicron has a number of variations vs Delta and other major variants. Is it possible that someone who is simultaneously infected with both Delta and Omicron to generate virus particles that utilize proteins from both variants in the same viral particle? If this can occur, would the genome of those viral particles get blended together, or would it just carry the genome of one or the other variants? i.e. would co-infection of multiple variants simultaneously increase mutation rate, or could hybrid variants appear?