Biochemical analysis determined that the UK variant (Alpha) could suppress a key innate immune mechanism for 1 to 2 days, and Indian variant (Delta) replicates about 10 times more strongly in the upper respiratory track. That seems increased fitness and explain why these two dominated over most other variants. Alpha less, but Delta ruled briefly supreme.
(I do agree that this obsession with S1 mutations is unwarranted. That is likely just a continuing result of the antibodies = immunity fallacy.)
So I'm not sure why you'd claim it doesn't have increased fitness. These low-data point graphs are not that convincing IMHO. Plus the amount of immune hosts also increased and are affected by testing rates which were all over the map.
But even if I grant you this, if not fitness and plenty of hosts, then why does a virus "decide" to no longer infect non-immune targets and simply give way to a new variant that isn't more fit but just different?
Without a convincing alternative, that still leaves me leaning towards fitness, even if we don't fully understand why VOC 1 was more fit than VOC2.
I do think however you are digging in the right place, as this is an area understudied. It seems to me this is a key opportunity to understand viral mutation and transmission mechanisms and greatly add to our general understanding. If anything, what I learned from your series so-far plus the preceding flu-series is how little we do know, and how much we just assume in the medical/scientific community. And likely there are some key aspects of this area we miss.
To continue my past 2 posts, I should clarify. If I understood Fleming correctly, and if indeed his observation was correct, that the variants are morphing the "virus" back to its original wild form (I have no way of figuring out if he's correct on this, but I'm sure some of you could!) , then what that might mean is that indeed the viruses are as a whole sentient and do have a purpose, which according to Smith's communication with them is to bring all life forms into balance. This is perhaps not so farfetched given how much of our DNA did come from viruses as we evolved! This is exciting and hopeful, because it means that no matter the degree of human ignorance and hubris, no matter our ability to wreak destruction and imbalance, there are more powerful and beneficient forces at work. I realize I am going seriously astray from the more technical flavor of this conversation, so please forgive me if so.
I am clearly a novice at this commenting and somehow posted my comment before finishing! To continue: ......I believe the following observation came from one of his talks. He was showing and discussing some of the early variants and his conclusion was that the changes he was seeing in the variants were significantly focused in the same areas where changes had been made in the lab to the original natural virus. In other words, the variants were moving the virus back towards it's non- chimeric form. He made no big deal out this, but it struck me because I had also been reading Penelope Smith's Animal Communicator Blog where there are a few articles on the true nature and purpose of viruses. This admittedly is a spiritual look at what's going on, but I think an important part of the big picture. If you are at all interested I can go back and find some exact links for you, which might otherwise be hard to find. Thanks again for your integrity, your sense of humor, and your work!
Hi Brian and Sage, thanks for what both of you are contributing to healthy dialogue. I wish I could follow and understand more of it, but regardless, I have a perspective that you might be interested in regarding the variants and the general direction of their evolution. This perspective is absolutely non-technical. It speaks to the bigger opportunities, that is, the bigger learnings that we might gain out of all of this craziness.
I have listened to a number of Peter Fleming interviews and talks, and I have read his book, "Is Covid-19 a Bioweapon?" I believe the following observation came from one of his talks.
One explanation for clades that appear and then fade out is that they were intentionally "seeded" within a population. I'm assuming this is where you are headed with this logic, and I almost suggested the same thing in my comment on your last post.
I'm curious, though, whether this phenomenon (many short-lived, local/regional evolutionary clades which fail to exhibit greater fitness on a global scale) is the exception or the rule in viral evolution - or even in evolutionary contexts more broadly.
The vast majority of mutations will be deleterious and will not be passed on from the host where they arise. A select few will confer greater fitness and will eventually gain dominance across the global viral population.
What lies in between these outcomes, though?
1. Mutations that confer a selective advantage *only within the host where they arise*. Perhaps they are better at infecting cells or making more copies but terrible at being transmitted. Presumably this explains many of the "one-off" sequences that are detected.
2. Mutations that confer a selective advantage within a particular spatiotemporal context, but not globally/permanently. It's quite possible to imagine, for example, a strain that could outcompete existing strains (and cause a wave of infection) in Manaus but not in New York City, or vice versa - in the context of differing innate/adaptive immunity in the populations (from past exposure to different pathogens/antigens) and different environmental and social conditions influencing transmission. It's also possible to imagine a strain that has an advantage in northern hemisphere winter but not in northern hemisphere spring/summer.
One of the main challenges here is that we have more detailed sequence data for SARS-CoV2 across space and time than for any other virus or organism ever, and so it's not always easy to find parallel comparisons to assess what is simply revealing the micro-, meso-, and macro-dynamics of natural selection and what is evidence of artificial intervention.
"A non-sterilizing vaccine WILL cause variants to emerge, as this is doing!"
So this is Paul channeling GVB, and Paul and GVB are quasi-homies or at least simpatico on this theme.
-----
Brian, I will confess to diligently trying to read through the first post in the series. I was doing pretty good through the Tony Hawk part and stuff. My head exploded, which is not unusual.
Biochemical analysis determined that the UK variant (Alpha) could suppress a key innate immune mechanism for 1 to 2 days, and Indian variant (Delta) replicates about 10 times more strongly in the upper respiratory track. That seems increased fitness and explain why these two dominated over most other variants. Alpha less, but Delta ruled briefly supreme.
(I do agree that this obsession with S1 mutations is unwarranted. That is likely just a continuing result of the antibodies = immunity fallacy.)
So I'm not sure why you'd claim it doesn't have increased fitness. These low-data point graphs are not that convincing IMHO. Plus the amount of immune hosts also increased and are affected by testing rates which were all over the map.
But even if I grant you this, if not fitness and plenty of hosts, then why does a virus "decide" to no longer infect non-immune targets and simply give way to a new variant that isn't more fit but just different?
Without a convincing alternative, that still leaves me leaning towards fitness, even if we don't fully understand why VOC 1 was more fit than VOC2.
I do think however you are digging in the right place, as this is an area understudied. It seems to me this is a key opportunity to understand viral mutation and transmission mechanisms and greatly add to our general understanding. If anything, what I learned from your series so-far plus the preceding flu-series is how little we do know, and how much we just assume in the medical/scientific community. And likely there are some key aspects of this area we miss.
https://anandamide.substack.com/p/quasi-species-swarms-in-sars-cov?utm_medium=email
Are you aware of Kevin McKernan’s substack?
Correction: I'm referring to Dr. Richard Fleming, not Peter! Sorry bout that.
To continue my past 2 posts, I should clarify. If I understood Fleming correctly, and if indeed his observation was correct, that the variants are morphing the "virus" back to its original wild form (I have no way of figuring out if he's correct on this, but I'm sure some of you could!) , then what that might mean is that indeed the viruses are as a whole sentient and do have a purpose, which according to Smith's communication with them is to bring all life forms into balance. This is perhaps not so farfetched given how much of our DNA did come from viruses as we evolved! This is exciting and hopeful, because it means that no matter the degree of human ignorance and hubris, no matter our ability to wreak destruction and imbalance, there are more powerful and beneficient forces at work. I realize I am going seriously astray from the more technical flavor of this conversation, so please forgive me if so.
In expansion pack terms, it's not exactly on the level of Lord of Destruction. But it does add some nice content.
I am clearly a novice at this commenting and somehow posted my comment before finishing! To continue: ......I believe the following observation came from one of his talks. He was showing and discussing some of the early variants and his conclusion was that the changes he was seeing in the variants were significantly focused in the same areas where changes had been made in the lab to the original natural virus. In other words, the variants were moving the virus back towards it's non- chimeric form. He made no big deal out this, but it struck me because I had also been reading Penelope Smith's Animal Communicator Blog where there are a few articles on the true nature and purpose of viruses. This admittedly is a spiritual look at what's going on, but I think an important part of the big picture. If you are at all interested I can go back and find some exact links for you, which might otherwise be hard to find. Thanks again for your integrity, your sense of humor, and your work!
Hi Brian and Sage, thanks for what both of you are contributing to healthy dialogue. I wish I could follow and understand more of it, but regardless, I have a perspective that you might be interested in regarding the variants and the general direction of their evolution. This perspective is absolutely non-technical. It speaks to the bigger opportunities, that is, the bigger learnings that we might gain out of all of this craziness.
I have listened to a number of Peter Fleming interviews and talks, and I have read his book, "Is Covid-19 a Bioweapon?" I believe the following observation came from one of his talks.
One explanation for clades that appear and then fade out is that they were intentionally "seeded" within a population. I'm assuming this is where you are headed with this logic, and I almost suggested the same thing in my comment on your last post.
I'm curious, though, whether this phenomenon (many short-lived, local/regional evolutionary clades which fail to exhibit greater fitness on a global scale) is the exception or the rule in viral evolution - or even in evolutionary contexts more broadly.
The vast majority of mutations will be deleterious and will not be passed on from the host where they arise. A select few will confer greater fitness and will eventually gain dominance across the global viral population.
What lies in between these outcomes, though?
1. Mutations that confer a selective advantage *only within the host where they arise*. Perhaps they are better at infecting cells or making more copies but terrible at being transmitted. Presumably this explains many of the "one-off" sequences that are detected.
2. Mutations that confer a selective advantage within a particular spatiotemporal context, but not globally/permanently. It's quite possible to imagine, for example, a strain that could outcompete existing strains (and cause a wave of infection) in Manaus but not in New York City, or vice versa - in the context of differing innate/adaptive immunity in the populations (from past exposure to different pathogens/antigens) and different environmental and social conditions influencing transmission. It's also possible to imagine a strain that has an advantage in northern hemisphere winter but not in northern hemisphere spring/summer.
One of the main challenges here is that we have more detailed sequence data for SARS-CoV2 across space and time than for any other virus or organism ever, and so it's not always easy to find parallel comparisons to assess what is simply revealing the micro-, meso-, and macro-dynamics of natural selection and what is evidence of artificial intervention.
https://palexander.substack.com/p/ba5-covid-sub-variant-being-replaced?pos=1
------
"A non-sterilizing vaccine WILL cause variants to emerge, as this is doing!"
So this is Paul channeling GVB, and Paul and GVB are quasi-homies or at least simpatico on this theme.
-----
Brian, I will confess to diligently trying to read through the first post in the series. I was doing pretty good through the Tony Hawk part and stuff. My head exploded, which is not unusual.
----
How far apart are we here on the Expert Scale?
Polar opposites?