Basically what has happened over the last 50 years is the emergence of some strains of Marek’s that kill unvaccinated birds extremely fast and at a young age. This is in contrast to the more classical Marek’s, that I am sure we have all read about, where tumors develop in slightly older birds causing paralysis.
I couldn’t get a handle on this exactly but it seems this more virulent disease is particularly marked in broiler intense farming operations.
The conclusion of these phylogenetic modeling wonks was that the use of vaccines has impacted the evolution of the virus such that these more virulent strains have emerged.
There is no discussion about how widespread the more virulent strains are, but a lot of discussion in the references is about broiler operations.

the genetic complexity of the Marek’s virus made it impossible to actually match specific mutations with virulence.

This is very interesting and I appreciate your diving into it! I hope you had a good nap and have recovered!

I have heard of genetic modeling and estimating time frames from that. I do accept the thought that Marek's seems to have some virulent strains that appear to be more widespread than previously observed "outbreaks." I come away from your synopsis thinking that they have correlated (but not found causation) Marek's vaccine prevalence and increased prevalence of virulent strains, along with intense broiler operations. Is that your thought too?

Because if they can't match any mutation with a virulent strain, probably because the data is limited, then they don't know which ones to trace back and identify its origins? For instance whether it existed before the beginning of the study time frame and became more widespread through repeated huge flocks of broilers on the same dirt, or if it developed out of a mild strain after the beginning of the study time frame and again spread from there.

I'm not denying that it is possible at all, but I'd like to understand better the theory how it happens. I don't see the evolutionary point of becoming a really virulent strain while happily coexisting inside a living chicken that's been vaccinated, shedding virus all over the place and multiplying in numbers. Why would the more virulent strain prevail? As opposed to quickly killing some poor unvaccinated 6 week old broiler and all it's flock-mates, which works out to be an evolutionary dead end. But I think this point has been made? By you I think. I suppose the virus could get more virulent and the vaccinated chicken wouldn't be affected, up to a point? Maybe there is another evolutionary through-line somewhere, like in the soil, perhaps?

Queenie's untended and hungry tribe, before people came and split them up and Queenie hid and wasn't caught. This was when I unsuccessfully tried to corral them all and get them to someone who was going to take them. I let them in, out and around the dog crate and couldn't see how to not panic anyone in collecting them. But I think part of them went to at least a good home, a family with kids. The rooster was magnificent, particularly his colorful legs, which I wish I'd gotten a picture of: pale yellow, blue and red.

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I have heard of genetic modeling and estimating time frames from that. I do accept the thought that Marek's seems to have some virulent strains that appear to be more widespread than previously observed "outbreaks." I come away from your synopsis thinking that they have correlated (but not found causation) Marek's vaccine prevalence and increased prevalence of virulent strains, along with intense broiler operations. Is that your thought too?

Because if they can't match any mutation with a virulent strain, probably because the data is limited, then they don't know which ones to trace back and identify its origins? For instance whether it existed before the beginning of the study time frame and became more widespread through repeated huge flocks of broilers on the same dirt, or if it developed out of a mild strain after the beginning of the study time frame and again spread from there.
I think it is not quite that straightforward. Virulence in Marek's is governed by numerous genes and they could not pinpoint all of them but some they could. And they observed (fascinating) that it got more virulent in Europe and the US but from different genes - so the virulent strains evolved independently in the two geographies.
Your point about whether the strain pre-existed or evolved for the first time in the last 50 years is I think exactly what they mean by saying in their paper that they would like to see more work to go back further, look at Jungle Fowl etc.

I'm not denying that it is possible at all, but I'd like to understand better the theory how it happens. I don't see the evolutionary point of becoming a really virulent strain while happily coexisting inside a living chicken that's been vaccinated, shedding virus all over the place and multiplying in numbers. Why would the more virulent strain prevail? As opposed to quickly killing some poor unvaccinated 6 week old broiler and all it's flock-mates, which works out to be an evolutionary dead end. But I think this point has been made? By you I think. I suppose the virus could get more virulent and the vaccinated chicken wouldn't be affected, up to a point? Maybe there is another evolutionary through-line somewhere, like in the soil, perhaps?
I still only partially understand this. There is another paper that all sources cite that sounds like it might address this topic but I didn't read it yet. I might tackle that tomorrow (though I also want to look into hormone treatments for Eli so will prioritize that).
And seriously, though I have some education in these areas, we are really close to the edge of my ability to understand the science!

And for tax I will share this very cute moment from earlier in the week. Eli got mashed potato over her face (the piece of beef leftover from dinner out came with mashed potato and onion). Bernie very gently cleaned it off Eli’s face.

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Nope, different herpes virus, there are actually many many of them. Look at it this way, there are thousands of bird species, they are all birds but not all are chickens.

The only thing you are catching from them is sore ankles from the too of yours 🤗.
Why can't you get "roo" right? Why?
 

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