What is Viral Fitness and How is it Measured?

[Giltil (Gilbert Thill)]

@RonSewell

The hemagglutinin head evolves faster than the stalk. There is more variation in the hemagglutinin stalk than transcription DNA. That is not loss of function, that is the virus adapting the function under immunological pressure and other host defenses, variation of the target sialic acid receptors, body temperature and serum pH across species, vaccination in human and food production, co-evolution of neuraminidase, and the progression of epidemics. There is positive selection

Of course there is some amount of positive selection in H1N1 history. Nobody deny that, even C&S. But the evenly distributed, gradual and linear accumulation of mutations over time observed in H1N1 is not what would be expected if only positive selection was at play. Rather, it is the sign that something else is happening, most probably the continuous erosion of genetic information.

[Rumraket (Mikkel R.)]

@Giltil

But the evenly distributed, gradual and linear accumulation of mutations over time observed in H1N1 is not what would be expected if only positive selection was at play. Rather, it is the sign that something else is happening, most probably the continuous erosion of genetic information.

Of course something more than only positive selection is at play. Be it purifying selection, genetic drift, reassortment, zoonotic events, all occurring under an arms-race between an ever-changing host and the parasite, and so on. It is ridiculous to think that just because this can’t all be reduced to continuous positive selection, then this means we have to jump to some phraseology emotionally tolerable to creationists about erosion, decay, rust, and entropy.

[Timothy_Horton]

@Giltil

Rather, it is the sign that something else is happening, most probably the continuous erosion of genetic information.

How do you quantify the genetic information in a genome to tell if it eroded, increased, or remained the same over time?

[Mercer (John Mercer)]

@Giltil

We have here a possible explanation of why genetic entropy…

They can’t assess genetic entropy if they are conflating mutation with reassortment.

@Giltil

Here is another quote from the same paper still more explicit:…

Evidence, Nigel. The quote refers to mutation rates. C&S aren’t looking at them. They are completely incompetent.

@Giltil

Rather, it is the sign that something else is happening, most probably the continuous erosion of genetic information.

Reassortment, which you are ignoring.

[dsterncardinale]

@Giltil

We have here a possible explanation of why genetic entropy of RNA viruses may be much slower in some of their natural reservoirs than during outbreaks in other host species.

Genetic entropy is not real. Just want to make sure we’re clear about that.

@Giltil

If it is the case that Influenza has been around a very long time, then you probably have a problem because long time is not what molecular clock estimates tell us about RNA virus origins. Interestingly, in the paper below, Holmes…

Very strongly recommend you read Holmes’ book on RNA viruses to clear up the misunderstanding here. The problem with small genomes and fast mutation rates is saturation; nobody thinks RNA viruses are young, but it is true that because of their rapid substitution rates, phylogenetic signals are lost more rapidly, which gives the illustion of recent emergence.

[RonSewell (RonS)]

@Giltil

If it is the case that Influenza has been around a very long time, then you probably have a problem because long time is not what molecular clock estimates tell us about RNA virus origins.

@dsterncardinale

Very strongly recommend you read Holmes’ book on RNA viruses to clear up the misunderstanding here. The problem with small genomes and fast mutation rates is saturation; nobody thinks RNA viruses are young, but it is true that because of their rapid substitution rates, phylogenetic signals are lost more rapidly, which gives the illustion of recent emergence.

Holme’s subsequent 2014 paper regarding molecular clock calibration…

According to our analysis, rates of evolution almost inevitably appear to decline over time because of the combined effects of natural selection and saturation. Consequently, and critically, estimates of rates are only applicable to the timeframe used to obtain them and cannot readily be extrapolated to other scales of analysis. In particular, short-term rate estimates will lead to underestimates of the timing of ancient divergence events, whereas using long-term rate estimates will cause the timing of recent events to be overestimated. These effects are particularly problematic in viruses, where the ages of many ssRNA virus families are probably orders of magnitude older than suggested by current estimates.

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates