Question from OG listener and supporter of microbe.tv:
Is dN/dS higher in the region of the SARS-CoV-2 genome that is targeted by the RT-PCR test?
Is it possible to detect a genetic conflict in the test regions? If so, would it be possible to use this to estimate how well testing works at a population level?
Based on listening to TWiEVO, I think the stock answer would be that evidence of genetic conflict can only emerge more slowly. But now with so many cases and such a large dataset, maybe the larger signal to noise ratio would enable quicker detection.
I think a measurable conflict would also suggest that the tests should not overuse the regions targeted by the vaccine. To anthropomorphize, the tests could train the virus to escape the vaccine. Perhaps this effect could be quantified with data or estimated in silico based on the mutation rate.
Since different countries use different primers, and at least six of the primer sequences are published, maybe there is enough data to begin to do statistics.
If this effect is masked by bias in the dataset, it would be interesting to quantify and track down the cause of the bias at the population level, and find possible policy implications.
“It should work perfectly the first time”
Just a curious engineer
PS: When I try to do this sort of thing in my field, I usually discover yet another inaccurate and expensive thermometer.
Mail sent after listening to TWiEVO EP 63.
Well, it’s an hour and a quarter, but it raises some really interesting points and questions.
Vincent, it also addresses a long standing theme in twiv of anthropomorphising virological processes, which maybe you could do more of, or at least be happy with that that you do. David thinks “transcription” is teleological.
Anyway, thanks for the work that you do. I almost said thanks for the fish.
Pete, Sydney, Australia.
Re: Evolution to less virulence
Dear Nels, dear Vincent,
Thank you for taking time to answer my letter in TWiEVO 61 regarding viruses trending to less virulence. I listened to your answer twice.
My understanding is now the following: “There is the theory that over evolutionary long time frames viruses might trend to less virulence. There is unfortunately only one data point that we have (the introduction of Myxoma virus to control Australien rabbits) and here the reason for changing virulence might be more on the host side. Due to the long time frames needed and due to the many factors involved, it won’t be easy to test this theory.”
Is this correct? Then I think it should only be communicated by scientists in such a weak form as stated above. From the letters to TWiV it can easily be seen that this theory causes confusion between laypersons as they try to use it to predict what will happen with SARS-CoV-2 / COVID 19 in the upcoming months or years. I liked what Dickson said in this context in one of the recent TWiV episodes.
By the way, I called it a Calcivirus, because I mixed that up with a second virus rabbit control experiment from the 1990s:
Thanks again and best regards,
Heard your request for origin of life books in episode 51. The books of Nick Lane, particularly Life Ascending and even more so, The Vital Question. The emphasis is on the role of energy in life’s formation and evolution. As a layman, it appears to me that most biologists think the use of an ion gradient was some weird affectation life picked up rather than a property as fundamental as DNA.
Listen to episode 49 of Big Biology for an interview of Lane and a discussion of the work.
To add to my email sent at 9:33 CST, I live in the St Louis Missouri metropolitan area. It probably came through with the email address, but my name is Mark. Full disclosure: I have been reading all of the books and articles and listening to the podcasts and watching the videos of Lane’s talks for over a decade. I wish I had learned this when I was in school.