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Dr Karl Sirotkin's avatar

As the other co-author, (of the peer reviewed work, not this article or the others on this substack, which are all Dan's work. And, in fact, he really did most of the work on that peer reviewed article, too, I just acted like an encouraging major professor with a student who picked his own project and whose work and energy did the work, with minor supervision.) I am hoping to engage with the readers. Dan was ahead of me, in spite of, and maybe because of my formal training as a microbiologist, as I worked with bacteriophage T4, not prone to being a quasi species. Or, staring in the 1970s. Loved this above piece, but perhaps I can add something by being available as a sort of "ask the professor" thread. After all, I did teach Molecular Virology at the University level, before designing and implementing internationally used genetic databases.

I will NEVER criticize or even critique answers. All I ask is for those to whom the material I present is well known, and there will be some, that I not be criticized for that.

So, when I say I did not see swarms, in my graduate work, it was because we wanted pure genomes which we could get by diluting phage solutions and spreading them on a lawn of bacterial hosts, in which one phage would eat a hole, leaving gobs of copies of itself.

This was the DNA phage T4 which recombines a lot, but whose genome is normally pretty stable.

The questions are:

1. What is different from T4 in flu and coronavirus?

2. Would a plaque (or equivalent) represent one genome, for these other viruses, of not, why not?

3. What experiments, or procedures should be done to measure swarms in RNA viruses?

(Happy to discuss all this.)

Hints:

https://en.wikipedia.org/wiki/Whole_genome_sequencing

https://en.wikipedia.org/wiki/Polymerase_chain_reaction

For those more familiar with these technology, what role would primer choice make?

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Squirrel's avatar

This is the level of understanding the world needs of this virus, and which has been lacking to date. The entire field of microbiology has lacked a theorist who can make the scales fall from their eyes. and this is the price we pay.

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