On another topic, I just came out of the Zoom of the NC Education committee. It looks like HB 324 is going to pass the committee. Supposedly this is an anti-CRT bill, but the wording of it should be troubling to all of us, because this certainly opens the door for assaults on the teaching of evolution and climate change.

About the same

Same

random

Bimodal at zero or one?

1 0 for alleles

BTW that was another Michigan guy giving that response. If only we were that good in football.

That’s the meaning of drift, no selection

That’s a compelling plot Michael and Katia. If you censor the noise your Ne is exactly what I would expect ~10

That it is a large bottleneck?

Bottlenecks are BOTH large and small!

This is the prediction you were making before on large bottleneck

Small bottleneck

mutation

Sorry if I missed this but when were these samples collected relative to exposure and clinical disease?

love my hard sweeps!

Agreed what was depth of sequencing?

That’s deep!

Feel free to virtually raise your hand to join the queue for discussion! (click “Reactions” at the bottom of your screen, then “Raise Hand.”)

Does a low bottleneck size tell us anything about transmission more generally? What about masks?

Do you expect that there is any relationship between exposure dose and transmission bottleneck size? For example, even if exposure doses are quite variable, is the transmission bottleneck likely always small?

Great work. How do your findings compare with similar work on other viruses or more specifically on other coronaviruses?

Perhaps related to Dana’s question: is there any evidence of variation in bottleneck size in viruses with different transmission modes?

Maybe this is a question for Vaughan as much as for Michael/Katia, but what was it about the ARTIC amplicon sequencing protocol that would lead to spurious sequencing errors outside of primer binding sites?

Does SARS-CoV-2 generated defective interfering particles. Would such particles affect your results?

Hi David, the errors come both from the PCR and from Illumina. Here’s one article about this: https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473

Can you explain the connection between tight bottlenecks and mutations--is it just probabilistic or does the low diversity allow for more "space" for mutants to evolve?

Vectors and mammalians hosts definitely have different selection pressures.

Thanks Vaughn!

For those posting questions in chat, please feel free to raise hand to ask your questions (otherwise, we will, but we like to hear form you!)

Here is reference to transmission of WNV through mosquito feeding:https://www.sciencedirect.com/science/article/pii/S2211124717304539?via%3Dihub

We sorta addressed relate questions….but how/would we detect evolutionary change *during* a pandemic with regards to overall transmissibility and/or route of transmission (e.g. droplet size, fomites) in the transmission bottleneck data

If all the samples were collected from those with symptoms (not sure if that’s true- I didn’t get to read the preprint- sorry), then that seems like it could bias toward higher exposure doses in your sample - although I guess you can’t get much lower than a transmission bottleneck of 1-3 virions, even if that’s somehow biased high

A lot of these data were, I believe, collected during contact tracing so I don’t think it’s all symptomatic and there was at least some range in the degree of symptoms, their Table S5 details this

https://stm.sciencemag.org/content/suppl/2020/11/20/scitranslmed.abe2555.DC1

Thanks!

Delta should have a right skewed Nb

A study of the initial Covid outbreak in New Orleans showed a single individual likely brought the pathogen into NOLA during Mardi Gras. This would support the bottleneck hypothesis and arise of dominant type https://www.nola.com/news/coronavirus/article_e4095910-6af1-11eb-a3bc-336456794a5b.html

I recommend this Radiolab episode for anyone interested in effects of immunosuppression on SARSCoV2 population sizes and genetic diversity. Exceptionally well done. https://www.wnycstudios.org/podcasts/radiolab/articles/dispatch-14-covid-crystal-ball

That Radiolab was excellent!

Thanks for a wonderful presentation and discussion!

Great job Michael and Katia!

Great conversation!