Logo

Club EvMed: SARS-CoV-2 transmission bottlenecks and why we care - Shared screen with speaker view
Joseph Graves Jr
22:29
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.
Joseph Graves Jr
36:52
About the same
Jonathan Runstadler
36:57
Same
Joseph Graves Jr
37:25
random
David Rasmussen
37:43
Bimodal at zero or one?
Joseph Graves Jr
37:56
1 0 for alleles
Joseph Graves Jr
38:35
BTW that was another Michigan guy giving that response. If only we were that good in football.
Joseph Graves Jr
39:03
That’s the meaning of drift, no selection
Vaughn Cooper
44:00
That’s a compelling plot Michael and Katia. If you censor the noise your Ne is exactly what I would expect ~10
Arka Pal
44:48
That it is a large bottleneck?
David Rasmussen
44:48
Bottlenecks are BOTH large and small!
Joseph Graves Jr
44:56
This is the prediction you were making before on large bottleneck
Joseph Graves Jr
45:44
Small bottleneck
Michael Reiskind
45:52
mutation
Dana Hawley
46:25
Sorry if I missed this but when were these samples collected relative to exposure and clinical disease?
Joseph Graves Jr
47:26
love my hard sweeps!
Joseph Graves Jr
52:03
Agreed what was depth of sequencing?
Joseph Graves Jr
52:48
That’s deep!
Meredith Spence Beaulieu, PhD (she/her/hers)
53:16
Feel free to virtually raise your hand to join the queue for discussion! (click “Reactions” at the bottom of your screen, then “Raise Hand.”)
Calen Ryan
53:58
Does a low bottleneck size tell us anything about transmission more generally? What about masks?
Dana Hawley
54:31
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?
Terence Taylor
55:36
Great work. How do your findings compare with similar work on other viruses or more specifically on other coronaviruses?
Charles Nunn
55:56
Perhaps related to Dana’s question: is there any evidence of variation in bottleneck size in viruses with different transmission modes?
David Rasmussen
58:12
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?
Neil Greenspan
01:00:34
Does SARS-CoV-2 generated defective interfering particles. Would such particles affect your results?
Vaughn Cooper
01:01:40
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
Michael Reiskind
01:02:25
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?
Joseph Graves Jr
01:02:54
Vectors and mammalians hosts definitely have different selection pressures.
David Rasmussen
01:03:14
Thanks Vaughn!
Charles Nunn
01:03:34
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!)
Michael Reiskind
01:03:58
Here is reference to transmission of WNV through mosquito feeding:https://www.sciencedirect.com/science/article/pii/S2211124717304539?via%3Dihub
Brandon Ogbunu
01:04:14
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
Dana Hawley
01:07:38
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
Michael Martin
01:11:17
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
Michael Martin
01:11:27
https://stm.sciencemag.org/content/suppl/2020/11/20/scitranslmed.abe2555.DC1
Dana Hawley
01:12:43
Thanks!
Bernie Crespi
01:13:41
Delta should have a right skewed Nb
Jean Ristaino
01:13:43
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
Vaughn Cooper
01:13:47
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
Meredith Spence Beaulieu, PhD (she/her/hers)
01:14:03
That Radiolab was excellent!
Dana Hawley
01:14:15
Thanks for a wonderful presentation and discussion!
Michael Reiskind
01:15:02
Great job Michael and Katia!
Joe Alcock
01:15:05
Great conversation!