Georgia writes:
Hi Nels and Vincent,
Just listened to episode #64 for the second time in 24 hours. So good. In the episode you touched on something I’ve been thinking about. I don’t have a science background but I appreciate the scientific method and the approach to truth as evidence-based point in time, that is to say, varying degrees of certainty and always open to new evidence and reevaluation.
I’m not certain if I understood you correctly about the B 117 variant. My thinking has been that it is unlikely that all of the world wide examples of the B 117 variant are based upon a single original source, then transmitted by infected travellers, but rather, multiple spontaneous originations that persisted in multiple places because it “apparently” is more transmissible. I’ve thought that with the millions of people who have been infected by SARS COV 2, the billions/trillions (?) of replications the virus has undergone, the inevitable small number of errors per replication are bound, eventually, to be repeated randomly, and if they provide an advantage in transmission would be found more often over time. Am I understanding this correctly?
Thank you for all you do,
Georgia
Per writes:
Hej Nels and Vincent,
Great episode 64 about variants and lineages!
Here is an official webpage for the Danish SARS-CoV-2 sequencing effort, which is quite impressive. B.1.1.7 increased from 4.1% to 7% of all sequenced samples from week 1 to week 2, with some regional variation.
https://www.covid19genomics.dk/statistics
Best wishes,
Per
Per Jemth
Uppsala University
Department of Medical Biochemistry and Microbiology
Uppsala, Sweden
John writes:
Hi Folks –
If I appear rude, I don’t mean to. It’s just that I have the diplomatic skills of a cinder block. I admire the work that all of you do.
A little snow here – I’m currently in Derbyshire, England. It’s about 0°C. The rosy-fingered dawn is spreading a pink light across the white landscape. The waves in the cloud make the dawn truly rosy-fingered.
In TWiEVO 64, at about 1:09:23, Nels Elde says:
“When we say B-one-seventeen [sic], what are we actually talking about? It’s actually not a single virus, it’s a lineage … and there’s variants constantly getting spit out. The original version of B-one-seventeen was described for its 23 mutations compared to the reference strain, out of Washington, and of course that’s slightly arbitrary as well. 17 of those mutations which are non-synonymous – or lead to coding changes – and there are some deletions in there – and those mutations are thought to be – potentially – the most consequential.”
Here’s a cued-up YouTube link: https://www.youtube.com/watch?t=4163&v=FPo2BAq4H-8
I’ll let that “B-one-seventeen” faux pas pass.
More seriously, following on from a point Amy Rosenfeld alluded to in TWiV A&V, this is an RNA virus. So synonymous mutations can affect secondary and tertiary RNA structure, with meaningful chemical effects such as changes in rates and reliability of transcription – and so rates of further mutations – and translation, stability e.g. 2′ hydrolysis, and conceivably even ribozymatic activity of the RNA itself, though if the last were true, we’d expect high conservation or convergent evolution, I guess.
Minor comment: I get the significance of dN/dS, but when it was spoken as “DNDS” – which I heard as “DMDS” – I found it hard to make sense of. “DN by DS” would have been clearer and more explicit. If Mr Racaniello didn’t take so much trouble over the sound quality, this kind of problem would be a lot worse. “Paperese” can be hard to understand when spoken. I know journals still require papers to be written in clumsy and unnatural paperese, but now nearly everything is read via the web, it’s time to start writing – and speaking – in a simple, clear style, whether the journals like it or not.
[My background. I mostly do “electronics stuff” in Cambridge, occasionally in California. I have degrees that say “Maths”, but if you squint at my undergraduate degrees from the right angle, they might look like Physics or Engineering degrees. I’ve had an armchair interest in molecular biology since I did Chemistry A-level – I guess a bit like freshman chemistry in the US. I maybe know just enough molecular biology to know that I’m kinda clueless about it.
With many thanks, and best wishes,
John
Sheila writes:
Dear Vincent and Nels,
Greetings from Oxford, where it is a chilly 6 degrees Celsius. I have been a TWIV listener since last Spring, when a friend recommended it to me, and look to you for clear explanations of what is going on. I’m no scientist, but my levels of understanding have definitely gone up, thanks to TWiV.
Thanks so much for episode 64 of TWiEVO. It is the first episode I have listened to, but gave me a great deal of information about what you understand about the current new variant in the U.K. There has been so much scaremongering, and I have been hoping to hear something on TWIV about it, so was delighted when I came upon TWiEVO.
I felt I needed to write and thank you, as Vincent referred to unpleasant mail from people. You are doing the right thing by sticking to the science, and giving the wider public a balanced view of where the science is right now.
As someone living in the U.K. it does feel as though something different is going on with the pandemic at the moment. The people I know aren’t behaving differently, but we all now know people who have recently caught the virus. On the other hand, the vaccine rollout appears to be going really well.
Thank you again for all you do to communicate science.
Sheila