---
type: Conversation
title: Private channel session 703
description: "slack conversation, 33 messages, 2020-12-20."
tags:
  - conversation
  - slack
medium: slack
message_count: 33
started_at: "2020-12-20T12:31:18"
ended_at: "2020-12-20T14:33:01"
duration_seconds: 7303
sources:
  - { id: slack_pm, resource: /sources/slack-pm.md, title: Slack / Private Message Drop, author: "process:senate-hsgac-release" }
generated: { by: randpaul-corpus-pipeline/1.0, at: "2026-08-01T12:42:27Z" }
status: stable
---

A slack conversation of 33 messages spanning 2h 1m.

# Metadata

- **Started:** 2020-12-20T12:31:18
- **Ended:** 2020-12-20T14:33:01
- **Duration:** 2h 1m
- **Participants:** 3
- **Source:** [slack_pm](/sources/slack-pm.md)
- **Pages:** 328-331

# Participants

* [Andrew Rambaut](/people/andrew-rambaut.md)
* [Edward C. Holmes](/people/edward-c-holmes.md)
* [Kristian G. Andersen](/people/kristian-g-andersen.md)
* [Robert F. Garry](/people/robert-f-garry.md)

# Transcript

**[2020-12-20T12:31:18] Edward C. Holmes:** Thanks Bob, a lot to think about.

**[2020-12-20T13:10:00] Kristian G. Andersen:** Thanks Bob - this is very helpful. One nagging question I have is that it doesn't seem to me that N501Y _alone_ can explain the 'spreader' phenotype, yet, the lineages in the UK and SA are quite distinct - and as far as I can tell, only share N501Y. However, it's entirely plausible that different mutations can lead to similar conformational changes, that might give the virus a 'spreader' phenotype if N501Y pops up on that genetic backbone.We have seen N501Y before (e.g., Australia), but I don't know that any of those are associated with increased spread? With that said, Australia isn't exactly representative when it comes to the question of spread, and I don't believe N501Y has been…

**[2020-12-20T13:16:45] Andrew Rambaut:** There are actually 2 501Y lineages in the UK - the other one in South Wales (now up to about 500 genomes but associated with a hospital outbreak as well). Again only N501Y in common. As you say - there was a cluster in Australia - 37 genomes from beginning of June to beginning of July.

**[2020-12-20T13:18:32] Kristian G. Andersen:** I missed that - I thought same lineage, but two separate emergence events (from a common source, I assumed). ButI see the differences on Emma's Nextstrain build - very interesting.

**[2020-12-20T13:19:10] Andrew Rambaut:** There are 5 from Massachusetts with a shit load of mutations

**[2020-12-20T13:19:20] Andrew Rambaut:** Spike A1020S, Spike C15del, Spike D614G, Spike G142del, Spike I870V, Spike L18del, Spike L141del, Spike N17del, Spike N440D, Spike N501Y, Spike Q14del, Spike Q183H, Spike Q493K, Spike S12del, Spike S13del, Spike S494P, Spike T478K, Spike V16del, Spike V143del, Spike Y144F, E T30I, M A2V, N A208S, NS3 Q57H, NS7a S83L, NSP2 I21V, NSP2 T85I, NSP4 A307V, NSP12 P323L, NSP13 T115I

**[2020-12-20T13:19:38] Andrew Rambaut:** I bet that is a chronic patient

**[2020-12-20T13:20:12] Andrew Rambaut:** Yes all from the same dead 45 year old man

**[2020-12-20T13:20:17] Kristian G. Andersen:** Holy moly - a lot of mutations there...

**[2020-12-20T13:20:22] Andrew Rambaut:** Is that the NEJM case?

**[2020-12-20T13:20:35] Andrew Rambaut:** Seems to be an increasing number over time.

**[2020-12-20T13:20:38] Kristian G. Andersen:** Lemme check - don't think so

**[2020-12-20T13:21:41] Kristian G. Andersen:** Actually, probably is... https://www.nejm.org/doi/full/10.1056/NEJMc2031364

**[2020-12-20T13:22:01] Kristian G. Andersen:** We don't see N501Y in our chronic patient - big difference, no treatment in that person.

**[2020-12-20T13:24:57] Kristian G. Andersen:** @Andrew Rambaut - question here, as I see this coming up in many many news articles. Do folks understand that there are two separate concerns here? (1) Increased transmission, possibly due to N501Y, and (2) Concerns about 'immunity' due to the mutations and deletions on the same haplotype? I see many people commenting that "we shouldn't expect SARS-CoV-2 to evolve towards immune evasion", but the problem here is that what we're seeing here isn't 'normal' SARS-CoV-2 evolution - it's a different process and it may _specifically_ be related to immune evasion. Can't assume our normal priors are appropriate here.

**[2020-12-20T13:26:42] Andrew Rambaut:** I have brought this up a few times but I still don't think people get it.

**[2020-12-20T13:26:58] Andrew Rambaut:** I am leaving it until the lab work is done.

**[2020-12-20T13:27:23] Kristian G. Andersen:** Yeah, same here - until I see data, no point in speculating, however, let's not trust our priors 100%

**[2020-12-20T13:28:24] Kristian G. Andersen:** Do you know if Wendy is going to be able to test neutralization from vaccinees in addition to convalescent patients?

**[2020-12-20T13:29:28] Andrew Rambaut:** Worse case would if it had selected for immune evasion, and was more transmissible, and ended up at high frequency, which could make vaccines less efficient and require a higher coverage for the higher R.

**[2020-12-20T13:30:17] Andrew Rambaut:** @Kristian Andersen Yes. Convelescent plasma from natural infections and vaccinees will be tested.

**[2020-12-20T13:30:25] Kristian G. Andersen:** Yup - exactly. Under a 'normal' evolution scenario I'd say that would be extremely unlikely - however, in this particular case, I'm not so sure.

**[2020-12-20T13:31:19] Andrew Rambaut:** Exactly. Basically it would be best to knock it out but that is likely too late.

**[2020-12-20T13:31:36] Kristian G. Andersen:** Australia managed to do it :wink:

**[2020-12-20T13:32:40] Kristian G. Andersen:** But yeah - we're not going to be able to completely stop this now - sure, put the brakes on, but we'll likely see this become the dominant lineage over the next few months.

**[2020-12-20T13:32:50] Andrew Rambaut:** Best we can hope for is that it isn't more transmissible and gets eliminated by the new lock down measures. A worse case is that the measures knock every thing else out.

**[2020-12-20T13:33:13] Kristian G. Andersen:** Yup!

**[2020-12-20T13:33:43] Andrew Rambaut:** I hope it turns out we are wrong and it is not transmissible - it is the right decision not to wait to find out I think.

**[2020-12-20T13:35:16] Kristian G. Andersen:** Agreed - this is a perfect example where we can't wait for scientific certainty, but need to react immediately anddecisively. No pussyfooting around. Also, I find it hilarious that we find ourselves in 1/"Virologists look at a mutation and assume it is adaptive,evolutionary biologists assume it isn't. Neither are right all the time" :wink:

**[2020-12-20T14:11:06] Edward C. Holmes:** That is weird. The Australian (from Victoria) cluster didn't take off but the circumstances here are not like US/Europe because there is strong intervention. The lineage that did take off in Victoria a little later did so because it was associated with a super-spreading event.

**[2020-12-20T14:12:37] Edward C. Holmes:** As if by magic: [shared file(s): Victoria_trends.pdf]

**[2020-12-20T14:23:56] Kristian G. Andersen:** Yeah, I don't think we can compare - Australia has this under control, we don't - I'm sure that with Aussie like control measures in place, N501Y wouldn't have had a chance to take off either.

**[2020-12-20T14:33:01] Kristian G. Andersen:** From all of this, I had the most concise question from Biden TF members this morning "should we ban travel from the UK". I guess when it comes down to it, we all need to be able to take all the science and distill it down into a simple yes/no answer. Easy.