---
type: Conversation
title: Private channel session 1023
description: "slack conversation, 23 messages, 2021-02-24."
tags:
  - conversation
  - slack
medium: slack
message_count: 23
started_at: "2021-02-24T07:16:41"
ended_at: "2021-02-24T09:47:25"
duration_seconds: 9044
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 23 messages spanning 2h 30m.

# Metadata

- **Started:** 2021-02-24T07:16:41
- **Ended:** 2021-02-24T09:47:25
- **Duration:** 2h 30m
- **Participants:** 3
- **Source:** [slack_pm](/sources/slack-pm.md)
- **Pages:** 544-546

# 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

**[2021-02-24T07:16:41] Robert F. Garry:** Pompeo [shared file(s): China's Reckless Labs Put the World at Risk - WSJ.pdf]

**[2021-02-24T07:34:39] Andrew Rambaut:** So much insinuation without actually accusing them of anything

**[2021-02-24T07:41:25] Kristian G. Andersen:** Hah, this is sooooo terrible. I'm pretty sure that Pompy looked up "Biosafety Level", thought, "That's some scary shit- let's blame China", and grabbed the keyboard.US politicians (and intelligence) actually used to be widely respected in the world. Boy, has that gone downhill.

**[2021-02-24T07:44:38] Kristian G. Andersen:** We now have an "NYC" variant... Sigh. Any concerns about any of these mutations - especially the ORF1s? [shared file(s): Screen Shot 2021-02-24 at 7.38.07 AM.png]

**[2021-02-24T07:45:20] Kristian G. Andersen:** Here's the report on it - rising in NYC (yes, of course there's a preprint...) https://outbreak.info/situation-reports?country=United%20States&division=California[...]20York&pango=B .1.526&selected=New%20York&selectedType=division

**[2021-02-24T08:11:33] Andrew Rambaut:** There are 2 subclades of B.1.526 - one has E484K, the other S477N. https://github.com/cov-lineages/pango-designation/issues/6

**[2021-02-24T08:26:29] Kristian G. Andersen:** Ah, interesting - need to dig a little further then (we can now do pango lineage + mutation on outbreak.info, so that's pretty nifty). If this is the one with, especially, eek, then that's interesting - a lot of standing immunity in large parts ofNYC.

**[2021-02-24T08:51:17] Robert F. Garry:** That's a really good point about all the pre-existing immunity in NYC. E484K doing double duty - ACE2 binding plusa neutralizing epitope. S477N likely the same/overlapping epitope, but NO interaction with ACE2 at least directly. [shared file(s): image.png]

**[2021-02-24T09:02:19] Robert F. Garry:** @Andrew Rambaut Q957R is interesting - Q957 probably forms a salt bridge with K304. Put another positive charge there make clash and likely "loosens up" the monomer more than a bit. Like Eddies corridor analogy though - variants finding their way down to a common path,

**[2021-02-24T09:22:50] Kristian G. Andersen:** Yeah, B.1.526 with eek is definitely rising in New York. This might be real. https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3 AE484K&selected=New%20York&selectedType=division

**[2021-02-24T09:27:32] Robert F. Garry:** Speaking of the WSJ - they just requested an interview to discuss our Virological post.

**[2021-02-24T09:27:44] Andrew Rambaut:** It is weird the V701A reverting in the S477N lineage - maybe the tree is wrong

**[2021-02-24T09:29:14] Robert F. Garry:** HMMMM - that is interesting.

**[2021-02-24T09:29:17] Kristian G. Andersen:** Oh... We have identified a MAJOR issue with Illumina's consensus caller - it's calling reference calls if there are _any_ mismatching reads at a variant site. That might be why

**[2021-02-24T09:29:38] Kristian G. Andersen:** If this is from NYC, it's possible they used Illumina's DRAGEN pipeline

**[2021-02-24T09:29:55] Kristian G. Andersen:** (I have reached out to them - crickets).

**[2021-02-24T09:30:49] Kristian G. Andersen:** shared file(s): image (1).png, Screen Shot 2021-02-24 at 09.30.29.png

**[2021-02-24T09:34:16] Andrew Rambaut:** Interesting - we have seen quite a lot of 'reversions' in some of the VOCs. Who would be using this consensus caller? Is there a way to find out?

**[2021-02-24T09:34:20] Kristian G. Andersen:** Preprint on the NYC sequences - pretty interesting. https://www.biorxiv.org/content/10.1101/2021.02.14.431043v2.full.pdf

**[2021-02-24T09:34:43] Kristian G. Andersen:** I'm worried A LOT of people are using the Illumina pipeline - and there's no way to find out in most cases

**[2021-02-24T09:35:27] Kristian G. Andersen:** Any lab that hasn't previously been involved in virus sequencing and isn't as comfortable with command line tools would likely use this caller. It's a big big problem.

**[2021-02-24T09:46:44] Kristian G. Andersen:** B.1.526 with S477N: https://outbreak.info/situation-reports?country=United%20States&division=California[...]1.526&muts=S%3AS477N&selected=New%20York&selectedType=division

**[2021-02-24T09:47:25] Kristian G. Andersen:** Interestingly, none with both (kinda supporting this is a real effect - since they're independent events): https://outbreak.info/situation-reports?pango=B.1.526&muts=S%3AE484K&muts=S%3AS477N