Thread by @firefoxx66

The 'Texas Paper' is getting sensationalist headlines. Remember:
- D614G is same mutation we've known about since spring & been in media all summer
- It happened in ~Jan & most of Europe & much of US had it
- Great to confirm previous work, but not 'breaking'

#SARSCoV2 #COVID19

Worth noting that the authors of this study sat on 5,000 sequences *all summer* meaning they couldn't be used by other scientists to explore any findings in these sequences. Or to better understand Texas's epidemic during its biggest spike.

The author laments the low sequencing rates of #SARSCoV2:

“I think we need to be doing this pretty aggressively in multiple locations on a real-time basis,” Musser said. “I think it’s shameful that we’re not doing that.”

/It's shameful to sit on sequences that could be public./

I maintain a #Texas @nextstrain build (I grew up partially in Texas; my mom lives there). I've repeatedly put out calls to connect to anyone willing to do TX sequencing to gather better information during the summer peak.

There are about ~600 sequences.

nextstrain.org/community/emma…

Using *only* 10% of the sequences of the new paper, what can we tell about the mutation they make such a fanfare about?

Here it is, plotted on the tree. D is ancestral (green), G is the new variant (yellow). Pie chart shows proportion of each, in Texas

nextstrain.org/community/emma…

As we already know: the G mutation arises very early in the pandemic (~Jan - where yellow starts). And, as in many other places in the west, it became the most common variant. From mid-April there were extremely few (if any) D (green) strains in Texas.

These trees alone can't show /why/ that happened - though many studies have been done that increasingly indicate the G variant has higher transmissibility (which could explain this pattern).

There's no evidence that it has changed clinical outcomes though - & def not recently

Certainly, since that variant has been circulating since early 2020 & since its the variant most people in Europe & USA had in spring - & the one circulating now - we can be confident it isn't responsible for things like a lower death rate - since it's the same variant.

The authors talk about seeing many mutations in their sequences. #SARSCoV2 mutates. We know this. We already see diversity in the sequences.

Here's all the amino-acid changes in the 600 TX seqs up until June. Quite a few! No different from what we see elsewhere, though.

Still - you can see how many sequences we lack from TX during the worst of the summer peak.

Those 5000 seqs might have helped us better understand imports vs local transmission, & connections within Texas & to other states, at a time when maybe that could have been useful.

We're in a pandemic. We're in this together. #Openscience & #opendata is responsible for *so much* of the research we've achieved on #SARSCoV2.

We need to put the greater good ahead of ourselves & our career goals. We need to do what's *right*. It's our best chance to succeed.