1/ The things we don’t yet know about the newly discovered sarscov2 variant have been well characterized in a number of places, by a number of excellent people. My favorite was this one by @kakape: https://www.sciencemag.org/news/2020/12/mutant-coronavirus-united-kingdom-sets-alarms-its-importance-remains-unclear

2/ To summarize: we don’t know if it’s truly more transmissible (seems likely), or if its growing prevalence in UK is the result of external forces like human behavior. We don’t know if it’s more or less virulent than existing strains (seems unlikely).

3/ We don’t know for sure what impact will be on vaccine efficacy (hopeful that it’s nil in short term). We also don’t know how common it is for this particular virus to have this many mutations (20 > than you’d expect based on what’s known) at once.

4/ And we don't know how widespread variant actually is. And it’s worth thinking about why that is.

5/ The U.K. is home to the most sophisticated genomic surveillance program in the world. Since 12/1, UK folks hv sequenced some 2100 individual sarscov2 viruses. The U.S., which has probably the second best genomic surveillance, has sequenced 31 viruses in the same time frame.

6/ Why does this matter? W/out sequencing as many viruses as possible, we can’t tell what’s actually going on. We can’t detect new variants quickly or get a sense of how much this virus mutates or know how far or fast different variants are spreading within or across communities

7/ Sequencing can help us better manage local outbreaks, too. Eg: a bunch of incoming nursing home residents fall ill in quarantine. Did ea case bring frm outside, or is infection spreading? Sequencing wld help us know. But is often only employed after sm outbreaks become lg ones

8/ Why? Because health departments across the country do not have the resources to do rigorous routine sequencing. And it’s a painfully small group deciding how the NIH grant money that could plausibly be used for this gets allocated, and right now this hasn’t been prioritized.

9/ If they did, and if individual health departments were linked to each other through some modern computer system that was coordinated centrally by CDC, they could answer some questions.

10/ like: how far did the SARS-Cov-2 variants that touched off the Amy Coney Barrett Super Spreader Event actually spread? Did variants that were circulating around Trump's golf club make their way to DC metro area, and circulate widely from there? https://www.nytimes.com/2020/10/05/health/contact-tracing-white-house.html

11/ Right now advanced molecular detection program at CDC is being run by basically one guy. And has no coherent or reliable way to collect data from all the states and territories. Again: not enough resources.

12/The situation has been improving a bit in recent years, particularly with respect to flu surveillance, but it is still objectively terrible.

13/ Folks like @trvrb at nextstrain are doing heroic work collating sequencing data. But they can only collate what’s been sequenced and right now that’s not nearly as much as it could be.

14/ It’s like a giant canvass, where one corner has been painted in extraordinary detail but the rest is fuzzy or blank. No matter how pretty that one corner is, you still don’t know the whole picture.

15/ reason scientists have been surprised to see this variant, with all its crazy mutations, emerge, is that they haven't seen this w SARS-CoV-2 yet. reason they haven't seen is that they haven't looked. reason they haven't looked is that they haven't been able to.

16/ but also: evidence of greater mutagenicity than originally thought has been emerging for a little bit now: past few months have seen several "interesting variants" including one that might monoclonals.

17/ lastly some good news to keep in mind: if this new variant does turn out to be more transmissible, it could be because it's actually less virulent (meaning more likely to be asymptomatic) but again: we don't know yet.