Thread by @DrEricDing

📍“There’s clearly something going on with this mutation”: 7 striking new converging variants with same #677 mutations suddenly found. Experts across US independently found them & are worried—all 7 changed same spike protein amino acid—bad sign.🧵 #COVID19 nytimes.com/2021/02/14/hea…

2) It’s been circulating for a few months, but because of poor genomic surveillance in the US, it took a while to realize it’s becoming a problem and growing across the US. We barely do 1% sequencing in the US. medrxiv.org/content/10.110…

3) Q677H & Q677P as a group change the same Q (glutamine) amino acid inside the spike protein. All 7 mutations yield the same change replacing the glutamine. Convergent evolution usually always means it’s something advantageous to the organism’s survival. That’s usually bad sign.

4) “I think there’s a clear signature of an evolutionary benefit,” Dr. Kamil said.

“As the coronavirus now branches into new variants, researchers are observing Darwin’s theory of evolution in action, day in and day out.”

5) It’s difficult to answer even basic questions about the prevalence of these seven lineages because the United States sequences genomes from less than 1% of coronavirus test samples. The researchers found samples from the lineages scattered across much of the country.

6) “It’s also hard to say whether the increase in variants is actually the result of their being more contagious. They might have become more common simply because of all of the travel over the holiday season. Or they might have exploded during superspreader events.”

7) “The 677 mutation alters the spike protein next to the spot where our proteins nick the virus, conceivably making it easier for the spike to be activated.”

8) “Dr. Kamil and his colleagues are starting those experiments, hoping to see whether the mutation does indeed make a difference to infections. If the experiments bear out their suspicions, the 677 mutation will join a small, dangerous club.”

9) “Convergent evolution has transformed a few other spots on the spike protein as well. The 501st amino acid has mutated in a number of lineages, for example, including the contagious variants first observed in the United Kingdom and South Africa...”

10) “Experiments have revealed that the 501 mutation alters the very tip of the spike. That change allows the virus to latch onto cells more tightly, and infect them more effectively.”

11) The N501Y is also nicknamed “Nelly”, and also seen in Brazil #P1 variant. Similar with the E484K “Eeek” mutation—it is seen in South Africa 🇿🇦 and Brazil 🇧🇷 and in 2 other sublineages in Wales and England—4 times. Here is a nickname figure from @K_G_Andersen.

12) Back to the new 7 mutations that alter the 677th amino acid in the spike protein—@firefoxx66 smartly nicknamed them with bird names instead of calling some a Louisiana or Florida variant. GOOD IDEA 💡! We don’t really want geographic stigma.

14) Whisper... That said, I just hope the mass media doesn’t confuse people when it says “bluebird” or “pelican” variant, and then people mistakenly start killing real bluebirds & pelicans by mistake.

Silly? Well people thought drinking Corona beer 🍺 gives you Coronavirus. 🤦🏻‍♂️

15) “To really understand what the mutations are doing, scientists will need to analyze a much bigger sampling of coronaviruses gathered from across the country. But right now, only a relatively meager number of genomes collected by a patchwork of state & university labs.

16) “It’s ridiculous that our country is not coming up with a national strategy for doing surveillance,” Dr. Cooper said.

17) Questions on vaccine efficacy I’m seeing... we don’t know yet. Scientists will first do virus neutralization tests to see how convalescent blood and vaccinated blood neutralize the pseudovirus with 677 mutation in a lab study. Then we can guess. But true efficacy from trial.

18) We don’t know yet about the new set of 7 different 677 mutations might have on contagiousness, reinfections, vaccines. But I just hope and pray it is not like the #B1351 variant... see thread 🧵 below WHO’s wanting on that one...

https://twitter.com/drericding/status/1360264581982093318