Thread by @AlexJohnsonLi3

Waking up from my hibernation (just kidding, it was application that took up my time for the last month)
Today I would summarize some thoughts I had with JN.1, the first 2023 strain to scare me. Yet besides that I want to also say things about the general covid evolution.

Chapter 1: History reviews. The pandemic was divided into three eras. Pre-Alpha was marked by gradual, pseudorandom mutations added to strain WH, Alpha-Delta marked key mutations and their ability to greatly enhance the virus, then Omicron shifted the focus to immune escape.

Omicron Era got five epoches (geo time scale laughter intensifies). Epoch 1 BA.1, abrupt change, unstable reign. Epoch 2 BA.2, grandfather variant Epoch 3 BA.5/BQ.1.1 The stepladder of key mutations Epoch 4 XBB, birth of recombs and polyphyly, Epoch 5 BA.2.86/JN.1

Chapter 2: Mutation Themes. Although the virus has evolved far from Omicron origins, immune escape is still the main scheme for covid. The virus switched between hugging an escape mutation, and mediating the effect, usually mutations recovering some of its ACE2 binding lost.

Thus, each epoch's virus largely escape its precursor. BA.5 is not vastly distinct from BA.2 yet, but its Omega version BQ.1.1 dodge BA.2 quite well. While the two chronic-derived masters, XBB and BA.2.86 wreck previous immunities.

Chapter 3: A Changing Landscape Starting from last year, brilliant minds such as @yunlong_cao have discovered that repeated infections could sway antibodies, and the dynamic nature of omicron evolution were then shown. Now, we know that kairos is part of the covid evolution.

Best example of shifting preference came from the famous F456L mutation. It was first neglected as part of tier 2 RBD mutations, but then it started leading XBB evolution, and the so-called FLip combination of F456L and L455F was the major targets before BA.2.86/JN.1 rose.

Chapter 4: Manner of Reign From Alpha to BA.2, one clade tightly held the lion share. BA.5 was already counting numerous "rebellions", and XBB looked like an HRE for virus. We had to coin terms like Eris+FLip to describe the horrifying super-convergence.

Yet, the "democratic process of covid evolution" seemed reversed in the fifth epoch. Hardly anything put up strong resistance for JN.1, neither top XBB like HK.3 or HV.1 descendent, nor its BA.2.86 siblings.

Chapter 5: summary This would be my new attitude at dissecting variants: EG.5.1*, other XBB, JN.1*, other BA.2.86, other (mostly a mishap of DV.7.1* and weird recombinants of XBB, BA.2.86* and DV.7.1*s). And a peek of red is enough to make me nervous.

However, JN.1 would not be the end of covid evolution. Itself would continue to perfection by adding other mutaitons (and some familiar ones from XBB epoch already appeared), and new chronics never cease to show up, only a spark is needed for them to engulf the world in flames.