I was getting lag and constant desyncs showing up after throwing the biter creep capsule on my privately hosted server.
Factorio version: 0.18.21
Krastorio version: 0.9.16

I reverted the save to before I threw the capsule and everything is working fine

Here is my local log:
https://pastebin.com/FCWz1EEJ

I also just ran into this issue. Well, not the desync since it is not a hosted server. However, the lag. I typically maintain 60 fps at all times, now it keeps pausing and dipping down to 46 fps every other second.
Factorio version: 0.18.22
K2 version: 0.9.16

Screen shot of stats before dropping the creep capsule: https://imgur.com/a/GRF00cs
Screen shot of stats after dropping the creep capsule: https://imgur.com/a/EzqFjVR

This is normal with slow pc or slow server connections. We can't imrpove it because Factorio don't provide tool to iterate the entities in better ways.

hmm, cant speak for the OP here, but I have a ryzen 2700x, 32gb of ddr4-3200, and rtx 2070. i dont think that falls into the "slow pc" category.

Do u know that Factorio use only one core (to be precise one thread) of ur CPU to the entities processing? :)
So no multithreading-per-core ALU feature, no complete use of CPU multi-level cache, no forkjoin threads management, no master-slave threads management, no multithreading work-stealing.. also Factorio require around 1 GB of ram to work and not fast GPU but only some VRAM, and mods don't use the main language of the engine that is C++, use LUA, that is slower.

I tried variuos implementations of this code and I didn't find a way to optimize this more.

I suggest u to leave the game play until the virus die (not more than 10 minutes), if u can't really play not use the virus at all (is not mandatory use virus to play), I'm sorry but we can't optimize this more...

and that why I keep repeat that for gaming having a high frequency CPU is better than have one with more core, because multi threading is not always possible/implemented/better.

Should be improved a lot in the latest update.