I've never known anyone who has been tested for a variant of any kind. I don't know anything about how variant tests look different from a generic Covid test. So where are these numbers for variant spread coming from? Maybe hospitals do have special genetic tests and reliably do those? But then isn't there going to be a pretty strong bias based on the fact that these are only for people who are getting hospitalized?

For the US there is a surveillance program run by the CDC in which each week they get specimens from all US states to be sequenced. CDC’s Role in Tracking Variants

"Specimens will ideally represent a variety of demographic and clinical characteristics and geographic locations. Selection of a diverse set of specimens will help ensure a representative set of sequences are generated for national monitoring." National SARS-CoV-2 Strain Surveillance (NS3)

I guess that for other countries there are similiar surveillance programs in place.

I've personally known many people who have had serious medical problems that sure looked clearly like vaccine reactions.

I'm curious how that coincides with no such person reporting their experiences at https://www.lesswrong.com/posts/XnRTP4dq3dkdwwtdS/which-rationalists-faced-significant-side-effects-from-covid. For me this thread was a test about whether I should look more into vaccine site-effects and the lack of reporting suggests that they aren't very common.

Are all those people you are talking about outside of the rationality community? One thing that I would see plausible is that people, who are generally psychologically suggestible and who believe the vaccine is dangerous, have their bodies overreact when they are faced with the more normal vaccine side-effects. Such a dynamic might produce more vaccine side-effects in people you know from a spiritual context than appear in the rationalist community.

One step that could be taken to verify an existing pattern of a lot of vaccine side-effects would be to simply hire a SurveyMonkey audience and see what people report when asked through that channel.

But how in the bajeezus can anyone possibly extrapolate from there to how long it takes to become symptomatic? In need of hospitalization, sure, but how is anyone getting not-heavily-biased data on symptom strength below the hospitalization threshold?

We have people we pay to do contact tracing. There are likely cases where that comes with both asking for symptoms and doing testing.

There was, best as I could tell, active (if unintentional) data destruction quite early on in the pandemic. Maybe it's still going on? Hospitals had financial incentives to find reasons why people who died had died of Covid. Lots of bodies got cremated before autopsies could happen. 

From a conversation I had with a doctor, it seems that our medical system generally does a lot fewer autopsies than we did 20 years ago. There seems to be a general culture change here. The question of how much resources our medical system should invest into doing more autopsies however isn't trivial. It would raise health care costs if we give hospitals more money if they do more autopsies. 

Maybe hospitals do have special genetic tests and reliably do those? But then isn't there going to be a pretty strong bias based on the fact that these are only for people who are getting hospitalized?

Hospitals aren't the only places that run tests besides at-home tests. The labs that do PCR testing retest some of the positive tests with variant-specific tests. Different countries have different policies about that. 

Hooooo boy.

Here is how I have been evaluating data, curious to know if other people are making judgments based on similar inputs:

• Primary source material (CDC data tracker) is better than secondary source interpretation (CNN COVID newsfeed).
• Small-scale primary source material, such as state or county data, is better than large-scale aggregate primary source material.
• Secondary source interpretation can be more, not less valuable when created by a single person (as opposed to a news site) (even if that individual does not have a medical background), as an individual is more likely to look for useful information that can help them decide whether or not to take a specific action and share useful detail that explains how they came to that conclusion.
• Assume something is lost/miscalculated/false-priored with every aggregation.
• Assume all primary source material and all interpretations thereof are compromised for some reason (biases, incentives, etc.). Ignore actual numbers. Watch for trends.

I've also been doing a fair amount of on-the-ground evaluation, e.g.:

• Do I know people who currently have COVID?
• Are people around me (strangers in grocery stores, etc.) visibly ill?
• Do I know people who have had post-vaccine health issues?
• How does my experience correlate with the experience the data says I should be having?

I'm afraid I only have time for a short, partial response today. Short version: Covid surveillance is hard, and there's lots of noise in the data. But there are lots of smart people working hard on this, and in the aggregate we actually have a pretty good idea what's going on.

I'll address one of the questions you asked specifically:

So where are these numbers for variant spread coming from? Maybe hospitals do have special genetic tests and reliably do those? But then isn't there going to be a pretty strong bias based on the fact that these are only for people who are getting hospitalized?

In Washington, much of the variant prevalence data comes from UW, which sequences a subset of the samples they receive. This is a bit complicated: some samples are fully sequenced, and some are tested for S-Gene Target Failure, which is a faster, easier test that is a fairly good (but not perfect) proxy for Omicron vs Delta. The UW sequencing is a good but not perfect sample of what's actually happening in Washington. For details on this project, the person to follow is Pavitra Roychoudhury. Details vary, but there are multiple other institutions with largely similar programs.

More general answer: you're asking good questions. They are all important, and they're obvious to any smart person who thinks about the issue for a moment. Although I don't have time to answer them all, I assure you that the smart people working on Covid have thought of every single one of your questions, and have good answers to every single one. Many of the answers are in Zvi's excellent series of Omicron updates.

There is a correlation between several types of reported data and the real situation. Raw data is not very reliable if we don't account for biases of all kinds. For example, there is an a known difference between reported deaths and excess mortality, which is often 2-3 times larger.

Anyway, I am disturbed by your words about inability to report adverse effects to vaccines. It should not be this way.