A continuation of Dave Dixon’s attempt, despite data obfuscation by DOH, to identify likely case rates among the vaxed, previously infected and unvaxed. Note that the analysis is confounded by not knowing overlap between the previously infected and vaxed. That could help make vaxed group look good, or could make the unvaxed look better than they are. But I think directionally it is very accurate and consistent with the research–infection immunity is better than vax immunity and both are much better than being unvaxed.
Dave’s notes, and again we do these so anyone can repeat the analysis, point out our errors and make any suggestions on importants. Trying to be transparent, unlike DOH:
Comments, Sources, and Methods:
1. Since 11/2/2021 Minnesota Department of Health (MDH) has published Covid reinfection data on the Minnesota Situation Update for COVID-19 web page: https://www.health.state.mn.us/diseases/coronavirus/situation.html Reinfections are defined as a person testing positive for Covid more than 90 days after a prior positive test.
“Confirmed” reinfections are defined as a positive PCR test following a positive antigen test. Probable is defined as a negative PCR test following a positive antigen test. It is implied, similar to Cases, that a PCR positive test is considered “Confirmed” and a positive antigen test is considered “Probable”. For purposes of this analysis all Confirmed and Probable reinfections will be included.
2. The weekly Covid reinfection rate displayed on the chart is calculated as the number of weekly reinfections (confirmed and probable) divided by the cumulative Total Positive Cases 90 days prior to the start of the week being considered, and the result multiplied by 100k to yield the reinfection rate per 100k per week. This is the red curve on the chart.
3. The Fully Vaccinated Age Adjusted Case Rate Per Week (green curve) and Not Fully Vaccinated Age Adjusted Case Rate Per 100k (blue curve) are taken directly without modification from the Vaccine Breakthrough Report https://www.health.state.mn.us/diseases/coronavirus/stats/vbt.html from the data file for Cases, Hospitalizations, and Deaths Over Time graphic (vbtaarates.xlsx linked on this page).
Data is plotted starting 5/2/2021, the earliest date we have breakthrough data. Reinfection data goes back to 6/28/2020, but the earlier data is more variable possibly due to the smaller population of previously infected people.
4. We have no knowledge of what age adjustments are performed in order to calculate the Age Adjusted Rates, and we have not yet submitted a formal query to MDH for this information.
5. It is likely that there are people who may have contracted a mild enough Covid infection that they did not seek medical attention or get tested, causing an undercount of the true number of breakthrough infections, non-breakthrough infections, and reinfections.
6. We do not know how thorough and comprehensive MDH’s process is in identifying reinfections or breakthrough infections.
7. The main purpose in generating this chart is to try to compare the relative infection rates for previously infected people to vaccinated people, and then to unvaccinated people. We can see that throughout the Summer of 2021 the three rates were all low, during the time period in Minnesota when Covid cases were very low in general. However, unvaccinated infection rates were always the highest of the three, and for several months the reinfection rate was higher than the vaccinated breakthrough rate. On 11/07/2021, the most recent date where we can be considered to have complete breakthrough case data, the reinfection rate was 89.4 per 100k, the vaccinated infection rate was 325.7 per 100k, and the unvaccinated infection rate was 1246.5 per 100k. The ratios between these rates are an indicator of the relative risk of infection for the different classifications of the population. It might be concluded from these rates that natural immunity provides better immunity than vaccination, but the uncertainties and possible incompleteness of the underlying data is a cause for concern. Similarly, the lower infection rate of vaccinated people compared to unvaccinated people is a measure of the relative protection provided by vaccination, again with some uncertainties about the underlying data.
8. As of 12/13/2021 a total of 1,361,606 Minnesotans had received a booster vaccination shot. It is not known how many of these people with booster shots have tested positive if any.
The Healthy Skeptic is a website about the health care system, and is written by Kevin Roche, who has many years of experience working in the health industry. Mr. Roche is available to assist health care companies through consulting arrangements through Roche Consulting, LLC and may be reached at 
Apple Podcasts
Google Podcasts
Spotify
Overcast
PocketCasts
Radio Public
Stitcher
Anchor
RSS - Posts
In the spring of this year CDC changed the guidelines for the cycle threshold on the PCR tests for vaccinated people. They lowered it to 28 for vaccinated people, but no mention of the change for people who were not vaccinated. The information for the change came from a zero-hedge article and within the article there was a link to the CDC web site with the information. Like you mentioned several times along with others it would be helpful to know what the cycle threshold was on each individual positive PCR test. If in fact, there was a dual testing standard and the testing laboratories followed through with the recommendation from the CDC it makes it difficult to work with the data on hand.
“CDC changed the guidelines for the cycle threshold on the PCR tests for vaccinated people. They lowered it to 28 for vaccinated people, but no mention of the change for people who were not vaccinated.”
And this could be the explanation as to what happened to me. 5 of us had dinner, I was the only vaxed person. 3 days later we all get sick. The 4 unvaxed people tested positive for covid while I tested negative. I got retested elsewhere a few days later, while even more sick than before, and again tested negative even though I know damn well that all 5 of us have covid. Of course they ask you before testing whether you’ve been vaxed or not and it’s in their interest to find covid in unvaxed people and NOT find covid in vaxed people.
Responding to James Zuck.
It would be nice if you had a link for that. My understanding for the last several months has been
1) the CDC does NOT set the PCR cycle threshold which defines a positive test. The testing lab does that.
2) there is no “dual testing standard”. For one thing (and this is just my thought), there is no reliable way a lab could tell if a test sample was from an unvaccinated or vaccinated person.
3) Reference to the 28 cycle threshold appears at this link, which concerns the National SARS-CoV-2 Strain Surveillance (NS3). The document is part of the Association of Public Health Laboratories website.
https://www.aphl.org/programs/preparedness/Crisis-Management/COVID-19-Response/Pages/Sequence-Based-Surveillance-Submission.aspx
Under the heading “Guidance Documents”, the page states
“CDC requests that state public health laboratories provide, on a weekly basis, confirmed, deidenfied, diagnostic specimens to CDC to support the NS3 program. CDC prefers specimens with Ct values < 28 that have not already been sequenced."
If you click the link "Guidance for submitting SARS-CoV-2 positive samples to CDC's NS3 Program" you get to this page:
https://www.aphl.org/programs/preparedness/Crisis-Management/Documents/NS3-Submission-Guidance.pdf
Search for "Appendix 1" and you'll find this wording in paragraph 5a:
"The quality of the specimen directly affects sequencing and virus culture success. Ideally,
specimens should have an RT-PCR Ct value of ≤28. If Ct values are not available, specimens that are
positive/strong positive for SARS-CoV-2 may be sent (avoid weakly positive samples)."
The CDC wants samples from positive tests for genomic sequencing. So, if a sample tests positive AND the cycle count is 28 or less, the CDC is confident there will be enough whole virus in the sample to make genomic sequencing possible. Positive samples with cycle counts higher than 28 may not have enough whole virus to do this.
It's certainly true that tells you something about the value of testing. But it doesn't appear the CDC is "fixing" the tests to make the vaccines look good. They just want to monitor for variants.
I've seen this issue come up for months. It's just not a valid criticism from us "skeptics".