Corona Policy in Times of High Vaccination Rates and Delta Variant
===

The Covid-19 pandemic featured two, maybe two basic phases, with the latest and hopefully last being defined by the successful developement of a vaccine. Furthermore subdeviding this phase into intervals of low and ready availability of doses supplies us with our current political climat. One in which the most important political objects related to ensuring high vaccination rates, which was hoped to bring about herd immunity.
There are plenty of different positions to examine and just as many sorry attempts at justification to the populace.

## Citations (before 2021-07-15)
1. [heute journal: shrinking effectiveness of vaccinations (Israeli Health Ministry)][1]
1ab. [haaretz: dwindling effectiveness of pfizer jab][1.1] compared to [haaretz: effectiveness was high in march][1.1b]
2. [npr: attribution of lessening effectiveness to __time passing and delta variant__][1.2]
2. [heute: gutenberg cross-sectional study][2]
1. [panorama: __old / immunized people rarely tested__][2.1]
3. [uni-lübbeck: Increased testing catches 70% of cases (all time high)][3]
4. [thebmj: likely _more_ young people hospitalized, even if less deadly nhs still busy with care "backlog" and thus a new wave be dangerous][4]
5. [PHE: monitoring the effectiveness of COVID-19 vaccinations][5]
1. [phe: two-dose-vaccination slightly less effective at preventing symptoms for delta variant, but when it comes to hopitalization more effective against delta than alpha.][5.1]
6. [icl: uk epedemic progressing faster, 13-17,18-24 yo most effected with 1.33%,1.40% infected over 11 days, "fully" vaccinated 1/3 as likely to be infected][6]

[1]: <https://youtu.be/sFoJEdQ-Das?t=156> "hj 2021-07-06"
[1.1]: <https://www.haaretz.com/israel-news/israel-pfizer-vaccine-less-effective-preventing-delta-covid-variant-infection-1.9971842> "haaretz effectiveness"
[1.1b]: <https://www.haaretz.com/israel-news/.premium-israeli-study-pfizer-coronavirus-vaccine-is-91-percent-effective-after-second-dose-1.9643859> "haaretz past effectiveness"
[1.2]: <https://www.npr.org/2021/07/06/1013496220/protection-provided-by-the-pfizer-vaccine-may-might-be-fading-israeli-officials-?t=1625933818358> "npr reasons for dwindling effectiveness"
[2]: <https://youtu.be/8WNsETdilI4?t=243> "h 2021-07-07"
[2.1]: <https://www.zdf.de/nachrichten/panorama/corona-gutenberg-covid-19-studie-100.html> "zdfheute panorama 2021-07-07"
[3]: <https://www.uni-luebeck.de/aktuelles/nachricht/artikel/corona-langzeitstudie-elisa.html> "uni-luebeck"
[4]: <https://www.bmj.com/content/373/bmj.n1513.full> "thebmj predictions for the next wave"
[5]: <https://www.gov.uk/government/publications/phe-monitoring-of-the-effectiveness-of-covid-19-vaccination> "public health england vaccination effects aggregator"
[5.1]: <https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/995101/Vaccine_surveillance_report_-_week_24_v2.pdf> "public health england comparative vaccination efficacy"
[6]: <https://www.imperial.ac.uk/news/225873/coronavirus-infections-continue-grow-exponentially-england/> "icl: trends in uk public health strategy"

## Citations (2021-07-24)

7. (overly) optimistic statement from us (left wing) media on vaccine efficacy
1. [cbs: 99.7% of cases supposedly among non Vaccinated (2021-07-10)][7.1]
1. [ln \w Seth Meyers][7.1.1]
2. [tls \w steven colbert: "among the unvaccinated in the united states covid cases are once again are on the rise"][7.2] (Somewhat implying, that this might not be the case for the vaccinated)
9. [us cdc: vaccination efficacy (among other things against infections)][8]
Different study types are used as evidence consider for example:
1. [Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data **(Public Suveillance Data)**][8.1]
- Surveillance Data sufferes from differing base rates in testing of vaccinated and unvaccinated people
- Because the need for vaccinated people of negative tests is eliminated these people just get tested less often.
3. [Association Between Vaccination With BNT162b2 and Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infections Among Health Care Workers **(common testing policy + discretionary testing)**][8.2]
- Same Problem as with the public surveillance data: Significant difference between cohorts likely skewing the data:
5. Decreased infectivity following BNT162b2 vaccination: A prospective cohort study in Israel **(Situational Testing)** ^{[[preprint]][8.3a] [[published]][8.3b]}
- Two Ways of analysing the data:
1. Restricting to tests after dangerous encounters is a formal process with common rule, eliminating differences of propencity to test.

2. Admitting all tests, but correcting for pandemic situation based on case numbers

- This all goes to show, that the more you test, the more the gap between vaccinated and unvaccinated people is likely to close.
- One expanation for the difference in even the best designed population wide sudies [REACT (see 6)][6] would be because the infection is over faster meaning randomly selected samples are likely to test negative even though them having been infected before is just as likely.
- If infection is defined as presence of a pathogen, then vaccination was never going to be an effective way to prevent it.
- _The proportion of vaccinated among the newly infected is also dependent on their (increased) propencity to mingle / their (reduced) care in social situations and their (reduced) likelyhood of being tested._
- _The concrete impact of which is dependent on local contexts, as this is much less a property of the disease but one of societal sensitivity / knowledge on the issue._
- If different variant infect vaccinated people more easily, then this should have no bearing on the vaccines usefullness, since it was never its goal in the first place.
- _However the aside from the effectiveness to protect the vaccinated it is very much relevant whether it lowers infectivity and duration of infectivity._
## Citations 2021-08-01

1. Infectivity and CT-Values
1. [Journal of Clinical Microbiology: Culture-Based Virus Isolation To Evaluate Potential Infectivity of Clinical Specimens Tested for COVID-19][9]
<details>
<summary> CT-Values correlate with culturability and ratio of present genes might be used to determine infectivity, as inactive cultures seem to have different proportions present. </summary>
<br>

**From the Discussion Section:** In this study, we investigated the infectivity of clinical specimens by virus culture and examined whether the infectivity was correlated with the level of viral nucleic acids. We provided quantitative results to show that specimens for which viral culture was successful contained more viral RNAs than those for which culture did not succeed. [...] Since some nonculturable specimens also contained high genome copy numbers, the presence of viral nucleic acid alone cannot be used to assess the infectivity directly. [...]
[...] Viral shedding of SARS-CoV-2 has been estimated to occur more than 30 days after symptom onset (13, 23). Such prolonged and persistent detection of viral RNA in stool specimens, even after the negative conversion of respiratory specimens, led some researchers to suggest the potential for fecal-oral transmission of SARS-CoV-2 (10, 24), and the virus was recently proven to replicate in the human small intestinal epithelium and organoids (25). However, direct evidence for the infectiousness of these specimens collected long after symptom onset is lacking, and no virus culture from stool specimens has been achieved to date (9). _Therefore, caution is needed when evaluating the infectivity of specimens simply based on the detection of viral nucleic acids (14)._ [...] however, culture remains the most reasonable approach to assess the infectivity of clinical specimens (26, 27).
As expected, specimens containing high copy numbers of the viral genome (suggesting high viral loads) tended to be culturable compared with those with fewer genome copies. [...] The lowest genome copy number detected in our culturable specimens was 5.4 log10 genome copies/ml sample of the nsp12 gene. [...] **Another feature associated with culturable specimens was the strong linear correlation between copy numbers of structural and nonstructural genes, indicating that the viral genome of cultural specimens was intact, possibly reflecting an infectious virion.** In contrast, the considerably higher RNA level of structural genes detected in nonculturable specimens might reflect the presence of replication intermediates retained in epithelium cells (21), while the nonculturable specimens characterized by highly nonstructural genes might contain viral genomes yet to be degraded. For specimens containing high viral loads with a high correlation among genes, the virus can be inactivated by neutralizing antibodies that might cause aggregation of the virus to prevent nucleic acid degradation (14). This hypothesis was supported by the finding that seroconversion occurred 7 to 14 days after symptom onset when no rapid decline in viral load was observed (9).
Overall, this study provides evidence that the infectiousness of clinical specimens from COVID-19 patients can potentially be determined by both the SARS-CoV-2 gene copy numbers and genome integrity. Nucleic acid detection is undoubtedly valuable in detecting SARS-CoV-2; however, other serological tests should be performed in parallel to best evaluate the disease course of a COVID-19 patient as demands of health care systems are robustly increasing due to the pandemic.</details>

[7.1]: <https://www.cbsnews.com/news/new-covid-19-cases-united-states-almost-all-among-people-unvaccinated/> "cbs: Almost all new COVID-19 cases are among people who have not been vaccinated"
[7.1.1]: <https://www.youtube.com/watch?v=m87Z2sd2zDw&list=UUVTyTA7-g9nopHeHbeuvpRA&index=46> "Don Jr. Bombs at CPAC as Crowd Cheers Low Vaccination Rates: A Closer Look"
[7.2]: <https://www.youtube.com/watch?v=T-Xdaru5Ato> "the late show 2021-07-22"
[8]: <http://web.archive.org/web/20210724032631/https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/fully-vaccinated-people.html> "us cdc: evidence for vaccination efficacy (captured 2021-07-24)"
[8.1]: <https://www.sciencedirect.com/science/article/pii/S0140673621009478> "the lancet: Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data"
[8.2]: <https://jamanetwork.com/journals/jama/fullarticle/2779853> "Jama: Association Between Vaccination With BNT162b2 and Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infections Among Health Care Workers"
[8.3a]: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3815668> "The Lancet Regional Health - Europe: Decreased infectivity following BNT162b2 vaccination Preprint"
[8.3b]: <https://www.sciencedirect.com/science/article/pii/S2666776221001277> "The Lancet Regional Health - Europe: Decreased infectivity following BNT162b2 vaccination: A prospective cohort study in Israel"
[9]: <https://journals.asm.org/doi/full/10.1128/JCM.01068-20> "Journal of Clinical Microbiology: Culture-Based Virus Isolation To Evaluate Potential Infectivity of Clinical Specimens Tested for COVID-19"