Research links and discussion on mouthwash, gargling and SARS-COV-2 prevention

Senator Ron Johnson is taking quite a bit of flack over his remarks on mouthwash and SARS-CoV-2 prohibition. It is worth noting that Japan (which has a very low Covid19 death rate[1]) has a long history of gargling  povidone iodine (PVP-I) to prevent respiratory infections[2]. Some American physicians are also suggesting gargling could be helpful [3] especially for school children. Molecular iodine and other anti-septic mouthwashes are in use as SARS-COV-2 prohibition in dental practices across the US [4].  'Disrupting SARS-CoV-2 transmission' with mouthwash has been and is being actively studied at Dental schools and other research institutions across the US.[5] 

First Month of Pediatric Covid Vaccination: Some select 'SYMPTOM_TEXT' stories and some stats

These are some select stories from the first month of Pediatric vaccinations in the US. There is a select group of syncope (fainting or 'loss of consciousness') in the little ones.

PRO TIP: Stay right by your kid before and after the vax. Vaccinate one kid at a time if possible. If they faint, don't let them fall and hit their head on the floor. Because then you have the child head injury on top of the child vaccine injury.  The HCW who are administering the pediatric injections are having some trouble confusing adult with pediatric dosing. Many kids are getting adult doses and adult saline preparation doses, among other administration errors. This doesn't seem to result in too much (immediate) injury. I guess. Maybe.

Full spreadsheet here and code here and here.  *Read the code first* if you don't understand my output or what I have done. All the paragraphs immediately below are separate AE ('Adverse Event') reports. 

Some critical markers, data, charts for 10/08/2021 VAERS DB report

 Click to enlarge charts and graphs.  All my data analysis removes duplicate VAERS_ID. The table directly below uses the 'symptom fields' for the term greps. Various symptoms, fatality, age, gender and other markers have missing or inappropriate fields in some of the data. The missing/inappropriate data is ignored. Code:

• HeaderCode.with.Analysis.r
• CriticalMarkers.r

Some critical markers, data, charts for 09/24/2021 VAERS DB report

Click to enlarge charts and graphs.  All my data analysis removes duplicate VAERS_ID. The table directly below uses the 'symptom fields' for the term greps. Various symptoms, fatality, age, gender and other markers have missing or inappropriate fields in some of the data. The missing/inappropriate data is ignored. Code:

• HeaderCode.with.Analysis.r
• CriticalMarkers.r

US Covid19 daily vaccinations don't reveal any significant or predictable statistical correlation with daily US Covid19 deaths/cases

 

Chart Data for cases, deaths, vaccinations from  "Our World in Data" Mathieu, E., Ritchie, H., Ortiz-Ospina, E. et al. A global database of COVID-19 vaccinations. Nat Hum Behav (2021) Code for this post here.

The long term data for US Covid-19 daily vaccinations, deaths and cases *is scaled* and plotted below in a seven day rolling average. A table of the R language correlation coefficient (using 'cor' which is scaled 1 to -1) is far below.   The table and visual inspection reveal a fairly strong correlation between daily Covid cases and daily Covid deaths. For 2021 only, US Covid daily vaccinations have a correlation coefficient with both cases and deaths close to '0'. This would indicate no correlative relationship between daily vaccinations with either daily cases or daily deaths.

In the second chart,  three overlay rectangles represent three distinct and separate temporal relationships between daily vaccinations and daily cases/deaths over the course of the pandemic:

1. The green rectangle graphs daily vaccinations increasing while daily cases/deaths decrease.
2. The purple rectangle graphs daily vaccinations decreasing while daily cases/deaths continue to decrease.
3. The blue rectangle graphs daily vaccinations increasing while daily cases/deaths increase.

Click to enlarge the charts.

Recent articles and research on Vaccine Induced Immune Escape

Questions about Global Vaccination

Two charts with regression lines below  the break are from a data download from "Our World in Data".  Code is available on request. The charts are intended to show both daily and 7 day averages of:

• scaled new vaccinations (red)
• scaled new deaths (black)
• new cases since the start of vaccinations per daily and  for seven day average (blue).

By visual inspection, the world is apparently climbing its third ladder of cases/deaths peak since the start of mass vaccinations in late 2020. There is little question for some of us that the onslaught of highly transmissible variants means that cases, deaths, hospitalizations will continue to both accumulate and rise as mass vaccination continues. I have these questions:

• Are the vaccines actually helping us fight Covid-19?
• Are the vaccines creating through 'immune escape' continuing cycles of more virulent and/or more transmissible variants?
• Is global vaccination a strategy that will bring continued death to many?

Far below the charts are recent posts and papers that help examine these questions. Click to enlarge the charts.

U.S. State Population Level Musings from CDC Vaccination/Cases/Death Data (Unfinished)

Unfinished and Under Construction

https://github.com/rferrisx/Covid-19/blob/master/VaccinationEfficiency

States

Click to enlarge charts

VAERS analysis and snapshots from the Friday, 06/11/2021 VAERS drop

Some VAERS snapshots analysis from the Friday, 06/11/2021 VAERS drop  representing data to 6/4/2021. These tables and charts are produced with R packages (libraries) from CRAN and Bioconductor including data.table, tm, graph, Rgraphviz, wordcloud.  Some of my R code can be found here.  Click to enlarge the screen shots, charts, and word clouds. View this blog on a wide screen.

The B.1.617 Storm is Coming to All the World

Screenshot from: https://nextstrain.org/groups/neherlab/ncov/20A.S.154K.S.478K?c=pango_lineage&f_pango_lineage=B.1.617.1,B.1.617.2,B.1.617.3&l=clock 

Nextstrain Data: Top 20 variants WA State and Whatcom County as 05.13.2021

From https://nextstrain.org/groups/blab/ncov/wa/2m . For dates April 2021 and later as of 05.12.2021. Click to enlarge the console screenshot:

Some COVID19 VAX_TYPE VAERS data and analysis: 05.07.2021

Some VAERS snapshots analysis from the Friday, 05/07/2021 VAERS drop (updated to 04/30/2021). These tables and charts are produced with R packages (libraries) from CRAN and Bioconductor including data.table, tm, graph, Rgraphviz, wordcloud. Post under construction. Click to enlarge the jpgs.

Papers/Presentations that discuss the use of Machine Learning and the haemocytometric diagnosis of Covid-19

Papers/Presentations that discuss the use of Machine Learning 
and the 'haemocytometric' diagnosis of Covid-19.  

List in progress:

Lattice and Bar chart graphs of Cases and Deaths for all U.S. states and territories from 01.01.2020 - 04.12.21

Below the break find lattice and bar chart graphs of cases and deaths for all U.S. states and territories from 01.01.2020 -  04.12.21. Read lattice charts top to bottom over time. Read bar charts left to right over time. Data from CDC Cases and Deaths. https://data.cdc.gov/Case-Surveillance/United-States-COVID-19-Cases-and-Deaths-by-State-o/9mfq-cb36 Abbreviations for  U.S. territories are:

Territory Abbreviations:
American Samoa   AS
Federated States
of Micronesia    FSM 
Guam GU
Marshall Islands MH
Northern Mariana
Islands  MP
Palau PW
Puerto Rico PR
Virgin Islands   VI

Select links on Green Tea and EGCG

Green Tea and EGCG (Epigallocatechin Gallate)

03.15.2021 Update: Successful Mass Vaccinations or Mass Deaths?

 "The vast majority of V2 and V3 variants and some more recent V1 variants also have a spike E484K mutation. Whereas in the presence of 501N, 484K has a modest positive impact on ACE2 binding 9, when present with 501Y, these mutations together synergistically increase ACE2-RBD binding affinity ~12.7 fold ... Crucially, E484K and other mutations at S/484 also frequently confer protection from neutralization by both convalescent sera ... , vaccine elicited antibodies ... , and some monoclonal antibodies ... There is therefore increasing evidence that viruses carrying the E484K mutation (with or without 501Y) will be able to more frequently infect both previously infected ... and vaccinated individuals ..." 

"The most important issue here is not whether this particular 'super variant' ever arises, but rather that the convergent mutations that have already arisen in members of the different 501Y lineages implies that these viruses are presently on, and are actively scaling, a broad new peak in the fitness landscape. Whatever SARS-CoV-2 variants eventually summit that peak could be a considerably bigger problem for us than any variants that we currently know in that they might have any combinations of increased transmissibility, altered virulence and/or increased capacity to escape population immunity."

"The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape" https://www.medrxiv.org/content/10.1101/2021.02.23.21252268v2 

VAERS deaths and symptoms for Covid-19 reported to 01.15.2021: Some questions for Medical Professionals on Vaccine Risk Assessments

Frequent Terms over 20 in Current VAERS Symptoms field for Covid19

Click to enlarge.

VAERS deaths and symptom word clouds for Covid-19 reported to 01.08.2021

Data Source: https://vaers.hhs.gov/data/datasets.html (Read the documentation for data caveats!)

My Code: https://github.com/rferrisx/VAERS/blob/main/Covid19_wordcloud.r

Screenshots and Word Clouds after the break. Click to enlarge each:

Update on thoughts on mask tech and mask use

I don't know how much my general thoughts on mask use for the general public have really changed in the last six months. I suspect the Swedish stance (https://www.reuters.com/article/us-health-coronavirus-sweden-cases/sweden-says-no-need-for-face-masks-as-covid-19-deaths-top-7000-idUSKBN28D1TH) on mask use is probably still being followed in many countries like Sweden, Norway, New Zealand. Immediately below there are some links to some earlier articles I wrote on mask use for the general public and farther below that are some new thoughts I have had on the new 'Covid-19 killing' mask tech: 

• https://www.ncovd.org/2020/05/more-thoughts-on-masks-for-infection.html
• https://www.ncovd.org/2020/05/thoughts-on-mask-for-general-public.html
• https://www.ncovd.org/2020/05/mask-wars.html

In line with the results of Danish RCT study (https://www.acpjournals.org/doi/full/10.7326/M20-6817), I doubt whether most current mask or 'face covering' use by the general public is actually slowing the spread of Covid-19 in the United States. But I think if you are going to wear a mask in the general public, you should take advantage of the latest tech in masks. Some have suggested N95 or KN95 lines of mask because they are now more available. Without a doubt approved N95 masks, if you can buy or afford them, can provide high levels of protection if fitted correctly. 

Personally, I find 3M N95 masks are excellent to wear while cleaning your heating system, vacuuming your garage, sweeping the patio. But I think it is improbable that the general public will don the tight fitting N95s as they pull masks in and out of their pockets between storefronts. What is more intriguing to me are the advances in 'germ killing' masks whose design appears to take into consideration the contamination dangers of most 'mask for the general public' usage.  Google "masks that kill Covid-19" for more information. 

CNN has a long article on this here: https://www.cnn.com/style/article/antimicrobial-fashion-coronavirus/index.html.  An article on designing better masks is here: https://hbr.org/2020/06/we-need-better-masks . These two vendors below are selling masks they claim can kill Covid-19 on contact: 

• https://shop.livinguard.com/
• https://www.acteev.com/acteev-technology

Here is the big problem I have with my mask use:  Many of those of us with Asthma (reputedly some ~25M or 1 out of every 13 in the US - see https://www.aafa.org/asthma-facts) simply can't breathe well with masks on. The snot, flem and the moisture start to pile up inside the mask which really invalidates the effectiveness of the mask and quite possibly makes a face mask a dangerous harbor of bacteria and a possible infection source; although about this danger is some debate. 

If you are going to use a face mask, you should at least follow the CDC recommendations here: https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/how-to-wear-cloth-face-coverings.html. Depending on your budget, I would recommend having some number of high quality, comfortable masks that work for you so you can get through the week without washing or reusing old or unclean masks.