Notes About COVID-19 and SARS-Cov-2
Recommended site: https://project-evidence.github.io/
I've aggregated notes I was making in 2020 while we were staying home from work. They are shared below in case you need them for your own research:
Terminology
These are my working notes (probably some cut-and-paste from other sources) about terminology - which is a bit fluid in the literature.
- Virologists don't have very specific terminology, and media is not using these words consistently adding to confusion regarding discussions of origin of transmission. This seems to be how the most pedantic use the terms:
- Microbe = small nasty things like bacteria or virus
- Phylogenesis = the evolutionary development and diversification of a species or group of organisms, or of a particular feature of an organism. For viruses, the anscestry is studied based on their genetic makeup and formed in a phylogenetic tree. In a phylogenetic tree, related viruses are grouped together on branches. The distance of branches is a measure of the degree to which variants are similar. For influenza, viruses whose HA genes’ share the same genetic changes and who also share a common ancestor (node) are grouped into specific 'clades' and 'sub clades.'
- Clade (group) = a group of organisms composed of an ancestor and its descendants (clades show phylogeny). A clade can be headed by a strain or a variant.
- Sub-clade (subgroup) = another group on a phylogenic tree with a common anscestor.
- Strain = genetic change that induces functional changes in microbe. A virus strain is a variant that possesses unique and stable phenotypic characteristics. According to some researchers SARS-CoV-2 is all one strain; however according to other researchers there are more than one strain with the L-strain as the original from Wuhan becoming extinct as the European strain G is more viral. (https://www.sciencedaily.com/releases/2020/08/200803105246.htm) As of last August 2020, 'there are six strains of coronavirus. The original one is the L strain, that appeared in Wuhan in December 2019. Its first mutation -- the S strain -- appeared at the beginning of 2020, while, since mid-January 2020, we have had strains V and G. To date strain G is the most widespread: it mutated into strains GR and GH at the end of February 2020.'
- Genotype = genetic makeup of the virus
- Genome = There are hundreds of thousands of complete SARS-CoV-2 genomes.
- Variant = is an isolate whose genome sequence differs from that of a reference virus. Pretty much every time SARS-CoV-2 is transmitted into a person it evolves a bit, so there is a new variant.
- Variant of Concern = a loosely held definition is 'variant of concern' is one that has a higher transmission rate, death rate, etc.
- Serotype = differentiates viruses of the same species that are antigenically different (if the virus mutates a new serotype, vaccinations might no longer work on the new ones)
There are many coronaviruses, and they've been known for decades. There are divided into sub groups of alpha, beta, gamma, delta, etc. The currently known human coronaviruses are:
- 229E (alpha)
- NL63 (alpha)
- OC43 (beta)
- HKU1 (beta
- MERS-CoV, a beta virus that causes Middle East respiratory syndrome (MERS)
- SARS-CoV, a beta virus that causes severe acute respiratory syndrome (SARS)
- SARS-CoV-2, which causes COVID-19
Each can be referred to as a 'strain' or 'type'.
It appears that researchers of COVID19 are currently using the genome structure Wuhan-Hu-1 (Wuhan-Hu-1/2019) as the progenetor of all the variants/clades, etc.
https://www.ncbi.nlm.nih.gov/nuccore/MN908947
The genommic epidemiology of SARS-CoV-2 is kept up to date here the clades are shown: auspice
Timeline of Outbreak
24 Nov 2019 Follow-up Post - discovered new and terrible virus and want to recruit people to study it Li 'bat woman'
First cases are in November, 2019 (Infected 55 year old in Hubei Province) [SkyNews Stefanovic, 2020]
Over 200 cases in Wuhan in 2019, and 5 million people had been in that region [SkyNews Stefanovic, 2020]
Mayor of Florence and Milan had 'hug a chinese person' day to stop racism, stigmatization
This report from CNN traces the origin (acc. to Dr. Leo Poon, Hong Kong University) to animals, perhaps from a market where they were sold for human consumption:
05 April 2020 Wet markets are still operating in Wuhan and other regions of China [SkyNews Stefanovic, 2020]
SkyNews Special COVID19: Ground Zero, Peter Stefanovic, https://www.youtube.com/watch?v=pKmUxSlOoUE
Please, read pages 10 and 11 "101. A Transformed WHO" and "3. Health Security" of : https://www.who.int/dg/election/cv-tedros-en.pdf
Changing Political Narrative About Pandemic Funding
About Pandemic Preparation Funding
These are some notes I was taking about the changing media and congressional narrative about the funding for pandemic response:
Before the pandemic of COVID19, the media was largely favorable to changes that were made between 2016 and 2018 for funding to, as an example, the PREVENT pilot program.
According to an online publication at UC Davis:
Ambitious Global Virome Project Could Mark End of Pandemic Era
Project Aims to Find the Majority of Unknown Viruses Before They Find Us
By Kat Kerlin on February 22, 2018 in Human & Animal Health
https://www.ucdavis.edu/news/ambitious-global-virome-project-could-mark-end-pandemic-era
The Global Virome Project is an international partnership to identify and halt the spread of the majority of the planet’s unknown viruses. The goal of the Global Virome Project is ambitious: to end the panedemic era.
Since many recent pandemics began with animal-to-human transmission, the effort involves understanding animal viruses. According to researchers, there are an estimated 1.6 million viral species are yet to be discovered in mammal and bird populations. Of those, an estimated 650,000 to 840,000 have the capacity to infect and cause disease in humans. The proof of concept was validated through USAID’s PREDICT program, which operated in more than 35 countries and was led by UC Davis One Health Institute directed by Dr. Mazet, has found more than 1,000 unique viruses in animals and humans. This viral discovery program is led by the UC Davis One Health Institute and directed by Mazet. PREDICT focuses on high-risk areas, where people and wildlife share changing landscapes and increasing pathogen transmission risks. The purpose of the Global Virome Project is designed to dramatically scale up PREDICT’s efforts and accelerate viral discoveries.
The description of the Global Virome Project is given in the journal Science:
The Global Virome Project
Dennis Carroll, Peter Daszak, Nathan D. Wolfe, George F. Gao, Carlos M. Morel, Subhash Morzaria, Ariel Pablos-Méndez, Oyewale Tomori, Jonna A. K. Mazet
Science 23 Feb 2018:
Vol. 359, Issue 6378, pp. 872-874
DOI: 10.1126/science.aap7463
That narrative suggests that PREDICT was a pilot program that evolved into the Global Virome Project as a natural progression of success.
http://www.globalviromeproject.org/our-history
According to the Global Virome Project website:
Between 8 and 11 August 2016, representatives from across the globe – high level policy and decision makers, thought leaders, subject matter experts, researchers, and representatives from international organizations (including those involved with human, animal, and environmental health), academia, donors, foundations, and the private sector – gathered at the Rockefeller Foundation’s Bellagio Conference Center to develop a vision on the importance and feasibility of the GVP in building a world safe from the threat of emerging viral diseases. Below is the report on this effort.
The Global Virome Project (GVP) Bellagio forum attendees (see list below) support the development of a global alliance to carry forward the GVP, an international effort to identify and characterize, within a decade, 99% of all zoonotic viruses with epidemic/pandemic potential in order to better predict, prevent, and respond to future viral pandemic threats and to protect us all from their worst consequences.
<snip>
- Detecting and identifying at least 99% of potential zoonotic viral threats to human health and food security;
- Characterizing the host range of the detected viruses (reservoirs and transmission hosts);
- Determining the geographic distribution and ecologic scope of nearly all zoonotic viruses to inform on risk and surveillance in human and animals;
- Promoting the monitoring of the movement of detected viruses across hosts and regions;
- Improving the assessment of the risk of spillover and epidemic potential;
- Prioritizing high-risk viruses for further characterization, surveillance targeting, research, and mitigation development;
- Strengthening global surveillance networks through local and global capacity enhancements (e.g. surveillance, field biology, lab proficiencies, biosafety);
- Enabling in-country/regional laboratory and surveillance capacities to monitor for high-risk viruses across animal-human interfaces;
- Establishing sample biobank(s) for further research;
- Creating open-access databases that include sequence and metadata;
- Making data and samples available for public health risk assessments and mitigation, as well as further detailed pathogen studies;
- Providing new insights into virus and host biology, conservation and ecology;
- Identifying markers for transmission and pathogenicity for high-risk viruses; and
- Establishing an ethical framework for sample, data, information, and benefit sharing, including authorship and intellectual property.
Thus, the transition from pilot PREDICT to Global Virome Project seems a natural course of action of a successful and much needed technology and this transition was taking place during the Obama administration era. Note that Dennis Carroll and Jonna Mazet are part of the Global Virome Project.
Forecasting Community Infection Rates
Models:
Timeline of the Vitamin D Controversy
APRIL 2020
Some members of the media and medical community expressed dismay that Fauci was not acknowledging and advocating for boosting immunity systems. For example, in this Enewletter, 'What Dr. Fauci Is Not Telling You - Nutritional Concepts,' the question is posed [1] :
"DID YOU KNOW that current director of NIH's National Institute of Allergy and Infectious Diseases, Dr. Anthony Fauci, and former director of the Centers Disease Control, Dr. Thomas Frieden, tout the benefits of vitamins to stave off infection?
Former CDC director Thomas Frieden said recently that taking vitamin D, or making sure your vitamin D level is optimal, is crucial during the coronavirus pandemic. Here is the link to the interview.
In this interview with The Washingtonian in 2016, when asked how to avoid getting sick when you're around people all day, Dr. Fauci mentioned four things. One of them was to take 1000 mg. of vitamin C, which he takes himself. Fauci also mentioned taking vitamin D.
Why, in all the press briefings and interviews he has done throughout the coronavirus pandemic, has he not mentioned vitamin C and D? We have no idea, but as the most visible US public health expert, he is doing the public a disservice."
MAY 2020
This wasn't all 'new science.' This is what Dr. Fauci's comments were suppressing - from Feb - Sept 2020. This report from May 2020 says Vitamin D deficiencies in slightly more than 40% of USA.
Dr. John Campbell, Nurse Lecturer: Vitamin D deficiency rates are 42% of Americna, 70% Hispanic Americans, and 82% African Americans. UN correlation studies suggest potential to reduce death rate to COVID19 by 50% if everyone had enough Vitamin D. [2]
Dr. Anthony Cardillo, CEO Of Mend Urgent Care and ER physician, joined ABC7 via Skype to explain the latest research showing why vitamin D levels may be linked to a person's risk of COVID-19. [3]
But at that time in the USA, this knowledge was being suppressed presumably because it was being associated with homeopathic remedies and with denial that COVID-19 was a severe pandemic. Here's an example: https://www.ftc.gov/system/files/warning-letters/covid-19-letter_to_dap_eric_nepute.pdf
JUNE 2020
Dr. Fauci's position on Vitamin D was that the USA would not really benefit from it because 'Most people in the developed world are not Vitamin D deficient'. He didn't say 88% of African Americans are deficient in Vitamin D, a statistic given above in the video from Dr. John Campbell. At this time, the WH Task Force was not suggesting that people use Vitamin D to prevent COVID-19, yet doctors elsewhere were strongly suggesting to. Here's the quote from the Fauci interview [5]:
"Dr Bauchner: People always raise the issue about vitamin D and whether or not it could be helpful in treatment. Do you have a sense of vitamin D and its role with COVID-19?
Dr Fauci I think it really relates to the importance of vitamin D in host defense against infection. There’s no doubt that if you are vitamin D deficient, you might have a poor outcome or a greater chance of getting into trouble with an infection. Most people in the developed world are not vitamin D deficient, so adding additional vitamin D may not actually have a substantial clinical effect. That doesn’t lessen the importance of a normal level of vitamin D. In some of the developing countries, there have been studies with tuberculosis and other diseases. Those who are vitamin deficient, including vitamin D and vitamin A, they do worse.
Dr Bauchner: Azithromycin has come up repeatedly. Some people have said, “Well, the reason azithromycin isn’t working is because you’re not combining it with zinc.” I’m not sure if there’s much of a basis for that argument. Do you have a sense of zinc and azithromycin?
Dr Fauci: I don’t think there’s enough data at all to give you any firm conclusion as to the benefit of azithromycin alone vs the benefit of azithromycin plus zinc. There’s anecdotal stuff all over the place, as you well know. There are studies now that are looking at a combination of hydroxychloroquine and azithromycin compared to a placebo to see if there’s any effect there. That’s what we need, as you well know, and you and I have both said that many times."
AUGUST 2020
The outcome was, this was just being said on other publications, but the WH Task Force did not mention nutrition importance in their daily briefings, and no initiative was undertaken to distribute vitamins (like D, A, B, zinc, magnesium, etc.) to the public, especially the most vulnerable. These comments (and the lack of acknowledgement or mention of public deficiencies, and the ease of overcoming it, being a significant contribution to the pandemic). This was written about in an article in Informed Choice Washington, titled 'Why is Dr. Fauci unaware of Vitamin D insufficiency in U.S. populations hit by COVID-19?' [6], here are some quotes:
* While Dr. Fauci did acknowledge the importance of Vitamin D, he seems unaware that those hit hardest in the United States are populations known to be Vitamin D insufficient.
* “Vitamin D insufficiency (VDI) meets every one of the above [mortality risk factors] criteria. VDI affects 80-90% of the African American population.” [7]
* “While MUSC [Medical University of South Carolina (MUSC) ] is not suggesting that vitamin D cures or prevents COVID-19 infection, officials say the body of prior and emerging scientific evidence would suggest that individuals with low vitamin D levels who contract COVID-19, including African Americans and elderly nursing home residents, might experience worse clinical outcomes than other groups with normal vitamin D levels.” [8]
* Instead of dismissing this as a concern only in developing countries, Dr. Fauci should be waging Vitamin D awareness campaigns, with emphasis in African American communities and nursing home facilities, and drastically reducing disease severity and fatalities.
The article continues citing numerous articles in support of Vitamin D.
SEPT 2020
The first time Dr. Fauci acknowledged that Vitamin D could be beneficial in the USA for COVID-19 was not during a WH Task Force briefing but during and Instagram (September 2020) [9]:
* “If you are deficient in vitamin D, that does have an impact on your susceptibility to infection. So I would not mind recommending, and I do it myself taking vitamin D supplements,” Dr Fauci said during an Instagram Live session: https://www.instagram.com/p/CE7tWzinTI8/
* Says that transmission is person-to-person and not through objects/surfaces.
* Says that contrary to some false claims, transmission to children is possible.
(Notes: WH Task Force didn't really talk as much about that finding in the WH Task Force briefings, they didn't inform much about how long the virus survives as a viable transmission on different surfaces. It peeves me that they didn't have better information after Diamond Princess because if they have labs studying coronaviruses then how can the be safe if they don't already know how long a virus is viable on different common surfaces and food products? Also, where was his proof that 'people' were saying that children do not get COVID-19? I don't remember anyone say that, and I suspect that it is a political attack called a strawman wherein false statements are given to opposition - I don't know whetehr that was his intent or someone tricked him that way - but where is his proof that people actually were saying that?)
It was at the pressure from the US House Reps (mostly Republicans) that have forced that issue. Republican Rep. Grothman (Wisconsin) insisted that 40% of USA citizens are Vitamin D deficient and cited publications, and this is important [10]
DECEMBER 2020
My favorite video about Vitamin D is reference [12]- the links in the description of that video are to numerous peer-reviewed articles. From their description: "Professor Roger Seheult, MD explains the important role Vitamin D may have in the prevention and treatment of COVID-19. Dr. Seheult illustrates how Vitamin D works, summarizes the best available data and clinical trials on vitamin D, and discusses vitamin D dosage recommendations." He carefully explains why this is a factor in what we see today as lack of equity in medical care. The references below also give the time links from one commenter to serve as an outline.
Some people got upset about the lack of acknowledgement to Vitamins and immunity and more to the suppression of their voice to spread this knowledge. Look at the comments in the Vitamin D video (long one) that is my favorite. Someone said their Facebook account was suspended for sharing it. That video gives the peer-reviewed articles that it references. By that time I was off of Facebook and Twitter because I just couldn't take it anymore all the politics and false information, then the suppression of facts and peer-reviewed science.
APRIL 2021
Perhaps the most insulting to the people advocating that society distribute Vitamin D (and other nutrients) widespread, was the claim that it was part of some conspiracy theory about a cover-up about COVID-19. It wasn't. Yet, that's the claim of Schraer (2021, April 4, BBC News) in her article 'Vitamin D: The truth about an alleged Covid 'cover-up'. There was never in any of the statements above about Vitamin D, a suggestion that it would completely prevent COVID-19, that it required homeopathics, or that COVID-19 was some sort of big-pharma hoax. What was being said was substantiated by medical research that is decades old.
TIMEMACHINE JOURNEY BACK TO 2016
But the sad thing is Dr. Fauci did know that the USA was deficient in Vitamin D and that it impacts immunity. Here's a 2016 article where he said that:
https://www.washingtonian.com/2016/01/15/how-to-avoid-getting-sick-when-youre-around-people-all-day/
How to Avoid Getting Sick When You're Around People All Day
Dr. Anthony Fauci shares his pro tips.
www.washingtonian.com
Our expert: Dr. Anthony Fauci, director of NIH’s National Institute of Allergy and Infectious Diseases since 1984, who oversees research in preventing, diagnosing, and treating infectious diseases from flu to HIV.
“Wash your hands often. Use soap, and rub it around for 15 to 20 seconds to kill germs. You don’t want to miss a spot. Make sure to dry thoroughly. If you can’t get to a restroom, use hand sanitizer, again for 15 to 20 seconds. If you can’t wash your hands, don’t touch your face, eyes, or nose after shaking hands or even taking a file from someone.
“I clip my nails often because I don’t want to carry germs around. If you have long nails, scrape a little soap or sanitizer under the nails.
“Take vitamin C. It can enhance your body’s defense against microbes. I take 1,000 milligrams a day. Many people also do not get enough vitamin D, which affects a lot of body functions, so that would be helpful, too.
“Take care of yourself. Get seven to eight hours of sleep—most of us, including myself, don’t sleep as much as we’d like. Exercise, eat well, and keep well hydrated.”
How to Avoid Getting Sick When You’re Around People All Day
WRITTEN BY WASHINGTONIAN STAFF | PUBLISHED ON JANUARY 15, 2016
References:
[1] Nutritionalconcepts.com. (2020, April 13). What Dr. Fauci Is Not Telling You. Nutritional Concepts. https://www.nutritionalconcepts.com/post/what-dr-fauci-is-not-telling-you.
[2] Campbell, J. (2020, May 22). Vitamin D on the news. YouTube. https://www.youtube.com/watch?v=esDfuS8JdE0
[3] Copyright © 2021 KABC-TV. (2020, May 15). COVID-19 and vitamin D: SoCal doctor explains the connection. ABC7 Los Angeles. https://abc7.com/vitamin-d-and-coronavirus-sunshine-sun-role/6182232/.
[4] https://www.ftc.gov/system/files/warning-letters/covid-19-letter_to_dap_eric_nepute.pdf
[5] Abbasi, J. (2020, July 21). Anthony Fauci, MD, on COVID-19 Vaccines, Schools, and Larry Kramer. JAMA. https://jamanetwork.com/journals/jama/article-abstract/2767208. doi:10.1001/jama.2020.9222
[6] Icwa. (2020, September 6). Why is Dr. Fauci unaware of Vitamin D insufficiency in U.S. populations hit by COVID-19? Informed Choice Washington. https://informedchoicewa.org/education/why-is-dr-fauci-unaware-of-vitamin-d-insufficiency-in-u-s-populations-hit-by-covid-19/.
[7] Vitamin D insufficiency is prevalent in severe COVID-19 https://www.medrxiv.org/content/10.1101/2020.04.24.20075838v1
[8] DeRobbio, D. (2020, April 28). MUSC vitamin D research team to study connection to COVID-19 prevention and treatment. WCIV. https://abcnews4.com/news/coronavirus/musc-vitamin-d-research-team-to-study-connection-to-covid-19-prevention-and-treatment.
[9] Garner, J. (2020, September 9). jennifer.garner Verified Conversation with Dr. Fauci. Instagram Account of Jenifer Garner. https://www.instagram.com/p/CE7tWzinTI8/
[10] Congressman Glenn Grothman, Update on Vitamin D, COVID-19 and Dr. Fauci. (2020, Sept. 18) YouTube. https://www.youtube.com/watch?v=uE8R4ATCqnM
[11] Seheult, R. (2020, Dec 10). Vitamin D and COVID 19: The Evidence for Prevention and Treatment of Coronavirus (SARS CoV 2). MedCram - Medical Lectures Explained CLEARLY. YouTube. https://www.youtube.com/watch?v=ha2mLz-Xdpg
[12] Schraer, Rachel. (2021, April 4). Vitamin D: The truth about an alleged Covid 'cover-up'. BBC News. https://www.bbc.com/news/health-56180921.
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