New page with thoughts on People Interactions. Currently holds thoughts on the Russian military actions/invasion into the Ukraine: https://github.com/forestgrape/people_interactions/blob/situation0705/conflicts/ru_ukr_conflict.md (some of the notes were originally published here.) It’s just personal thoughts but not a scientific or political work.

Understanding Betacoronaviruses and their Diseases

This page contains topics around Covid and Coronaviruses. The content discussed is broad and reaches from practical tips to current re-search topics including new hypotheses which are tagged as ‘explorative’.

The section bird view of content overviews the overall content and in the content section the topics discussed are presented in more detail. Usually it is possible to cherry pick content and most chapters have a summary outlining the concepts. The more ‘in depth’ content often is written in technical jargon.

A goal of this page is to motivate critical and independent thinking and to contribute to accessible explanations. As noted, currently some parts are very technical, improvements planned. Both questions and help are welcome!

Sections of this Chapter (index)

• Bird View of Content: Gives a short overview of the different topics.
• Updates: Lists the most recent topics added and changes of content:
  • Recent Topics Added
  • Recent Updates
• Notes on Reading: Notations used and how the page is written.
• Content. Detailed content overview including twittering summaries.

Bird View of Content

This section overviews the entire content. The content section lists the topics discussed in more detail. The links point there.

1. Introductory Topics. Public Suggestions and Tips. Day to day tips how to handle ‘Covid times’. Covid transmits with the air, similar to smoke. A healthy lifestyle helps to prevent and overcome Covid. Situations assessments are also grouped here.
2. Biological Topics. Forms of life on earth including viruses. How life forms relate and interact with a focus on coronaviruses.
3. Medical Topics. What Covid-19 is and how to diagnose it.
4. Immunological Topics: The interplay between coronaviruses and their hosts where the immune system plays a central role.
5. Epidemiological Topics: Where and when coronaviruses spread and how they spread (transmission paths). Individual factors such as age relevant for the transmission of SARS-CoV-2.
6. Treatment and Prevention. Ideas to prevent and treat virus diseases including Covid. A good prevention with positive ‘side-effects’ is a healthy lifestyle. For young and healthy people this is a reliable and recommended prevention against severe Covid.
7. Social Topics. Thoughts about measures to reduce the spread.
8. Data Topics.
9. Topics in Physics: How atoms and molecules aggregate (e.g. to droplets) which is relevant for transmission and viability of viruses.
10. Vaccines: Thoughts on the safety of vaccines.

Updates

Recent Topics Added

• 17.12.: New Chapter on Omicron. Omicron is noteworthy different from the previous SARS-CoV-2 lineages: 1) Higher Transmission 2) reports for changed disease symptoms and 3) very high number of mutations in the spike. Two possible explanations are discussed:
  • Explanation 1 (speculative): The Omicron Variants has a changed tropism away from airways epithelial cells towards immune cells such as macrophages. From biology this is possible since various members of coronaviruses (and other members of Nidovirales) are known to replicate in immune cells. The changed symptoms, the increased transmissibility especially in immunized people and the mutations observed provide evidence for the change of tropism.
  • Explanation 2: The Omicron variant mutated to escape spike binding antibodies and thereby gained a transmission advantage. This could also have been or be an intermediated step towards explanation 1.

• 24.11.: Interferon Treatment: Early interferon treatment helps to reduce the viral load and prevents more than half of severe disease cases. Interferon alpha treatment shows the best results with a mortality reduction above 75% if used early. Topical administration to the respiratory tract (spray or nebulized) shows benefits even in mid to advanced disease stages. Systemically applied interferons (especially IFN beta) on the other hand yield adverse outcomes when applied late.
  => 1) Topical IFN alpha is recommended to treat SARS-CoV-2 infection and treatment should start as early as possible.
  => 2) Systemic or topical IFNs are recommended as prophylaxis for risk groups upon exposure or at high incidence rates of severe Covid.

• 12.11.: Respiratory Tract Microbiota with a focus on Virobiota and some notes PCR diagnosis.
• 12.11.: Split up the spread analyses chapter into
  • Spread Analyses regarding Transmission Environments
  • Individual Susceptibility and Transmission. Added sections:
    • Effects of acquired immunity
    • Extended many section e.g. transmission by age groups.
    • updates still in work
• 12.11.: Proposal for an Advisory Covid App

News Board

• 31.1.22: Possibly changed IFN treatment effects with Omicron and with acquired immunity present. Looking at individuals treated with IFNs for other indications, could elucidate changes in treatment effects.

• 17./30.1.22: Findings and interpretations are stated, to the best knowledge, even-handed. Biased thinking may happen nevertheless, please point out. Human rights are kept in mind.

• 14.-31.1.22 How this page was communicated/marketed or not communicated often was bad/didn’t work. To re-search and to work on content went (and goes) often easier here than the vitally important communication, this especially if times are stressful or communication possibly had been appropriate earlier or unsure about. Also many successful projects/concepts were done good enough they spread on their own - which is challenging in many aspects. Here, some awkwardness, a messy presentation, missing rigor and controversial and/or not well founded content may not have helped. To communicate more is a major goal and to publish selected chapters on searchable science portals (some polishing will be done first). The content focus will be on basic science such as Virion Viability or Development and Localization of the Immunity.

• 7.-11.1.22: Rolling updates of the Omicron Chapter: Summary updated: 1) Omicron infects the lungs less. In agreement, in vitro experiments show Omicron replicates less in the lungs. Likely since Omicron enters cells mainly via the endosomal cathepsin primed pathway and not through the TMPRSS2 primed cell surface pathway. 2) A few month after vaccination the efficacy against infection can turn negative (once infected, the vaccine induced immunity still protects against severe disease). Both observations provide evidence for immune cell infection. 3) The levels of ABs inducing phagocytosis decay slower than the levels of ABs inducing other functions such as cytotoxicity after natural infection (if the mechanism is independent of the way of immunization, likely too after vaccination).

• 1.1. - 12.1. Clarifications and formulations across the page. E.g. Suggestions and Tips clarified and most content was written in the first and second wave in 2020 when the Covid situations were different.

• 7.1.(announced here) Individual Transmission and Susceptibility: Added evidence for the hypothesis that the average viral and the positivity rate are correlated. // online since 27.12.21

• 20-22/27.12. Sorry. Without the peace of mind for careful considerations and concise, factual and tactful formulations, the page was rushed out to a wider audience. For example, some statements regarding the safety of vaccines were much to dramatic (and partly still are) - these mostly were formulated in a different situation. Corrections in work.

  To keep in mind, the focus of this page is on (corona)viruses what they do, how they transmit and how to handle them. Mistakes of any form [are likely to] happen regularly on this page.

• 20/21/22.12. Help & Feedback of any kind, especially improvements suggestions including pointing out mistakes, is always welcome (witotraub@gmail.com/@runbox.com).

• 20.12. Correctly linked Omicron chapter and moved the announcement to section Recent Topics.

  Omicron is a new Chapter and not just an Update, both biological and organizational.

• 27.11. (pinned): Restrictions should be nearly no for children, very relaxed teenagers and relaxed for the twenties. //as of January 2022, few restriction are necessary anyways.

Notes on Reading

• Many parts are hypothesis and ideas but not [double] checked facts. They are put here as ideas to be checked and evaluated. The chapters with not well founded content are tagged with (explorative).
• The writing often is conversational and some parts aren’t rigorous.
• This is work in progress. Parts under heavy work are mostly marked with ‘[in work]’. Mistakes of any form are likely.
• Support Support on ko-fi.com is welcome, to enable full-time re-searching on coronaviruses.
• License The license is Creative Commons Attribution 4.0. Relaxation: For any use with the main purpose of public health and public information no attribution is required (as long as its not copy & paste) but referencing is always welcome (most content is founded enough by now).
• Questions, pointing out mistakes, improvement suggestions and feedback are welcome.
• Table of Content The content is ordered mostly by dependencies i.e. content founding other sections is ahead. The dependencies are often circular however.
• Source This page is open source on GitHub: https://github.com/forestgrape/coronavirus/blob/master/index.md, where it can be read both as Markdown and GitHub Preview and hosted on GitHub Pages: https://forestgrape.github.io/coronavirus
• References
  • Often references are summarized. Word-by-word extracts are in “_ _ _”. The summaries are biased towards to results relevant for this page. To capture the essence of the research is tried too.
  • The references are named by the first author.
  • References are usually grouped by topic. If several topics apply, one is chosen.
  • For term definitions and general topics, wikipedia (English), encyclopedia britannica and the oxford dictionary are frequently consulted. Currently they omitted as reference at each location. It is planned to improve this.
• Formulations Some are subjective and marked as comments. Sometimes words are not weighted carefully or formulations are unclear/ambiguous. Upon discovery, unfitting formulations are improved. Feedback is appreciated and questions welcome.

  • No Ambiguity: Some formulations especially in comments are general but ambiguity is not indented. The reason is clarity. (In the beginning, a few comments were ambiguous but this is not intended anymore, since this neither works nor fits a project like this.)

• Symbols
  • ’=’ denotes ‘equals’ or ‘has the meaning of’ or ‘set equal to’
  • ’=>’ = implies
  • ’->’ = points to further content/explanations
  • ‘a := b’ = a defines b (to emphasize a definition or specify the order)
  • ‘&’ := and
  • {hello} = Repetition of hello e.g. hello, hello, hello
  • [to check] = Annotation if something is in work or needs checking.
  • [good] morning = facultative word (same syntax as work annotations, distinction upon context)

Definitions

Definitions are written like this and are valid throughout this page; sometimes only throughout this page.

New Definition

‘New’ definitions are written like this. ‘New’ means it is defined on this page and not a definition commonly used in literature (introduced on 15.5.21).

Redefinition of an existing terms is not done on purpose, unless explicitly noted. Please point out!

Comments

• Comments, often subjective, are formatted the same as definitions and sometimes additionally marked with programming style ‘//’. Otherwise distinction is done by context/content.
• Off Topic Remarks: Sometimes subjective off topic remarks are added. One reason for subjective off-topic remarks is transparency and background for the mindset behind suggestions.

Mindset in Short

• We all should be able to live the life we want, as long that’s respecting the rest of the world doing so too.
• Fairness is important. Attitudes or group memberships - as long as they respect others - should only matter if directly relevant and really necessary for the task of interest.

More on the mindset follow on this page in the chapters:

• Respect and Take Care on the Suggestion and Tips page.
• Baseline Principles to design an Economic System on the Economic page.

Content

Sometimes out of date, newest sections are announced in recent topics and recent updates].

In the source on github the topics correspond to folders and the chapters correspond to files.

1 Introductory Topics

• Illustrative Resources: A subjective list of especially helpful, insightful and/or extraordinary Resources.
• Suggestions and Tips Keep distance and hygiene. Then outdoors is safe. Inside ventilate well and/or wear a mask. Transmission of severe Covid is mostly smoke-like. Don’t burden the immune system.
• Covid and Social Life
• Situation Assessments.
• Update History: Content and updates as published in reverse chronological order.

2 Biological Topics

• Life Forms. Principles and concepts of life on earth.
  • Mobility of Life Forms How life form move or get moved to cross distances.
• Viruses. What viruses are and what they can do and do. Viruses are defined as life forms which are dependent on extern enzymes. Aspects such as life cycle and behavior are discussed.
• Virion Viability
  • Virions decay fast in sunlight, soap and disinfectants (the halflife time is a few minutes).
  • From 0 to 40 degrees the decay is faster at increased temperature and depends on the biochemical environment. In saliva, nasal mucus and sputum the halflife time is about 8 hours at 4 degrees and about 2 hours at a room-temperature of 22 degrees.
  • Above 45 degrees the decay fastens and is less dependent on the biochemical environment since the spring-loaded proteins loose their energy.
  • A fast decay occurs when the concentration of salts is very low in the surrounding water. This is the case in distilled water and in situations with a lot of condensation. Possible mechanisms: osmotic pressure or increase of degrees of freedom of movement especially of the single stranded RNA/DNA.
• Coronaviruses. Life cycle, distinguishing features and capabilities of coronaviruses.
  • Coronavirus Evolution
  • Backtracing Sars-CoV-1/2 (explorative) The natural habitat of SARS-CoV-1/2 may include domestic animals and/or insects in the region northern Yunnan. Possibly the life cycle of SARS-like is alternating in hosts and follows nutrient cycles.

3 Medical Topics

• Covid-19 The Covid-19 results from the interplay between the immune system and SARS-CoV-2. SARS-CoV-2 can infect different locations throughout the respiratory tract and the immune response experienced depends on the location. Therefore Covid-19 is a disease with many faces.
• Diagnosis and Viral Load How to diagnose Covid with a focus on methods detecting parts of viruses (virus RNA with PCR or virus proteins with antigen test) at different locations (e.g. in the nose, mouth, lungs).
  • Immunological Detection Methods: Antibodies bind very specifically to certain substance (mostly proteins), immuno assays use this property to detect specific substances. Antigen and antibody tests for by this principle.
  • PCR Detection: Some notes on the detection of viruses by PCR. PCR usually have an error rate of a few cycles (95% confidence interval). Low viral loads have a certain probability to go undetected.
• Infection Locations and Disease Patterns (explorative)

4 Immunological Topics

• A conceptual View of Immunology Selected topics of the immune protection with a focus protection versus coronaviruses are discussed.
• Immune Evasion Mechanism of Coronaviruses How coronaviruses circumvent immune system obstacles.
• Development and Localization of the Immune System during Life: How the immune system developes during lifetime and how the pathogen exposures induce immune adaptions which are often localized. During childhood SARS-CoV-2 is just another new virus as each virus is encountered once for the first time. With increasing age the immune system increasingly relies on the previously seen pathogens and looses capabilities to handle new viruses.

5 Epidemiological Topics

• Transmission of Sars-CoV-2 with Focus on a Proposed Dry Form Transmission Sars-CoV-2 is mostly transmitted airborne and even a Dry Form aerosol infection is possible.
  • A summary of airborne transmission,
  • Proposal of a new dry from transmission model,
  • describe how particles behave in the respiratory tract,
  • analyse spread pattern of Covid-19 which indicate aerosol transmission
  • and based on the discussed transmission pathways, protection measures are suggested: smoke protection and masks.
• Situation specific Spread Analyses Situations where Covid-19 spreading is observed or is not observed are described. High transmission of severe Covid is observed in situations where much air is exchanged between people. Much air is exchanged when spending a lot time indoors without ventilation, crowded confined settings, at high altitude and when deep breathing (e.g. sports, singing).
• Individual Susceptibility and Transmission: How much individual factors such as age, dirty air exposure and acquired immunity (either by natural infection or vaccination) influence the susceptibility and the onwards spread.
• Microbiota with a Focus on Virobiota in the Respiratory Tract: The mucosal surfaces such as the intestine and the respiratory tract form habitats to a variety of microorganisms. The focus is on viruses in the respiratory tract and their roles in health and disease.
• Evidence for Increased Immune Protection against Sars-CoV-2 from Exposure to BCoVs (explorative section)

6 Treatment and Prevention

• Treatment Overview: Which treatments at which time.

• Interferon Treatment: Early interferon treatment helps to reduce the viral load and prevents more than half of severe disease cases. Interferon alpha treatment shows the best results with a mortality reduction above 75% if used early. Topical administration to the respiratory tract (spray or nebulized) shows benefits even in mid to advanced disease stages. Systemically applied interferons (especially IFN beta) on the other hand yield adverse outcomes when applied late.
  => 1) Topical IFN alpha is recommended to treat SARS-CoV-2 infection and treatment should start as early as possible.
  => 2) Systemic or topical IFNs are recommended as prophylaxis for risk groups upon exposure or at high incidence rates of severe Covid.

• Movement How movement helps to get a better immune reaction upon a Covid infection and to recover faster and better.

• Masks. Mask both reduce the spread and prevent infections. Not only from SARS-2 but from all viruses which infect through the respiratory tract e.g. influenza.

• Topical Treatments of the Respiratory Tract to prevent and cure respiratory infections including Covid. Coronaviruses (and other respiratory viruses) live on the surface of the respiratory tract and release their progeny as delicate virions to the covering fluids. The idea is to reduce these virions by local treatments. Similar as we disinfect wounds - the medications need to be adapted of course. (explorative)
  • Temperature and Humidity Modulation is proposed as a topical treatment: It reduces the number of infectious virions and enhances the immune response. There is solid biological and epidemiological evidence that it works if used early on! (explorative)
  • Increase the mucus Flow by humidified air: Humidify inhaled air early on to increase the mucus flow and wash the virions out. The goal is a reduce viral load and better prognosis. (explorative)

7 Social Topics

• Thoughts about Controlling Sars-CoV-2: Thoughts how to tackle and control Covid-19. Different kinds of measures are discussed from physical (mask, ventilation) to social measures such as an early closure of nightlife.
• Thoughts on Economical Systems: How to design an economical system which enables free choice for the economic life.
• Considerations on Individual Measures: Consideration on measures targeting individuals. E.g. splitting societies by the immune status or vaccine status is discussed.
• Good Air Certificate: Severe Covid mainly spreads from lung to lungs through dry air. Thoughts how to reduce this spread by ventilation, air humidification and air cleaning.
• Advisory Covid App: Proposal of an advisory app that estimates the exposure risk. Upon high exposure risk a test can be adequate to early detect a possible infection either to initiate a treatment for risk groups or to reduce ongoing transmission.

8 Data Topics

• Monitoring: About testing, monitoring, gathering and publishing data.
• Data: On publishing and analyzing data.

9 Topics in Physics

• Aggregation of Atoms. How atoms aggregate to form the different kinds of matter.

10 Vaccines

• Immunization: How to prepare the immune system to pathogens.
• Vaccine Safety Considerations: Open safety question and possible adverse effects of ‘mRNA’ vaccines and adenovirus vaccines.
• Effect of Covid-Vaccines on SARS-CoV-2 Infections: What effects the current have or can have on SARS-2 infections. The knowns and the unknowns.

Explorative Chapters

• Modifying Temperature and Humidity
• Topical Treatments for Respiratory Infections
• Infection Locations and Disease Pattering
• Backtracing Sars-CoV-1/2: on the page Hosts of Nidovirales.
• Infection Tropism and Disease Patterns
• Bovine Farming and Covid
• Early On Prevent Mucus Accumulations