Jeff Gilchrist Profile picture
Mar 29, 2022 19 tweets 4 min read Read on X
COVID-19: Causes unprecedented autoimmunity

Several studies have shown indicators and markers of autoimmunity (immune response attacking body's own health cells or tissues) present with and after COVID-19 infection. 🧵1/
One study found that CD8+ T-cells expressing killer cell immunoglobulin-like receptors (KIRs) are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases, including COVID-19 ( science.org/doi/10.1126/sc… ). 2/
They found elevated levels of KIR+CD8+ T-cells but not CD4+ regulatory T-cells in COVID-19 patients which correlated with disease severity, vasculitis (inflammation of blood vessels) and were associated with autoimmune-related complications. 3/
Their results indicate that these regulatory CD8+ T-cells act uniquely to suppress pathogenic T-cells in autoimmune and infectious diseases. When they destroyed these cells in virus infected mice, it led to autoimmunity post-infection. 4/
Another study looked at 147 hospitalized COVID-19 patients and found autoantibodies in 50% of patients but less than 15% of healthy controls ( nature.com/articles/s4146… ).  Autoantibodies mistakenly target and react with a person's own tissues or organs. 5/
They hypothesize that prolonged inability to eradicate and clear the virus expands the adaptive immune response to target non-structural viral proteins, some of which might physically interact or cross-react with components of the body. 6/
A new publication from @fitterhappierAJ discusses superantigens and COVID-19 ( mdpi.com/2076-0817/11/4… ).  It has been suggested that the COVID-19 virus contains at least one superantigen-like pattern that is unique and not found in any other SARS or endemic coronaviruses. 7/
Why is this an issue? Superantigens can send the immune system into overdrive since multiple immune cells already trained for other pathogens might think it looks similar enough and activate. Normally a very small fraction of T-cells will be stimulated during an infection. 8/
A superantigen can stimulate up to 30% of naive T-cells which can also lead to a number of issues including anergy (T-cells become unresponsive), inflammation, cytotoxicity (kill cells), deletion of T-cells, and autoimmunity. 9/
"SARS-CoV-2 causes many of the biological and clinical consequences of a superantigen, and we believe in the context of reinfection and waning immunity,..." 10/
"... it is important to better understand the impact of a widely circulating, airborne pathogen that may be a superantigen, superantigen-like or trigger a superantigenic host response." 11/
Superantigens have differing effects on immature and mature CD4 and CD8 T-cells (see figure).  They can deplete immature T-cells but hyperstimulate mature cells.  12/
They can also cause differentiation of naive T-cells and stimulation of CD8 memory cells from bystander activation which can also lead to T-cell death. 13/ Image
The possibility of deletion of antiviral memory warrants investigation given the thymus loses its ability to produce new naive T-cells as we age and could compromise the ability for the immune system to clear pathogens. 14/
COVID-19 has been found to persist in the body for months after infection therefore chronic exposure to superantigen could continually stimulate T-cells, keeping them in a perpetual state between anergy and hyperstimulation.  15/
This could also manifest in an observed naive T-cell depletion and could explain the low quantities found in some Long COVID patients. 16/
The evidence of autoimmunity with COVID-19 keeps mounting. Studies have found immunological dysfunction following even mild to moderate infection, including depletion of naive T-cells and B-cells in individuals with Long COVID. 17/
Another study found the depletion of naive T-cells and higher levels of T-cell death (apoptosis) in COVID-19 infection than HIV. 18/
"Some countries seem willing to tolerate high levels of infection provided their healthcare systems can cope... If SARS-CoV-2 contains a superantigen, superantigen-like protein or triggers a superantigenic host response, this strategy may prove a grave error." 19/

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More from @jeffgilchrist

Nov 10
COVID-19: Stats, Guides, Articles, Calculators

COVID-19 guides, useful info, stats, calculators & 600+ scientific articles: covid.gilchrist.ca

Ottawa, Canada weekly stats: covid.gilchrist.ca/Ottawa.html

Ontario, Canada weekly stats: covid.gilchrist.ca/Ontario.html

🧵1/ Graph of COVID-19 wastewater levels in Ottawa, Ontario, measured from Sept. 1, 2021. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Sankey graph (height of each bar is # of sequences for that variant) showing top variants and their lineages over the past 6 weeks from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D&pageName=ReportSection32240d6b62ba73667e98 )
A sample of some threads listed on the website ( covid.gilchrist.ca ):

How do variant designations work and relate to our immunity ( x.com/jeffgilchrist/… )? 2/
Why should we care about a virus with a "99.8% survival rate" ( )? 3/
Read 16 tweets
Nov 10
#Variant update for #Ontario, #Canada (to Oct 29, 2024)

The KP.3.1.1 #DeFLuQE variant is having some competition from XEC and MC.1 now. Graph tools by @Mike_Honey_ 🧵1/ Graph of top 7 COVID variants from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
XEC is a combination of KP.3.3 and KS.1.1 that recombined together. MC.1 is a direct descendant of KP.3.1.1 with one spike mutation at T571I. To learn more about how variant naming works, you can read this article I wrote with @paulseaman31 ( ). 2/docs.google.com/document/d/1q0…
This Sankey graph shows the proportion of variants from PCR test genomic sequencing in Ontario since September 15, 2024. You can follow the lineage backwards to see where a variant is a descendant from. 3/ Sankey graph (height of each bar is # of sequences for that variant) showing top variants and their lineages over the past 6 weeks from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D&pageName=ReportSection32240d6b62ba73667e98 )
Read 9 tweets
Sep 22
Ceilings fans can reduce short-range viral concentrations close to the infected (54%-77%) while increasing long-range levels (5%-14%). Only recommended when # people in room is less than decision tool for various ventilation rates with not highly contagious pathogens (e.g. cold).

Decision tool for using or not using fans to mix the air in the room. Decision tool for using or not using fans under various ventilation rates (200, 400, and 800 m³/h) on reducing overall airborne transmission risk, considering occupants with and without the use of masks. The logarithmic scale on the left vertical axis shows the contagiousness of the pathogen, which indicates the quanta emission rate. The horizontal axis measures the number of people at long-range distances in relation to per person ventilation rates. The range of conditions that using fans is beneficial is filled in turqu...
The number concentration of lumped tracer particles between 0.3 and 5.0 μm for both short-range and long-range routes, respectively.
Link to full study here ( ).sciencedirect.com/science/articl…
There are some important caveats in this research. "Fans are beneficial in well-ventilated rooms with not highly contagious pathogens." 3/
Read 4 tweets
Sep 19
Variants: JN.1 vs KP.2 vs KP.3.1.1

What do the variant designations like KP.3.1.1 mean and how does it compare to JN.1? How important is just 1 mutation? Can 1 mutation potentially affect our immunity and how vaccines are designed? Read on to find out more. @paulseaman31 🧵1/ Structural alignment of the AF2-predicted RBD conformational ensembles in the complexes with ACE2 for JN.1 (A), KP.2 (B) and KP.3 variants (C). Structural alignment of the AF2-predicted conformations with high pLDDT values > 80.0 and the cryo-EM structure of the BA.2.86 RBD-ACE2 complex (pdb id 8QSQ). The RBD conformations are shown in ribbons. The sites of unique BA.2.86 mutations D339H, K356T, R403K, V445H, G446S, N450D, L452W, N460K, N481K, A484K, F486P, R493Q are shown in blue spheres on panels (A-C). Mutation L455S in JN.1 is shown in red spheres on panel A. The positions of KP.2 mutat...
The web version of this article with nice table of contents and is easy to share with others can be found here ( ) or ( ). 2/ tinyurl.com/VariantsSummer…
docs.google.com/document/d/1q0…
Table of Contents Variant Designations (e.g. KP.3.1.1) - Parent & Child Lineages - KP.3 vs KP.3.1 vs KP.3.1.1 - Variants that Start with X How does this relate to our immunity? How important is 1 mutation? What variants are circulating now? - Canada - USA - United Kingdom - Europe - Asia - South America -Oceania
Variant Designations (e.g. KP.3.1.1)

You have probably seen people refer to COVID-19 variants with specific codes containing both letters and numbers like JN.1 or XBB.1.5, but what does that mean? 3/
Read 89 tweets
Aug 28
Virus update for Ottawa, Canada (Aug 28, 2024)

COVID-19 #Wastewater levels in #Ottawa are up again with the circulation of a new KP.3.1.1 DeFLuQE variant ( ). Wastewater is still being updated but on a weekly basis now. 🧵1/3 covid.gilchrist.ca/Ottawa.html
Image
New hospitalizations in Ottawa *due* to COVID-19, Flu or RSV are unfortunately increasing again. There were two big spikes over the past month ( ). 2/3 ottawapublichealth.ca/en/reports-res…
Graph of New Hospitalizations in Ottawa *due to* COVID-19, Influenza or RSV. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
One virus is causing a lot more hospitalizations than the other two over the past year. Even at the lowest point at the end of March 2024, COVID-19 still accounted for more than 40% of hospitalizations between the three viruses and more than 80% for almost half the year. 3/3 Graph of % of New Hospitalizations in Ottawa *due to* COVID-19, Influenza or RSV. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Read 4 tweets
Aug 23
#Variant update for #Ontario, #Canada (to Aug 13, 2024)

Today's variant show is brought to you by the letters KP... Looks like KP.3.1.1 has really taken off and separated from the pack at 40% prevalence in Ontario. Graph tools by @Mike_Honey_ 🧵1/ Graph of top 7 COVID variants from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
KP.3.1.1 has the #FLuQE mutations and also a key point in the spike protein deleted which gives it much more immune evasion than other variants. 2/
Testing with a recently released monoclonal antibody treatment (pemivibart) found that while it neutralized JN.1 and KP.2 with similar performance... ( ). 3/biorxiv.org/content/10.110…
Read 14 tweets

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