Jeff Gilchrist Profile picture
Dec 22, 2022 36 tweets 13 min read Read on X
What is going on with our immune cells after COVID-19 infection?

This thread will explore some of the impacts of COVID infection on our immune system even after people are recovered including:
- Missing naive T-cells
- Exhausted T-cells
- Loss of B-cell maturation

🧵1/ Image of Shark eating T-cell
- Hyper-activated inflammatory response
- Immune system is impeded post-infection
- Immunological dysfunction persists 8+ months
- Depletion and dysfunction of dendritic cells
- Impairs ability to fight fungal infection
- Unprecedented autoimmunity

2/
- Infected immune cells (monocytes)
- Persistent loss of smell from T-cells
- Persisting CD4+ and CD8+ T-cell activation 12+ months

An unrolled one-page web view for this long thread that may be easier to read or share can be found here ( ). 3/
A new study found that a subset of naive T-cells usually found in healthy individuals were absent from recovered people, suggesting a post-infection inflammatory stage ( frontiersin.org/articles/10.33… ). H/T: @vipintukur 4/ Image of the summary of the...
Naive immune cells are important when you get infected by a new pathogen so they can be activated and develop/differentiate into T and B-cells that are specific to that pathogen to fight it. Without enough naive cells, the response from your immune system is weakened. 5/
To learn more about how your immune system works, you can watch this Immunology 101 for Non-immunologists video by @VirusesImmunity ( ). 6/
People who recovered from COVID-19 exhibited a hyper-activated response with loss of B-cell maturation which suggests an impeded post-infection stage. 7/
The study also found a higher expression of T-cell exhaustion markers in the recovered compared to healthy individuals and those with active COVID-19 infection. "This indicates that a larger population of the T cells are exhausted post recovery from the COVID-19." 8/ Chart showing expression of...
COVID-19 patients exhibited a reduced presentation of the pathway that alerts the immune system to virally infected cells (MHC Class-I) to killer T-cells (CD8+ receptors) and dysregulated presentation (MHC Class-II) to helper T-cells (CD4+) which was restored in the recovered. 9/
They also found both COVID-19 *and* recovered patients exhibited inflammatory responses in monocytes and T-cells, and elevation of immunological, stress, and antiviral responses in T-cells, Natural Killer (NK) cells, and monocytes. 10/ Chart showing the distribut...
A study found that immunological dysfunction persists for more than 8 months following initial mild-to-moderate COVID-19 infection ( ). 11/ Graphs showing elevated lev...
Dendritic cells (DC) recognize viral infections and trigger multiple parts of the immune system to respond. They activate helper T-cells which then stimulate B-cells to create antibodies against the pathogen. 12/
A study found a long-lasting reduction in dendritic cells and functional impairment of those cells in the blood of COVID-19 patients ( journals.plos.org/plospathogens/… ). 13/
"Depletion and functional impairment of DCs beyond the acute phase of the disease may have consequences for susceptibility to secondary infections and clinical management of COVID-19 patients." 14/
A second study confirms the impaired functions and reduced numbers of dendritic cells persist even 7 months after infection resulting in "a catastrophe for the immune system during SARS-CoV-2 infection." ( frontiersin.org/articles/10.33… ). H/T: @TRyanGregory 15/ Diagram showing interaction...
What else can go wrong? It turns out that dendritic cells are important in starting the immune response to RSV infection and help determine the impact on the adaptive immune response ( ncbi.nlm.nih.gov/pmc/articles/P… ). 16/
On top of that they are important contributors to defending against Strep bacterial infection ( journals.asm.org/doi/10.1128/IA… ). 17/
COVID-19 also impairs the immune response to the fungus Candida albican including showing signs of T-cell exhaustion ( frontiersin.org/articles/10.33… ) and a second study found defective antifungal immunity in patients with COVID-19 ( frontiersin.org/articles/10.33… ). H/T: @fitterhappierAJ 18/
This leaves people at higher risk for secondary infections from fungal infections that the WHO has warned is becoming a major issue and where thousands of people died from fungus after COVID infection in India ( ). 19/
Nocardiosis is a disease caused by bacteria that can be found in soil and water which can affect the lungs, brain, and skin that is most common in people with weakened immune systems who have difficulty fighting off infections ( cdc.gov/nocardiosis/ ). 20/ Photo of Nocardiosis microg...
Dr. Fisman wrote COVID-19 does appear to be an immune-injuring virus after reviewing a report of disseminated (two or more sites on the body) nocardiosis following infection, with post-viral leukopenia (lower than normal white blood cell count) ( ). 21/
It looks like persistent post-COVID smell loss which can last months to years is associated with immune cell infiltration and altered gene expression in olfactory epithelium ( science.org/doi/10.1126/sc… ). H/T: @EricTopol 22/ Image of T cell infiltrates...
"These findings indicate that T cell–mediated inflammation persists in the olfactory epithelium long after SARS-CoV-2 has been eliminated from the tissue, suggesting a mechanism for long-term post–COVID-19 smell loss." 23/
Several studies have shown indicators and markers of autoimmunity (immune response attacking body's own health cells or tissues) present with and after infection ( ). 24/
In the summer I wrote a whole week's worth of tweets about how COVID impacts T-cells and other parts of the immune system
including COVID infecting monocytes which you can find here ( ). 25/
@RaffyFlynnArt was kind enough to put together a thread of important papers on post-COVID immune dysregulation including ones showing dramatically reduced numbers of T-cells and persistently activated T-cells 12+ months later (
). 26/
@AndrewEwing11 put together a list of 25 papers/articles ( ) providing evidence for post-COVID immune deficiency and another thread with 36 more references ( ). 27/
Dr. Anthony Leonardi (@fitterhappierAJ) has been trying to warn the scientific community about the negative impact of COVID-19 infection and harms on the immune system since 2020 ( frontiersin.org/articles/10.33… ). 28/
Earlier this year @fitterhappierAJ published a paper on a potential mechanism for how this might be happening ( frontiersin.org/articles/10.33… ). 29/
Dr. Leonardi points out that T-cell exhaustion is not limited to just people with Long COVID and you can go from "normal" to having Long COVID and the exhausted T-cells ( ). 30/
The research study he is referring to found an unexpected result where people with milder COVID-19 infections had a weaker CD8+ T-cell response which also showed signs of T-cell exhaustion ( science.org/doi/10.1126/sc… ). 31/ Click "Show replies" 👇 to continue.
The T-cells got so much immune system stimulation that they become less effective. 32/
The people who survived severe disease had higher numbers of memory immune cells while people with milder disease still had some memory cells but appear to be exhausted and dysfunctional so may not be effective for long enough ( lji.org/news-events/ne… ). 33/
Something important to note is that while all of these impacts on the immune system have been found, it is not yet known just how broad the impact is on the population, how long each of them might last or if they will eventually heal on their own. 34/
For a virus that governments no longer seem to consider a problem, there doesn't seem to be much funding to investigate these kinds of things in more depth. 35/
Does the virus cause some kind of negative impact on everyone's immune system to some extent or only certain subgroups of people? How do reinfections impact the immune system, do vaccines reduce the chance of immune issues and to what extent? Lots of questions still remain. 36/

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More from @jeffgilchrist

Jun 6
Pollution levels in Ottawa are very high from wildfire smoke. The particulate matter (PM)2.5 levels surpassed 140 ug/m^3 Thursday evening and are still above 130 on my VisiblAir Model X outdoor sensor ( ). 🧵1/ #iaq #wildfire #smoke visiblair.comLine graph showing PM2.5 levels in Ottawa increasing above 140 ug/m^3 and still above 130 now
Readings from a VisiblAir Model X outdoor air quality monitor showing levels in Ottawa above 130 ug/m^3 for PM2.5 wildfire smoke pollution
The EPA maps fine particulate pollution to their Air Quality Index where anything above 125.5 PM is Very Unhealthy which is a "Health alert: The risk of health effects is increased for everyone" ( ). 2/airnow.gov/aqi/aqi-basics/
EPA Categories:
* Unhealthy for Sensitive Groups (Orange) = 35.5-55.4 PM ug/m^3
* Unhealthy for everyone (Red) = 55.5 to 125.4 PM ug/m^3
* Very Unhealthy (Purple) = 125.5 to 225.4 PM ug/m^3
* Hazardous (Brown) = 225.5+ PM ug/m^3

3/
Read 13 tweets
Feb 10
#Ottawa, #Ontario, #Canada Virus Update:

You can see in the graph, COVID makes up the majority of new hospitalizations due to #Flu, #RSV or #COVID throughout the year, and even stays ahead during winter respiratory virus season. 🧵1/ A line graph displaying the percentage of patients hospitalized due to COVID-19, Influenza, or RSV over time, from September 1, 2023, to January 26, 2025. The x-axis represents weeks within this period, and the y-axis shows percentages from 0% to 100%. The graph has three colored lines: blue for COVID-19, purple for Influenza, and teal for RSV. The graph shows fluctuations in the percentage of hospitalizations due to each cause over time, with COVID-19 consistently having the highest percentage, followed by Influenza and RSV.
New hospitalizations are increasing again. This last update was the first time Flu hospitalizations (42) were significantly higher than COVID (34) in the same week with RSV at 14 people. 2/ The bar chart shows the number of new hospitalizations per week in Ottawa from August 27, 2023, to January 26, 2025. The y-axis represents the number of patients, ranging from 0 to 100. The x-axis represents the weeks. The bars are color-coded: blue for COVID-19, purple for Influenza, and teal for RSV. The chart shows fluctuations in hospitalizations over time, with notable peaks around December 2023 and January 2025.
In Ottawa, test positivity for Flu A (bright green) has really increased, COVID is still in second place, but seasonal human coronavirus is almost the same level, followed by Entero/Rhinovirus, and then RSV for the top 5. 3/ A stacked area chart displaying the percentage of positive tests for various viruses over time, from October 1, 2022, to January 26, 2025. The x-axis represents weeks within this period, while the y-axis represents the percentage, cumulatively stacked to 100%. The chart features the following viruses, each depicted in a distinct color: COVID-19 (red), Entero/Rhinovirus (yellow), Seasonal human coronavirus (purple), RSV (green), Parainfluenza (all types) (blue), Influenza B (dark purple), Influenza A (light green), Human metapneumovirus (pink), and Adenovirus (dark blue). The data shows fluc...
Read 6 tweets
Jan 20
Similar to #Canada, babies in the #UK are at higher risk for #hospitalization and #ICU admission from #COVID. Their data looks deeper at infants < 6 months old which have higher ER attendance, hospital admission and severe hospitalisation rates than the oldest adults 90+! 🧵1/
That data from the UK was taken from this pre-print study ( ). 2/medrxiv.org/content/10.110…
In Canada, babies < 1 years old had the highest ICU admission rates of all age groups from Aug. 27, 2023 to Aug. 24, 2024. Read on to see more details including Flu and RSV too ( ). 3/
Read 7 tweets
Jan 19
The @elastomaskpro () is a NIOSH approved reusable N95 elastomeric respirator. It is made of silicone so a higher chance it will fit and seal well and is super breathable at the same time. Read on to find out more about my experience with it. 🧵1/ elastomaskpro.comA blue respirator mask, called ElastoMaskPro, rests on top of a blue and white box. The mask has a smooth, curved design with two circular filters on each side. The mask's straps are neatly arranged.
A light blue ElastoMaskPro N95 reusable respirator mask with a soft, flexible facepiece rests on top of its packaging box. The mask features a large opening in the center, showcasing white pleated filters. Two elastic straps are attached to the mask for securing it to the face.
Full disclosure: ElastoMaskPro sent me a unit to evaluate. There were no strings attached, they just asked that I provided feedback after I tried it. This thread is the first time they are seeing my feedback, they did not review anything before it being posted here. 2/
The ElastoMaskPro is very cost effective at the current sale price of $29.99 which includes two N95 filtering pucks. You can continue using the filters until they either get too dirty or there is increased breathing resistance. 3/ ElastoMaskPro Filter Puck. Filter Pucks are constructed using an adhesive-free process that incorporates a large volume of long-lasting, highly durable mechanical filtration media.
Read 43 tweets
Jan 6
#Ottawa, #Ontario, #Canada Virus Update:

Ottawa updated its #respiratory #virus data again after a break for the holidays, respiratory related ED visits are up especially in kids 0-3, then 4-11 and age 80+. 🧵1/ A line graph showing the number of respiratory-related emergency department (ED) visits per 100,000 population by week, from September 1, 2023, to November 1, 2024, across different age groups. Six lines represent the age groups: Age 0-3 (purple), Age 4-11 (blue), Age 12-17 (green), Age 18-54 (yellow), Age 55-79 (red), and Age 80+ (orange). The Age 0-3 group shows the highest number of visits, peaking around 1000 visits per 100,000 population, while other age groups generally have rates below 250 visits per 100,000 population. The graph exhibits seasonal fluctuations, with peaks in the wint...
Quite a mixture of different viruses testing positive in the lab right now so people can pick up a variety of bugs in the air. 2/ A stacked area chart displaying the percentage of positive tests for various viruses over time, from October 1, 2022, to December 22, 2024. The x-axis represents weeks within this period, while the y-axis represents the percentage, cumulatively stacked to 100%. The chart features the following viruses, each depicted in a distinct color: COVID-19 (red), Entero/Rhinovirus (yellow), Seasonal human coronavirus (blue), RSV (green), Parainfluenza (purple), Influenza B (light blue), Influenza A (light green), Human metapneumovirus (pink), and Adenovirus (dark blue). COVID-19 maintains a high posit...
New hospitalizations also jumped a lot in the last two reporting weeks, not just due to #RSV but a big spike in #COVID as well.

Follow the latest updates here ( ). 3/ covid.gilchrist.ca/Ottawa.htmlThe bar chart shows the number of new hospitalizations per week in Ottawa from August 27, 2023, to December 22, 2024. The y-axis represents the number of patients, ranging from 0 to 100. The x-axis represents the weeks. The bars are color-coded: blue for COVID-19, purple for Influenza, and teal for RSV. The chart shows fluctuations in hospitalizations, with peaks around late 2023 and early 2024, and another peak towards the end of 2024.
A line graph displaying the percentage of patients hospitalized due to COVID-19, Influenza, or RSV over time, from September 1, 2023, to December 22, 2024. The x-axis represents weeks within this period, and the y-axis shows percentages from 0% to 100%. The graph has three colored lines: blue for COVID-19, purple for Influenza, and teal for RSV. COVID-19 consistently shows the highest percentage of hospitalizations, with fluctuations throughout the period.
Read 4 tweets
Dec 24, 2024
#Variant update for #Ontario, #Canada (to Dec 10, 2024)

The KP.3.1.1 #DeFLuQE variant has finally been surpassed with XEC now in top place above 20% while the other 5 (MC.* and XEC.* descendants) remain < 7%. Graph tools by @Mike_Honey_ 🧵1/ A line graph showing the lineage frequency of the top 7 COVID-19 genomes in Ontario, Canada, up to December 10, 2024. The graph includes data from 4,928 sequenced genomes. The x-axis represents dates from October 27 to December 08, while the y-axis represents lineage frequency percentages from 0% to 35%. Different colored lines represent different genome lineages: KP.3.1.1 (blue), MC.1 (green), MC.13 (purple), MC.16 (pink), MC.24 (orange), XEC (brown), and XEC.8 (yellow). Below the main graph, there is a bar chart showing the number of samples (n) collected each day, ranging from 0 to 200 s...
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 October 27, 2024. You can follow the lineage backwards to see where a variant is a descendant from. 3/ The Sankey diagram visually displays the evolution and distribution of sequenced genomes in Ontario, Canada, up to December 10, 2024. The diagram uses colored bars and curved lines to show the flow and relationships between different genome variants over time. Each variant is labeled, such as "XEC," "BA.2," "BA.2.86," "JN.1," "KP.3," and various sub-variants. These bars and lines illustrate the transitions and derivations from one variant to another. The total number of sequenced genomes depicted is 4,928. This visualization helps to underst...
Read 16 tweets

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