Jeff Gilchrist Profile picture
Sep 24, 2022 43 tweets 13 min read Read on X
COVID-19: Things everyone should know (Part 1: Immune System)

With poor public health messaging, the general public doesn't seem to know some important things about how COVID-19 and the immune system actually works. 🧵1/ Image
This thread will highlight some at a very high level without going into too much scientific jargon and references will be left for the end. 2/
Did you know that the COVID-19 virus (SARS-CoV-2) actually has the ability to actively suppress and hide from multiple parts of your immune system? Even if you have been vaccinated or previously infected, some immune cells that were trained to identify the virus will not see...3/
...that your cells are infected because the virus can turn off the early warning system of the infected cell to call for help. Normally your infected cells can trigger an alarm and immune cells will kill them, but have now become invisible. 4/
Not only that but the virus is pretty sneaky and sets up a secret compartment inside the cell to replicate where it can't easily be detected by some of the immune system sensors. 5/
That is one of the reasons why the COVID-19 vaccines don't completely prevent infection because the virus can hide long enough from your immune system to replicate in large enough numbers to be infectious to others even if you don't get seriously ill. 6/
The newer COVID-19 variants are getting better and better at suppressing and evading the immune system which is why so many people are becoming reinfected again. 7/
The current COVID-19 vaccines you get in your arm, generate blood antibodies throughout your body which provide protection in most organs but do not generate many antibodies in your nose and upper airway where the virus enters your body. 8/
It turns out you need local (mucosal) antibodies in these areas to protect your upper airway and brain from infection, which is another reason why the intramuscular vaccines do not completely stop infection. 9/
New nasal spray COVID-19 vaccines are being developed and now approved in some countries (India, China) that will generate these mucosal antibodies. You may have heard that vaccine protection "wanes" over time but what does that mean? 10/
When your immune system first encounters a new virus (whether you get infected or get your first vaccine dose) your immune system will generate antibodies to fight the virus and prevent them from infecting your cells. 11/
The first exposure takes longer to generate antibodies (10-20 days depending on type) so it takes a while to fight off the virus (or build immunity from a vaccine dose). Naturally over time the antibody levels drop after the virus is gone since your body can't use energy... 12/ Image
...to keep high levels of antibodies for every pathogen it has ever encountered. Instead, it creates memory immune cells so it can create more antibodies to fight off the virus should you get exposed again. 13/
The next time your immune system encounters the same virus, it can respond much faster, mobilizing the memory cells to generate new antibodies and this time it only takes 3-10 days instead of 10-20 days. 14/ Image
With COVID-19 actively suppressing and hiding from parts of the immune system, it can replicate long enough and fast enough for you to become infectious even if you were previously infected or vaccinated before the antibody levels get high enough to fight off the virus. 15/
Thankfully immune system memory can generate antibodies fast enough to protect most people from serious illness, even if it doesn't stop you from being contagious. 16/
Since immune memory takes time to build up antibodies when exposed to the virus, people have more protection from infection and severe disease when antibody levels are still relatively high so they can spring into action immediately. 17/
Antibody levels tend to hit their maximum levels within a month of getting exposed and then slowly decline over time with much faster declines between 4 and 6 months. 18/
This is why you typically see recommendations to get booster doses between 3 and 6 months after your last dose because antibody levels have decreased significantly by 6 months. 19/
What happens when you get multiple doses of vaccines? First, most of the vaccines people received as children to protect against other diseases needed multiple doses. 20/
Vaccines for measles, mumps, rubella, HPV, hepatitis B are all 2 doses, and Diphtheria, Tetanus, and Pertussis are all 4 dose vaccines, with tetanus needing a booster every 10 years. 21/
For the COVID-19 mRNA vaccines specifically, the first dose generates antibodies to a certain level and immune cells look at certain parts of the COVID virus spike that is given in the vaccine and memorize it. 22/
The second dose generates antibodies to an even higher level than the first, and the immune system memorizes even more parts of the spike protein. 23/
So far this has continued where subsequent doses generate higher and higher levels of antibodies which then take longer to decrease below a minimum threshold because they start out higher. 24/
Since the immune system continues to learn about different parts of the virus spike even though the virus has been mutating, it will still recognize the virus and generate a response, but antibodies are less effective against newer variants that have mutated significantly. 25/
Getting a booster dose after 6 months restores and likely increases your antibody levels to a higher level which temporarily provides more immediate protection should you be exposed to the virus again. 26/
The new bivalent booster doses also include one of the newer variants like BA.1 (Canada, UK) or BA.5 (USA) so your immune system will learn about some of the mutations and hopefully be able to identify new variants more easily. 27/
If you do get infected, do you know how long you are contagious for? Studies have found that with the Omicron variant, 75% of people they tested after 5 days from symptom onset were still contagious, 50% of people after 8 days, and 24% of people after 10 days. 28/
This is not just testing positive, but they actually cultured the virus to see if it was still viable and replicating. So that means if people only isolate for 24 hours or even 5 days after testing positive, they are likely still contagious and could be infecting others. 29/
Rapid Antigen Tests (RATs) are great for this purpose since they only test positive when there is a high viral load detected which means you are likely contagious. 30/
Have you heard or been told that tests can be positive for weeks or months after infection? That is the PCR test which amplifies the RNA signal and is usually done in a lab. 31/ 👇Click "Show Replies" to continue thread...
Since PCR tests can detect very low levels of virus, testing positive doesn't tell you if you are still contagious and can test positive long after you are no longer contagious. 32/
But since RATs testing positive almost always means you are contagious, they can be used to help see when you stop being contagious and then safely leave isolation. 33/
But... What you really want to do is prevent becoming infected in the first place. Each time you get infected or reinfected there is a chance you can develop long-term consequences or possibly permanent damage to your body as COVID-19 is not a cold. 34/
While being vaccinated can reduce the chance of developing Long COVID, even 1 in 10 vaccinated people who got infected developed Long COVID. 35/
Infection puts people at increased risk of heart attack, stroke, cardiovascular issues, blot clots, brain damage, neurological and many more issues even months after infection. This happens in both adults and children, and even with mild infections. 36/
This means that we can't rely on vaccines alone, but need to invest in additional measures that are variant proof. Part 2 will discuss how the virus is transmitted and ways to help reduce the risk of becoming infected. 37/
For people who want a web link to share, you can find it here: threadreaderapp.com/thread/1573772…
Part 2 of this thread on transmission and protection is now available here:

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More from @jeffgilchrist

Dec 24
#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
Dec 22
Population rate vs raw numbers

This is a good example of why it is useful to understand the importance of population *rate* and not just look at raw numbers. The first graph shows raw numbers and the second graph population rate. 🧵1/ #ED #Respiratory #Virus #Population #Ottawa Chart of Respiratory Related ED Visits by Week and Age (Ottawa, ON, Canada) with raw numbers
Chart of Respiratory Related ED Visits by Week and Age (Ottawa, ON, Canada) with population rate per 100K
Ottawa Public Health makes only the raw data available for All causes and respiratory-related emergency department visits to Ottawa hospitals by age group and week ( ). 2/open.ottawa.ca/datasets/ottaw…
If I take the data and plot all the ages together, you can at least see all of the age groups at the same time but it is just the raw numbers. 3/
Read 12 tweets
Dec 17
This is amazing, not only a lower cost CPC for measuring mask fit and ultrafine particles in a room, but also a new probe to measure fit of a respirator without destroying it, check out the video from @OpenAeros and @masknerd to see how it works ( ). 🧵1/ Woman wearing N95 head band respirator inserting new probe design in side of respirator so you don't have to puncture the front, the new OpenAeros OpenCPC machine operating on the table showing the ultrafine particle levels and Aaron Collins (@masknerd) holding the new blue probe against his face to show what it looks like.
@masknerd also demonstrates how you can use OpenCPC to measure how well an air cleaner is filtering particles when you insert the probe into the output vent where particles dropped to 6.4/cm^3 from the regular 700-800/cm^3 for the room. 2/ Aaron Collins (@masknerd) holding the OpenCPC probe inside the fins of a portable air cleaner to measure particle concentration showing it has dropped significantly.
When Aaron Collins moves the probe to a couple of feet in front of the portable air cleaner, levels go back up to 785/cm^3 which is the same as the room concentration indicating this type is filtering the air but doesn't create a "clean bubble" in front of it. 3/ Aaron Collins (@masknerd) holding the OpenCPC probe a couple of feet in front of a portable air cleaner to measure particle concentration, showing it has gone back up to room concentrations.
Read 6 tweets
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

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