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Jeff Gilchrist Profile picture
Jeff Gilchrist
@jeffgilchrist
PhD Biomedical researcher, data scientist, and finder of large prime numbers. Views are my own. @jeffgilchrist@mstdn.science @jeffgilchrist.bsky.social
87 subscribers
Oct 25 • 25 tweets • 5 min read
How does various mask fit compare to filter the air and protect you or others?

Most masks, even baggy blue procedure masks use filtering material that can filter 95%+ of particles that pass through it, but the key is "pass through it". 🧵1/ Bar chart titled “Equivalent Exposure Time to Unmasked Person.” The chart compares how long different masks/respirators extend the equivalent exposure time relative to being unmasked. The x-axis shows unmasked infection times of 1, 5, and 10 minutes. The y-axis shows equivalent masked exposure time, ranging up to 5000 minutes. Seven mask types are represented by colored bars: - Procedure mask (loose fit, FF=2) - Ear loop mask (tight fit, FF=6) - Vertical bifold headband mask (FF=30) - N95 headband masks with fit factors of 100, 200, and 500 Key pattern: higher fit factor masks dramatically ... Protection mostly depends on how well that mask fits your specific face and one that does not fit well, much of the air you breathe will go around the filter material and filter 0% of those particles. 2/
Oct 19 • 10 tweets • 3 min read
** Ontario Variant Update (to Oct. 3, 2025) **

The XFG.* "Stratus" family is accounting for 83% while the next closest variant family NB.1.8.1.* "Nimbus" is 12.8% of sequenced genomes from COVID tests. 🧵1/ Line graph showing COVID-19 variant family frequencies in Ontario, Canada, from June to October 2025, based on 3,722 sequenced genomes. Looking at specific variants, XFG.3 has dropped considerably and its descendent XFG.3.15 now takes first place at 6.2%, followed by XFG.3 at 5.2% and XFG.2 at 4.5%. 2/ Line graph showing specific COVID-19 variant frequencies in Ontario, Canada, from June to October 2025, based on 3,722 sequenced genomes.
Sep 9 • 18 tweets • 5 min read
*** Ontario Variant Update (to: Aug. 16, 2025) ***

Ontario COVID sequence updates have been more frequent over the past month with the XFG.* "Stratus" family of variants now at 74% of sequences, NB.1.8.1.* "Nimbus" at 22% and LP.8.1.* down to 3%. #Variants #XFG #Stratus 🧵1/ Line graph showing COVID-19 variant frequencies in Ontario, Canada, from May to mid August 2025, based on 1,772 sequenced genomes. The XFG.* Stratus variant rises sharply to dominate over 70% by August. Other variants, including FLiRT and LP.8.1.*, decline over the same period, while NB.1.8.1.* Nimbus remains steady around 20% and several minor variants remain at low levels. Looking at specific variants as of mid August, XFG.5.1 is most prevalent at 13%, NB.1.8.1 in second at 10%, XFG.2 in third at 8.6% and XFG.3 in fourth at 7.4%. 2/ Line graph showing COVID-19 variant frequencies in Ontario from 5 July to 16 August 2025, based on 750 sequenced genomes. Seven variants are tracked: NB.1.8.1, XFG.2, XFG.3, XFG.3.4.1, XFG.3.1, XFG.4.1, and XFG.5.1. Frequencies range from 0% to about 14%, with some variants rising, others falling, and some fluctuating over time. A bar chart below shows the number of samples collected on each date.
Jun 9 • 41 tweets • 10 min read
Understanding Canadian Air Quality Health Index (AQHI) & Wildfire Smoke

Wildfire smoke consists of toxic gases and particulate matter (PM) when breathed in gets into our lungs, bloodstream, and even our brain. 🧵1/
#iaq #wildfire #smoke #AQI #AQHI #Canada Bar chart of Canadian Air Quality Health Index (AQHI) - Equivalent # Cigarettes after Exposure ranging from 0.5 cigarettes after 8 hours exposure at AQHI level 3 to 0.9 cigarettes at level 6 and 1.5 at level 10.
Graph of Particulate Matter (PM) Levels in Ottawa from June 6, 2025 to June 8, 2025 from a VisiblAir Model X air quality sensor ( https://visiblair.com/ ). The web version of this article with nice table of contents and easy to share with others can be found here ( tinyurl.com/AQHIwildfire ) and ( docs.google.com/document/d/1s9… ). 2/ Table of Contents: * Introduction * Air Quality Health Index (AQHI) * Health impact of Wildfire Smoke * Protect Yourself
Jun 6 • 13 tweets • 4 min read
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/
Feb 10 • 6 tweets • 2 min read
#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.
Jan 20 • 7 tweets • 2 min read
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…
Jan 19 • 43 tweets • 9 min read
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/
Jan 6 • 4 tweets • 2 min read
#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...
Dec 24, 2024 • 16 tweets • 5 min read
#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…
Dec 22, 2024 • 12 tweets • 3 min read
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…
Dec 17, 2024 • 6 tweets • 2 min read
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.
Nov 10, 2024 • 16 tweets • 5 min read
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/
Nov 10, 2024 • 9 tweets • 3 min read
#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…
Sep 22, 2024 • 4 tweets • 2 min read
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…
Sep 19, 2024 • 89 tweets • 20 min read
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
Aug 28, 2024 • 4 tweets • 2 min read
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 )
Aug 23, 2024 • 14 tweets • 4 min read
#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/
Jul 25, 2024 • 10 tweets • 3 min read
No Novavax JN.1 vaccine for Canada?

It seems Canada has not ordered any Novavax JN.1 vaccine doses for the fall which means this protein based vaccine option may not be available to anyone who wants or needs it. We are hoping you can help us change that. 🧵1/ English executive summary: A group of concerned stakeholders advocating for broader access to diverse COVID-19 vaccine options for Canadians, particularly those beyond the mRNA vaccines currently dominating the public offering wrote a letter to the Public Health Agency of Canada (PHAC), all the provinces/territories and immunization providers to address the pressing need for enhanced COVID-19 awareness and education, increased availability and access to protein-based vaccines, such as Novavax, which are currently limited in distribution. A group of concerned stakeholders advocating for broader access to diverse COVID-19 vaccine options for Canadians, particularly those beyond the mRNA vaccines currently dominating the public offering wrote a letter to the Public Health Agency of Canada (PHAC)... 2/ Resume francais: Nous vous écrivons en tant que parties prenantes revendiquant un accès plus large aux différentes options de vaccins contre la COVID-19 pour les Canadiens, particulièrement au-delà des vaccins à ARNm qui dominent présentement l’offre publique. Nous exhortons l’Agence de la santé publique du Canada (ASPC), toutes les provinces et tous les territoires ainsi que tous ceux qui fournissent des vaccins à s’attaquer au besoin pressant d’une meilleure sensibilisation et éducation sur la COVID-19, ce qui inclut une plus grande disponibilité et un meilleur accès aux vaccins à base de...
May 22, 2024 • 34 tweets • 8 min read
Novavax JN.1 Vaccine Neutralization

Novavax revealed they had selected the original JN.1 variant as their fall booster and recently released neutralization results on non-human primates (Macaques) including a more recent KP.2 FLiRT variant. 🧵1/
Graph of JN.1 vaccine neutralizing response against JN.1 and JN.1 subvariants in non-human primates (macaques)
Graph of Novavax JN.1 Vaccine Neutralization Dose Schedule Recall that the JN.1 variant became dominant in many parts of the world in December 2023 so by the time the fall 2024 vaccine program rolls out it will be almost a year old. 2/
May 20, 2024 • 84 tweets • 21 min read
Indoor Air Quality: Wildfire Smoke & Cooking

With wildfire smoke season here, we all need to think about air quality inside where we spend most of our time. This thread provides multiple examples measuring the air quality inside my home from wildfire smoke and cooking. 🧵1/

Wildfire smoke making it difficult to see buildings in New York City from ( https://www.theguardian.com/environment/2023/jun/08/air-quality-record-smoke-hazard-wildfire-worst-day-ever-canada-new-york ).
Graph of PM 2.5 Wildfire Smoke Pollution Levels Inside & Outside House with significantly higher levels of PM outside and in garage, and higher levels of PM in unfinished sections of basement with very little PM in finished rooms and those with HEPA filters.
Graph from co2.click portal showing a massive spike in particulate matter (PM) levels past 50 ug/m3 on Christmas Eve. More info at: https://co2.click/ The web version of this article with nice table of contents and easy to share with others can be found here ( ) or ( ). 2/ tinyurl.com/AirQualityPoll…
docs.google.com/document/d/1x0…
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