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jeffgilchrist.bsky.social
Jeff Gilchrist
@jeffgilchrist.bsky.social
6.9K followers 250 following 1.3K posts
PhD Biomedical researcher, data scientist, and finder of large prime numbers. Views are my own. Twitter: @jeffgilchrist Mastadon: @jeffgilchrist@mstdn.science

COVID-19 guides, stats, calculators & 600+ scientific articles: http://covid.gilchrist.ca
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jeffgilchrist.bsky.social
Jeff Gilchrist @jeffgilchrist.bsky.social · 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 )
Reposted by Jeff Gilchrist
ukhadds.bsky.social
The risk of the airborne transmission of disease correlates with the amount of infectious exhaled aerosol. Since people exhale CO2 with aerosol, its conc has been used as proxy for exhaled aerosol

In this article, researchers propose a new way to estimate risk of transmission
February 7, 2026 at 6:46 PM
jeffgilchrist.bsky.social
*** Ontario Virus & Variant Update | Jan 11 ***

Hospitalizations due to COVID increased from 176 to 241 in the last update. Influenza hospitalizations have start dropping from the peak of 1,400 to 1,095 with RSV increasing from 121 to 156. 🧵1/
Graph of New hospitalizations in Ontario due to COVID, Influenza or RSV.
January 11, 2026 at 9:25 PM
Reposted by Jeff Gilchrist
siamosolocani.bsky.social
BA.3.2 Era new deisgnations:
we have a new branch of Ba.3.2.2 named RE.3 emerged in Mozambique and then spread to Europe (RE.3.1),
We have also a new RE.2 branch named RE.2.3 defined by ORF1a:T2648N & ORF1a:T4065I
RD.1.1.1 is a BA.3.2.1 with N:T271I
RE.1.1.1 was discussed by @ryanhisner.bsky.social
January 7, 2026 at 12:38 PM
Reposted by Jeff Gilchrist
ajtevelthuis.bsky.social
Congratulations to @karishmabisht.bsky.social with her paper on the effect of fever on influenza replication and innate immune activation! www.science.org/doi/10.1126/...
Febrile temperature activates the innate immune response by promoting aberrant influenza A virus RNA synthesis
Fever promotes aberrant influenza A virus RNA synthesis and innate immune activation.
www.science.org
January 2, 2026 at 7:09 PM
Reposted by Jeff Gilchrist
jeffgilchrist.bsky.social
If you thought that was bad, the next update was even worse...
Graph of Flu A wastewater levels in Ottawa showing the highest spike recorded with the latest data.
January 1, 2026 at 4:51 PM
Reposted by Jeff Gilchrist
countrybee2.bsky.social
"If HCWs wear N95 respirators and surgical masks throughout, the total infection risk can be reduced by 94.7 % and 53.9 %, respectively Increasing the ventilation rate from 1 ACH to 6 ACH reduced the infection risk. ."

FYI NSW Health & @racgp.bsky.social et al

www.sciencedirect.com/science/arti...
Transmission of respiratory infectious diseases based on real close contact behavior in an emergency room
The risk of transmission of respiratory infectious diseases in emergency rooms is high, posing a severe threat to the health of healthcare workers (HC…
www.sciencedirect.com
December 19, 2025 at 3:26 AM
jeffgilchrist.bsky.social
There is a new study from Poland looking at children hospitalized for COVID during the 2023/2024 and 2024/2025 epidemiological years ( link.springer.com/article/10.1... ). 🧵1/
Differences in the clinical course of COVID-19 in children and adolescents hospitalized in the 2023/2024 and 2024/2025 seasons – a retrospective real-world study - BMC Infectious Diseases
BMC Infectious Diseases - This multicenter retrospective study was designed to track changes in the clinical presentation of COVID-19 in children that occurred in the last two infectious seasons,...
link.springer.com
December 18, 2025 at 11:45 PM
Reposted by Jeff Gilchrist
donatemask.bsky.social
Did you know? Donate A Mask works with mask blocs across Canada. 🇨🇦 Help us continue to put #masks on faces by donating today. 😷 Your donation will be matched until December 14.

donatemask.ca/fundraiser

#GivingTuesdayCa #MaskBloc #MaskDistro #StillMasking #Charity #MaskUp
Photo of a man wearing a white N95 respirator mask. He is outside and wearing a red winter jacket. "DYK? Donate A Mask works with mask blocs across Canada. Help us continue to put masks on faces by donating today." Donate A Mask Canada - donatemask.ca
December 14, 2025 at 12:17 AM
jeffgilchrist.bsky.social
New hospitalizations in Ontario due to COVID, Flu, and RSV are starting to increase rapidly, especially Influenza. @donatemask.bsky.social helps vulnerable people in need and donations are currently being doubled if you can help.
A stacked bar graph showing **New Hospitalizations in Ontario due to COVID-19, Influenza, or RSV** from November 27, 2022, to November 23, 2025, broken down by week. The **y-axis** is the number of patients, and the **x-axis** is the week ending date. The data shows three distinct annual peaks, corresponding to the fall/winter seasons: 1. **2022-2023 Season:** A peak around December 2022/January 2023, with total hospitalizations reaching nearly 2,000. 2. **2023-2024 Season:** A larger, more drawn-out peak around January to March 2024, with total hospitalizations reaching around 1,500. 3. **2024-2025 Season:** A peak around December 2024/January 2025, with total hospitalizations reaching around 1,400. 4. **Current Season (2025-2026):** Shows a sharp increase starting in November 2025, reaching nearly 500 hospitalizations in the last week shown (11/23/2025). The bars are stacked by virus: * **COVID-19 (Blue):** Generally the largest contributor, especially during the 2022-2023 and 2023-2024 peaks, but appears to be a smaller portion of the current 2025 surge. * **Influenza (Purple):** Rises sharply during the winter peaks, contributing significantly, particularly in the 2024-2025 season. * **RSV (Teal/Green):** Generally the smallest component, peaking alongside the other viruses. For data description, source, and more Ontario related graphs, please visit ( https://covid.gilchrist.ca/Ontario.html ).
December 6, 2025 at 2:14 PM
Reposted by Jeff Gilchrist
donatemask.bsky.social
Our Request Program makes #masking more accessible. 😷 Help us continue this work by donating today. Your donation will be matched so your money will go further! 💙

donatemask.ca/fundraiser

#GivingTuesdayCa #Masks4All #MaskingIsCaring
Close-up photo of white KN95 respirator masks stacked and resting on a table. Donate A Mask and Giving Tuesday logos at the top of the photo. "Double your Donation. Donations up to $5,000 will be matched by a generous sponsor."
December 4, 2025 at 8:25 PM
Reposted by Jeff Gilchrist
donatemask.bsky.social
Our #GivingTuesday campaign starts today! 💙 Help spread #masks, not illness. 😷 Donate by December 14 and your donation will be matched by the GKE Foundation. 🎉

donatemask.ca/fundraiser

#GivingTuesdayCa #StillMasking #MaskUp #Charity #Fundraiser
Close-up photo of a young boy wearing a white N95 respirator with teddy bears illustrations on it. He is looking at the camera. Donate A Mask Canada and Giving Tuesday logos at the bottom of the image on a red background. donatemask.ca/fundraiser
December 2, 2025 at 2:12 PM
jeffgilchrist.bsky.social
Thread @virusesimmunity.bsky.social "A ground breaking paper by Shady Younis et al. @stanfordimmunology.bsky.social provides an answer to the long-standing question about how EBV infections are linked to lupus. A short thread to explain the key findings." ( threadreaderapp.com/thread/19891... )
Thread by @VirusesImmunity on Thread Reader App
@VirusesImmunity: A groundbreaking paper by @younis_sh1 et al. @stanfordimmuno provides an answer to the long-standing question about how EBV infections are linked to lupus. A short thread to explain ...
threadreaderapp.com
November 14, 2025 at 1:05 PM
Reposted by Jeff Gilchrist
northboxsystems.bsky.social
After some finagling to get the assembly procedure just right we are finally releasing the aluminum bodied POLARIS air purifier, made-in-Canada and based on the open-source design by Zack Deis.

1/3

#airpurifier #indoorairquality #covidisairborne
November 11, 2025 at 12:05 AM
Reposted by Jeff Gilchrist
jeffgilchrist.bsky.social
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". Continue to learn more... 🧪🧵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 increase equivalent exposure time. For example, at 10 minutes unmasked, a procedure mask extends exposure to 20 minutes, while an N95 with FF=400 extends it to 5000 minutes.
October 25, 2025 at 11:09 AM
Reposted by Jeff Gilchrist
epiellie.bsky.social
What was life really like before vaccines? The story of what happened to 8-year old George Williams in August 1852 gives us a glimpse.

open.substack.com/pub/epiellie...
Here's what life before vaccines was really like
The morning of August 2nd 1852 promised a lovely summer’s day in London. But not for 8 year old George Williams.
open.substack.com
October 26, 2025 at 2:11 PM
jeffgilchrist.bsky.social
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". Continue to learn more... 🧪🧵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 increase equivalent exposure time. For example, at 10 minutes unmasked, a procedure mask extends exposure to 20 minutes, while an N95 with FF=400 extends it to 5000 minutes.
October 25, 2025 at 11:09 AM
jeffgilchrist.bsky.social
** 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.
October 19, 2025 at 12:18 PM
jeffgilchrist.bsky.social
Health Canada has published Guidance for Indoor Air Quality Professionals, a practical, science-based resource for Indoor Air Quality (IAQ) experts, building operators, and employers.

Article ( ospe.on.ca/advocacy/pol... )

Guidelines ( www.canada.ca/en/health-ca... )
Policy Win: Health Canada Releases New IAQ Guidance
Health Canada announces new IAQ guidance, providing essential insights for improving indoor air quality and safety in buildings.
ospe.on.ca
October 15, 2025 at 8:14 PM
Reposted by Jeff Gilchrist
jbloomlab.bsky.social
In new study led by @bdadonaite.bsky.social, we measure how spike mutations affect function & antigenicity of spike of KP.3.1.1 strain of SARS-CoV-2.

Sheds light on how key neutralizing epitopes are changing & importance of RBD up/down motion.

www.biorxiv.org/content/10.1...
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants
SARS-CoV-2 is under strong evolutionary selection to acquire mutations in its spike protein that reduce neutralization by human polyclonal antibodies. Here we use pseudovirus-based deep mutational sca...
www.biorxiv.org
August 20, 2025 at 5:22 AM
Reposted by Jeff Gilchrist
jbloomlab.bsky.social
The final published version of this study is now available in Journal of Virology at journals.asm.org/doi/10.1128/...
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants | Journal of Virology
This study measures how mutations to the spike of a SARS-CoV-2 variant that circulated in early 2025 affect its function and recognition by both the polyclonal antibodies produced by the human immune ...
journals.asm.org
October 14, 2025 at 4:22 PM
Reposted by Jeff Gilchrist
jbloomlab.bsky.social
In new study led by @ckikawa.bsky.social, we provide near real-time data on human neutralizing antibody landscape to influenza by measuring ~26,000 titers to >100 recent viral strains

Data can inform vaccine selection & evolutionary/epidemiological modeling
www.biorxiv.org/content/10.1...
Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025
The hemagglutinin of human influenza virus evolves rapidly to erode neutralizing antibody immunity. Twice per year, new vaccine strains are selected with the goal of providing maximum protection again...
www.biorxiv.org
September 8, 2025 at 9:48 PM
Reposted by Jeff Gilchrist
brendancrabb.bsky.social
Such an important piece. The positive momentum behind clean indoor air is palpable. But we’re not there yet as my last post demonstrates. Please read and share and get behind this cause.

theconversation.com/why-investme...
Why investment in clean indoor air is vital preparation for the pandemics and climate emergencies to come
Unchecked airborne infections cost billions in lost health and productivity each year – likely more than the cost of better ventilation to clean up indoor air.
theconversation.com
October 1, 2025 at 11:12 PM
jeffgilchrist.bsky.social
I found out for Ontario that "the Ministry of Health updated the age groups on the I9 bed census data collection forms" so some data in the Ontario Respiratory Virus Tool ( www.publichealthontario.ca/en/Data-and-... ) will be grouped differently starting in September. 🧵1/
Table of age groups before September 2025 Table of age groups starting September 2025
September 29, 2025 at 12:22 PM
Reposted by Jeff Gilchrist
smcgrath.phd
🧪 Can researchers stop AI from fabricating citations? Probably not entirely.

While models like GPT-5 are improving, hallucination is fundamental to their statistical design, shifting the burden onto users to build new intuitions for an AI age.
#MLSky #AcademicSky
Can researchers stop AI making up citations?
OpenAI’s GPT-5 hallucinates less than previous models do, but cutting hallucination completely might prove impossible.
www.nature.com
September 9, 2025 at 3:27 PM
jeffgilchrist.bsky.social
*** 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 #COVID #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.
September 9, 2025 at 12:08 PM