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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

To learn how to see what variants are circulating in your area, please read this guide ( bsky.app/profile/jeff... ). 9/

Jeff Gilchrist @jeffgilchrist.bsky.social · Oct 16

How To: See what variants are circulating in your country/province/state

This thread will walk you through how to see which variants are circulating in your area using Mike Honey's visualization tool. 🧪🧵1/

On page unrolled version here ( pingthread.com/thread/16472... ).

Graph of COVID variant families frequency from PCR test genomic sequencing. Visualization tool was created by Mike Honey @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )

Graph of top 7 specific COVID variant frequencies from PCR test genomic sequencing. Visualization tool was created by Mike Honey @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )

Graph of specific BA.2.86.1 variant frequency from PCR test genomic sequencing. Visualization tool was created by Mike Honey @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

To learn how to create a Sankey diagram of variants circulating in your area, please read this guide ( bsky.app/profile/jeff... ). 8/

Jeff Gilchrist @jeffgilchrist.bsky.social · Jan 11

How To: Create a Sankey diagram of variants circulating in your area

This thread will walk you through the process of using Mike Honey visualization tool to generate a Sankey diagram for your country, province or State. 🧪🧵1/

Unrolled version: threadreaderapp.com/thread/17454...

Filtered Sankey diagram view with "Lineage Level" set to 3 and 11 and the Minimum # Samples per Lineage to show" to 60 and all labels shown. Visualization tool was created by Mike Honey @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

The visualization tool for variants was created by @mikehoney.bsky.social and the source of this data can be found at ( app.powerbi.com/view?r=eyJrI... ). 7/

Power BI Report

Report powered by Power BI

app.powerbi.com

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

You can find weekly Ontario stats including variants at ( covid.gilchrist.ca/Ontario.html ). 6/

covid.gilchrist.ca

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

You can learn more about variant naming and mutations from this document ( docs.google.com/document/d/1... ). 5/

How do variant designations work and relate to our immunity?

How do variant designations work and relate to our immunity? Variants: JN.1 vs KP.2 vs KP.3.1.1 Written by: Jeff Gilchrist & Paul Seaman Link to this document: https://tinyurl.com/VariantsSummer2024 L...

docs.google.com

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

The SanKey diagram shows you variant lineages and you can follow back where that variant came from. 4/

Sankey diagram showing the evolution of 1,897 sequenced viral genomes in Ontario, Canada, from June to October 2025.

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

It looks like PY.1.1.1 was trying to make a run for the top in mid-September but has decreased significantly. PY.1.1.1 is a descendant of LF.7 while the XFG variant is a recombination of LF.7 and LP.8.1.2 so they would share some mutations in common. 3/

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

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.

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Jeff Gilchrist @jeffgilchrist.bsky.social · 1d

** 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.

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Jeff Gilchrist @jeffgilchrist.bsky.social · 5d

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

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Reposted by Jeff Gilchrist

Bloom lab @jbloomlab.bsky.social · Aug 20

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

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Reposted by Jeff Gilchrist

Bloom lab @jbloomlab.bsky.social · 6d

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

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Reposted by Jeff Gilchrist

Bloom lab @jbloomlab.bsky.social · Sep 8

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

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Reposted by Jeff Gilchrist

Prof Brendan Crabb AC @brendancrabb.bsky.social · 19d

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

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Jeff Gilchrist @jeffgilchrist.bsky.social · 13d

Not sure where you are but some parts of the world including Japan are getting an updated Novavax LP.8.1 formula while USA is reusing the same formula as last year due to regulatory issues. Almost no reaction for Novavax for me too but mRNA this fall is using an updated LP.8.1 formula.

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Jeff Gilchrist @jeffgilchrist.bsky.social · 21d

They are supposed to update their technical notes with more details in the next month. The last update was a year ago ( www.publichealthontario.ca/-/media/Data... ). 4/

www.publichealthontario.ca

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Jeff Gilchrist @jeffgilchrist.bsky.social · 21d

I'm glad at least they didn't merge the 0-4 group into the other kids. It should already be broken down as <1 and 1-4 since that first year of life is vastly different for rates and impact on health than the kids 1-4 so it looks much less serious for infants when it gets averaged out. 3/

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Jeff Gilchrist @jeffgilchrist.bsky.social · 21d

You can see that the latest data grouped the 5-11 and 12-17 into one age category of 5-17, the 18-39 & 40-59 categories have been grouped into 18-49 and the older adults are now grouped as 50-64, 65-74, and 75+. That is going to change the populate rates with the new groups. 2/

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Jeff Gilchrist @jeffgilchrist.bsky.social · 21d

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

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Jeff Gilchrist @jeffgilchrist.bsky.social · Sep 10

It is interesting how companies are now highlighting just the fold increase in neutralizing antibodies since the absolute levels are many fold lower than what the original formula gave against the original variant and don't want to draw attention to that.

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Reposted by Jeff Gilchrist

Scott McGrath @smcgrath.phd · Sep 9

🧪 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

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Jeff Gilchrist @jeffgilchrist.bsky.social · Sep 9

It depends on what part of the world you are in, but in Ontario during August 2024 the KP.3.1.1 variant (or some form of DeFLuQE mutation variant) would have been common.

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Jeff Gilchrist @jeffgilchrist.bsky.social · Sep 9

To learn how to see what variants are circulating in your area, please read this guide ( bsky.app/profile/jeff... ). 18/

Jeff Gilchrist @jeffgilchrist.bsky.social · Oct 16

How To: See what variants are circulating in your country/province/state

This thread will walk you through how to see which variants are circulating in your area using Mike Honey's visualization tool. 🧪🧵1/

On page unrolled version here ( pingthread.com/thread/16472... ).

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Jeff Gilchrist @jeffgilchrist.bsky.social · Sep 9

To learn how to create a Sankey diagram of variants circulating in your area, please read this guide ( bsky.app/profile/jeff... ). 17/

Jeff Gilchrist @jeffgilchrist.bsky.social · Jan 11

How To: Create a Sankey diagram of variants circulating in your area

This thread will walk you through the process of using Mike Honey visualization tool to generate a Sankey diagram for your country, province or State. 🧪🧵1/

Unrolled version: threadreaderapp.com/thread/17454...

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Jeff Gilchrist @jeffgilchrist.bsky.social · Sep 9

The visualization tool for variants was created by @mikehoney.bsky.social and the source of this data can be found at ( app.powerbi.com/view?r=eyJrI... ). 16/

Power BI Report

Report powered by Power BI

app.powerbi.com

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