Jeff Gilchrist
@jeffgilchrist.bsky.social
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
*** Ontario Virus Update | July 26 *** Hospitalizations due to COVID have decreased from 16 to 6 in the last update. Influenza hospitalizations increased from 5 to 8 and RSV finally decreased from 3 to 0. 🧵1/ #Ontario #Virus #COVID #Hospital #Wastewater
*** Ontario Virus Update | July 12 *** Hospitalizations due to COVID have increased from 14 to 15 in the last update. Influenza hospitalizations dropped from 18 to 5 and RSV increased from 2 to 6. 🧵1/ #Ontario #Virus #COVID #Hospital #Wastewater
A mysterious, unusually diverse saltation lineage descended from KP.3.1.1 (last seen early 2025) has circulated at a low level for ~8 months in Ontario (see 🧵 on next post). Seemed a local anomaly, but @solidevidence.bsky.social just spied a weird spike in NYC wastewater—& it's the same one! 1/14
Solid Evidence@solidevidence.bsky.social · last mo.This is kind of weird. A new cryptic showed up in two different NYC sewersheds this month. Low coverage. RBD piece is: 403K-405N-408S-417N-435S-439N-445P-446T-450D-452K-455S-456L. Also a deletion at 621-622. 1/
** Ontario Virus Update | June 30 ** Hospitalizations due to COVID have increased from 9 to 18 in the last update. Influenza hospitalizations remained stable at 13 and RSV increased from 3 to 5 so not quite finished for the season yet for those two.🧵1/ #Ontario #Virus #COVID #Hospital #Wastewater
** Ontario Virus Update | June 30 ** Hospitalizations due to COVID have increased from 9 to 18 in the last update. Influenza hospitalizations remained stable at 13 and RSV increased from 3 to 5 so not quite finished for the season yet for those two.🧵1/ #Ontario #Virus #COVID #Hospital #Wastewater
Successfully appealed the biorxiv rejection and today our paper (co-authors @darrenmartin.bsky.social & Ravi Gupta) is posted. The paper's too long to do a single summary thread, but I'll do a cursory overview here, then more detailed subsection threads later. 1/16 www.biorxiv.org/content/10.6...
Coevolving Mutations in Chronic SARS-CoV-2 Infections
The SARS-CoV-2 pandemic has been marked by two outstanding features that have had major impacts on global public health: the repeated emergence and growth of highly divergent saltation variants with n...
biorxiv.org
Ryan Hisner@ryanhisner.bsky.social · 2mo agoSpend 3+ years painstakingly working on a paper, doing original analysis, writing 10,000s of lines of custom code, etc, only to be rejected by a preprint server, which derides it as "automated/computational analyses of public data, facile database searches, sequence alignments"...
The basis for the last sentence below: New data from David Ho's lab showing that while adults & kids have ~equal antibody responses to XFG & NB.1.8.1, children have essentially no neutralizing antibodies to BA.3.2. This seems to solve the BA.3.2 + kids mystery. 1/14 www.biorxiv.org/content/10.6...
Ryan Hisner@ryanhisner.bsky.social · 2mo agoMy best guess is dead-end virus evolution combined with a continually broadening global population antibody response that makes it more difficult for novel variants to completely escape—except in those with few exposures (such as children).
New modelling shows upgraded ventilation can sharply cut airborne exposure for staff on respiratory wards. Engineering controls matter. We need this ambition across the NHS. Study by Zachreson, Geard, Sheena Sullivan, et al., @unimelb.edu.au et al. www.journalofhospitalinfection.com/article/S019...
Room-return ventilation and N95 respirator policies for reducing airborne pathogen exposure on hospital wards
Understanding interactions between the components of bundled mitigation measures can aid the prospective evaluation of hospital infection control programs. This work provides a prospective, simulation...
journalofhospitalinfection.com
Healthy Air at Home: What You Can Monitor, Filter, and Fix A new webinar by @theingredientslist.bsky.social, founder of Clean Indoor Air Toronto ( www.youtube.com/watch?v=45sk... ). #IAQ #IndoorAirQuality #Ventilation #CO2 #PM #Pollution #Home 🧪
Health Air at Home: What You Can Monitor, Filter, and Fix
YouTube video by Toronto Home Energy Network
youtube.com
Healthy Air at Home: What You Can Monitor, Filter, and Fix A new webinar by @theingredientslist.bsky.social, founder of Clean Indoor Air Toronto ( www.youtube.com/watch?v=45sk... ). #IAQ #IndoorAirQuality #Ventilation #CO2 #PM #Pollution #Home 🧪
Health Air at Home: What You Can Monitor, Filter, and Fix
YouTube video by Toronto Home Energy Network
youtube.com
Filtering the air may help prevent your own infection from becoming more severe If everyone in a household becomes infected with the same virus, does it help to isolate from each other and can you be a danger to yourself? Read on to find out... 🧪🧵1/ #AirQuality #IAQ #Ventilation #Infection #COVID
Anyone looking for access to #Novavax in #Canada - it’s been approved federally but now we need our provinces/territories to purchase it, educate on it, and make it available to anyone who wants it. Time is of the essence. Time to #MakeYourNoise! stillcoviding.ca/en/take-acti...
Novavax now! We need access to the Novavax COVID-19 vaccine in 2026/2027!
stillcoviding.ca
Tue, May 26, 2026 @ 6:30-7:30pm EDT, a Zoom Webinar: "Healthy Air at Home: What You Can Monitor, Filter, and Fix" Register and more info here ( www.thenetwork.to/event-detail... )
Researchers show TMPRSS2 cuts the SARS-CoV-2 spike only after it shifts shape, triggering membrane fusion and entry, while antibodies that block this cut can stop infection and inspire vaccine design. www.nature.com/articles/s41...
TMPRSS2-mediated coronavirus spike activation and inhibition - Nature Structural & Molecular Biology
Here, the authors elucidate TMPRSS2 protease recognition of the SARS-CoV-2 spike S2′ cleavage site, revealing the molecular basis of activation of membrane fusion, and show that antibodies recognizing...
nature.com
*** Ontario Variant Update | Apr 28 *** In Ontario, there was some competition for variant dominance during the month of March but the NB.1.8.1.* "Nimbus" family currently holds first place with 49.5% while the XFG.* "Stratus" family sits at 38.1% of sequenced genomes from COVID tests. 🧵1/
*** Ontario Virus Update | Apr 28 *** Hospitalizations due to COVID have gone down from 109 to 68 in the last update. Influenza hospitalizations decreased from 71 to 63 and RSV decreased from 83 to 75. 🧵1/
A really important critique of the flawed @AnnalsofIM masks vs respirators trial. Good on @bmj_latest for publishing it www.bmj.com/content/393/...
bmj.com
So it's clear that BA.3.2 preferentially infects children, something we have never seen before in a SARS-CoV-2 variant. Why? The question's baffled me, but after a suggestion from @darrenmartin.bsky.social, I think I have an explanation that makes sense. 1/16
Ryan Hisner@ryanhisner.bsky.social · 4mo agoSomeone suggested BA.3.2 might preferentially infect kids. I think they're right. Ages of SARS-2 sequences since Dec 1 in Ireland: non-BA.3.2 6/66 (9.1%) age 0-19, (0/1 hospital tests) BA.3.2 43/91 (47.3%) age 0-19 (1/3 hospital tests) 1/4
Quick elaboration on this. The disproportionate rate at which BA.3.2 infects children is not driven by infants. The 0-1 age group is less overrepresented (by a large margin) than the 2-5 and 6-17 age groups in the countries we have data for. 1/4
Ryan Hisner@ryanhisner.bsky.social · 4mo agoSo it's clear that BA.3.2 preferentially infects children, something we have never seen before in a SARS-CoV-2 variant. Why? The question's baffled me, but after a suggestion from @darrenmartin.bsky.social, I think I have an explanation that makes sense. 1/16
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/
