Jeff Gilchrist Profile picture
Dec 10, 2022 27 tweets 9 min read Read on X
Toilets, wastewater COVID-19, RSV, and Influenza all increasing

This thread will be wastewater related, looking at new variants, levels, and what happens in the air after you flush that wastewater down the toilet with some cool video/graphics. 🧵1/ Image of aerosol plumes over a flushed toilet.
The wastewater levels in Ottawa, Canada are increasing for all measures ( ). RSV and Influenza A levels continue to increase which means even more pressure will be put on the hospitals that are already overwhelmed. 2/ covid.gilchrist.ca/Ottawa.html
Graphs showing increasing RSV and Influenza A wastewater levels in Ottawa, Canada
To make matters worse, COVID-19 levels have started increasing again. You can see in the graph that levels never actually returned to low levels but are on the rise again ( ). 3/ covid.gilchrist.ca/Ottawa.html
Graphs showing increasing COVID-19 wastewater levels in Ottawa, Canada
What might be making the difference now? New Omicron BQ based variants have rapidly been increasing in Ontario and as of 10 days ago already made up more than 40% of sequenced cases ( ). Graphs by @Mike_Honey_ 4/ app.powerbi.com/view?r=eyJrIjo…
Graph showing increasing levels of BQ.* variants in Ontario
The BQ.1 Typhon and BQ.1.1 Cerberus variants specifically have overtaken all the other circulating variants in Ontario and are much more immune evasive than previous variants. 5/ Graph showing increasing levels of BQ.1 and BQ.1.1 variants now dominant in Ontario
If wastewater levels are going up again it could be because more people are susceptible to this newer variant and is being more easily transmitted amongst people, even those that have been previously infected. 6/
Speaking of wastewater, a very cool study used lasers to actually see and measure the aerosol plumes that come out of toilets when you flush ( ). H/T: @yaneerbaryam 7/ nature.com/articles/s4159…
Image of aerosol plumes over a flushed toilet.
Aerosols can transmit infectious diseases including COVID-19, influenza and likely most respiratory viruses and even Strep bacteria has airborne spread ( ). H/T: @ELHopkins 8/thelancet.com/journals/lanmi…
When you flush a toilet, it releases plumes of tiny water aerosols into the air around you which can spread pathogens from human waste and expose people in public washrooms to contagious disease ( ). 9/ theconversation.com/toilets-spew-i…
Image of aerosol plume over a flushed toilet.
A typical commercial toilet generates a strong upward jet of air with velocities exceeding 2m/sec rapidly carrying particles up to 1.5m (5 feet) above the bowl within 8 seconds of the start of the flush which you can see in this video ( ). 10/
Toilet bowl water contaminated by feces can have pathogen concentrations that persist after dozens of flushes but it is still an open question as to how much of a transmission risk toilet aerosol plumes present. 11/
Particle size matters, the smaller aerosols can stay floating in the air for sometimes hours. Particles smaller than 5 microns can be breathed directly into your lower respiratory tract and those 6-12 microns can deposit in the upper airways ( ). 12/thelancet.com/journals/lanre…
The study measured a massive increase in particles smaller than 2.5 microns with most particles being less than 1 micron. 13/
Over the bowl (Loc 1 and 2 in diagram) particle counts increased more than 10x pre-flush rates and decreased afterwards, while 1.5m away from the bowl the particle count increase was lower but remained constant after flushing ( ). 14/ nature.com/articles/s4159…
Charts of aerosol particle size measurements from various locations.
While the visible aerosols in the video (5-10 microns) scatter more light from the lasers, they also captured the dimmer light scattered by smaller aerosols which found they move within the same envelope as the larger ones ( ). 15/ nature.com/articles/s4159…
Image showing small aerosol particles staying within plume with larger droplets fall quickly outside of plume.
Most interesting is they show large droplets follow ballistic trajectories, remain outside the aerosol plume envelope and drop quickly. Yet another blow to droplet theory being a significant contributor to transmission <darn laws of physics>. 16/
Closing the lid before flushing helps but does not completely eliminate plumes as there are still large gaps of space between the lid and the bowl when closed and many commercial toilets do not have lids at all. 17/
The researchers suggest that UV disinfection systems and better ventilation could help mitigate exposure to aerosol plumes in the bathroom. The next time you visit a public washroom, think of all the aerosolized human waste you are breathing in if you aren't wearing a mask... 18/
A lot of people have been saying to close the toilet lid first which doesn't stop the aerosols coming out and contaminates the underside of the lid that people touch as pointed out by this comment ( ). 19/
As @rnaguru points out, each pathogen is different, and so far studies haven't found much infectious COVID-19 particles in urine or feces so while the risk is not zero it may be very low. This may not be the case for other viruses/pathogens though ( ). 20/
But you will still want to wear your mask in public bathrooms to at least protect yourself from respiratory aerosols from the other people using the bathroom who may be infected (COVID, RSV, Influenza, etc...). 21/
It is not just breathing in aerosols released from flushing toilets that people need to worry about, but bacteria that gets deposited on your hands from hot-air hand dryers ( ). 22/ cnbc.com/2022/12/19/how…
Image showing person drying their hands using a hot air dryer in a bathroom
A study before the pandemic found that test plates exposed to bathroom air for 2 minutes with hand dryers off averaged < 1 bacteria colony while plates exposed to hand dryer air for 30 seconds averaged 18-60 colonies ( ). 23/journals.asm.org/doi/10.1128/AE…
When researchers swabbed the interior hand dryer nozzle, they found surfaces had minimal bacterial levels so they added HEPA filters to the hand dryers which reduced bacterial deposition by 4x. 24/
This implies the bacteria was coming from the bathroom air so just after washing your hands you get pathogens deposited on them right after again. 25/
Health experts recommended using paper towels to dry their hands instead and remind everyone that acquiring infection from direct contact with other people is much more likely than from drying your hands. 26/
This study found during contact tracing that someone got infected after using a shared bathroom 40 minutes after the index case left. A good example of it isn't just the people currently there in a public bathroom you need to worry about ( … ). 27/icjournal.org/DOIx.php?id=10…

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More from @jeffgilchrist

Jul 25
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...
...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. 3/
Read 10 tweets
May 22
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/
Lets look more closely at the neutralization results that Novavax did provide in slide 14 of their investor presentation on May 10th ( ). 3/novavax.widen.net/s/gvwfqkhbhm/2…
Read 34 tweets
May 20
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…
Image
Particulate Matter (PM) Pollution

People now spend the vast majority of the time indoors. Adults in the USA with a 79 year life expectancy will spend on average 69 years inside of buildings and 54 of those years inside their own homes/residences ( ). 3/nap.nationalacademies.org/catalog/27341/…
Read 84 tweets
May 13
#Variant update for #Ontario, #Canada (to May 12 2024)

The JN.1.* +FLiRT variants now make up 27% of sequences and XDK.* which is recombinant of JN.1.1.1 and XBB.1.16.11 is remaining at 5% for now. Graph tools by @Mike_Honey_ 🧵1/
Sankey graph (height of each bar is # of sequences for that variant) showing top variants and their lineages over the past couple of months 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 )
Graph of top 7 COVID variant clans from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D
JN.1 #Pirola has dropped to 7% frequency and JN.1.4 down to 9% while KP.3 FLuQE is now most prevalent at 26% while the FLiRT variants are much lower at KP.2 (6%) and KS.1 (5%). 2/ Graph of top 8 COVID variants (JN.1, JN.1.4, JN.1.7, JN.1.8.1, KP.2, KP.3, KS.1) 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 has the F456L and Q493E mutations (FLuQE nickname) while the FLiRT variants have the same F456L mutation but a different R346T mutation. Ryan Hisner explains how FLiRT is a typical stepwise mutation but Q493E is very rare and may be different ( ). 3/
Chart of BA.2.86* variant convergence and latest FLiRT and FLuQE/SLuQE mutations. Chat by @dfocosi ( https://twitter.com/dfocosi/status/1789535645515313244 )
Read 15 tweets
Apr 29
People are rightfully concerned about the high case fatality rate (CFR) of the H5N1 influenza virus but did you know fatalities from COVID infection (which already spreads easily between humans) with the elderly are as high as 40% ( )? 🧵1/
Virus infection can damage the body, we have seen this with Long COVID and this can happen with other viruses as well such as Influenza causing increased risk of cardiovascular events among other things. 2/
This study tries to indirectly measure the impact of influenza infection by looking at cardiovascular events and then measuring the risk people had if they received the influenza vaccine or not( … ). 3/ H/T: @JaninePaynterncbi.nlm.nih.gov/pmc/articles/P…
Read 12 tweets
Apr 28
#Variant update for #Ontario, #Canada (to Apr. 17, 2024)

The JN.1.* +FLiRT variants now make up 20% of sequences and XDK.* which is recombinant of JN.1.1.1 and XBB.1.16.11 has made an appearance at 5%. Graph tools by @Mike_Honey_ 🧵1/
Sankey graph (height of each bar is # of sequences for that variant) showing top variants and their lineages over the past couple of months 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 )
Graph of top 7 COVID variant clans from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D
FLiRT is a nickname for variants with F456L & R356T mutations which seem to provide an advantage over the JN.1 Pirola variants without them. You can see the current FLiRT variants here from @dfocosi. 2/ Chart of BA.2.86* variant convergence and latest FLiRT mutations. Chat by @dfocosi ( https://twitter.com/dfocosi/status/1780183036853690596 )
JN.1 #Pirola has dropped to around 20% frequency and JN.1.4 is hovering at 14% while the FLiRTs are gaining: KS.1 at 10%, KP.1.1 at 4%, KP.2 at 3% and XDK.1 at 4%. 3/ Graph of top 8 COVID variants (JN.1, JN.1.16.1, JN.1.4, KP.1.1, KP.2, KS.1, XDK.1) from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
Read 17 tweets

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