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Jeff Gilchrist Profile picture
@jeffgilchrist
Apr 20 • 13 tweets • 4 min read • Read on X
#Variant update for #Ontario, #Canada (to Apr. 9, 2024)

The regular BA.2.86.*/JN.1.* #Pirola clan of variants as you know them are starting to go down in Ontario. This is because descendants are picking up two very useful FLiRT mutations. 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 )
Now that most variants with FLiRT have designations, you can see that JN.1 has dropped to 20% frequency while the new KP.3 FLiRT has jumped to 17.5%. The KS.1 FLiRT variant has also increased to 11% and KP.2 FLiRT is in the mix as well. 3/ Graph of top 8 COVID variants (JN.1, JN.1.13.1, 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 )
@Mike_Honey_ is now automatically generating new variant reports when he updates his data for various locations so it is easy to just click on a link and get the latest PDF version of the report instead of having to navigate through his tool. 4/
You can get the latest Ontario variant report here ( ). 5/mike-honey.github.io/covid-19-genom…
You can get the latest Canada variant report here ( ). 6/mike-honey.github.io/covid-19-genom…
Despite many hospitals declaring the end of respiratory virus season in Ontario and relaxing or removing mask requirements already, there is still a lot of viral activity going on. 7/
The % positivity in Ontario from viral tests ( ):
6.3% = Seasonal Human Coronavirus
6.2% = Entero/Rhinovirus
6.0% = COVID-19
5.5% = Human metapneumovirus
5.1% = Influenza
5.0% = Parainfluenza
1.1% = Adenovirus
0.6% = RSV

8/publichealthontario.ca/en/Data-and-An…
You can find weekly Ontario stats including variants at ( ) and ( ). 9/covid.gilchrist.ca/Ontario.html
gilchrist.great-site.net/jeff/COVID-19/…
The visualization tool for variants was created by @Mike_Honey_ ( ). 10/app.powerbi.com/view?r=eyJrIjo…
To learn how to create a Sankey diagram of variants circulating in your area, please read this guide ( ). 11/
To learn how to see what variants are circulating in your area, please read this guide ( ). 12/
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More from @jeffgilchrist

Jeff Gilchrist Profile picture
Mar 25
PHO is reminding HCWs, even those who have been vaccinated, to wear an N95 while providing care to people with confirmed or suspected cases because they know N95s can prevent infection from infectious aerosols. Works for other airborne viruses as well and non-HCW too.
Respirators protect individuals who are healthy and help reduce the chance of individuals who are sick from infecting others even in well ventilated places where short-range transmission is a concern. 2/
Yes, respirators actually work, read this thread to learn how ( ). 3/
Read 7 tweets
Jeff Gilchrist Profile picture
Mar 25
Virus update for Ottawa, Canada (Mar 25, 2024)

COVID-19 #Wastewater levels in #Ottawa have finally declined significantly but lower does not mean gone as PCR test positivity rates are still at 7.6% ( ). 🧵1/ covid.gilchrist.ca/Ottawa.html
Graph of COVID-19 wastewater levels in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
RSV WW levels are 7.7x lower than the peak which was much lower than last year. Influenza had much higher peaks this year than last year and while Flu A levels are low, Flu B hit its peak at the beginning of March and is now declining but still above the peak from last year. 2/ Graph of RSV, Influenza A & B wastewater levels in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Ottawa Public Health (OPH) stopped updating its COVID dashboard and now produces new stats on their updated respiratory virus dashboard ( ). 3/ottawapublichealth.ca/en/reports-res…
Read 12 tweets
Jeff Gilchrist Profile picture
Mar 24
#Variant update for #Ontario, #Canada (to Mar. 14, 2024)

The BA.2.86.* #Pirola clan of variants has made most other lineages extinct in Ontario. The SanKey shows the situation is now much simpler and almost exclusively JN.1 and descendants. 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
Right now the JN.1 and JN.1.4 Pirola variant are still the most prevalent. The JN.1.11.1 variant, its descendants (KP.*) and other FLiRT variants will be the ones to watch as they start growing in Ontario and may be able to escape immunity from JN.1 infections. 2/ Graph of top 8 COVID variants (JN.1, JN.1.1, JN.1.11.1, JN.1.2, JN.1.22,, JN.1.4, JN.1.7, JN.1.8.1) from PCR test genomic sequencing in Ontario, Canada. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
The % positivity from viral tests is quite a mixture now, the original Coronavirus in lead at 8.2% with COVID-19 in 2nd (6.3%) then Entero/Rhinovirus (5%), Human metapneumovirus (4.6%), Influenza A (4%), Influenza B (3.8%), Parainfluenza (3.4%) ( ). 3/ publichealthontario.ca/en/Data-and-An…
Table showing percentage positivity of respiratory virus activity in Ontario. Table from: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool
Read 8 tweets
Jeff Gilchrist Profile picture
Mar 23
Public Health Ontario (PHO) using different age categories for updated RV tool data

PHO now combines children <1 into a 0-4 age group while before they had separate <1 and 1-4 age categories which makes a big difference in how the impact of children is perceived. 🧵1/
Graph of Ontario hospitalization rate by age group for the 2023-24 surveillance period. Image from: http://covid.gilchrist.ca/Ontario.html
Graph of COVID-19 average bed occupancy per 100k population by age group in Ontario for the 2023-24 surveillance period. Image from: http://covid.gilchrist.ca/Ontario.html
PHO stopped updating COVID-19 hospital admissions and now provide bed occupancy in their recent Respiratory Virus Tool update which uses different age categories ( ). 2/publichealthontario.ca/en/Data-and-An…
You can see from the previous Ontario hospitalization rate by age group that children <1 were hospitalized at 81.8 per 100k population which is more than age 60-79 at 77.2 per 100k population. The 1-4 age group is massively smaller at 7.7 per 100k population. 3/ Graph of Ontario hospitalization rate by age group for the 2023-24 surveillance period. Image from: http://covid.gilchrist.ca/Ontario.html
Read 7 tweets
Jeff Gilchrist Profile picture
Mar 20
A nine year old boy named Matt in Singapore was infected with COVID in January 2024. Unfortunately he developed myocarditis (inflammation of the heart muscle) from the COVID infection and then had a stroke which weakened his left side ( ). 🧵1/ straitstimes.com/life/triple-wh…
From Jan 5 to 16, Matt Aeron Semodio was on ECMO, a life support system that temporarily does the job of the heart and lungs. PHOTO: COURTESY OF MATT AERON SEMODIO’S FAMILY. Image from: https://www.straitstimes.com/life/triple-whammy-nine-year-old-boy-in-singapore-suffers-covid-19-myocarditis-and-stroke
After being admitted to hospital, his heart failed and he was required to be put on the most invasive form of life support extracorporeal membrane oxygenation (ECMO), which temporarily does the job of the heart and lungs. H/T: @MeetJess 2/
His initial stay in the hospital was 5 weeks before he was discharged on Feb. 8, 2024 to recover but then was readmitted again twice for other virus infections on Feb. 11, 2024 for 3 days and then on Feb. 22, 2024 for another infection. 3/
Read 8 tweets
Jeff Gilchrist Profile picture
Mar 3
Increased Measles in Canada - Are you protected?

As Public Health crumbles and too few people are getting vaccinated for measles our herd immunity levels have dropped too much and now many people are at risk for a disease we almost eradicated in Canada. 🧵1/ Various symptoms of measles. Fever, Cough, Blocked or running nose, red, sore and watery eyes, spots in mouth, measles rash. Image from: https://www.dailymail.co.uk/health/article-12991379/Symptoms-measles-runny-nose-rash-tell-apart.html
Contents of Post:
* Worldwide Outbreaks
* Symptoms
* How is it Transmitted
* How to prevent Infection
* Damage from Measles
* Measles Depletes Immune Memory
* How long does Vaccine Last
* Breakthrough Infections
* Cleaning the Air

2/
There has been a huge surge in measles cases around the world including cases in the UK and USA. The government is strongly advising everyone in Canada to be vaccinated with 2 doses of measles vaccine, especially before travelling ( ). 3/canada.ca/en/public-heal…
Read 61 tweets

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