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Jeff Gilchrist Profile picture
@jeffgilchrist
May 13 • 15 tweets • 5 min read • Read on X
#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 )
@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 ( ).

You can get the latest Canada variant report here ( ). 5/mike-honey.github.io/covid-19-genom…
mike-honey.github.io/covid-19-genom…
How well can people with previous vaccines and/or infections neutralize these new mutations? Pre-print studies are starting to come out evaluating this. XBB infection on its own provides almost no neutralization against FLiRT and FLuQE ( ). 6/
The results show someone infected with JN.1 only has half the neutralization with the KP.3 FLuQE variant and people who had a previous XBB infection was even worse at 2.4x lower. 7/ 50% neutralization titers (NT50) of plasma samples from seven different cohorts against SARS-CoV-2 variant pseudoviruses. Plasma source cohorts and corresponding number of samples are labeled above each panel. Dashed line indicates limit of detection (NT50 = 10). Numbers of negative samples are labeled below the dashed lines. Geometric mean titers (GMT) values are labeled as black bars and shown above each group of points, with fold-changes and significance compared to JN.1 labeled. Image from ( https://www.biorxiv.org/content/10.1101/2024.04.19.590276v1.full ).
Note, these neutralization levels are 37x lower (NT50 around from 51 to 177) for KP.3 compared to the levels against BA.5 which were 1833 to 1902 so while there is some neutralization it isn't much. 8/
These results are the mutations we are seeing today. In another 4 months when a new vaccine is supposed to be deployed, results could be a lot worse than 50% lower than an already low number so new vaccines should at least catch up with current escape mutations. 9/
Despite many hospitals declaring the end of the respiratory virus season in Ontario and relaxing or removing mask requirements already, there is still a lot of viral activity going on and COVID rising again. 10/
The % positivity in Ontario from viral tests ( ):
8.1% = Entero/Rhinovirus
7.3% = COVID-19
5.9% = Parainfluenza
5.3% = Seasonal Human Coronavirus
4.6% = Human metapneumovirus
2.9% = Influenza
0.9% = Adenovirus
0.4% = RSV

11/publichealthontario.ca/en/Data-and-An…
You can find weekly Ontario stats including variants at ( ) and ( ).

The visualization tool for variants was created by @Mike_Honey_ ( ). 12/covid.gilchrist.ca/Ontario.html
gilchrist.great-site.net/jeff/COVID-19/…
app.powerbi.com/view?r=eyJrIjo…
To learn how to create a Sankey diagram of variants circulating in your area, please read this guide ( ). 13/
To learn how to see what variants are circulating in your area, please read this guide ( ). 14/
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More from @jeffgilchrist

Jeff Gilchrist Profile picture
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
Jeff Gilchrist Profile picture
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
Jeff Gilchrist Profile picture
Apr 20
#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 )
Read 13 tweets
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

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