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Oct 20 17 tweets 6 min read Twitter logo Read on Twitter
Virus update for Ottawa, ON, Canada (Oct 20, 2023)

#Viral indicators continue to increase for #Ottawa, #Canada ( ). #Wastewater levels in Ottawa are now higher than the peak of the first #Omicron BA.1 wave. 🧵1/ covid.gilchrist.ca/Ottawa.html
Graph of wastewater levels in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Unfortunately that means increases in hospitalization as well. Ottawa has had significantly elevated levels of hospitalization *for* COVID-19 during the past 2 months now. 2/ Graph of # of people currently hospitalized *for* COVID-19 in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Our youngest children are especially vulnerable to respiratory virus infections. In Ottawa there were 361 respiratory related ED visits the week of Oct. 8th which accounted for 60% of ED visits in the <4 age group, up from 282 the previous week ( ). 3/ottawapublichealth.ca/en/reports-res…
Ottawa MPP Chandra Pasma @ChandraPasma yesterday tabled a private members bill, "Improving Air Quality for Our Children Act" to help address air quality issues in schools to monitor and ensure our children have the best safest learning conditions ( ). 4/
Which respiratory viruses are already circulating wildly? Since the symptoms are often very similar or the same, many people think they have a "cold" but will often have COVID-19. 5/
Right now in Ontario there is a similar percent test positivity for COVID-19 and Entero/Rhinovirus while very little of anything else yet ( ). 6/ publichealthontario.ca/en/Data-and-An…
Table of respiratory virus activity showing viruses and percent positivity from tests in Ontario. Stats available at ( https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool )
If you have something that feels like a really bad flu, in Ottawa there has been *no* Influenza A or B detected in wastewater in the past 2 weeks, and only very low amounts of RSV, so it is very unlikely to be Flu or RSV at the moment. 7/ Graph showing very little RSV, and no Influenza A or B wastewater levels in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
In Ottawa you can get free COVID-19 rapid tests (RATs) from Ottawa Public Health at libraries and community centres ( ). 8/
What about current variants? More than 60% of sequences are from the EG.5.* [Eris] family with the others at or below 10% but there is still quite a mixture of variants circulating with different immune evasion capabilities. 9/ Graph of top 7 COVID variant family frequencies from PCR test genomic sequencing. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
If you look at individual variants, HV.1 has increased very rapidly and is actually the top variant in Ontario at >15% of sequences. HV.1 is a descendant of Eris (EG.5.1.6) which itself is a descendant of XBB.1.9.2 [Hyperion]. 10/ Graph of 7 COVID variant frequencies from PCR test genomic sequencing. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
Unfortunately since there is still so much uncontrolled transmission of the virus, it is constantly mutating to evade immunity built up by previous variants which can lead to some people becoming reinfected again within weeks not months or years ( ). 11/
If you have been infected, don't assume you have months of protection before the next infection and increase risky behaviour of exposure thinking you are safe. You might be getting all the damage from the virus and very little protection. 12/
The BA.2.86.* [Pirola] variant which is very different from the other currently circulating variants was found in Ontario in late August and is starting to increase more rapidly now and picking up more immune evasive mutations in its offspring JN.1 (BA.2.86.1.1). 13/ Graph of BA.2.86.1 from PCR test genomic sequencing in Ontario. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
The visualization tool for variants was created by @Mike_Honey_ ( ). 14/app.powerbi.com/view?r=eyJrIjo…
To learn how to see what variants are circulating in your area, please read this guide ( ). 15/
It is long past time to start implementing other ways to reduce transmission and new variants besides relying on a chasing the variants vaccine-only policy ( ). 16/
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More from @jeffgilchrist

Oct 22
If there are 1 in 23 people infected in Ontario like @MoriartyLab estimates, that means any group of 10 people has a 36% chance at least 1 person is infected, increases to almost 50% for 15 people and 67% for 25 people. Online calculator available here: tinyurl.com/2emnj8nj

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You can use the calculator to estimate the chance in your area by updating the values. If you are in Canada, you can use Dr. Moriarty's COVID hazard index to find the current rates in your province here ( ). 2/covid19resources.ca/covid-hazard-i…
You can read the unrolled 1 page version of the latest report from @MoriartyLab here ( ). 3/threadreaderapp.com/thread/1715930…
Read 4 tweets
Oct 16
Did you know that Dogs can get infected by COVID?

Unfortunately a study observed substantial brain pathology in infected dogs which you can read more about here ( ). H/T: @arijitchakrav 🧵1/ wwwnc.cdc.gov/eid/article/29…
Image
"We observed substantial brain pathology in SARS-CoV-2–infected dogs, particularly involving blood–brain barrier damage resembling small vessel disease, including changes in tight junction proteins, reduced laminin levels, and decreased pericyte coverage." 2/
"Furthermore, we detected phosphorylated tau, a marker of neurodegenerative disease, indicating a potential link between SARS-CoV-2–associated small vessel disease and neurodegeneration." 3/
Read 6 tweets
Oct 15
Variant update for Ontario, Canada (October 15, 2023)

More than 60% of sequences are from the EG.5.* [Eris] family with the others at or below 10% but there is still quite a mixture of variants circulating with different immune evasion capabilities. 🧵1/ Graph of top 7 COVID variant family frequencies from PCR test genomic sequencing. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
If you look at individual variants, HV.1 (purple) has increased very rapidly and is actually the top variant in Ontario at 15% of sequences. HV.1 is a descendant of Eris (EG.5.1.6) which itself is a descendant of XBB.1.9.2 [Hyperion]. 2/ Graph of 7 COVID variant frequencies from PCR test genomic sequencing. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D )
Unfortunately since there is still so much uncontrolled transmission of the virus, it is constantly mutating to evade immunity built up by previous variants which can lead to some people becoming reinfected again within weeks not months or years ( ). 3/
Read 8 tweets
Oct 4
Some are describing the #Novavax #vaccine having the ability to target the parts of the #virus that stay the same. This is a little misleading since Novavax + #adjuvant and your immune system have no idea what parts of the #spike are going to change in new #variants. 🧵1/ Graphic of virus with multiple tattoos on its body wearing a procedure mask. Image created by Bing Image Creator and DALL-E 3
Instead, the adjuvant in Novavax (Matrix-M) helps your immune system target a larger set of unique parts on the spike so new variants may have less of an impact with Novavax vaccines depending on where the mutations happen ( ). 2/
While the original Novavax elicited antibodies that target parts of the spike that happened to be conserved in BA.1 and BA.5 ( ), those parts got changed with the latest XBB variants requiring an updated formula. 3/ medrxiv.org/content/10.110…
Neutralizing (ID50) antibody titers by dose for the ancestral, BA.1, and BA.4/BA.5 variants. Dotted line represents approximate correlates of protection titers as derived for the ancestral strain.22 (C) Antigenic cartography by dose for the ancestral and variants strains of SARS-CoV-2. SARS-CoV-2 antigens are depicted as circles and sera are depicted as squares. Each grid square represents one antigenic unit representing a two-fold change in neutralization titers from ancestral to variant. CoP, correlate of protection; VE, vaccine efficacy.
Read 15 tweets
Oct 1
Virus update for Ottawa, ON, Canada (Sep 30, 2023)

#Viral indicators continue to increase for #Ottawa, #Canada ( ). #Wastewater levels in Ottawa have almost reached the same as the peak of the first #Omicron BA.1 wave. 🧵1/ covid.gilchrist.ca/Ottawa.html
Graph of wastewater levels in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Unfortunately that means increases in hospitalization as well. Ottawa has seen significantly elevated levels of hospitalization *for* COVID-19 for the past 2 months now. Remember, this virus is not seasonal, it transmits easily all year long. 2/ Graph of # of people currently hospitalized *for* COVID-19 in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Our youngest children (age < 4) are especially vulnerable to respiratory infections. There were 304 respiratory related Emergency Department visits the week of Sep. 17th (49% of ED visits in that age group) and the season is just starting ( ). 3/ottawapublichealth.ca/en/reports-res…
Read 19 tweets
Sep 23
@Friesein The adjuvant helps your immune system target a larger set of unique parts on the spike than vaccines like mRNA that don't use an adjuvant so new variants may have less of an impact with Novavax vaccines depending on where the mutations happen. 2/
@Friesein While the original Novavax elicited antibodies that target parts of the spike that were conserved in BA.1 and BA.5, those parts got changed with the latest XBB variants requiring an updated formula. 3/
@Friesein People will be more confused as to why they can't just keep getting the original Novavax and if they think it targets parts that don't change which are and have been changing and now require an updated formula. 4/
Read 13 tweets

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