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Jeff Gilchrist Profile picture
@jeffgilchrist
Nov 12 • 8 tweets • 4 min read Twitter logo Read on Twitter
Virus update for Ottawa, ON, Canada (Nov 12, 2023)

#Wastewater levels in #Ottawa remain higher than the peak of the first #Omicron BA.1 wave and hospitalization *for* COVID-19 continues to increase ( ). 🧵1/ covid.gilchrist.ca/Ottawa.html

Graph of wastewater levels in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Graph of # of people currently hospitalized *for* COVID-19 in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Our young children are especially vulnerable to respiratory virus infections. In Ottawa there were 1110 respiratory related Emergency Department visits the week of Oct. 22 of which 50% were children aged 0-11, and a third were age 0-3 ( ). 2/ ottawapublichealth.ca/en/reports-res…
Graph showing % of total respiratory related ED visits by week in Ottawa, Ontario with children <12 making up 50% of all visits. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
Which respiratory viruses are already circulating wildly? COVID-19 is by far the highest at 17% test positivity, followed a distant second by Entero/Rhinovirus (8.4%) and then RSV (5.8%)( ). 3/ 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 )
Graph showing COVID-19 PCR test positivity and # of tests over time in Ottawa, Ontario. Weekly stats available at ( http://covid.gilchrist.ca/Ottawa.html )
RSV levels in Ottawa wastewater are picking up and Influenza A has now made an appearance but still no sign of Influenza B yet. 4/ Graph showing RSV levels increasing, Influenza A levels starting and no 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 ( ). 5/
If you are sick right now, it is highly unlikely to be to flu and a recent study found that half of people's COVID-19 viral loads peaked on day 4 of symptoms so may not test positive on a rapid test in the first few days ( ). 6/cidrap.umn.edu/covid-19/evolv…
Recall that rapid tests do not amplify the virus like PCR tests so they will only test positive after you have a high viral load which may take several days to get to while your symptoms are from your immune response which can start right away even when viral loads are low. 7/
When a rapid test is positive it is almost always correct so assume you have COVID-19, but if it is negative there are many ways to get a false negative so RATs cannot be used to rule out a virus infection ( ). 8/

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More from @jeffgilchrist

Jeff Gilchrist Profile picture
Nov 5
Variant update for Ontario, Canada (Nov. 5, 2023)

This sankey diagram shows the amount of variants being sequenced and their family lineage since Sep. 1, 2023 using @Mike_Honey_'s new addition to his visualizer. COVID-19 still has highest virus activity and almost no flu.🧵1/
Sankey graph showing top variants and their lineages from PCR test genomic sequencing. Visualization tool was created by @Mike_Honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D&pageName=ReportSection32240d6b62ba73667e98 )
Table showing percentage positivity of respiratory virus activity in Ontario with COVID-19 at 18.6% positive and Influenza at <= 0.5% positivity. Table from: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool
If you are sick right now, it is highly unlikely to be to flu and a recent study found that half of people's COVID-19 viral loads peaked on day 4 of symptoms so may not test positive on a rapid test in the first few days ( ). 2/ cidrap.umn.edu/covid-19/evolv…
Table showing percentage positivity of respiratory virus activity in Ontario with COVID-19 at 18.6% positive and Influenza at <= 0.5% positivity. Table from: https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool
Recall that rapid tests do not amplify the virus like PCR tests so they will only test positive after you have a high viral load which may take several days to get to while your symptoms are from your immune response which can start right away even when viral loads are low. 3/
Read 11 tweets
Jeff Gilchrist Profile picture
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
Jeff Gilchrist Profile picture
Oct 20
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…
Read 17 tweets
Jeff Gilchrist Profile picture
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…
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"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
Jeff Gilchrist Profile picture
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
Jeff Gilchrist Profile picture
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

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