Mastodawn

Jeff Gilchrist Jan 6, 2024

#Variant update for #Ontario, #Canada (up to Dec. 26, 2023)

The BA.2.86.* #Pirola clan of variants is now the majority of sequences at 56%. JN.1 "Pirola" has taken 1st place at 38% with HV.1 #Eris down to 18%. The next closest is JG.3.2 "Eris" at 7%. Graph tools by @mike_honey_ 🧵 1/

The one page easier to share version of this thread can be found at: https://threadreaderapp.com/thread/1743652837102354561.html

Thread by @jeffgilchrist on Thread Reader App

@jeffgilchrist: #Variant update for #Ontario, #Canada (to Dec. 26, 2023) The BA.2.86.* #Pirola clan of variants is now the majority of sequences at 56%. JN.1 Pirola has taken 1st place at 38% with HV.1 "Eris" down...…

You can find weekly Ontario stats including variants at ( http://covid.gilchrist.ca/Ontario.html ) and ( https://gilchrist.great-site.net/jeff/COVID-19/Ontario.html ). 2/

Jeff Gilchrist Jan 6, 2024

Public Health Ontario got rid of their COVID data tool and replaced it with a respiratory virus tool making some of the previously reported data no longer available.

They are now using the "viral season" calendar instead of year and only producing hospitalization rates by age group for entire viral seasons. I finally got around to making these stats (along with death rate). 3/

Jeff Gilchrist Jan 6, 2024

You can see that ever since the first Omicron BA.1 variant arrived in January 2022 that hospitalization rates for our youngest children (< 1) are higher or similar to older adults 60-79. 4/

Jeff Gilchrist Jan 6, 2024

This viral season to date children < 1 years old are being hospitalized for COVID at a rate of 50.8 per 100,000 population, almost the same as adults 60-79 are 52.8 per 100k population. Adults 80+ are being hospitalized 6x more than those aged 60-79 and children aged 1-4 are being hospitalized almost 10x more than teens 12-19. 5/

Jeff Gilchrist Jan 6, 2024

Now that PHO is updating their data again after the holidays, we can see that RSV positivity has gone down a lot (4.6%) while Flu A has increased significantly (15.4%) but COVID-19 remains in the lead (18.5%) ( https://www.publichealthontario.ca/en/Data-and-Analysis/Infectious-Disease/Respiratory-Virus-Tool ). 6/

Ontario Respiratory Virus Tool | Public Health Ontario

This tool provides comprehensive epidemiological information of respiratory virus activity in Ontario, including COVID-19, influenza and other respiratory viruses. Explore case trends, laboratory testing, and outbreaks, as well as COVID-19 outcomes and vaccination.

Public Health Ontario

Jeff Gilchrist Jan 6, 2024

There are a lot of people who are sick right now, and with multiple viruses circulating if you get a negative result on a rapid test (RAT) it might be tempting to think you only have a cold.

It is important to remember a recent study found that half of people's COVID-19 viral loads peaked on day 4 of symptoms so you may not test positive on a rapid test in the first few days ( https://www.cidrap.umn.edu/covid-19/evolving-peak-sars-cov-2-loads-relative-symptom-onset-may-influence-home-test-timing ). 7/

Evolving peak SARS-CoV-2 loads relative to symptom onset may influence home-test timing

Median SARS-CoV-2 viral loads, as measured by polymerase chain reaction cycle threshold and antigen concentrations, rose from symptom onset, peaking on the fourth or fifth day of symptoms.

Jeff Gilchrist Jan 6, 2024

Recall that rapid antigen tests (RATs) 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. 8/

Jeff Gilchrist Jan 6, 2024

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 ( https://pingthread.com/thread/1563118397633597440 ). 9/

Thread by jeffgilchrist: COVID-19: FDA updates advice on rapid test (RAT) u... - PingThread

COVID-19: FDA updates advice on rapid test (RAT) usage at home A couple of weeks ago the FDA released updated guidance on taking multiple rapid antigen tests (RAT) at home to reduce the risk of false negatives ( ). 🧵1/

PingThread

Jeff Gilchrist Jan 6, 2024

If you do test positive for COVID-19 or suspect you might be infected, the Salisbury Hospital advises that mouth/oral care is very important as research has demonstrated the mouth is a reservoir for the virus and a site where it replicates.

Research also suggests the virus could pass from saliva into the blood vessels of the mouth and travel to the lungs or heart via the bloodstream. The COVID-19 mouth care guide available from Salisbury Hospital here ( https://www.salisbury.nhs.uk/coronavirus/covid-19-mouth-care/ ). 10/

Microguide Viewer - Web Viewer

Jeff Gilchrist Jan 6, 2024

People need to be very careful to understand what kind of statistics are being made available by their governments and their context. It seems Alberta is now using different criteria for reporting their COVID and RSV/Flu hospitalization and ICU rates ( https://twitter.com/GosiaGasperoPhD/status/1743450303771328931 ). 11/

Malgorzata (Gosia) Gasperowicz (@GosiaGasperoPhD) on X

Wow. Tricky & not a clean move. Before, both the reported Covid & Flu hospitalizations numbers didn’t include incidentals. Now Flu includes incidentals Covid doesn’t So they can’t be compared 🍎to🍏anymore The false narrative “flu worse than COVID, TBH” can be spread wildly 🥳/s

X (formerly Twitter)

Jeff Gilchrist Jan 6, 2024

Alberta only reports COVID numbers if it was the primary or contributing cause while influenza and RSV numbers include incidental hospitalizations which means that numbers will be much higher than if they used the same criteria as COVID and are not directly comparable. 12/

Jeff Gilchrist Jan 6, 2024

The visualization tool for variants was created by @mike_honey_ ( https://app.powerbi.com/view?r=eyJrIjoiNzE5YzczODItMDQzMS00M2EzLWFjNWYtMjg3OTY3NTNhZDM3IiwidCI6ImRjMWYwNGY1LWMxZTUtNDQyOS1hODEyLTU3OTNiZTQ1YmY5ZCIsImMiOjEwfQ%3D%3D ).

To learn how to see what variants are circulating in your area, please read this guide ( https://mstdn.science/@jeffgilchrist/110203494274348811 ). 13/

Power BI Report

Report powered by Power BI

Jeff Gilchrist Jan 7, 2024

I forgot to include the link to the latest mouth guide here ( https://www.salisbury.nhs.uk/coronavirus/covid-19-mouth-care/ ) and here is the thread discussing the importance of mouth care ( https://threadreaderapp.com/thread/1579972594320945152.html ). 14/

Microguide Viewer - Web Viewer

Jeff Gilchrist Jan 7, 2024

Also additional details about the Oral-Vascular-Pulmonary Infection Route: a Pathogenic Mechanism Linking Oral Health Status to Acute and Post-Acute COVID-19 ( https://threadreaderapp.com/thread/1725557784752619633.html ). 15/

Thread by @DrGrahamLJ on Thread Reader App

@DrGrahamLJ: Summary thread of the oral-vascular-pulmonary model of #COVID-19 lung disease, why this is important and what to do about it. Also potentially relevant in #LongCOVID @SpringerNature review - 1/21 bit.ly...…

neutron_chick Jan 7, 2024

@jeffgilchrist Thank you for this!!

I've tried CPC mouthwash before, and after a couple of days I started to get fairly painful mouth irritation, so I stopped using it. I wonder if there's different "strengths" of it. Maybe I'll look into that and see about trying again...

Lynne Jackier Jan 7, 2024

Do you know where we can get similar information in the U.S.?

Jeff Gilchrist Jan 7, 2024

@YourNeighbor57 which information are you talking about specifically, which variants are circulating or hospitalization levels or both?

Carol LK Jan 6, 2024

@jeffgilchrist do you know if there evidence for this routine? I'm curious about why the cpc mouthwash at a different time from brushing teeth.

Jeff Gilchrist Jan 7, 2024

@carolinthegarden I'm not sure but would guess it spreads out and provides more chances throughout the day to clean out the mouth?

Here is the thread the Dr. from Salisbury wrote about this ( https://threadreaderapp.com/thread/1579972594320945152.html ) and also a newer one from him about why this is important ( https://threadreaderapp.com/thread/1725557784752619633.html ).

Thread by @DrGrahamLJ on Thread Reader App

@DrGrahamLJ: 1/ A thread to explain the reasons why it is important to care for the mouth if you have #COVID. If you don't have time to read is all, here is the mouth care guidance...

Siderea, Sibylla Bostoniensis Jan 7, 2024

@jeffgilchrist
They're recreating the Nonoxynol-9 catastrophe all over again.

If they are correct that SARS-CoV-2 can enter the bloodstream via lesions in the mouth, leading to vascular COVID infection, then brushing the teeth (and maybe some mouthwash!) would be contraindicated in people who already have gum disease. Toothbrushing reduces lesions in the mouth due to gum disease only long-term, in the short term it exacerbates them.

This is a textbook example of why RCTs are necessary.

Humble Fan of Atty. Woo Jan 9, 2024

that's some scary shit. Passing the chart onto my FB page. Thanks for posting this. carry on

alastair87 (old account)Jan 7, 2024

@jeffgilchrist Just to confirm is this saying that approximately 1 in 5/6 of the Ontario population respectively (though probably with some overlap) have COVID-19 or flu-A? This isn't just a subset that were tested who were symptomatic? (the link is to wastewater analysis but I find it sufficiently extraordinary that I wanted to check).

Jeff Gilchrist Jan 7, 2024

@alastair sorry if you are talking about the "Respiratory virus activity" chart from PHO, it is not based on wastewater, but on the percent of virus testing that come back positive. So When it says COVID-19 18.5% it means that of all the PCR tests they did for COVID-19, 18.5% came back positive while the rest were negative, and for Influenza A at 15.4% that was people who were tested for Flu A, 15.4% of tests came back positive. Not percentage of population.

alastair87 (old account)Jan 7, 2024

@jeffgilchrist That makes more sense!! Thank you.

50sFarmGirl 🇨🇦Jan 6, 2024

@jeffgilchrist Complete failure on the part of public health. Sacrifice the vulnerable for the sake of the economy.

Jonathan Jan 6, 2024

@jeffgilchrist ye olde u shaped mortality like so many pathogens