Patrickthebiosteamist
@patbiosteamist.bsky.social
Engineer & Scientist.
Breaks down Covid papers & data.
Masked fitness series.
All views expressed are my own, I speak from a US perspective.
Not a Covid researcher nor a Covid scientist.
youtube.com/@patrickthebiosteamist?si=FoWeCh6fdBWY5jEt
Breaks down Covid papers & data.
Masked fitness series.
All views expressed are my own, I speak from a US perspective.
Not a Covid researcher nor a Covid scientist.
youtube.com/@patrickthebiosteamist?si=FoWeCh6fdBWY5jEt
Reposted by Patrickthebiosteamist
Your new motto should be: if it’s fine for disabled people, it’s fine for me.
November 11, 2025 at 3:52 AM
Your new motto should be: if it’s fine for disabled people, it’s fine for me.
WastewaterSCAN is terminating sites from their program again.
Now they are down to 147 active sites.
Most recent loss from their Mendhall, Juneau, AK facility.
Now they are down to 147 active sites.
Most recent loss from their Mendhall, Juneau, AK facility.
November 11, 2025 at 3:16 AM
WastewaterSCAN is terminating sites from their program again.
Now they are down to 147 active sites.
Most recent loss from their Mendhall, Juneau, AK facility.
Now they are down to 147 active sites.
Most recent loss from their Mendhall, Juneau, AK facility.
Reposted by Patrickthebiosteamist
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 2:41 PM
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
Reposted by Patrickthebiosteamist
Tracking SARSCoV2 Lineage BA.3.2* over time
Total BA.3.2* - Globally: 63
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark
Tracker: public.tableau.com/app/profile/...
Total BA.3.2* - Globally: 63
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark
Tracker: public.tableau.com/app/profile/...
November 9, 2025 at 6:39 PM
Tracking SARSCoV2 Lineage BA.3.2* over time
Total BA.3.2* - Globally: 63
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark
Tracker: public.tableau.com/app/profile/...
Total BA.3.2* - Globally: 63
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark
Tracker: public.tableau.com/app/profile/...
Reposted by Patrickthebiosteamist
Praying on the downfall of everyone who smokes on the train 😭 at least I look cute tho
November 9, 2025 at 7:07 AM
Praying on the downfall of everyone who smokes on the train 😭 at least I look cute tho
I learned an important lesson that you also should change the bobbin thread color to match when hemming your pants.
But, successfully hemmed my first pair of pants - turning them into shorts 😊
But, successfully hemmed my first pair of pants - turning them into shorts 😊
November 9, 2025 at 3:39 AM
I learned an important lesson that you also should change the bobbin thread color to match when hemming your pants.
But, successfully hemmed my first pair of pants - turning them into shorts 😊
But, successfully hemmed my first pair of pants - turning them into shorts 😊
Dark humor things I think about lately is the fact that I haven’t heard people say the phrase “we have the tools” regarding Covid anymore.
National stockpiles haven’t been replenished, variant surveillance is dying, wastewater surveillance isn’t standardized, mask bans are being pushed…
National stockpiles haven’t been replenished, variant surveillance is dying, wastewater surveillance isn’t standardized, mask bans are being pushed…
November 8, 2025 at 4:53 PM
Dark humor things I think about lately is the fact that I haven’t heard people say the phrase “we have the tools” regarding Covid anymore.
National stockpiles haven’t been replenished, variant surveillance is dying, wastewater surveillance isn’t standardized, mask bans are being pushed…
National stockpiles haven’t been replenished, variant surveillance is dying, wastewater surveillance isn’t standardized, mask bans are being pushed…
Reposted by Patrickthebiosteamist
#COVID19 #VariantDashboard - #USA| 11/07/25
#SARSCoV2 #Lineages #30DAYTRENDS
XFG.2 (10.9%)
XFG.3.4.1 (4.7%)
XFG.3 (4.7%)
XFG.14.1 (4.3%)
XFG.4.1 (3.8%)
XFG.5.1 (3.8%)
XFG.5.2 (2.8%)
XFG.3.4.3 (2.6%)
XFG.6 (2.6%)
XFG.3.4 (2.4%)
Tracker tinyurl.com/mryj4uu7
1/n
#SARSCoV2 #Lineages #30DAYTRENDS
XFG.2 (10.9%)
XFG.3.4.1 (4.7%)
XFG.3 (4.7%)
XFG.14.1 (4.3%)
XFG.4.1 (3.8%)
XFG.5.1 (3.8%)
XFG.5.2 (2.8%)
XFG.3.4.3 (2.6%)
XFG.6 (2.6%)
XFG.3.4 (2.4%)
Tracker tinyurl.com/mryj4uu7
1/n
November 8, 2025 at 7:08 AM
#COVID19 #VariantDashboard - #USA| 11/07/25
#SARSCoV2 #Lineages #30DAYTRENDS
XFG.2 (10.9%)
XFG.3.4.1 (4.7%)
XFG.3 (4.7%)
XFG.14.1 (4.3%)
XFG.4.1 (3.8%)
XFG.5.1 (3.8%)
XFG.5.2 (2.8%)
XFG.3.4.3 (2.6%)
XFG.6 (2.6%)
XFG.3.4 (2.4%)
Tracker tinyurl.com/mryj4uu7
1/n
#SARSCoV2 #Lineages #30DAYTRENDS
XFG.2 (10.9%)
XFG.3.4.1 (4.7%)
XFG.3 (4.7%)
XFG.14.1 (4.3%)
XFG.4.1 (3.8%)
XFG.5.1 (3.8%)
XFG.5.2 (2.8%)
XFG.3.4.3 (2.6%)
XFG.6 (2.6%)
XFG.3.4 (2.4%)
Tracker tinyurl.com/mryj4uu7
1/n
This is the exact issue I foresee for Covid vaccines next year, and what I have also been harping on for the past year.
Surveillance is important. We need to invest in it - this includes participation and cooperation on the global scale (aka proactive participation with the WHO).
Surveillance is important. We need to invest in it - this includes participation and cooperation on the global scale (aka proactive participation with the WHO).
The US withdrawal from WHO could impact the flu shot.
Flu samples sent to CDC from around the world are down 60% this year, as of July.
"When those viruses are not coming in, we don't know what to put in the vaccine, and you're going to have less effective vaccines."
www.npr.org/sections/goa...
Flu samples sent to CDC from around the world are down 60% this year, as of July.
"When those viruses are not coming in, we don't know what to put in the vaccine, and you're going to have less effective vaccines."
www.npr.org/sections/goa...
Why next year's flu shot might not be as good as it should be
America's withdrawal from the World Health Organization is affecting the ability of U.S. scientists to track flu and other pathogens. That could be a blow to the development of the 2025 flu vaccine.
www.npr.org
November 8, 2025 at 1:48 AM
This is the exact issue I foresee for Covid vaccines next year, and what I have also been harping on for the past year.
Surveillance is important. We need to invest in it - this includes participation and cooperation on the global scale (aka proactive participation with the WHO).
Surveillance is important. We need to invest in it - this includes participation and cooperation on the global scale (aka proactive participation with the WHO).
Reposted by Patrickthebiosteamist
When the data speaks for itself (source: www.alberta.ca/stats/dashbo... ):
November 7, 2025 at 9:47 PM
When the data speaks for itself (source: www.alberta.ca/stats/dashbo... ):
This is another large loss to our surveillance capabilities.
At this point I have no clue how we will pick the variant for next years Covid vaccine.
We will lose the ability to know when convergence (XFG) or other high mutation changes occur (BA.3.2 we’ve been monitoring)
Cryptic lineages too.
At this point I have no clue how we will pick the variant for next years Covid vaccine.
We will lose the ability to know when convergence (XFG) or other high mutation changes occur (BA.3.2 we’ve been monitoring)
Cryptic lineages too.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 9:07 PM
This is another large loss to our surveillance capabilities.
At this point I have no clue how we will pick the variant for next years Covid vaccine.
We will lose the ability to know when convergence (XFG) or other high mutation changes occur (BA.3.2 we’ve been monitoring)
Cryptic lineages too.
At this point I have no clue how we will pick the variant for next years Covid vaccine.
We will lose the ability to know when convergence (XFG) or other high mutation changes occur (BA.3.2 we’ve been monitoring)
Cryptic lineages too.
Reposted by Patrickthebiosteamist
BA.3.2 has arrived in the UK. One BA.3.2.2, collected October 5, was uploaded from Scotland today.
Same branch as recent BA.3.2.2 from Germany & Slovenia.
It has a few errors (S:ins214:ASDT is misread & ORF1a:E4388K is an artifact). Ignoring those, the one notable new mutation is N:N126K.
Same branch as recent BA.3.2.2 from Germany & Slovenia.
It has a few errors (S:ins214:ASDT is misread & ORF1a:E4388K is an artifact). Ignoring those, the one notable new mutation is N:N126K.
November 7, 2025 at 12:10 PM
BA.3.2 has arrived in the UK. One BA.3.2.2, collected October 5, was uploaded from Scotland today.
Same branch as recent BA.3.2.2 from Germany & Slovenia.
It has a few errors (S:ins214:ASDT is misread & ORF1a:E4388K is an artifact). Ignoring those, the one notable new mutation is N:N126K.
Same branch as recent BA.3.2.2 from Germany & Slovenia.
It has a few errors (S:ins214:ASDT is misread & ORF1a:E4388K is an artifact). Ignoring those, the one notable new mutation is N:N126K.
Reposted by Patrickthebiosteamist
GISAID on providing data to @Nextstrain.org: "After consulting with our staff and advisors on the feasibility of keeping your global tree up-to-date, there was a clear consensus that continuing to generate, zip and move big files back and forth is not sustainable and a waste of resources."
🙃
🙃
Nextstrain: Interruption to GISAID-based SARS-CoV-2 sequence analyses
Nextstrain blog post from 2025-11-06; author(s): Trevor Bedford, Richard Neher and the Nextstrain team
next.nextstrain.org
November 7, 2025 at 12:19 PM
Reposted by Patrickthebiosteamist
This is a total outrage and has crippled SARS-CoV-2 variant tracking and evolutionary analysis.
Updating a file and giving access to Nextstrain & Cov-Spectrum does not require extensive resources, so the official justification is a lie. There has to be an ulterior motive here.
Updating a file and giving access to Nextstrain & Cov-Spectrum does not require extensive resources, so the official justification is a lie. There has to be an ulterior motive here.
Nextstrain's daily-updated tree of SARS-CoV-2 genomes was my gateway into the world of viral phylogenetics in early 2020, and Nextstrain's beautiful interactive tree display is crucial to making usher.bio results usable. GISAID cutting off data harms global surveillance efforts. 🧵👇
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 12:18 PM
This is a total outrage and has crippled SARS-CoV-2 variant tracking and evolutionary analysis.
Updating a file and giving access to Nextstrain & Cov-Spectrum does not require extensive resources, so the official justification is a lie. There has to be an ulterior motive here.
Updating a file and giving access to Nextstrain & Cov-Spectrum does not require extensive resources, so the official justification is a lie. There has to be an ulterior motive here.
Next sewing project for the weekend is going to be learning to hem some pants as I while be cutting down some pants into shorts that my legs are now too big for and some napkins.
Planning to do a Covid description of all the various phases as I think it’s important to show the nuanced nature of it
Planning to do a Covid description of all the various phases as I think it’s important to show the nuanced nature of it
November 7, 2025 at 4:21 AM
Next sewing project for the weekend is going to be learning to hem some pants as I while be cutting down some pants into shorts that my legs are now too big for and some napkins.
Planning to do a Covid description of all the various phases as I think it’s important to show the nuanced nature of it
Planning to do a Covid description of all the various phases as I think it’s important to show the nuanced nature of it
A communication point of the article that needs to be corrected is the initial/direct comparison between Covid, the vaccine, and risk.
People hear “heart issues more than vaccination” and go the vaccine causes these issues.
When it should read - covid causes heart issues in children as the focus
People hear “heart issues more than vaccination” and go the vaccine causes these issues.
When it should read - covid causes heart issues in children as the focus
Our current medical establishment all said the opposite was true.
Full article: www.newscientist.com/article/2502...
Full article: www.newscientist.com/article/2502...
November 6, 2025 at 12:15 AM
A communication point of the article that needs to be corrected is the initial/direct comparison between Covid, the vaccine, and risk.
People hear “heart issues more than vaccination” and go the vaccine causes these issues.
When it should read - covid causes heart issues in children as the focus
People hear “heart issues more than vaccination” and go the vaccine causes these issues.
When it should read - covid causes heart issues in children as the focus
Mask for Mamdani!
Congrats NY on the win!
But also, please mask while you’re out celebrating tonight to prevent the transmission of diseases like Covid.
Congrats NY on the win!
But also, please mask while you’re out celebrating tonight to prevent the transmission of diseases like Covid.
November 5, 2025 at 2:39 AM
Mask for Mamdani!
Congrats NY on the win!
But also, please mask while you’re out celebrating tonight to prevent the transmission of diseases like Covid.
Congrats NY on the win!
But also, please mask while you’re out celebrating tonight to prevent the transmission of diseases like Covid.
I’ve been spending time imagining what the future could be for Covid monitoring and surveillance.
1) Standardization of all facilities in NWSS program to same methods, processing techniques (like NY state just did).
2) Viral ‘weather reports’ in the news like with meteorologists…
1/
1) Standardization of all facilities in NWSS program to same methods, processing techniques (like NY state just did).
2) Viral ‘weather reports’ in the news like with meteorologists…
1/
November 2, 2025 at 7:58 PM
I’ve been spending time imagining what the future could be for Covid monitoring and surveillance.
1) Standardization of all facilities in NWSS program to same methods, processing techniques (like NY state just did).
2) Viral ‘weather reports’ in the news like with meteorologists…
1/
1) Standardization of all facilities in NWSS program to same methods, processing techniques (like NY state just did).
2) Viral ‘weather reports’ in the news like with meteorologists…
1/
Love to see a masked face (and in this case two!).
I’m very pleased to share that I've joined the Office of the Mayor at the City of Calgary as Communications Advisor.
I am so grateful for the opportunity to serve Calgarians alongside our amazing team and the exceptional people at the City of Calgary.
(The cake was delicious.)
I am so grateful for the opportunity to serve Calgarians alongside our amazing team and the exceptional people at the City of Calgary.
(The cake was delicious.)
November 1, 2025 at 1:44 AM
Love to see a masked face (and in this case two!).
Reposted by Patrickthebiosteamist
Sad day for the folks who staked their reputations on lab leak conspiracy theories.
www.telegraph.co.uk/global-healt...
www.telegraph.co.uk/global-healt...
October 31, 2025 at 3:51 PM
Sad day for the folks who staked their reputations on lab leak conspiracy theories.
www.telegraph.co.uk/global-healt...
www.telegraph.co.uk/global-healt...
Reposted by Patrickthebiosteamist
wishin you a berry good (n safe!!!) halloween 🍓✨ #CaliforniaGrown
October 31, 2025 at 11:00 PM
wishin you a berry good (n safe!!!) halloween 🍓✨ #CaliforniaGrown
As of today, one month of no new Covid variant data from the CDC and one month plus a week and a half of no new wastewater data through the CDC’s NWSS program due to the government shutdown.
October 31, 2025 at 5:50 PM
As of today, one month of no new Covid variant data from the CDC and one month plus a week and a half of no new wastewater data through the CDC’s NWSS program due to the government shutdown.
Learning how to sew and made my first pillow today.
October 30, 2025 at 11:37 PM
Learning how to sew and made my first pillow today.
Reposted by Patrickthebiosteamist
XFG.17.2.1 is undergoing multiple similar recombination events with other XFG sub-branches.
I say similar because in all of them it got Orf1ab lost and kept Spike and N*TRS double mutation
This in my 2 cents view could point at a real advantage of the XFG.17.2.1 spike combined with that N* muts:
I say similar because in all of them it got Orf1ab lost and kept Spike and N*TRS double mutation
This in my 2 cents view could point at a real advantage of the XFG.17.2.1 spike combined with that N* muts:
October 29, 2025 at 5:52 PM
XFG.17.2.1 is undergoing multiple similar recombination events with other XFG sub-branches.
I say similar because in all of them it got Orf1ab lost and kept Spike and N*TRS double mutation
This in my 2 cents view could point at a real advantage of the XFG.17.2.1 spike combined with that N* muts:
I say similar because in all of them it got Orf1ab lost and kept Spike and N*TRS double mutation
This in my 2 cents view could point at a real advantage of the XFG.17.2.1 spike combined with that N* muts: