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
Fascinating 🧵. The grotesquely mutated spike of this NJ Cryptic binds ACE2 very tightly.
It raises a broader question: Can cryptic wastewater-like lineages transmit?
YES
We knew it happened once. Now we know it's happened at least twice. The results in both cases were not pretty. 1/15
It raises a broader question: Can cryptic wastewater-like lineages transmit?
YES
We knew it happened once. Now we know it's happened at least twice. The results in both cases were not pretty. 1/15
This is wild.
Remember the NJ crytic lineage?
I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.
Some colleagues took me up on it.
Guess what they found?
1/
Remember the NJ crytic lineage?
I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.
Some colleagues took me up on it.
Guess what they found?
1/
November 22, 2025 at 7:19 PM
Fascinating 🧵. The grotesquely mutated spike of this NJ Cryptic binds ACE2 very tightly.
It raises a broader question: Can cryptic wastewater-like lineages transmit?
YES
We knew it happened once. Now we know it's happened at least twice. The results in both cases were not pretty. 1/15
It raises a broader question: Can cryptic wastewater-like lineages transmit?
YES
We knew it happened once. Now we know it's happened at least twice. The results in both cases were not pretty. 1/15
Phases of Covid Infection - Part 1
youtu.be/rLOJm8dNbvU
youtu.be/rLOJm8dNbvU
Phases of Covid Infection - Part 1
YouTube video by PatricktheBioSTEAMist
youtu.be
November 22, 2025 at 9:18 PM
Phases of Covid Infection - Part 1
youtu.be/rLOJm8dNbvU
youtu.be/rLOJm8dNbvU
Zohran Mamdani and I are the same age.
So for the New Yorkers out there.
Once more I say…
Mask for Mamdani! 😷
So for the New Yorkers out there.
Once more I say…
Mask for Mamdani! 😷
November 22, 2025 at 3:41 PM
Zohran Mamdani and I are the same age.
So for the New Yorkers out there.
Once more I say…
Mask for Mamdani! 😷
So for the New Yorkers out there.
Once more I say…
Mask for Mamdani! 😷
Reposted by Patrickthebiosteamist
This is wild.
Remember the NJ crytic lineage?
I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.
Some colleagues took me up on it.
Guess what they found?
1/
Remember the NJ crytic lineage?
I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.
Some colleagues took me up on it.
Guess what they found?
1/
November 21, 2025 at 3:19 PM
This is wild.
Remember the NJ crytic lineage?
I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.
Some colleagues took me up on it.
Guess what they found?
1/
Remember the NJ crytic lineage?
I posted 18 months ago that the Spike was too divergent to predict ACE2 binding, and asked if someone else could figure it out.
Some colleagues took me up on it.
Guess what they found?
1/
I know I’ve got several different on-going educational series, but what’s one more!
Going to start a video series later today breaking down everything that goes into a Covid infection from acute infection to the potential of long Covid - from a conceptual level with simple hand drawn figures
Going to start a video series later today breaking down everything that goes into a Covid infection from acute infection to the potential of long Covid - from a conceptual level with simple hand drawn figures
November 21, 2025 at 5:39 PM
I know I’ve got several different on-going educational series, but what’s one more!
Going to start a video series later today breaking down everything that goes into a Covid infection from acute infection to the potential of long Covid - from a conceptual level with simple hand drawn figures
Going to start a video series later today breaking down everything that goes into a Covid infection from acute infection to the potential of long Covid - from a conceptual level with simple hand drawn figures
To those of us that have been following Covid and Long Covid, it is not a surprise to see rampant misinfo on the CDC pages.
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
The CDC updated its vaccine page to claim "vaccines do not cause autism" is "not evidence-based" and studies were "ignored." This is an outrage. Decades of research have found no link. This isn't science, it's RFK Jr. using the CDC as propaganda. Children will die because of this.
November 20, 2025 at 4:39 PM
To those of us that have been following Covid and Long Covid, it is not a surprise to see rampant misinfo on the CDC pages.
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
To those of us that have been following Covid and Long Covid, it is not a surprise to see rampant misinfo on the CDC pages.
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
November 20, 2025 at 4:28 PM
To those of us that have been following Covid and Long Covid, it is not a surprise to see rampant misinfo on the CDC pages.
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
With the autism/vaccine page, know this is not their first instance of this, it’s just the first time you have taken notice or care of it.
It’s not too late to mask up 😷
Reposted by Patrickthebiosteamist
Robert Malone says the MMWR -- the CDC's venerated journal -- is being scaled back. He also says he is now the chair of the influenza vaccine working group.
November 20, 2025 at 3:08 AM
Robert Malone says the MMWR -- the CDC's venerated journal -- is being scaled back. He also says he is now the chair of the influenza vaccine working group.
ACIP is having a last minute December meeting covering the childhood vaccine schedule, “adjuvants and contaminants”, and the Hep B vaccine.
Public comment ends in 5 days.
Public comment ends in 5 days.
If anyone would like to submit a written comment to the ACIP for the upcoming meeting on December 4/5 here is the link. Comments are open until 11/24/25.
I already submitted one regarding Hep B prior to the news about the CDC vaccine website changes from today.
www.regulations.gov/commenton/CD...
I already submitted one regarding Hep B prior to the news about the CDC vaccine website changes from today.
www.regulations.gov/commenton/CD...
Regulations.gov
www.regulations.gov
November 20, 2025 at 5:17 AM
ACIP is having a last minute December meeting covering the childhood vaccine schedule, “adjuvants and contaminants”, and the Hep B vaccine.
Public comment ends in 5 days.
Public comment ends in 5 days.
Reposted by Patrickthebiosteamist
Tracking SARSCoV2 Lineage BA.3.2* over time | 11/19/2025 update
Total BA.3.2* sequences: 91
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* sequences: 91
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark
Tracker: public.tableau.com/app/profile/...
November 20, 2025 at 4:14 AM
Tracking SARSCoV2 Lineage BA.3.2* over time | 11/19/2025 update
Total BA.3.2* sequences: 91
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* sequences: 91
Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark
Tracker: public.tableau.com/app/profile/...
I’m nervous about this new classification scheme NY is doing now that they’ve transitioned to a new method of quantifying Covid in the wastewater.
Regions that I have rarely seen low (like the Long Island area) are now consistently low.
I worry this is an artifact of their new classifications
Regions that I have rarely seen low (like the Long Island area) are now consistently low.
I worry this is an artifact of their new classifications
November 18, 2025 at 9:01 PM
I’m nervous about this new classification scheme NY is doing now that they’ve transitioned to a new method of quantifying Covid in the wastewater.
Regions that I have rarely seen low (like the Long Island area) are now consistently low.
I worry this is an artifact of their new classifications
Regions that I have rarely seen low (like the Long Island area) are now consistently low.
I worry this is an artifact of their new classifications
Reposted by Patrickthebiosteamist
two new BA.3.2.2 from NSW clustering with previous samples from there, likely local circualtion has started:
nextstrain.org/fetch/genome...
nextstrain.org/fetch/genome...
nextstrain.org
November 17, 2025 at 9:27 AM
two new BA.3.2.2 from NSW clustering with previous samples from there, likely local circualtion has started:
nextstrain.org/fetch/genome...
nextstrain.org/fetch/genome...
Reposted by Patrickthebiosteamist
Our recent study on BA.3.2 is now available. Thanks to Markus Hoffmann, Lu Zhang and Georg Behrens for the great collaboration. Here’s a brief summary of our findings:
November 17, 2025 at 10:55 AM
Our recent study on BA.3.2 is now available. Thanks to Markus Hoffmann, Lu Zhang and Georg Behrens for the great collaboration. Here’s a brief summary of our findings:
I don’t know about y’all but virtually everything at the grocery store was a few more dollars expensive today.
Spent about $60 more than I usually do on the same types of items.
Spent about $60 more than I usually do on the same types of items.
November 17, 2025 at 1:59 AM
I don’t know about y’all but virtually everything at the grocery store was a few more dollars expensive today.
Spent about $60 more than I usually do on the same types of items.
Spent about $60 more than I usually do on the same types of items.
Reposted by Patrickthebiosteamist
Here's the latest I have on XFZ.*. A very robust growth advantage of 5.9% per day (41% per week) vs XFG.*. Broad geographical distribution.
Nova Scotia, Canada is the recent hotspot (OG XFZ).
Is this the one to drive the next wave?
Nova Scotia, Canada is the recent hotspot (OG XFZ).
Is this the one to drive the next wave?
November 15, 2025 at 3:29 AM
Here's the latest I have on XFZ.*. A very robust growth advantage of 5.9% per day (41% per week) vs XFG.*. Broad geographical distribution.
Nova Scotia, Canada is the recent hotspot (OG XFZ).
Is this the one to drive the next wave?
Nova Scotia, Canada is the recent hotspot (OG XFZ).
Is this the one to drive the next wave?
Reposted by Patrickthebiosteamist
New designations
XFZ.1 is a fast recombinant that got S:M153V
its spike is quite divergent 22N 31P 153V 182R 190S 346T 445R 456L 478E 493E 679R 1104L 1264L deriving from past variants circualting in Latin America. It keeps also the N/Orf9b from KP.3.3 as XEC.
XFZ.1 is a fast recombinant that got S:M153V
its spike is quite divergent 22N 31P 153V 182R 190S 346T 445R 456L 478E 493E 679R 1104L 1264L deriving from past variants circualting in Latin America. It keeps also the N/Orf9b from KP.3.3 as XEC.
November 14, 2025 at 10:55 AM
New designations
XFZ.1 is a fast recombinant that got S:M153V
its spike is quite divergent 22N 31P 153V 182R 190S 346T 445R 456L 478E 493E 679R 1104L 1264L deriving from past variants circualting in Latin America. It keeps also the N/Orf9b from KP.3.3 as XEC.
XFZ.1 is a fast recombinant that got S:M153V
its spike is quite divergent 22N 31P 153V 182R 190S 346T 445R 456L 478E 493E 679R 1104L 1264L deriving from past variants circualting in Latin America. It keeps also the N/Orf9b from KP.3.3 as XEC.
Reposted by Patrickthebiosteamist
BA.3.2.2 nearly 50% of recent Western Australia sequences—perhaps on a path to dominance there?
In this latest batch, there's another furin-cleavage site (FCS)-adjacent ∆QT sequence. It's very closely related to the first one, so there's now no doubt that the deletion is real. 1/3
In this latest batch, there's another furin-cleavage site (FCS)-adjacent ∆QT sequence. It's very closely related to the first one, so there's now no doubt that the deletion is real. 1/3
November 13, 2025 at 12:23 AM
BA.3.2.2 nearly 50% of recent Western Australia sequences—perhaps on a path to dominance there?
In this latest batch, there's another furin-cleavage site (FCS)-adjacent ∆QT sequence. It's very closely related to the first one, so there's now no doubt that the deletion is real. 1/3
In this latest batch, there's another furin-cleavage site (FCS)-adjacent ∆QT sequence. It's very closely related to the first one, so there's now no doubt that the deletion is real. 1/3
😢
The American penny died on Wednesday in Philadelphia. It was 232. The cause was irrelevance and expensiveness, the Treasury Department said. Nothing could be bought any more with a penny, as the cost to mint the penny had risen to more than 3 cents. nyti.ms/48bFd5K
November 12, 2025 at 7:41 PM
😢
Reposted by Patrickthebiosteamist
+4 From Germany two regions BA.3.2.2 different branch from WA found by HynnSpylor github
New batch from WA AUS 9/22 are BA.3.2.2
In November 8/20 samples there have been BA.3.2.2
nextstrain.org/fetch/genome...
In November 8/20 samples there have been BA.3.2.2
nextstrain.org/fetch/genome...
nextstrain.org
November 12, 2025 at 4:16 PM
+4 From Germany two regions BA.3.2.2 different branch from WA found by HynnSpylor github
Walgreens has a new updated respiratory illness index.
Will comment my thoughts when I have a min to look through it.
Check it out in the link below
⬇️
Will comment my thoughts when I have a min to look through it.
Check it out in the link below
⬇️
@patbiosteamist.bsky.social Did you see that Walgreens has a Respiratory Illness Index Tracker again? It says it's updated once a week. The last update was November 8. It's different from their old one. Don't know if it's useful or not. It's *something*.
Respiratory Illness Index | Walgreens
Track flu and COVID-19 with our Respiratory Illness Index map. Get local updates and find links to virtual care, and vaccines and testing at a Walgreens near you.
www.walgreens.com
November 11, 2025 at 10:42 PM
Walgreens has a new updated respiratory illness index.
Will comment my thoughts when I have a min to look through it.
Check it out in the link below
⬇️
Will comment my thoughts when I have a min to look through it.
Check it out in the link below
⬇️
Reposted by Patrickthebiosteamist
Quick variant update special watch for :
XFG.17.2.1 rising in Italy and Uk
XFG.10.4
XFZ especially with S:M153V
XFW.1.1
PQ.2.8.1
Everything with 679R
Everything with 1174V
Everything with the double nuc mut enhancing N* TRS
BA.3.2
XFG.17.2.1 rising in Italy and Uk
XFG.10.4
XFZ especially with S:M153V
XFW.1.1
PQ.2.8.1
Everything with 679R
Everything with 1174V
Everything with the double nuc mut enhancing N* TRS
BA.3.2
November 11, 2025 at 2:27 PM
Quick variant update special watch for :
XFG.17.2.1 rising in Italy and Uk
XFG.10.4
XFZ especially with S:M153V
XFW.1.1
PQ.2.8.1
Everything with 679R
Everything with 1174V
Everything with the double nuc mut enhancing N* TRS
BA.3.2
XFG.17.2.1 rising in Italy and Uk
XFG.10.4
XFZ especially with S:M153V
XFW.1.1
PQ.2.8.1
Everything with 679R
Everything with 1174V
Everything with the double nuc mut enhancing N* TRS
BA.3.2
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/...