Sam Scarpino
@scarpino.bsky.social
Scientist. Director of AI + Life Sciences and Professor of Public Health Sciences at Northeastern University. External Faculty at the Santa Fe Institute and Vermont Complex Systems Institute. scarpino.github.io
1/ The CDC's Center for Forecasting and Outbreak Analytics has also posted estimates of influenza growth.
Their analysis similarly shows widespread growth.
www.cdc.gov/cfa-modeling...
Their analysis similarly shows widespread growth.
www.cdc.gov/cfa-modeling...
November 14, 2025 at 5:23 PM
1/ The CDC's Center for Forecasting and Outbreak Analytics has also posted estimates of influenza growth.
Their analysis similarly shows widespread growth.
www.cdc.gov/cfa-modeling...
Their analysis similarly shows widespread growth.
www.cdc.gov/cfa-modeling...
3/ The CDC is also reporting that 50% of sub typed H3 viruses are the "K" variant. Importantly, that number is cumulative since May, so I suspect the current prevalence of the K variant is much higher.
November 14, 2025 at 5:01 PM
3/ The CDC is also reporting that 50% of sub typed H3 viruses are the "K" variant. Importantly, that number is cumulative since May, so I suspect the current prevalence of the K variant is much higher.
2/ The CDC is reporting that 2% of clinical samples are flu positive and 2% of outpatient visits had symptoms typically associated with influenza.
For both positive samples and outpatient visits the trend is increasing.
www.cdc.gov/fluview/surv...
For both positive samples and outpatient visits the trend is increasing.
www.cdc.gov/fluview/surv...
November 14, 2025 at 5:01 PM
2/ The CDC is reporting that 2% of clinical samples are flu positive and 2% of outpatient visits had symptoms typically associated with influenza.
For both positive samples and outpatient visits the trend is increasing.
www.cdc.gov/fluview/surv...
For both positive samples and outpatient visits the trend is increasing.
www.cdc.gov/fluview/surv...
Good news from the UK on the influenza "K" variant.
As expected, vaccine-derived antibodies show reduced effect against the K variant.
But, preliminary real-world data shows that the vaccine is protecting against severe disease.
Especially in kids!
www.gov.uk/government/p...
As expected, vaccine-derived antibodies show reduced effect against the K variant.
But, preliminary real-world data shows that the vaccine is protecting against severe disease.
Especially in kids!
www.gov.uk/government/p...
November 13, 2025 at 2:30 PM
Good news from the UK on the influenza "K" variant.
As expected, vaccine-derived antibodies show reduced effect against the K variant.
But, preliminary real-world data shows that the vaccine is protecting against severe disease.
Especially in kids!
www.gov.uk/government/p...
As expected, vaccine-derived antibodies show reduced effect against the K variant.
But, preliminary real-world data shows that the vaccine is protecting against severe disease.
Especially in kids!
www.gov.uk/government/p...
4/ Wastewater SCAN data from Georgia also shows a sharp rise in influenza concentrations, which is being driven by H3 SCAN doesn't subtype the Ns, but is seems like safe bet that this is the H3N2 K variant I discussed in my thread yesterday. www.wastewaterscan.org/en
November 10, 2025 at 6:50 PM
4/ Wastewater SCAN data from Georgia also shows a sharp rise in influenza concentrations, which is being driven by H3 SCAN doesn't subtype the Ns, but is seems like safe bet that this is the H3N2 K variant I discussed in my thread yesterday. www.wastewaterscan.org/en
3/ Interestingly, Walgreens data through Nov 1st, showed no signs of influenza-specific activity. That has changed with the data through Nov 8th. While rates are still quite low, they trend is consistent with us entering the flu season.
November 10, 2025 at 6:50 PM
3/ Interestingly, Walgreens data through Nov 1st, showed no signs of influenza-specific activity. That has changed with the data through Nov 8th. While rates are still quite low, they trend is consistent with us entering the flu season.
2/ Walgreens data through Nov 8th shows much higher levels of generalized respiratory infection and also the first signs of influenza activity.
You can see the dashboard and learn about their methods (not very transparent, but at least we have something) here: www.walgreens.com/seasonal/res...
You can see the dashboard and learn about their methods (not very transparent, but at least we have something) here: www.walgreens.com/seasonal/res...
November 10, 2025 at 6:50 PM
2/ Walgreens data through Nov 8th shows much higher levels of generalized respiratory infection and also the first signs of influenza activity.
You can see the dashboard and learn about their methods (not very transparent, but at least we have something) here: www.walgreens.com/seasonal/res...
You can see the dashboard and learn about their methods (not very transparent, but at least we have something) here: www.walgreens.com/seasonal/res...
10/ I looked at publicly available flu genomes from the US. There are 68 genomes from H3N2 viruses that have been posted online recently.
In the figure, I look at the raw proportion of those genomes that belong to the K variant/clade.
But, you should take these data with a HUGE grain of salt...
In the figure, I look at the raw proportion of those genomes that belong to the K variant/clade.
But, you should take these data with a HUGE grain of salt...
November 10, 2025 at 2:16 AM
10/ I looked at publicly available flu genomes from the US. There are 68 genomes from H3N2 viruses that have been posted online recently.
In the figure, I look at the raw proportion of those genomes that belong to the K variant/clade.
But, you should take these data with a HUGE grain of salt...
In the figure, I look at the raw proportion of those genomes that belong to the K variant/clade.
But, you should take these data with a HUGE grain of salt...
8/ Walgreens reports weekly on COVID, flu, and respiratory activity.
They use data collected from their stores (like sales and positive tests).
As of Nov 1st, they are reporting essentially ZERO flu activity.
It looks like they update on Sat or Sun, so I'll add last week's data to this thread.
They use data collected from their stores (like sales and positive tests).
As of Nov 1st, they are reporting essentially ZERO flu activity.
It looks like they update on Sat or Sun, so I'll add last week's data to this thread.
November 10, 2025 at 2:16 AM
8/ Walgreens reports weekly on COVID, flu, and respiratory activity.
They use data collected from their stores (like sales and positive tests).
As of Nov 1st, they are reporting essentially ZERO flu activity.
It looks like they update on Sat or Sun, so I'll add last week's data to this thread.
They use data collected from their stores (like sales and positive tests).
As of Nov 1st, they are reporting essentially ZERO flu activity.
It looks like they update on Sat or Sun, so I'll add last week's data to this thread.
7/ Here are the data from Newark.
One thing I don't understand about the wastewaterscan data is that they don't always seem to subtype. My guess is that it's because the sample quality wasn't sufficiently high, so I tend to pay attention to the positives and take the negatives with a grain of salt.
One thing I don't understand about the wastewaterscan data is that they don't always seem to subtype. My guess is that it's because the sample quality wasn't sufficiently high, so I tend to pay attention to the positives and take the negatives with a grain of salt.
November 10, 2025 at 2:16 AM
7/ Here are the data from Newark.
One thing I don't understand about the wastewaterscan data is that they don't always seem to subtype. My guess is that it's because the sample quality wasn't sufficiently high, so I tend to pay attention to the positives and take the negatives with a grain of salt.
One thing I don't understand about the wastewaterscan data is that they don't always seem to subtype. My guess is that it's because the sample quality wasn't sufficiently high, so I tend to pay attention to the positives and take the negatives with a grain of salt.
6/ But....
We are seeing some concerning signs in Boston and Newark where flu activity in the wastewater has been steadily increasing for the past two weeks.
Unfortunately, we can't tell what variant/clade is causing the signal (although in Newark we know it's H3 and not H1, no data from Boston)
We are seeing some concerning signs in Boston and Newark where flu activity in the wastewater has been steadily increasing for the past two weeks.
Unfortunately, we can't tell what variant/clade is causing the signal (although in Newark we know it's H3 and not H1, no data from Boston)
November 10, 2025 at 2:16 AM
6/ But....
We are seeing some concerning signs in Boston and Newark where flu activity in the wastewater has been steadily increasing for the past two weeks.
Unfortunately, we can't tell what variant/clade is causing the signal (although in Newark we know it's H3 and not H1, no data from Boston)
We are seeing some concerning signs in Boston and Newark where flu activity in the wastewater has been steadily increasing for the past two weeks.
Unfortunately, we can't tell what variant/clade is causing the signal (although in Newark we know it's H3 and not H1, no data from Boston)
5/ We can see from the WastewaterScan dashboard the across-the-US, influence activity is quite low (although note higher levels in a sampling sites in a handful states).
Data from: www.wastewaterscan.org/en/about
Data from: www.wastewaterscan.org/en/about
November 10, 2025 at 2:16 AM
5/ We can see from the WastewaterScan dashboard the across-the-US, influence activity is quite low (although note higher levels in a sampling sites in a handful states).
Data from: www.wastewaterscan.org/en/about
Data from: www.wastewaterscan.org/en/about
3/ As the BBC article above reported, the UK is seeing an earlier and dramatic rise in flu activity.
I haven't seen any genome sequencing data from the UK*, but the article suggests that the rise is due to this "K" variant/clade.
*I haven't looked, but I suspect there are plenty of sequences.
I haven't seen any genome sequencing data from the UK*, but the article suggests that the rise is due to this "K" variant/clade.
*I haven't looked, but I suspect there are plenty of sequences.
November 10, 2025 at 2:16 AM
3/ As the BBC article above reported, the UK is seeing an earlier and dramatic rise in flu activity.
I haven't seen any genome sequencing data from the UK*, but the article suggests that the rise is due to this "K" variant/clade.
*I haven't looked, but I suspect there are plenty of sequences.
I haven't seen any genome sequencing data from the UK*, but the article suggests that the rise is due to this "K" variant/clade.
*I haven't looked, but I suspect there are plenty of sequences.
My mom, @bettyscarpino.bsky.social, has a piece going on display at the Smithsonian’s Renwick Gallery!!!
The @washingtonpost.com mentioned her in their great review of the show.
She’s many of our biggest social media booster, so let’s show her lots of love ❤️
www.washingtonpost.com/dc-md-va/202...
The @washingtonpost.com mentioned her in their great review of the show.
She’s many of our biggest social media booster, so let’s show her lots of love ❤️
www.washingtonpost.com/dc-md-va/202...
September 3, 2025 at 3:42 PM
My mom, @bettyscarpino.bsky.social, has a piece going on display at the Smithsonian’s Renwick Gallery!!!
The @washingtonpost.com mentioned her in their great review of the show.
She’s many of our biggest social media booster, so let’s show her lots of love ❤️
www.washingtonpost.com/dc-md-va/202...
The @washingtonpost.com mentioned her in their great review of the show.
She’s many of our biggest social media booster, so let’s show her lots of love ❤️
www.washingtonpost.com/dc-md-va/202...
“Your scientists were so preoccupied with whether they could, they didn't stop to think if they should.”
May 10, 2025 at 8:37 PM
“Your scientists were so preoccupied with whether they could, they didn't stop to think if they should.”
Boston outdoor dining phenology update. It’s started!!!
March 11, 2025 at 3:30 PM
Boston outdoor dining phenology update. It’s started!!!
How are public health messaging frames shaped during an emergency?
@yaassakka.bsky.social presenting their work on how the US media interacted and framed the 2022 Mpox PHEIC at #netscix2025.
Sharaj is the first joint @nunetsi.bsky.social x @foucaultwelles.bsky.social x me PhD student!
@yaassakka.bsky.social presenting their work on how the US media interacted and framed the 2022 Mpox PHEIC at #netscix2025.
Sharaj is the first joint @nunetsi.bsky.social x @foucaultwelles.bsky.social x me PhD student!
January 17, 2025 at 5:49 AM
How are public health messaging frames shaped during an emergency?
@yaassakka.bsky.social presenting their work on how the US media interacted and framed the 2022 Mpox PHEIC at #netscix2025.
Sharaj is the first joint @nunetsi.bsky.social x @foucaultwelles.bsky.social x me PhD student!
@yaassakka.bsky.social presenting their work on how the US media interacted and framed the 2022 Mpox PHEIC at #netscix2025.
Sharaj is the first joint @nunetsi.bsky.social x @foucaultwelles.bsky.social x me PhD student!
Big announcement at #NetSciX2025 is that India will join many countries by having its own Network Science Society country chapter!!!
January 17, 2025 at 5:10 AM
Big announcement at #NetSciX2025 is that India will join many countries by having its own Network Science Society country chapter!!!
NetSciX 2025 continuing the network science society tradition of an outstanding social dinner band!
January 16, 2025 at 2:55 PM
NetSciX 2025 continuing the network science society tradition of an outstanding social dinner band!
How do the neuronal dynamics in the mouse brain differ from those in a neural net when they learn the same association task?
@jesseba.bsky.social (@nunetsi.bsky.social x @lordgrilo.bsky.social x me PhD student) presenting her amazing new work at #netscix2025!
@jesseba.bsky.social (@nunetsi.bsky.social x @lordgrilo.bsky.social x me PhD student) presenting her amazing new work at #netscix2025!
January 16, 2025 at 11:07 AM
How do the neuronal dynamics in the mouse brain differ from those in a neural net when they learn the same association task?
@jesseba.bsky.social (@nunetsi.bsky.social x @lordgrilo.bsky.social x me PhD student) presenting her amazing new work at #netscix2025!
@jesseba.bsky.social (@nunetsi.bsky.social x @lordgrilo.bsky.social x me PhD student) presenting her amazing new work at #netscix2025!
What is a “typical” graph given a specified generative model?
@nunetsi.bsky.social PhD student, Narayan Sabhahit, presenting a new method for answering this question for hidden variable random graphs at #netscix2025.
@nunetsi.bsky.social PhD student, Narayan Sabhahit, presenting a new method for answering this question for hidden variable random graphs at #netscix2025.
January 16, 2025 at 10:42 AM
What is a “typical” graph given a specified generative model?
@nunetsi.bsky.social PhD student, Narayan Sabhahit, presenting a new method for answering this question for hidden variable random graphs at #netscix2025.
@nunetsi.bsky.social PhD student, Narayan Sabhahit, presenting a new method for answering this question for hidden variable random graphs at #netscix2025.
January 16, 2025 at 6:30 AM
Our ability to identify mechanisms in higher-order systems is dependent on the observation scale (which depends on the network and dynamical model).
Prof @lordgrilo.bsky.social presenting at #NetSciX2025 on reconstructing higher order mechanisms.
Prof @lordgrilo.bsky.social presenting at #NetSciX2025 on reconstructing higher order mechanisms.
January 16, 2025 at 6:09 AM
Our ability to identify mechanisms in higher-order systems is dependent on the observation scale (which depends on the network and dynamical model).
Prof @lordgrilo.bsky.social presenting at #NetSciX2025 on reconstructing higher order mechanisms.
Prof @lordgrilo.bsky.social presenting at #NetSciX2025 on reconstructing higher order mechanisms.
What do the predictability limits of epidemics have to do with limits on our us of AI study biology?
Tomorrow at 9am in Indore (1030pm today in Boston), I'm going to try and connect these dots during my #netscix2025 keynote lecture.
Tune into the live feed here: www.youtube.com/live/frY8luh...
Tomorrow at 9am in Indore (1030pm today in Boston), I'm going to try and connect these dots during my #netscix2025 keynote lecture.
Tune into the live feed here: www.youtube.com/live/frY8luh...
January 15, 2025 at 2:50 PM
What do the predictability limits of epidemics have to do with limits on our us of AI study biology?
Tomorrow at 9am in Indore (1030pm today in Boston), I'm going to try and connect these dots during my #netscix2025 keynote lecture.
Tune into the live feed here: www.youtube.com/live/frY8luh...
Tomorrow at 9am in Indore (1030pm today in Boston), I'm going to try and connect these dots during my #netscix2025 keynote lecture.
Tune into the live feed here: www.youtube.com/live/frY8luh...