Important read on challenges of continued SARS-CoV-2 surveillance provided by tools like Nextstrain, using GISAID data. Just one comment as someone who is using Nextstrain for my research, for keeping up to date and for scientific talks:
nextstrain.org/blog/2025-11...
nextstrain.org/blog/2025-11...
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
nextstrain.org
November 17, 2025 at 10:37 AM
Important read on challenges of continued SARS-CoV-2 surveillance provided by tools like Nextstrain, using GISAID data. Just one comment as someone who is using Nextstrain for my research, for keeping up to date and for scientific talks:
nextstrain.org/blog/2025-11...
nextstrain.org/blog/2025-11...
SARS-CoV-2 lineage LP.8.1 (KP.1.1.3.8.1; JN.1.11.1.1.1.3.8.1) has been designated Clade 25A by Nextstrain github.com/nextstrain/n.... (1/3)
github.com
January 25, 2025 at 3:07 PM
SARS-CoV-2 lineage LP.8.1 (KP.1.1.3.8.1; JN.1.11.1.1.1.3.8.1) has been designated Clade 25A by Nextstrain github.com/nextstrain/n.... (1/3)
I use CovSpectrum & Nextstrain every day—& I'm not the only one. Every Covid thread I've ever posted has relied largely on CovSpectrum & Nextstrain for information & visuals. These vital resources have now been stolen from us by a world-class grifter. 2/ www.thinkglobalhealth.org/article/to-f...
December 22, 2025 at 5:00 PM
I use CovSpectrum & Nextstrain every day—& I'm not the only one. Every Covid thread I've ever posted has relied largely on CovSpectrum & Nextstrain for information & visuals. These vital resources have now been stolen from us by a world-class grifter. 2/ www.thinkglobalhealth.org/article/to-f...
GISAID is now blocking genomic sequencing access to critical resources like Nextstrain, Covspectrum, Outbreak-info, & others.
This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
Bad. No justification, no communication, no standard procedures for making changes—just arbitrary pronouncements cutting off access to some of the most valuable resources we have.
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
October 30, 2025 at 10:53 PM
GISAID is now blocking genomic sequencing access to critical resources like Nextstrain, Covspectrum, Outbreak-info, & others.
This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
This makes us less safe, as live tracking of viral evolution remains critical for assessment of emerging threats. This needs to be escalated.
I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland.
Please interpret with caution.
By segment:
S: nextstrain.org/groups/hodcr...
M: nextstrain.org/groups/hodcr...
L: nextstrain.org/groups/hodcr...
Please interpret with caution.
By segment:
S: nextstrain.org/groups/hodcr...
M: nextstrain.org/groups/hodcr...
L: nextstrain.org/groups/hodcr...
May 8, 2026 at 8:22 PM
I've built some initial Nextstrain phylogenies of the Andes Hantavirus variant, which include the sequence generated by HUG & UniZurich, Switzerland.
Please interpret with caution.
By segment:
S: nextstrain.org/groups/hodcr...
M: nextstrain.org/groups/hodcr...
L: nextstrain.org/groups/hodcr...
Please interpret with caution.
By segment:
S: nextstrain.org/groups/hodcr...
M: nextstrain.org/groups/hodcr...
L: nextstrain.org/groups/hodcr...
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 6, 2025 at 9:51 PM
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."
🙃
🙃
For more on the fantasies conjured by the "GISAID Secretariat"—Bogner—to justify the unjustifiable, including the risible notion that a few mouse clicks & file transfers is "not sustainable & a waste of resources," see this @nextstrain.org blog post. 18/
nextstrain.org/blog/2025-11...
nextstrain.org/blog/2025-11...
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
nextstrain.org
December 22, 2025 at 5:00 PM
For more on the fantasies conjured by the "GISAID Secretariat"—Bogner—to justify the unjustifiable, including the risible notion that a few mouse clicks & file transfers is "not sustainable & a waste of resources," see this @nextstrain.org blog post. 18/
nextstrain.org/blog/2025-11...
nextstrain.org/blog/2025-11...
Designation of lineage NB.1.8.1 as Nextstrain Clade 25B has been merged to the main branch. I would consider this the official designation of Clade 25B. See github.com/nextstrain/n....
github.com
April 23, 2025 at 3:49 PM
Designation of lineage NB.1.8.1 as Nextstrain Clade 25B has been merged to the main branch. I would consider this the official designation of Clade 25B. See github.com/nextstrain/n....
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 6, 2025 at 9:46 PM
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
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
October 16, 2025 at 7:48 PM
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
🙏Thanks to support from swissuniversities & help from TNG Tech, particularly Simon - we've got a very exciting update to CoVariants! 📢
🎉You can now switch between Nextstrain & Pango lineages!! 🎚️
1/3
🎉You can now switch between Nextstrain & Pango lineages!! 🎚️
1/3
April 20, 2025 at 11:37 AM
🙏Thanks to support from swissuniversities & help from TNG Tech, particularly Simon - we've got a very exciting update to CoVariants! 📢
🎉You can now switch between Nextstrain & Pango lineages!! 🎚️
1/3
🎉You can now switch between Nextstrain & Pango lineages!! 🎚️
1/3
In 2025, GISAID cut off access to many critical SARS-CoV-2 resources, incl. our outbreak.info.
A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts.
Our joint response:
blog.outbreak.info/joint-respon...
A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts.
Our joint response:
blog.outbreak.info/joint-respon...
February 24, 2026 at 11:06 PM
In 2025, GISAID cut off access to many critical SARS-CoV-2 resources, incl. our outbreak.info.
A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts.
Our joint response:
blog.outbreak.info/joint-respon...
A month ago, GISAID leveled accusations against us, Cov-Spectrum, Nextstrain, and members of COG-UK, which are false and misrepresent known facts.
Our joint response:
blog.outbreak.info/joint-respon...
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.
Nextstrain #ANDV trees updated with a few improvements:
- 2 outbreaks marked
- host scientific/common name added
- province now visible on map
- date colouring added
Here's a quick tour of how to change colours, geography & names!
Links to trees here (scroll down):
nextstrain.org/groups/hodcr...
- 2 outbreaks marked
- host scientific/common name added
- province now visible on map
- date colouring added
Here's a quick tour of how to change colours, geography & names!
Links to trees here (scroll down):
nextstrain.org/groups/hodcr...
May 14, 2026 at 11:01 AM
Nextstrain #ANDV trees updated with a few improvements:
- 2 outbreaks marked
- host scientific/common name added
- province now visible on map
- date colouring added
Here's a quick tour of how to change colours, geography & names!
Links to trees here (scroll down):
nextstrain.org/groups/hodcr...
- 2 outbreaks marked
- host scientific/common name added
- province now visible on map
- date colouring added
Here's a quick tour of how to change colours, geography & names!
Links to trees here (scroll down):
nextstrain.org/groups/hodcr...
The most valuable viral research tools—@nextstrain & CovSpectrum—are being destroyed—not only blocked from new data but now forbidden from even sharing info from the PAST. Why?
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
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
December 22, 2025 at 5:00 PM
The most valuable viral research tools—@nextstrain & CovSpectrum—are being destroyed—not only blocked from new data but now forbidden from even sharing info from the PAST. Why?
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
Because GISAID is run dictatorially by a con man, paranoid egomaniac, & liar named Peter Bogner. 1/
BA.3.2 wurde von der Weltgesundheitsorganisation (WHO) als SARS-CoV-2-Variante unter Beobachtung (VUM) eingestuft.
cdn.who.int/media/docs/d...
cdn.who.int/media/docs/d...
December 6, 2025 at 1:49 PM
BA.3.2 wurde von der Weltgesundheitsorganisation (WHO) als SARS-CoV-2-Variante unter Beobachtung (VUM) eingestuft.
cdn.who.int/media/docs/d...
cdn.who.int/media/docs/d...
Staying ahead of the next pandemic: Nextstrain, a new platform by scientists at the Univ of Washington, intends to boost tracking of virus evolution. It's a genomic epidemiology platform where phylogenetic analyses of virus evolution & transmission data are posted online👇
Nextstrain Aims to Boost Tracking of Virus Evolution
Leaders seek to better understand the needs of the public health community
www.medpagetoday.com
August 23, 2026 at 11:22 AM
Staying ahead of the next pandemic: Nextstrain, a new platform by scientists at the Univ of Washington, intends to boost tracking of virus evolution. It's a genomic epidemiology platform where phylogenetic analyses of virus evolution & transmission data are posted online👇
Last week, a teenager in British Columbia contracted H5N1, the first human case acquired in Canada. The BC CDC and and Canadian Food Inspection Agency have released sequences from this infected person and domestic and wild birds sampled in BC, which we've just added to Nextstrain. A thread:
auspice
nextstrain.org
November 17, 2024 at 7:59 PM
Last week, a teenager in British Columbia contracted H5N1, the first human case acquired in Canada. The BC CDC and and Canadian Food Inspection Agency have released sequences from this infected person and domestic and wild birds sampled in BC, which we've just added to Nextstrain. A thread:
We are pleased to announce the availability of the human metapneumovirus (hMPV) phylogenetic analysis on Nextstrain and its corresponding Nextclade dataset.
Read more on our blog: nextstrain.org/blog/2025-01...
Read more on our blog: nextstrain.org/blog/2025-01...
Nextstrain: Phylogenetic analysis of Human Metapneumovirus
Nextstrain blog post from 2025-01-09; author(s): Isabel Joia, Richard Neher
nextstrain.org
January 9, 2025 at 7:02 PM
We are pleased to announce the availability of the human metapneumovirus (hMPV) phylogenetic analysis on Nextstrain and its corresponding Nextclade dataset.
Read more on our blog: nextstrain.org/blog/2025-01...
Read more on our blog: nextstrain.org/blog/2025-01...
Tools like Nextstrain, CoV-Spectrum, UShER and outbreak.info facilitate a global community of experts to keep close tabs on the ongoing evolution of SARS-CoV-2. Support for outbreak.info ended in Jan 2025 and CoV-Spectrum hasn't been updated for >3 weeks. 3/5
November 6, 2025 at 9:46 PM
Tools like Nextstrain, CoV-Spectrum, UShER and outbreak.info facilitate a global community of experts to keep close tabs on the ongoing evolution of SARS-CoV-2. Support for outbreak.info ended in Jan 2025 and CoV-Spectrum hasn't been updated for >3 weeks. 3/5
The Nextstrain team has been focused on extending the usability of Auspice and auspice.us.
See the blog post for details: nextstrain.org/blog/2026-07...
See the blog post for details: nextstrain.org/blog/2026-07...
Nextstrain: Auspice and auspice.us updates
Nextstrain blog post from 2026-07-09; author(s): The Nextstrain team
nextstrain.org
July 9, 2026 at 10:41 PM
The Nextstrain team has been focused on extending the usability of Auspice and auspice.us.
See the blog post for details: nextstrain.org/blog/2026-07...
See the blog post for details: nextstrain.org/blog/2026-07...
As of yesterday, with a merge into the master branch of github.com/nextstrain/n..., SARS-CoV-2 lineage XFG.3.4.1 has been designated Nextstrain clade 26B.
github.com
July 8, 2026 at 2:13 AM
As of yesterday, with a merge into the master branch of github.com/nextstrain/n..., SARS-CoV-2 lineage XFG.3.4.1 has been designated Nextstrain clade 26B.
Designation of XFG as Nextstrain Clade 25C has now been merged to the master branch github.com/nextstrain/n..., so now I’d call designation of XFG as 25C official.
github.com
June 8, 2025 at 2:10 AM
Designation of XFG as Nextstrain Clade 25C has now been merged to the master branch github.com/nextstrain/n..., so now I’d call designation of XFG as 25C official.