Pinned
DoropFan
@doropfan.bsky.social
· Jan 30
SARS-CoV-2(fandorop
docs.google.com
BA.2.75やXBBだったグーグルシートの名前を今更変更
Renaming a sheet
SARS-CoV-2(fandorop
docs.google.com/spreadsheets...
- Spike
docs.google.com/spreadsheets...
- Orange Marmalade
docs.google.com/spreadsheets...
- A^Z
docs.google.com/spreadsheets...
Renaming a sheet
SARS-CoV-2(fandorop
docs.google.com/spreadsheets...
- Spike
docs.google.com/spreadsheets...
- Orange Marmalade
docs.google.com/spreadsheets...
- A^Z
docs.google.com/spreadsheets...
Reposted by DoropFan
"She and Chen sent GISAID three emails in the weeks after, but never received any response. (GISAID says the emails came from Chen, whereas its agreement was with Stadler.)"
www.science.org/content/arti...
www.science.org/content/arti...
Fresh conflicts erupt around giant database for flu and COVID-19 sequences
Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic
www.science.org
January 7, 2026 at 1:17 PM
"She and Chen sent GISAID three emails in the weeks after, but never received any response. (GISAID says the emails came from Chen, whereas its agreement was with Stadler.)"
www.science.org/content/arti...
www.science.org/content/arti...
Reposted by DoropFan
Mark Twain was a vehement anti-imperialist, often wielding his "pen warmed up in Hell" against the imperialist warmongers of his day.
"Patriotism... it is a word which always commemorates a robbery...."
"Patriotism... it is a word which always commemorates a robbery...."
"Patriotism... a word which always commemorates a robbery. There isn’t a foot of land in the world which doesn’t represent the ousting & re-ousting of a long line of 'owners' who each, as 'patriots' defended it against the next gang of 'robbers' who came to steal it & did—& became patriots in turn."
January 11, 2026 at 9:05 PM
Mark Twain was a vehement anti-imperialist, often wielding his "pen warmed up in Hell" against the imperialist warmongers of his day.
"Patriotism... it is a word which always commemorates a robbery...."
"Patriotism... it is a word which always commemorates a robbery...."
Reposted by DoropFan
ScienceInsider: Fresh conflicts erupt around giant database for flu and COVID-19 sequences
by @kakape.bsky.social @science.org
bit.ly/4puKXNI
by @kakape.bsky.social @science.org
bit.ly/4puKXNI
Fresh conflicts erupt around giant database for flu and COVID-19 sequences
Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic
bit.ly
January 7, 2026 at 3:19 AM
ScienceInsider: Fresh conflicts erupt around giant database for flu and COVID-19 sequences
by @kakape.bsky.social @science.org
bit.ly/4puKXNI
by @kakape.bsky.social @science.org
bit.ly/4puKXNI
Reposted by DoropFan
Zie hier het verloop van de precieze aantallen/percentages van BA.3.2 ten opzichte van het totaal aantal gesequencte samples in Nederland, Duitsland, Luxemburg en Nederland.
Bij het bereiken van 50% door een snel groeiende variant start er doorgaans een niewe golf.
ukcovid.xyz/2025/country...
Bij het bereiken van 50% door een snel groeiende variant start er doorgaans een niewe golf.
ukcovid.xyz/2025/country...
December 19, 2025 at 7:28 AM
Zie hier het verloop van de precieze aantallen/percentages van BA.3.2 ten opzichte van het totaal aantal gesequencte samples in Nederland, Duitsland, Luxemburg en Nederland.
Bij het bereiken van 50% door een snel groeiende variant start er doorgaans een niewe golf.
ukcovid.xyz/2025/country...
Bij het bereiken van 50% door een snel groeiende variant start er doorgaans een niewe golf.
ukcovid.xyz/2025/country...
Reposted by DoropFan
An independent group of experts, the TAG-CO-VAC meets twice a year to review the evolution of the virus, the performance of currently approved COVID-19 vaccines and implications for vaccine composition.
Read their recommendation:
bit.ly/3YBlVBe
Read their recommendation:
bit.ly/3YBlVBe
Statement on the antigen composition of COVID-19 vaccines
The TAG-CO-VAC reconvened on 8-9 December 2025 to review the genetic and antigenic evolution of SARS-CoV-2; immune responses to SARS-CoV-2 infection and/or COVID-19 vaccination; the performance of cur...
bit.ly
December 18, 2025 at 2:46 PM
An independent group of experts, the TAG-CO-VAC meets twice a year to review the evolution of the virus, the performance of currently approved COVID-19 vaccines and implications for vaccine composition.
Read their recommendation:
bit.ly/3YBlVBe
Read their recommendation:
bit.ly/3YBlVBe
Reposted by DoropFan
@corneliusroemer.bsky.social designated the sub branches of BA.3.2.1 and BA.3.2.2.
Respectively their aliases are RD* and RE*.
the Western Australia BA.3.2.2 branch is now RE.1.1
while the European BA.3.2.2 with Orf1a:E1015G is RE.2 with RE.2.1 having N:T296I and instead RE.2.2 having N:A173V
Respectively their aliases are RD* and RE*.
the Western Australia BA.3.2.2 branch is now RE.1.1
while the European BA.3.2.2 with Orf1a:E1015G is RE.2 with RE.2.1 having N:T296I and instead RE.2.2 having N:A173V
December 2, 2025 at 10:31 PM
@corneliusroemer.bsky.social designated the sub branches of BA.3.2.1 and BA.3.2.2.
Respectively their aliases are RD* and RE*.
the Western Australia BA.3.2.2 branch is now RE.1.1
while the European BA.3.2.2 with Orf1a:E1015G is RE.2 with RE.2.1 having N:T296I and instead RE.2.2 having N:A173V
Respectively their aliases are RD* and RE*.
the Western Australia BA.3.2.2 branch is now RE.1.1
while the European BA.3.2.2 with Orf1a:E1015G is RE.2 with RE.2.1 having N:T296I and instead RE.2.2 having N:A173V
Reposted by DoropFan
Humoral immunity induced by LP.8.1 monovalent vaccines against a broad range of SARS-CoV-2 variants including XEC, NB.1.8.1, XFG, and BA.3.2 https://www.biorxiv.org/content/10.1101/2025.11.18.689152v1
November 21, 2025 at 12:16 AM
Humoral immunity induced by LP.8.1 monovalent vaccines against a broad range of SARS-CoV-2 variants including XEC, NB.1.8.1, XFG, and BA.3.2 https://www.biorxiv.org/content/10.1101/2025.11.18.689152v1
Reposted by DoropFan
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 5:03 AM
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. 🧵👇
Reposted by DoropFan
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
そろそろ来るかな？ S:T1117I
T1117I←もうこれほとんど棒が６本立ってるのと変わらんな……
||||||
XFY
C24912T, T4714C, C6543T
NB.1.8.1
C22995C, C24912T, G25352T, C24990T
XFG.5.1.4
C22995C, C2485T, C6543T, C24990T
XFG.22
C24912T, C449T, G24434T
T1117I←もうこれほとんど棒が６本立ってるのと変わらんな……
||||||
XFY
C24912T, T4714C, C6543T
NB.1.8.1
C22995C, C24912T, G25352T, C24990T
XFG.5.1.4
C22995C, C2485T, C6543T, C24990T
XFG.22
C24912T, C449T, G24434T
November 1, 2025 at 12:29 AM
そろそろ来るかな？ S:T1117I
T1117I←もうこれほとんど棒が６本立ってるのと変わらんな……
||||||
XFY
C24912T, T4714C, C6543T
NB.1.8.1
C22995C, C24912T, G25352T, C24990T
XFG.5.1.4
C22995C, C2485T, C6543T, C24990T
XFG.22
C24912T, C449T, G24434T
T1117I←もうこれほとんど棒が６本立ってるのと変わらんな……
||||||
XFY
C24912T, T4714C, C6543T
NB.1.8.1
C22995C, C24912T, G25352T, C24990T
XFG.5.1.4
C22995C, C2485T, C6543T, C24990T
XFG.22
C24912T, C449T, G24434T
Reposted by DoropFan
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
Untargeted longitudinal ultra deep metagenomic sequencing of wastewater provides a comprehensive readout of expected and unexpected viral pathogens
Wastewater surveillance has become a powerful tool to monitor circulating viruses at a community level. Currently, most wastewater surveillance efforts use target-based approaches such as quantitative...
www.medrxiv.org
October 31, 2025 at 12:19 PM
Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
That is the question we asked in our latest pre-print.
Turns out you can.
1/
www.medrxiv.org/content/10.1...
Reposted by DoropFan
There was only one respiratory virus that was present year-round. You guessed it, SARS-CoV-2.
It’s still here.
9/
It’s still here.
9/
October 31, 2025 at 12:19 PM
There was only one respiratory virus that was present year-round. You guessed it, SARS-CoV-2.
It’s still here.
9/
It’s still here.
9/
Reposted by DoropFan
The final published version of this study is now available in Journal of Virology at journals.asm.org/doi/10.1128/...
Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants | Journal of Virology
This study measures how mutations to the spike of a SARS-CoV-2 variant that circulated
in early 2025 affect its function and recognition by both the polyclonal antibodies
produced by the human immune ...
journals.asm.org
October 14, 2025 at 4:22 PM
The final published version of this study is now available in Journal of Virology at journals.asm.org/doi/10.1128/...
October 12, 2025 at 11:50 AM
Reposted by DoropFan
Identification and characterization of a SARS-CoV-2 Mpro G23 deletion ensitrelvir-resistant mutant https://www.biorxiv.org/content/10.1101/2025.09.30.679586v1
October 7, 2025 at 8:16 PM
Identification and characterization of a SARS-CoV-2 Mpro G23 deletion ensitrelvir-resistant mutant https://www.biorxiv.org/content/10.1101/2025.09.30.679586v1
NB.1.8.1 + ORF1a:P1640S(BA.2.75)
S:I478T(rev, S:T1117I, S:V1264L
2 seq (Korea, Japan)
シーケンスが少ないからこれだけ変異しても隠れられていたと
日本がんばって～
nextstrain.org/fetch/genome...
cov-spectrum.org/explore/Asia...
S:I478T(rev, S:T1117I, S:V1264L
2 seq (Korea, Japan)
シーケンスが少ないからこれだけ変異しても隠れられていたと
日本がんばって～
nextstrain.org/fetch/genome...
cov-spectrum.org/explore/Asia...
October 3, 2025 at 10:31 AM
NB.1.8.1 + ORF1a:P1640S(BA.2.75)
S:I478T(rev, S:T1117I, S:V1264L
2 seq (Korea, Japan)
シーケンスが少ないからこれだけ変異しても隠れられていたと
日本がんばって～
nextstrain.org/fetch/genome...
cov-spectrum.org/explore/Asia...
S:I478T(rev, S:T1117I, S:V1264L
2 seq (Korea, Japan)
シーケンスが少ないからこれだけ変異しても隠れられていたと
日本がんばって～
nextstrain.org/fetch/genome...
cov-spectrum.org/explore/Asia...
Reposted by DoropFan
In Western Australia BA.3.2 has been around longer, but maybe we will see PE.1.4 and BA.3.2 competing against each other there soon.
September 25, 2025 at 1:01 PM
In Western Australia BA.3.2 has been around longer, but maybe we will see PE.1.4 and BA.3.2 competing against each other there soon.
Reposted by DoropFan
Attenuation of the SARS-2 furin-cleavage site (FCS) continues apace. It's beginning to look as if some form of FCS-weakening mutation might well become fixed in the near future. Collectively, they are at ~12% globally—a totally unprecedented level—& rising quickly. 1/4
September 25, 2025 at 11:57 PM
Attenuation of the SARS-2 furin-cleavage site (FCS) continues apace. It's beginning to look as if some form of FCS-weakening mutation might well become fixed in the near future. Collectively, they are at ~12% globally—a totally unprecedented level—& rising quickly. 1/4
Reposted by DoropFan
Reposted by DoropFan
VSA-2, a novel plant-derived adjuvant for SARS-CoV-2 subunit vaccine https://www.biorxiv.org/content/10.1101/2025.09.22.677856v1
September 25, 2025 at 2:17 AM
VSA-2, a novel plant-derived adjuvant for SARS-CoV-2 subunit vaccine https://www.biorxiv.org/content/10.1101/2025.09.22.677856v1
Reposted by DoropFan
"Je déclare que la France reconnaît aujourd'hui l'État de Palestine."
➡️ La #France, par la voix d'Emmanuel #Macron, a reconnu, ce lundi à l'ONU, l'État de #Palestine lors d'un sommet organisé par Paris et Riyad sur la solution à deux États.
➡️ La #France, par la voix d'Emmanuel #Macron, a reconnu, ce lundi à l'ONU, l'État de #Palestine lors d'un sommet organisé par Paris et Riyad sur la solution à deux États.
September 22, 2025 at 7:52 PM
"Je déclare que la France reconnaît aujourd'hui l'État de Palestine."
➡️ La #France, par la voix d'Emmanuel #Macron, a reconnu, ce lundi à l'ONU, l'État de #Palestine lors d'un sommet organisé par Paris et Riyad sur la solution à deux États.
➡️ La #France, par la voix d'Emmanuel #Macron, a reconnu, ce lundi à l'ONU, l'État de #Palestine lors d'un sommet organisé par Paris et Riyad sur la solution à deux États.
Reposted by DoropFan
BA.3.2.* rebounded to 10% in the wastewater, so a further +440 to my estimated BA.3.2.* infections in Perth. That takes my estimated total past 2,100.
Meanwhile, a possible BA.3.2 / NB.1.8.1 recombinant was shared in the clinical sample data from WA ... very worrying if true ...
Meanwhile, a possible BA.3.2 / NB.1.8.1 recombinant was shared in the clinical sample data from WA ... very worrying if true ...
September 19, 2025 at 8:06 AM
BA.3.2.* rebounded to 10% in the wastewater, so a further +440 to my estimated BA.3.2.* infections in Perth. That takes my estimated total past 2,100.
Meanwhile, a possible BA.3.2 / NB.1.8.1 recombinant was shared in the clinical sample data from WA ... very worrying if true ...
Meanwhile, a possible BA.3.2 / NB.1.8.1 recombinant was shared in the clinical sample data from WA ... very worrying if true ...
Reposted by DoropFan
EPI_ISL_20175638 is the first possible recombinant with Jn.1 if real and not artifact or contamination or coinfection it would be BA.3.2.2/NB.1.8.1/BA.3.2.2/NB.1.8.1 getting from 245 to 439 in the spike from NB.1.8.1 and getting back orf7ab/Orf8 and acquiring Orf9b:I5T all from NB.1.8.1
September 17, 2025 at 11:31 AM
EPI_ISL_20175638 is the first possible recombinant with Jn.1 if real and not artifact or contamination or coinfection it would be BA.3.2.2/NB.1.8.1/BA.3.2.2/NB.1.8.1 getting from 245 to 439 in the spike from NB.1.8.1 and getting back orf7ab/Orf8 and acquiring Orf9b:I5T all from NB.1.8.1
XFG.5.1.1(S:A688V) + S:V642G, S:L822F(1 seq)
S:A688*変異にS:V642Gって相性いい？
BA.3.2(S:A688D)
BQ.1.1.1(S:A688T)
S:A688*変異にS:V642Gって相性いい？
BA.3.2(S:A688D)
BQ.1.1.1(S:A688T)
September 15, 2025 at 12:05 AM
XFG.5.1.1(S:A688V) + S:V642G, S:L822F(1 seq)
S:A688*変異にS:V642Gって相性いい？
BA.3.2(S:A688D)
BQ.1.1.1(S:A688T)
S:A688*変異にS:V642Gって相性いい？
BA.3.2(S:A688D)
BQ.1.1.1(S:A688T)
XFG系統で発生回数はそれなりにあるのになかなか広がらないS:V642G
XFG.4 + S:V642G 3seq(Romania 2, England 1)
cov-spectrum.org/explore/Worl...
Romaniaで感染者数が低い水準でも増加傾向なのとシーケンスの少なさ
2seqながらも日付と親から獲得している変異の違いを考えると広がっている可能性も
www.digi24.ro/stiri/actual...
XFG.4 + S:V642G 3seq(Romania 2, England 1)
cov-spectrum.org/explore/Worl...
Romaniaで感染者数が低い水準でも増加傾向なのとシーケンスの少なさ
2seqながらも日付と親から獲得している変異の違いを考えると広がっている可能性も
www.digi24.ro/stiri/actual...
September 4, 2025 at 8:29 AM
XFG系統で発生回数はそれなりにあるのになかなか広がらないS:V642G
XFG.4 + S:V642G 3seq(Romania 2, England 1)
cov-spectrum.org/explore/Worl...
Romaniaで感染者数が低い水準でも増加傾向なのとシーケンスの少なさ
2seqながらも日付と親から獲得している変異の違いを考えると広がっている可能性も
www.digi24.ro/stiri/actual...
XFG.4 + S:V642G 3seq(Romania 2, England 1)
cov-spectrum.org/explore/Worl...
Romaniaで感染者数が低い水準でも増加傾向なのとシーケンスの少なさ
2seqながらも日付と親から獲得している変異の違いを考えると広がっている可能性も
www.digi24.ro/stiri/actual...