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
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...
Reposted by DoropFan
Uncovering the Hidden Yeast Diversity in Fermented Coffee: Insights from a Shotgun Metagenomic Approach https://www.biorxiv.org/content/10.1101/2025.09.01.673590v1
September 2, 2025 at 4:18 AM
Uncovering the Hidden Yeast Diversity in Fermented Coffee: Insights from a Shotgun Metagenomic Approach https://www.biorxiv.org/content/10.1101/2025.09.01.673590v1
XEC.27.2 + S:K478T(rev (6 seq, 3 countries)
T6763C, C22995C, C26028T
cov-spectrum.org/explore/Worl...
nextstrain.org/fetch/genome...
メキシコの1seqがミステリー
ORF7a:I100Vの枝からORF1ab:T1429K, ORF1ab:L1434Fを持っていて
ORF7a:I100Vを欠いていて
S:K182Nの別の枝のT6763C, S:K478Tを持っている
T6763C, C22995C, C26028T
cov-spectrum.org/explore/Worl...
nextstrain.org/fetch/genome...
メキシコの1seqがミステリー
ORF7a:I100Vの枝からORF1ab:T1429K, ORF1ab:L1434Fを持っていて
ORF7a:I100Vを欠いていて
S:K182Nの別の枝のT6763C, S:K478Tを持っている
August 25, 2025 at 5:38 AM
XEC.27.2 + S:K478T(rev (6 seq, 3 countries)
T6763C, C22995C, C26028T
cov-spectrum.org/explore/Worl...
nextstrain.org/fetch/genome...
メキシコの1seqがミステリー
ORF7a:I100Vの枝からORF1ab:T1429K, ORF1ab:L1434Fを持っていて
ORF7a:I100Vを欠いていて
S:K182Nの別の枝のT6763C, S:K478Tを持っている
T6763C, C22995C, C26028T
cov-spectrum.org/explore/Worl...
nextstrain.org/fetch/genome...
メキシコの1seqがミステリー
ORF7a:I100Vの枝からORF1ab:T1429K, ORF1ab:L1434Fを持っていて
ORF7a:I100Vを欠いていて
S:K182Nの別の枝のT6763C, S:K478Tを持っている
August 25, 2025 at 5:30 AM
Reposted by DoropFan
From The Atlantic, “COVID Revisionism Has Gone Too Far” www.msn.com/en-us/news/w...
And the pendulum swings…
And the pendulum swings…
MSN
www.msn.com
August 22, 2025 at 4:36 AM
From The Atlantic, “COVID Revisionism Has Gone Too Far” www.msn.com/en-us/news/w...
And the pendulum swings…
And the pendulum swings…
Reposted by DoropFan
Phenomenal work here.
I'm curious about the very small number of exceptions to this—non-RBD mutations that increase Ab evasion & ACE2 binding. For RBD muts, this is readily explainable. Any ideas how non-RBD mutations might achieve this?
Three in particular interest me: T22N, L629V, & A852K. 1/7
I'm curious about the very small number of exceptions to this—non-RBD mutations that increase Ab evasion & ACE2 binding. For RBD muts, this is readily explainable. Any ideas how non-RBD mutations might achieve this?
Three in particular interest me: T22N, L629V, & A852K. 1/7
August 21, 2025 at 10:54 AM
Phenomenal work here.
I'm curious about the very small number of exceptions to this—non-RBD mutations that increase Ab evasion & ACE2 binding. For RBD muts, this is readily explainable. Any ideas how non-RBD mutations might achieve this?
Three in particular interest me: T22N, L629V, & A852K. 1/7
I'm curious about the very small number of exceptions to this—non-RBD mutations that increase Ab evasion & ACE2 binding. For RBD muts, this is readily explainable. Any ideas how non-RBD mutations might achieve this?
Three in particular interest me: T22N, L629V, & A852K. 1/7
Reposted by DoropFan
A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells https://www.biorxiv.org/content/10.1101/2025.08.15.670620v1
August 19, 2025 at 3:16 AM
A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells https://www.biorxiv.org/content/10.1101/2025.08.15.670620v1
covspectrumで見たい変異が検索でヒットしないなーと思ったら全体の数がこんなことに…
データ更新中かな？
データ更新中かな？
August 17, 2025 at 2:30 AM
covspectrumで見たい変異が検索でヒットしないなーと思ったら全体の数がこんなことに…
データ更新中かな？
データ更新中かな？