Top Tweets for #NextClade
Additionally, we've updated the Nextclade datasets to appropriately call clade 23G, 23H, and 23I viruses at https://t.co/B8jU0VluU3.
If you use #Nextclade in the browser, make sure to reload the tab from time to time so that you get the most recent datasets.
8/9
Finally, if you have a #SARSCoV2 sequencing pipeline that uses the #Nextclade CLI, please *pull the latest update*, as it includes BA.2.86 & will help you quickly ID sequences.
This is also updated online if you scan sequences there!
https://t.co/F7RxloAQCi
9/9
Additionally, we've updated Nextclade datasets to appropriately call clade 23C, 23D, 23E and 23F viruses at https://t.co/B8jU0VluU3.
If you use #Nextclade in the browser, make sure to reload the tab from time to time so that you get the most recent datasets.
8/9
#SARSCoV2 Weekly #VariantDesignation Breakdown
This week there have been 36 designations
- 4 new aliases
- #NextClade lineage availability has been fully updated
#SARSCoV2 Weekly #VariantDesignation Breakdown
This past week there have been 42 designations
- 3 new aliases
- #NextClade availability: All but 2 designations
- This week saw 1,300 omicron-containing designations, and more recombinant designations than BA.2 designations
#SARSCoV2 #PhylogeneticTree for XBB, BA.2.3.20, and BQ.1
Black - Recognized by #NextClade
Red - Recently added designation
#SARSCoV2 #PhylogeneticTree for XBB
- First picture shows recently added variants.
- Second picture shows variants recognized by #NextClade
LINK: https://t.co/N4n63umME4
.@richardneher walking us through @nextstrain and #nextclade, which have now become essential tools for viral genomics/phylogeny/epidemiology (also my favorite pandemic hobby!) @vizbi
Also in the list are the much-requested @10xGenomics #CellRanger 🧫 , @CGAT_Oxford UMI-tools 🧬 and @nextstrain #Nextclade 🦠
This release has lots of new modules for long-read sequencing data, for all you @oxfordnanopore / @PacBio users 🔬
@EricTopol @RajlabN Note: this is only _predicted_ immune escape using @jbloom_lab's and @yunlong_cao's calculator using DMS data.
It only takes RBD into account, not NTD and test of Spike.
@RajlabN got the scores through Nextclade.
Actual neutralization data (available!) is much better than this.
Tracked #Convergent #lineages are predicted to be immune evasive and better ACE2 receptor binders than Omicron.BA2
Lineages to watch closely- CH.1.1*, XBB*, BM.1.1.1, CA.1, BQ.1.1*, BR.2, BN.1*
Note: Scores are from #Nextclade and predictions are based on RBD mutations.
4/n
@CorneliusRoemer @EricTopol @jbloom_lab @yunlong_cao Thanks to @CorneliusRoemer and the #LineageWatchTeam for quick lineage proposals to facilitate rapid @PangoNetwork designations.
Quick designations helped prioritize lineages for lab experiments.
This particular #Nextclade tool will help prioritize the next set to experiment!
You can hover on the bubbles and look at the partially aliased variant names (thanks to @CorneliusRoemer's #nextclade tool)
for example - CA.1 partially aliased BA.2.75.2.1
https://t.co/h8LP5wz5Rl
.@GenSpectrum has adapted to Include #nextclade pango calls immediately.
Probably @gisaid should too? #CovidTwitter #VariantHunters what say you?
None of the recently designated lineages feature is @GISAID yet especially the high flyers like XBB, BA.2.3.20, BM.1.1.1 & BQ*. GISAID Probably awaiting new @PangoNetwork release?
Most of us are using #Nextclade or Usher to make appropriate lineage calls. 1/n
@JPWeiland @JosetteSchoenma @CiscoRucinski @EllingUlrich @CorneliusRoemer Talking to different people from different backgrounds, from different regions.. nick names or group names comes handy.
Wish there were "nick names" for every clade designated by #NextClade/@nextstrain
Otherwise, we end with too many nick names and too many group names..
A plot of Immune Escape vs ACE2 Binding scores generated using the #NextClade tool (developed by
@CorneliusRoemer)
Closely watching recombinant XBB (aka #Gryphon), BM.1.1.1 (#Mimas, BA.2.75.2 (#Chiron), CA.1, BR.2, BN.1 (#Hydra), BR.3!!
A plot of Immune Escape vs ACE2 Binding scores generated using the #NextClade tool (developed by @CorneliusRoemer)
Most BA.2.75* sub-lineages have good ACE2 binding scores.
BN.1 (BA.2.75 with S:K356T, S:R346T & S:490S) is one of the lineages to watch!
@mildanalyst Austria uploaded 19322 XAS seqs in the last 3 months.. they were stuck in unassigned.
Thanks to #nextclade tool embedded in @CovSpectrum we can assign the unassigned with one simple tab click! .. @ChaoranChen_ @Asinickle1 @CorneliusRoemer @siamosolocani @nzm8qs @JosetteSchoenma
#SARSCoV2 lineages in USA (#15DayTrends)
Circulating #BA5*/#BA4* sub-lineages:
BA.5, BA.4.1, BA.5.2.1, BA.5.1, BA.4, BA.5.2, BA.5.3.1, BE.1, BF.1, BA.5.3
Assignments via: #Nextclade #PANGO - https://t.co/h2rKpc8y7K
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