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Jun 11, 2021 7 tweets 4 min read Read on X
We have just released a new version of the Nextclade web application clades.nextstrain.org for #SARSCOV2. We now use Nextalign (C++ via wasm) under the hood, which allows for many new exacting features!

A quick tour!

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Analysis now takes a few seconds to start, but overall it has become much faster and analyzing hundreds of sequences should be no problem. You can download the reference alignments, including translations of SARS-CoV-2 genes, for further analyses.

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You can now examine the diversity of the nucleotide alignment and alignments of different proteins. Select a gene from the drop-down or click on a gene in the genome annotation panel below.

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The tooltips to explore diversity have become much more informative. For amino acid changes, we now provide a nucleotide context view that is particularly helpful for complex mutations. Consecutive changes are merged into one tooltip.

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A little icon next to the sequence tells you whether some genes of the sequence have failed to translate, either because they weren't covered or because of frame shifts.

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As before, the samples are placed on a reference tree that now includes the updated #Nextstrain clades and a diverse set of lineages.

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Brought to you by the @nextstrain team.

Share your comments and suggestions at discussion.nextstrain.org or github.com/nextstrain/nex… or reach out to @ivan_aksamentov.

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More from @nextstrain

Aug 11, 2023
Based on their frequencies and rate of growth, we've designated 4 new Nextstrain clades from @PangoNetwork lineages:
23C (CH.1.1)
23D (XBB.1.9)
23E (XBB.2.3)
23F (EG.5.1)

1/9 Image
23C (CH.1.1) is a sublineage of 22D (BA.2.75) with additional spike RBD mutations at 346T, 444T, 452R & 486S. This non-XBB lineage has persisted despite the dominance of XBB descendants.
Currently most prevalent in Australia & New Zealand, it is also growing in Europe.

2/9 Image
23D (XBB.1.9) is primarily characterized by mutations in ORF1a and ORF9b.
While it does not have S:486P, its 2 main sublineages (XBB.1.9.1 & XBB.1.9.2) do & are most common. Since the sublineages differ only by synonymous mutations, we decided to designate the parent.

3/9 Image
Read 9 tweets
Apr 24, 2023
Based on its rapid growth, particularly in Asia, we've designated the recombinant @PangoNetwork lineage XBB.1.16 & its descendants as clade 23B, labeled "23B (Omicron)" on Nextstrain trees.

Like 23A, 23B is a descendant of the recombinant 22F (XBB).

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23B (XBB.1.16) is different from 22F (XBB) primarily through 3 new Spike mutations - S:E180V; S:K478R; & S:486P (acquired independently from other XBB sublineages).
In addition, S:G252V is inherited from ancestral XBB.1



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S:486P is already known to confer an advantage as in 23A / XBB.1.5.
What sets 23B apart is the additional receptor binding domain mutation S:478R. Any potential impact of S:180V is less clear.

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Read 9 tweets
Feb 9, 2023
Based on its rapid growth in multiple geographies, we've designated the recombinant @PangoNetwork lineage XBB.1.5 & its descendants as clade 23A, labelled "23A (Omicron)" on Nextstrain trees.

23A (XBB.1.5) is a descendant of the recombinant 22F (XBB).

1/7 Image
23A (XBB.1.5) is different from 22F (XBB) primarily through 2 new Spike muts - 1 in ancestor XBB.1 (S:G252V), & 1 in 23A itself S:486S -> S:486P. This 'P' change is associated with an increased ACE2 binding, which is likely why 23A is spreading.



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You can read more about what we know about mutations at position S:486, and the S:486P mutation in particular, in this thread:



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Read 7 tweets
Nov 3, 2022
Based on its rapid growth in multiple geographies, we've designed the recombinant @PangoNetwork lineage XBB & its descendants as clade 22F, labelled "22F (Omicron)" on Nextstrain trees.

Because 22F is a recombinant, its phylogenetic placement doesn't reflect its history.

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22F/XBB is the result of a recombination between BJ.1 (BA.2.10.1.1) & BM.1.1.1 (BA.2.75.3.1.1.1) with breakpoint in S1 (first part of spike).

Recombination occurs during co-infection with 2 different variants, when parts of two different genomes end up together.

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We can see the two 'parents' of 22F/XBB on the Nextclade phylogeny - parts of each of these genomes have combined to create a variant that has unique mutations from each parent lineage.

next.nextstrain.org/nextclade/sars…

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Read 6 tweets
Oct 20, 2022
Based on its rapid growth in multiple geographies, we've designed @PangoNetwork lineage BQ.1 and descendants (most notably BQ.1.1) as clade 22E, labelled as "22E (Omicron)" on Nextstrain trees.

1/4 Image
Clade 22E (lineage BQ.1) has been growing in frequency at a rate of 0.11 per day in USA, which is equivalent to the initial growth of 22B (BA.5) in the US & UK.
5-15% of recent samples in the USA & many countries in Europe are 22E & it might soon dominate in some places.

2/4 Image
These growth dynamics, along with mutational profile, strongly suggest this clade will continue to spread widely.
Further rationale for decision to designate this clade can be found here: github.com/nextstrain/nco…

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Read 4 tweets
Jul 22, 2022
Based on sustained logistic growth in frequency in India, we've designed @PangoNetwork lineage BA.2.75 as clade 22D, labeled as "22D (Omicron)" to denote it still being considered as "Omicron variant" by @WHO. 1/4
Lineage BA.2.75 / clade 22D has been growing in frequency at a rate of 0.12 per day in India, which is equivalent to initial growth of BA.5 in the US and the UK, and is now outcompeting BA.5 in India. 2/4
These growth dynamics, along with mutational profile, strongly suggest this clade will spread widely, though it may not ultimately displace BA.5 viruses globally. Further rationale for decision to designate this clade can be found here: github.com/nextstrain/nco… 3/4
Read 4 tweets

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