BELGIUM Genomic Surveillance: New update(10/5/23) Recombinant mix in Belgium: ➡️ XBB.* dominant variant ➡️ XBB.1.5📉 ➡️ XBB.1.9 📉 ➡️ XBB.1.16📈 ➡️Other variants/XBB* 📈-> is this partly XBB.2.3* ➡️The new incoming battle in Belgium: XBB.1.16/XBB.2.3*(Cov-Spectrum/ Nextclade

🌈CoVariants.org Update!🌈 The eagle-eyed among you may have already spotted, but we've just added a new feature - translations! Check out the top-right corner for a drop-down menu that translates many labels automatically, & more fully supports Chinese! 🙌🏻📖 1/5

A *huge* thank you to Ivan Aksamentov for implementing this feature, and to Tony Qu for suggesting this & for translating everything into Chinese! 🙏🏻🇨🇳 We hope this makes CoVariants.org even more accessible to people around the world!🌏 2/5

Based on their prevalence and rate of growth, we've designated 3 new Nextstrain clades from @PangoNetwork lineages: 23G (XBB.1.5.70) 23H (HK.3) 23I (BA.2.86) 1/9

After many months of work, we are releasing Nextclade v3 with major changes: - Splicing, slippage, and circular genomes - Local tree-building - Auto-suggestion of suitable datasets - Align more divergent sequences - Community datasets clades.nextstrain.org (desktop only) 1/9

3) The growth advantage estimates are shown in the provided charts. The inferred growth advantage is mapped onto the Nextclade-curated phylogeny, which only includes relatively competitive variants.

Mike Honey --Neon-Newton-- As sample size reduced to 20.. 25 samples per week, it's a bit...noisy 🤪🙈 My analysis with nextclade of RKI sequence data in the graphs below (x-axis: date of sample drawing/swab). So pretty likely we hit 50% around last week to now here in Germany.

Comparing JN.1* (Nextclade) + S:F456L vs. JN.1* (Nextclade) + S:R346T vs. JN.1* (Nextclade) + S:T572I vs. JN.1* (Nextclade) + S:S31-

Marc Johnson Here's the Nextclade nucleotide view.

To be clear: despite the bad FDA decision, we all should still 100% get the vaccine. It's still a big improvement over the XBB.1.5 shot. Single mutations can have big effects, but for perspective, see Nextclade visualizations for the S1 of WT, BA.5, XBB.1.5, JN.1, & KP.3.1.1 👇

Data from the human H5N2 case from Mexico are now available on GISAID. Here's an HA tree built using Nextclade, with all human H5 cases from GISAID highlighted. Unsurprisingly, this seq belongs to the Am-nonGsGd clade, and is very distinct from the dairy cattle outbreak in the US

Thanks to work by Kim Andrews, we've recently updated our analyses and resources for measles virus. We now include automatically updated views of evolution of both the full genome at nextstrain.org/measles/genome as well as the N450 segment at nextstrain.org/measles/N450. 1/2

We also include a new Nextclade dataset to call measles genotype at clades.nextstrain.org/?dataset-name=…. This work is described on the Nextstrain blog at nextstrain.org/blog/2024-06-1….

Following a Nextclade update, a further 172 lineages are now classified. I am grouping all the JN.1.* child lineages featuring the Spike Q493E mutation into a new "Lineage L2" group: JN.1.* +FLuQE. 🧵 ends

. Ben Murrell is doing the best variant growth modeling in the world, & his latest results confirm most of what we've thought: KP.3 is the fastest large variant, & its sublineage KP.3.1.1—w/the highly advantageous, glycan-creating S:∆S31—is easily the fastest in the world. 1/15

As visuals can often be helpful in interpreting what remain, to the vast majority of people, incomprehensible letter-numbers-letter combinations, I've annotated the Nextclade spike visualization for some sequences (all uploaded today), to provide some context. 4/

Check out this recent preprint on SC2 recombinants to learn more about their detection and characterization, as well as associated challenges for public health labs! We welcome any feedback as this goes through the peer review process👩🏻‍💻