Along the way, we discuss a few important topics:
- Approaches to sequencing arboviruses (Box 1)
- Discrete phylogenetic approaches for determining arbovirus transmission histories (Box 2, 👇 )
- How to deal with sampling biases (main text)
- Future directions of using phylogenetics (conclusions)

Finally, we discuss integrating ecological and epidemiological covariate data into the phylodynamic framework to discover the complex drivers of transmission and spread.

We then detail how using phylodynamic tools, including phylogeography, can reveal detailed patterns of spillovers from sylvatic cycles (e.g. below) and invasion into new regions.

We highlight how arbovirus genetic diversity can better inform classification & within-species dynamics and how some simple phylogenetic methods can help to answer important questions about virus emergence and spread.

Arboviruses are highly diverse in terms of virus families / genome structures and types of vectors and hosts. We tried to draw upon as many different examples as possible and learned a ton about some less studied viruses along the way! (e.g. Toscana and bluetongue are some of my new favs).

Interested in using phylogenetics to study arboviruses? Our new review in @natrevgenet.nature.com‬ by @viralverity.bsky.social‬, @sdellicour.bsky.social‬, and Marta Giovanetti has you covered!

📖 👉 rdcu.be/epH2U

Short 🧵

What a sequence

🤯

Sharing our work expanding SARS-CoV-2 style tiled amplicon sequencing for whole bacteria genomes directly from clinical samples, showing examples with M.tb (>4 mb) and Strep pneumo (>2 mb).

Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...

Unfortunately, this is my house right now

For transparency - here is everything that I said to @cofford.bsky.social - who wrote this very good article.

While i think that the names are mostly "silly and pompous", I don't think that this will really have much impact either way. Annoying, but meh.

Lab decorated the lab with sleigh of Handsome Dans 🎅

Pre-dinner cocktails: cranberry aperol spritz and cider mimosas.

After dinner: Apple pie old fashioneds using the infused bourbon in the jar.

Cheers!

Drop us a line if you have any questions, suggestions - or just want to collaborate.

dengue-lineages.org/contact.html

We also have several other resources:

Designate a new lineage: dengue-lineages.org/design.html

Track existing lineages: dengue-lineages.org/lineages.html

Genome surveillance resources: dengue-lineages.org/resources.html

You can assign lineages to your sequences using several tools that are available on our website.

Our system splits previously defined dengue virus serotypes and genotypes into major and minor lineages to better enable tracking and characterization of genetic diversity.

If you do dengue virus sequencing +/- phylogenetic analysis, check out our new system for classifying lineages.

Led by Verity Hill, this was a large collaborative effort by dengue researchers from 14 countries.

Paper -> journals.plos.org/plosbiology/...

Website-> dengue-lineages.org