Thread by @LucyvanDorp

Our paper on the emergence of genomic diversity and recurrent mutations in #SARSCoV2 is now out in #IGE tinyurl.com/yb4mxhes As with many others, we’ve been working hard tracing the evolution of #SARSCoV2 using thousands of genomes 🧬shared on @GISAID. Here's what we found👇/1

Here we analyse >7500 viral genomes from all around the 🗺️ We show that the time of the host-jump of #SARSCoV2 into humans dates to late last year, consistent with estimates by several others

Genetic data shows #SARSCoV2 only recently started infecting us & was detected fast. /2

Around the world we see large amounts of regional genetic diversity with marked & repeated intros to many countries

Eg. we place genomes sampled from UK patients throughout the global tree. There is no such concept as a patient zero (see @nextstrain also for visualisations) /3

Finally we screened for regions of the genome that tend to vary, focusing in particular on sites which have appeared multiple times independently ➡️ #homoplasies

These can signpost convergent #evolution but may also arise from recombination or sequencing/assembly artefacts /4

We therefore performed strict filtering (see paper) to identify a list of homoplasies that warrant further investigation🔎 Some sites fall within known epitopes and/or structural regions, others are hypervariable & some may yet result from to be determined sequencing artefacts /5

We hope our list of recurrent mutation candidates will provide a platform for further investigation into the nature of these changes & what they mean for our understanding of #SARSCoV2 adaptive evolution.

We will continue to monitor these sites aided by 📈data & raw seq reads /6

This work was only possible thanks to the contributions of many around the world uploading data & also because of the extraordinary effort of all co-authors (not all on Twitter) who dropped their ongoing projects to help out on this real (and almost real-time) team effort /7

Thanks in particular to @misac42 Damien @liampshaw and to Charlotte @louiseormond @ChrisJ_Owen @JuanitaPang @CedricCSTan1 @FlorenciaTetta1 Arturo @BallouxFrancois @UGI_at_UCL 🌟/8