musicaljoke
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TRAVIS BEDFORD
Genomic sequencing of viruses from the #COVID19 pandemic can help reveal transmission patterns. Thanks to data sharing through @GISAID from groups all over the world, @nextstrain is now showing 1882 #SARSCoV2 genomes. This is an update on a few aspects of what we're seeing. 1/14
Trevor Bedford on Twitter
To begin, Washington State has had 354 viruses sequenced (out of 453 in the US). Here we see that the large majority (83%) of sequenced viruses from Washington State appear to descend from a single introduction event in late Jan or early Feb. auspice 5/14 Trevor Bedford on Twitter
This transmission chain has gotten big enough to throw off its own sparks, with sequenced viruses showing up elsewhere in the US, Australia and Iceland. auspice 6/14 Trevor Bedford on Twitter
Sequenced cases from elsewhere in the US and Canada are sometimes related to this transmission chain, but most (77%) derive from separate more numerous and smaller introductions. However, it's possible that further sequencing of other regions will change this picture. 7/14 Trevor Bedford on Twitter
Next up, 201 genomes from the United Kingdom. These show a different pattern in which there are multiple clusters of related viruses, suggesting repeated introductions into the country followed by local spread. auspice 8/14
Trevor Bedford on Twitter
As you might expect, viruses from the UK show close genetic relationships to viruses from elsewhere in Europe indicating frequent mixing between the two regions.
9/14
Iceland has just released 334 virus genomes that are spread throughout the world's diversity and appear to represent a large number of recent separate introductions. auspice 10/14
Trevor Bedford on Twitter
For example, as expected, viruses sampled in Iceland from people with travel history to the United States group with viruses from the US. This can be seen as the red (US) branches leading to (blue) Iceland viruses here. 11/14 Trevor Bedford on Twitter
Generally, we see large regional transmission chains when there was an introduction that got successfully underway in late Jan or early Feb and much more mixed transmission of recent introductions from the growing pandemic. 12/14
Oh wow, it is absolutely fascinating how they can trace transmission chains. I wish that I had paid more attention in biology class.