Alli Black

Busy day on B.1.1.529 - a variant of great concern - The world should provide support to South Africa and Africa and not discriminate or isolate it! By protecting and supporting it, we will protect the world! A plea for billionaires and financial institutions. 1/8 tweets

@dmaccannell @firefoxx66 And just to note, that delta focal build is a HUGE Nextstrain tree but still represents a fraction of delta sequences. That means that there will be more cases of those delta viruses with 69/70 dels than there are tips showing that pattern in the tree.

@dmaccannell @firefoxx66 All those yellow tips are 69/70 dels that cluster phylogenetically within Delta. That phylogenetic clustering is key. While Pango won't call a lineage that hasn't been assigned yet, those 69/70 dels are way more closely related to other delta viruses than to omicron.

I can't comment on the plausibility of European origin, although I have seen similar conjecture. I'd happily take bets on whether omicron was circulating at low-levels in Minnesota and New York over the summer, however. Especially enough to cause a blip.

And the CDC job posting here: usajobs.gov/GetJob/ViewDet… 3/3

You can see the CZB job posting here: apply.workable.com/czbiohub/j/75D… 2/3

Hey genomic epi friends, looking for jobs? There is a position open on the capacity building side of genepi @czbiohub, and @adam_retchless lab at CDC is looking for a genomic epi to support SCV2 analysis! cc: @IDDjobs @Epijobs 1/3

As always, this work is the result of an enormous collaborative effort (see the Acknowledgements!). I'm very grateful that I get to support such meaningful work, and collaborate with fantastic people. /7

The take home message? Genomic surveillance is super useful at the local level. I'm thrilled about investments in genomic surveillance at the federal and state levels. We should also support extending that infra to other levels of jurisdictional authority. /6

Our paper describing how we've used genomic epidemiology to guide public health action in Humboldt County CA is up on medrxiv! medrxiv.org/content/10.110… /1

My amazing labmate @huddlej is defending his PhD on Monday Dec 7, 10am PST! In addition to doing really cool work forecasting flu, he also is a data viz nerd and gives great talks. So it's gonna be awesome. DM me if you want the Zoom link.

#OpenData & #OpenScience have been critical for allowing lightning-fast research on #SARSCoV2 #COVID19 during this pandemic. But making that data useful & accessible isn't easy! Led by @griffiemma, a fantastic outline of @pha4ge efforts to improve this! preprints.org/manuscript/202…

While I'm incredibly proud of this paper, I note that it's a starting point. I look forward to working as a part of this community to help bring this ecosystem to fruition.

And a huge thank you to everyone who participated in the long-form interviews and who discussed these recommendations at length at meetings.

Our paper describing ten recommendations for supporting open pathogen genomic analysis in public health is out today in Nature Medicine! nature.com/articles/s4159…