The COG-UK weekly reports are now getting posted up on the COVID-19 Genomics UK (COG-UK) Consortium site. The first report was back on 23rd March, 11 days after first meeting! Back then we saw a greater diversity of international lineages in UK, reflecting the multiple imports: cogconsortium.uk/wp-content/upl…

What?! What a terrible idea to terminate research funding on bat coronaviruses now... I am disappointed that such a decision was made by the NIH, likely under political pressure... sciencemag.org/news/2020/04/n…

#RECOMB2020 will take place entirely virtually on June 22-25, 2020, with required registration (at the link recomb2020.org/registration ) but no registration fee. More info on schedule and refunds at our website recomb2020.org .

I'm still not over the amazing work presented in mmbr.asm.org/content/84/2/e… and now accepted by ICTV (talk.ictvonline.org) to achieve a (near-complete) unification of viral taxonomy. This included coming up with (many) meaningful new names. Some of my favorites:

It's live! After years of work and more than 16 months in peer review, the gnomAD package is now up at Nature. We have seven papers in total, exploring different scientific aspects of this collection of more than 140,000 exomes and genomes: nature.com/collections/af…

I'll have tweets later in the day about the science that went into this package, but here are some excellent summaries: Broad Institute coverage: broadinstitute.org/news/internati… Great News and Views piece by Deanna Church (she/her): nature.com/articles/d4158… Nature editorial: nature.com/articles/d4158…

Massive thanks and congratulations to all of the lead authors on this collection of papers - Konrad Karczewski, Eric Vallabh Minikel, Beryl Cummings, Ryan Collins, Nicky Whiffin, Qingbo Seiha Wang, Irina Armean, PhD, Aaron Kleinman, and Harrison Brand.

As well as to everyone else who made this project possible, expecially Jessica Alfoldi, Laurent Francioli, Grace Tiao, Matthew Solomonson, Nick Watts, Ben Weisburd, Kristen Laricchia, and the teams from Broad DSP and Hail.

The gnomAD team are data parasites - we are completely dependent on the generosity of principal investigators willing to share their data from independent research projects. Without the 109 (!) PIs who donated data to this project there would be no gnomAD: gnomad.broadinstitute.org/about

It's been a long journey from the first inception of a new data aggregation database in 2012, through the creation of ExAC and gnomAD, to this moment. Here's a blog post covering some of the highlights: macarthurlab.org/2020/05/27/the…

Finally, as I settle into my new role in Australia, I am delighted to have left gnomAD leadership at Broad Institute in the very safest of hands - new co-directors Mark Daly and Heidi Rehm. Looking forward to working with them on many future data releases and much cool science!

And let’s not forget the false positives. Technically RTPCR is highly specific, but in the real world false positives happen. If we go with a conservative estimate of 0.8%, when we test the 71,000 students and staff, we’ll expect 568 false positives. 14/ medrxiv.org/content/10.110…

It's not been an easy ride by any means, but very proud of what COVID-19 Genomics UK (COG-UK) Consortium have achieved in a short timescale: article in The Lancet Microbe today describes the distributed and diverse sequencing and analysis model we chose for genomics of SARS-CoV-2: thelancet.com/journals/lanmi…

Despite the catchy headline, the mandate of the CDC is far broader than pandemics, and the problems at the CDC precede COVID-19. But yes, the response to the COVID-19 pandemic was deeply flawed and systemic 1/ nytimes.com/2020/06/03/us/…

New blogpost: The Octopaper 🐙 Eight papers with the same survival curves, table values, and similar line graphs. But published in different journals by different authors, at different institutes, on different patients, and different cancers. scienceintegritydigest.com/2020/06/03/the…

Really important point. Spread of a highly infectious virus won't stop until most people are immunized either through infection or a vaccine. The ~50% compliance we get with flu vaccines won't come close to cutting it

4 Ways That Scientists And Academics Can Effectively Combat Racism These four steps, as limited as they are, can play a major role in transforming science and academia into a safer, more inclusive environment. forbes.com/sites/startswi…

Finally, a plea again for solidarity - this a "humans vs the virus" situation - it is not about countries, less so even groups inside a country. Very simply we want to eliminate the virus or live comfortably alongside it. We should stay focused on that goal.

We developed a new method, CoronaHiT, for sequencing up to 95 SARS-CoV-2 genomes on a Oxford Nanopore MinION flowcell for our COVID-19 Genomics UK (COG-UK) Consortium work. Cheap and easy - using nextera and PCR barcoding of ARTIC Network PCR products. biorxiv.org/content/10.110… Dave Baker Andrew Page @andrewjpage.bsky.social

Agree, we do have therapeutics and vaccines on the way and testing will continue to expand. But we need to be smart, and we are going to need disciplined public health behaviors for months not weeks