After many months of hard work our analysis of the lineage structure and importation dynamics of the first wave of the #SARSCoV2 epidemic in the UK is out in @ScienceMagazine today! science.sciencemag.org/content/early/…
We use >50K genomes, 26K from the UK (thanks to @CovidGenomicsUK) representing ~10% of UK cases in the 1st wave, but still only ~0.5% of all estimated infections. Nonetheless this is a level of surveillance much higher than we’re used to and allows for unprecedented insights. pic.twitter.com/8tB1owxySc
We detect >1000 independently-introduced UK transmission lineages. However we expect this number to be an underestimate. Transmission lineage sizes follow a power-law distribution with the biggest 20% accounting for >75% of all UK genomes in our dataset. pic.twitter.com/ooMJPlM7Vo
Where do all these lineages come from and what does it mean? Pre-lockdown high travel volumes and few restrictions on arrivals coincided with growing epidemics in Europe, jointly contributing to accelerating the growth of the UK epidemic to exceed contact tracing capacity. pic.twitter.com/ubOrsS4xWD
We combined these 2 trends to generate an estimated importation intensity (EII) - an empirical measure of the intensity of #SARSCoV2 importation into the UK - which peaks in mid-March, before the national lockdown. pic.twitter.com/GaTVyRFzwl
By combining country-specific EIIs with genomic data and a statistical model we show that the rate and source of introductions changed rapidly through time. In total we find most lineages were imported from Spain, France and Italy, with China only accounting for a tiny minority. pic.twitter.com/2L3PHt82bL
The rate of imports slowed after lockdown, but we find earlier lineages were larger, more dispersed and harder to eliminate, highlighting the importance of rapid or pre-emptive interventions. Overdispersion in transmission likely led to even greater survival of larger lineages. pic.twitter.com/2rRNReUeru
We expect similar trends occurred in other countries with large epidemics and high travel volumes. These results and methods are changing our understanding of the lineage dynamics of epidemics and are already being used to track the spread of new variants: cov-lineages.org/global_report_…
@laduplessis @EvolveDotZoo @McCroneIV @aezarebski @viralverity @Chris3Ruis @arambaut @MOUGK Amazing work with this. And satisfying to get to watch the science develop from Virological post to preprint to published paper. Thank you!
Lastly, this wouldn’t have been possible without the hard work of hundreds of people working for @CovidGenomicsUK, sequencing 1000s of genomes/week. Most are on fixed-term contracts and have been working overtime since March. Really fantastic effort from them!
@laduplessis @ScienceMagazine Some amazing work has gone into this and one part I would like to highlight is the adaptation of BEAST to work on trees of this scale by @McCroneIV. He has even written a very nice tutorial on how to do it: beast.community/thorney_beast
@laduplessis @ScienceMagazine @McCroneIV The approach (a fast approximate likelihood) dates back to 1962 and a seminal paper by Zuckerkandl and Pauling but also the evergreen multidivtime by Jeff Thorne and some recent work by @XavierDidelot doi.org/10.1093/nar/gk…
Virologist, Associate Professor @LSUHS. I study human cytomegalovirus. (he, him). Opinions my own, not my employer's. #LoveVirology
Such an absolutely fantastic paper by @EvolveDotZoo @arambaut @AineToole & coworkers. Although I've helped ramp up sequencing of SARS-CoV-2, these types of analyses need to be done by the experts! 👏👏👏
An analysis of @CovidGenomicsUK & other #SARSCoV2 genomic data shows the virus was introduced to the United Kingdom over 1,000 times in early 2020. The rate & source of introduction of the virus changed quickly. @laduplessis @MOUGK @arambaut @EvolveDotZoo fcld.ly/80xh10wpic.twitter.com/9K61AHsm2R
Virologist and Infectious Diseases physician at the University of Michigan. Proud father of 3. Opinions are my own.
Fantastic work and super proud of former student @McCroneIV. >50,000 genomes and >25,000 from UK. I remember a few years back when we thought his study of 249 influenza viruses was a big dataset. science.sciencemag.org/content/early/…
Hugely timely large scale genomic analysis of the first wave of the pandemic in the UK from Louis du Plessis @arambaut @EvolveDotZoo and many others. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK science.sciencemag.org/content/early/…