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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this...
https://science.sciencemag.org/content/early/2021/01/07/science.abf2946

Louis du Plessis @laduplessis - Fri Jan 08

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/…

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Louis du Plessis @laduplessis - Fri Jan 08

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

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Louis du Plessis @laduplessis - Fri Jan 08

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

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Louis du Plessis @laduplessis - Fri Jan 08

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

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Louis du Plessis @laduplessis - Fri Jan 08

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

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Louis du Plessis @laduplessis - Fri Jan 08

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

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Louis du Plessis @laduplessis - Fri Jan 08

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

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Louis du Plessis @laduplessis - Fri Jan 08

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_…

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Louis du Plessis @laduplessis - Fri Jan 08

Thanks to @EvolveDotZoo, @McCroneIV, @aezarebski, @viralverity, @Chris3Ruis, @arambaut, @MOUGK and many many others for all their hard work on this project!

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Trevor Bedford @trvrb - Fri Jan 08

@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!

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Louis du Plessis @laduplessis - Fri Jan 08

@B_Gutierrez_G @jnaraghwani @_jordanash @rmcolq @tomrconnor @nmrfaria Ben Jackson @pathogenomenick @AineToole @samstudio8 @krisparag1 @DrEmilyScher @TanyaVasylyeva @erikmvolz @daanensen Alexander Watts @BogochIsaac Kamran Khan

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Louis du Plessis @laduplessis - Fri Jan 08

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! end;

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Andrew Rambaut 🦠🧬🌲🔮🤦‍♂️ @arambaut - Fri Jan 08

@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

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Andrew Rambaut 🦠🧬🌲🔮🤦‍♂️ @arambaut - Fri Jan 08

@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…

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Kristian G. Andersen @K_G_Andersen - Fri Jan 08

@laduplessis @evogytis @ScienceMagazine Big fan - awesome study! 👏

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Christophe Fraser 💙 @ChristoPhraser - Fri Jan 08

@laduplessis @ScienceMagazine Great study, congrats to you and whole team. Control of epidemics requires quick action, early.

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Jeremy Kamil @macroliter - Fri Jan 08

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! 👏👏👏 science.sciencemag.org/content/early/…

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Science Magazine @ScienceMagazine - Fri Jan 08

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/80xh10w pic.twitter.com/9K61AHsm2R

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Lauring Lab @LauringLab - Fri Jan 08

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/…

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Roland Baker @RolandBakerIII - Fri Jan 08

Rapid fluctuations in virus importation rates resulted in >1000 lineages Science: Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK science.sciencemag.org/content/early/…

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Ben Sheldon @Ben_Sheldon_EGI - Fri Jan 08

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/…

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