Our new paper, out now in @Eurosurveillanc, looks at #COVID19 #SARSCoV2 across Europe eurosurveillance.org/content/10.280…
A major part was reconciling different nomenclatures!
Working with @GISAID & @AineToole, we created a handy reference between @nextstrain, Pangolin & GISAID!
1/8
A major part was reconciling different nomenclatures!
Working with @GISAID & @AineToole, we created a handy reference between @nextstrain, Pangolin & GISAID!
1/8
Using ~39,000 seqs from 35 WHO Europe countries (up to 10 Jul), we found an avg of 40 days btwn sample collection & GISAID submission, with 8% published in 2 wks!
We can breakdown timing by country (worth viewing in manuscript - Supp Fig 2!)
2/8
We can breakdown timing by country (worth viewing in manuscript - Supp Fig 2!)
2/8
When we look at clades/lineages over time in Europe, we see 19A, L/V/O, A (Nextstrain, GISAID, Pangolin) dominating initially, concordant w early intros from Asia. However, must be mindful of small # samples from early epidemic & poss bias in who was tested (travellers)
3/8
3/8
We can also look at clade distribution (GISAID/Nextstrain) across countries (arranged by longitude). 19B/S is relatively rare except in Spain & Kazakhstan.
We can see the distinct Spanish 19B cluster in the Nextstrain Europe builds: nextstrain.org/groups/neherla…
4/8
We can see the distinct Spanish 19B cluster in the Nextstrain Europe builds: nextstrain.org/groups/neherla…
4/8
#Opendata #openscience has been critical to tracking #SARSCoV2 #COVID19. Since 10 Jul (our cutoff) another ~10,000 Europe seqs have been added!
Continued sequencing & supporting increased sequencing in countries w fewer seqs will help understand spread & impact of responses
5/8
Continued sequencing & supporting increased sequencing in countries w fewer seqs will help understand spread & impact of responses
5/8
Inferences are limited by sequencing delays & low # of seqs from some countries - we can get a more complete picture of #SARSCoV2 transmission in Europe, impacts of responses, & seasonal changes if we try to support more equal coverage
6/8
6/8
Further, in the future, rapid sequencing will enable real-time tracking, as well as real-time monitoring for mutations impacting future antiviral drugs & vaccines. Countries will also be able to better understand their own epidemics!
7/8
7/8
This work was a collaboration with a *huge* number of labs across Europe. However in particular this work was led by: @ECDC_EU @ErikAlm13 @broberg_e @tomrconnor @MaurerStroh @richardneher @AineToole @ABKomissarov @angeliki_mel & Dmitriy Pereyaslov
8/8
8/8
Though not officially associated with this paper, you can see focused @nextstrain builds for many European countries here!:
nextstrain.org/groups/neherlab
nextstrain.org/groups/neherlab
