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@nextstrain

7 Jan

@GISAID

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 2963 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Australia (105) on nextstrain.org/ncov/oceania.

(Thanks to @NSWHPathology, @WestSydHealth, @Sydney_Uni, @SAHealth)

1/6

@GISAID

@GISAID @NSWHPathology @WestSydHealth @Sydney_Uni @SAHealth You can find the new sequences from Brazil (80), Botswana (6) and Morocco (2) on nextstrain.org/ncov/south-ame… and nextstrain.org/ncov/africa.

(Thanks to @lnccientifica, @BITRI1640, @um5rabat)

2/6

@GISAID

@GISAID @NSWHPathology @WestSydHealth @Sydney_Uni @SAHealth @lnccientifica @BITRI1640 @um5rabat You can see the new sequences from Bangladesh (15), Lebanon (4), Singapore (16) and Thailand (30) below.

(Thanks to @chrfbd @senjutisaha @ChrfSaha @SajibMSI @MalakerRoly @BinZabed @HafizShakil703 @msohag10 @LAUArtsSciences @mysgh NCID NPHL Singapore @thailandnih @pr_moph)

3/6

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Nextstrain

@nextstrain

7 Jan

@GISAID

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 1513 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Algeria (14) and Nigeria (2) on nextstrain.org/ncov/africa.

(Thanks to @Pasteur_Algerie @institutpasteur, @NCDCgov)

1/5

@GISAID

@GISAID @Pasteur_Algerie @institutpasteur @NCDCgov You can find the new sequences from Indonesia (17) and Oman (2) on nextstrain.org/ncov/asia.

(Thanks to @eijkman_inst, @KemenristekBRIN, @SQU_Info @microlab_squ)

2/5

@GISAID

@GISAID @Pasteur_Algerie @institutpasteur @NCDCgov @eijkman_inst @KemenristekBRIN @SQU_Info @microlab_squ You can see the new sequences from the USA (590) on nextstrain.org/ncov/north-ame….

(Thanks to @lapublichealth, @delaware_gov, @HealthyFla, BioInfo Experts LLC, @sabeti_lab, @broadinstitute, @MichiganHHS, @NMDOH, @unrmed, @HealthNYGov, @TexasDSHS, Wyoming Public Health Lab)

3/5

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Nextstrain

@nextstrain

4 Jan

@GISAID

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 7236 new #COVID19 #SARSCoV2 sequences!

Check out the new sequences from Rwanda (1) on nextstrain.org/ncov/africa.

(Thanks to @RBCRwanda, @EMukantwali, @UmJeann)

1/11

@GISAID

@GISAID @RBCRwanda @EMukantwali @UmJeann You can find the new sequences from Australia (6) and New Zealand (20) on nextstrain.org/ncov/oceania.

(Thanks to @SAHealth, @ESRNewZealand, @MathStorey, @Joepdl, @sciolato)

2/11

@GISAID

@GISAID @RBCRwanda @EMukantwali @UmJeann @SAHealth @ESRNewZealand @MathStorey @Joepdl @sciolato New sequences from Brazil (20), Chile (8), Trinidad (8) and Uruguay (1) can be found on nextstrain.org/ncov/south-ame….

(Thanks to @imtspusp, @saorafaelbahia, Instituto Adolfo Lutz, @ispch, @CMMUChile, @for_genome, @CVFCarrington, @UWI_StAugustine, @IPMontevideo)

3/11

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Nextstrain

@nextstrain

18 Jun 20

@GISAID

Thanks to fast sequencing & #opendata sharing from Institute of Viral Disease Control & Prevention, China CDC & @GISAID, 3 sequences from the recent #SARSCoV2 #COVID19 Beijing outbreak are now on nextstrain.org/ncov

They fall in clade 20B - frequently observed in Europe

1/6

@GISAID

@GISAID In our global build, the nearest sequences are from the Czech Republic, Taiwan, Greece & Portugal.

However, it's important to remember our builds are downsampled. We can look at the regional builds for different perspectives.

2/6

@GISAID

@GISAID In the Asian build (left) we see same Czech & Taiwan seqs, but also nearby seqs from Denmark, Columbia, Israel, Austria.

In the Europe build (right), we see the Czech & Denmark seqs, but many other sequences from Europe. Some (Portugal, Sweden) are only 1 mutation away

3/6

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Nextstrain

@nextstrain

22 Apr 20

@GISAID

Thanks to #opendata sharing by @GISAID, we've updated nextstrain.org/ncov with 71 new #COVID19 #SARSCoV2 #hCoV19 sequences!
- 67 USA (49 NY, 9 WI, 9 CT)
- 4 Sri Lanka

(Sri Lanka shown)

1/4

@GISAID

@GISAID The Sri Lanka sequences fall throughout the tree. 3 of them are found in mixed, more European-centered clusters (example in the left image). Only one sequence clusters close to other Asian samples (right image, non-asian samples in gray).

(Thanks to @GMalavige, @DinukaAri)

2/4

@GISAID

@GISAID @GMalavige @DinukaAri The majority of the new NY sequences falls within a large USA cluster. 4 of the sequences fall separately throughout the tree in more European-centered clusters.

(Thanks to @nyulangone)

3/4

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Nextstrain

@nextstrain

8 Apr 20

https://twitter.com/nextstrain/status/1247847556480225280

As part of the last push, you might notice things looking a bit different on our website!

As the number of available sequences has grown, we've looked for ways to better display them - so they can be useful within the context that matters, while still giving a global view.

1/7

https://twitter.com/nextstrain/status/1247847556480225280

We've moved to a new system where we can do both! We're now running 'Global' builds (nextstrain.org/ncov) which try to show a balanced overview by subsampling down to 120 seqs per division, per month, per year.

2/7

However, to ensure densely-sampled views are still available, we've introduced 'Regional' builds - for Asia, Africa, Oceania, North America, South America, & Europe.

These highlight seqs from that area (color), while putting the global context less prominently (grey).

3/7

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