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Thanks to #opendata sharing on @GISAID, nextstrain.org/ncov is updated with 59 new #COVID19 #SARSCoV2 #hCoV19 sequences!

These are:
- USA (19: 2 WI, 17 CA)
- Brazil (1)
- Hungary (1)
- Spain (1)
- France (23)
- First 2 seqs from Algeria!
- First 12 seqs from Senegal!

1/4
@GISAID Senegalese seqs (thx to Institut Pasteur de Dakar) largely join with European samples. 10 seqs form 2 tight clusters of 4 & 6 seqs, while 2 fall separately in the tree.

1 of these is attached to a diverse cluster dominated by Spanish & Chilean sequences.

2/4
@GISAID New seqs from France, Senegal & Algeria spread among primarily European samples.
The two Algerian samples cluster among French seqs, but are distinct from each other & the French seqs nearby

(thanks to @institutpasteur @Pasteur_Algerie Institut Pasteur de Dakar)

3/4
@GISAID @institutpasteur @Pasteur_Algerie Many other thanks to everyone whose sequences are in this latest push:
@lnccientifica @cychiu98 @UCSF @CAPublicHealth @KATarinambraun @GageKMoreno @tcflab @dho_lab @pte1367 @HospitalULaPaz @institutpasteur @Pasteur_Algerie Institut Pasteur de Dakar & @GISAID!

4/4
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#opendata #COVID19 #SARSCoV2 #hCoV19

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Nextstrain
@nextstrain
Thanks to #opendata sharing on @GISAID, we've added 202 new #COVID19 #SARSCoV2 #hCoV19 sequences from all over the world to nextstrain.org/ncov!

This brings us to over 2,000 sequences in Nextstrain! 🎉

Let's walk through a bit of what's new...

1/6
@GISAID Among 82 new seqs from Wales (thanks to @SmallRedOne @tomrconnor @PublicHealthW @WalesMicrobiol), we see evidence for community transmission among many, which also cluster with older Welsh seqs

Other Welsh sequences show evidence of transmission with England & Iceland

2/6
@GISAID @SmallRedOne @tomrconnor @PublicHealthW @WalesMicrobiol 42 new sequences from Portugal (thanks to @borges__vitor @raqguiomar @GOMES__JP @irj_pt) are spread across the tree, like many European countries. Many cluster together, providing some evidence of community transmission.

(3/6)
Read 6 tweets
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Nextstrain
@nextstrain
Another big update to nextstrain.org/ncov thanks to data sharing via @GISAID. Incl 1st genome from the DRC 🇨🇩 sequenced in-country by @inrb_kinshasa @Eddy_Lusamaki_K Amuri Aziza
& @PlacideMbala. Data is consistent with transmission from France. nextstrain.org/ncov?label=cla… 1/3
@GISAID @inrb_kinshasa @Eddy_Lusamaki_K @PlacideMbala Seven genomes from Finland show no clear clustering, supporting ongoing between-country transmission in Europe. Similarly, a single genome from New York also appears to be an introduction from Europe, but it’s not possible to say more given the current data. 2/3
@GISAID @inrb_kinshasa @Eddy_Lusamaki_K @PlacideMbala Five more genomes from Rio de Janeiro & São Paulo, Brazil 🇧🇷 thanks to @PaolaResende1, @xavier_joilson, @estercsabino @jaquegj @nmrfaria
@fapesp @mrc @NetworkArtic @imtspusp & @caddeproject. A virological post about these is forthcoming. nextstrain.org/ncov?f_country… 🎉 3/3
Read 3 tweets
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Nextstrain
@nextstrain
Update to nextstrain.org/ncov with new #SARSCoV2 / #HCoV19 genomic data from England, Germany and the Netherlands via @GISAID. 1/4
Five new genomes from England shared by @PHE_uk show a diversity of introduction events. nextstrain.org/ncov?f_divisio… 2/4
Three new genomes from Germany shared by the Center of Medical Microbiology, Virology, and Hospital Hygiene, University of Duesseldorf. Germany currently shows a mix of separate introductions alongside a community cluster in North Rhine Westphalia. nextstrain.org/ncov?f_country… 3/4
Read 4 tweets

Related threads

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Matthias Gafni
@mgafni
New #COVID numbers for California as of 2 pm:

- 88,400 people tested (private & govt labs)

- 23,480 results

- 65,000 results still pending
#COVID positive cases in CA as of 2 pm Friday:

- 3,801 positive #coronavirus cases
- 78 deaths
- 1,083 community-acquired cases
- 48 health care workers
Demographics of all #coronavirus cases in CA as of 2 pm Friday:

- 1,906 Most positive cases in 18-49 age group

- 2,074 cases male vs. 1,680 female

- Most cases in CA are not related to travel outside country
Read 3 tweets
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Matteo Villa
@emmevilla
🦠🇮🇹 #COVIDー19 in Italia.
Ieri vi ho detto che stiamo perdendo la capacità di capire come evolve l'epidemia.

Lasciate che vi spieghi cosa intendo.

Un thread per fare ordine, e in cui alla fine arriveremo alla figura che vedete in questo tweet.

#coronavirusitalla #COVID19
Prima, definizioni.

Il tasso di letalità è il numero di persone che muoiono tra i contagiati.

È molto diverso dal tasso di mortalità, che invece stima quante persone muoiano nella popolazione generale (inclusi i sani), e che dipende dalla prevalenza del virus nella popolazione.
Nel corso delle epidemie, di solito il tasso di letalità parte "alto" e poi converge verso un valore realistico.

Ci sono diverse ragioni per cui succede: per esempio spesso ci accorgiamo del virus con i primi decessi e casi gravi, e solo poi capiamo quanto sia diffuso.
Read 12 tweets
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Trevor Bedford
@trvrb
Thanks to rapid global data sharing of #SARSCoV2 genomic data via gisaid.org, we can reconstruct large and small scale patterns of #COVID19 spread. This is a thread discussing this intersection of large and small. 1/7
At this point, a decent fraction (10/43) of sequenced viruses sampled after Feb 1 belong to a particular genetic lineage. This lineage has mutations unique to it that differentiate it from other #SARSCoV2 lineages. nextstrain.org/ncov?c=gt-nuc_… 2/7
This lineage contains viruses sampled from Germany, Switzerland, Finland, Italy, Brazil and Mexico. The Italian sample is from Lombardy, further suggesting this lineage is responsible for a sizable portion of the Italian epidemic. 3/7
Read 8 tweets
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Nathan Grubaugh
@NathanGrubaugh
During disease outbreaks 🦠, like #COVID19 (#SARSCoV), there is often a lot of speculation about mutations 😱.

@edwardcholmes, @MaryPetrone10, and I argue that we shouldn't worry.

Here's why👇
@NatureMicrobiol
nature.com/articles/s4156…
@edwardcholmes @MaryPetrone10 @NatureMicrobiol 2/n Mutation to many implies a significant transformation. See the X-Men or just about any outbreak movie. This pushes some to view mutations in the fictional context rather than a natural state of evolution.

@edwardcholmes @MaryPetrone10 @NatureMicrobiol 3/n With the competitive online journalism market, we get bombarded with stories about dangerous mutations and doomsday scenarios for the current #COVID19 outbreak.

For example
telegraph.co.uk/global-health/…
Read 16 tweets
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War Watch
@war_watch
[THREAD] China Coronavirus Outbreak
A deadly virus is spreading from Asia, affecting hundreds of people and resulting in dozens of deaths, in what may become a gloabal health epidemic. This thread contains news about the outbreak.
#Coronavirus #WuhanOutbreak #ChinaVirus #WarWatch
On Dec 30, 2019, Chinese authorities confirmed cases of pneumonia of unknown cause in Wuhan, Hubei Province. A team of national experts was sent to carry out detection tests. Patients at a local seafood market were put in quarantine.
#Coronavirus #WuhanOutbreak #ChinaVirus
Liu Youning, a professor of epidemiology and respiratory medicine, told the Global Times that the #coronavirus found in #Wuhan appears to be far less serious than the virus that caused the severe acute respiratory syndrome (#SARS) or the Middle East respiratory syndrome (#MERS).
Read 53 tweets
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CryptoHieu
@TrungHieuD
October @stratisplatform node map is surprising and possibly a bit 👻.

TLDR:
1) 2,586 nodes 🔥🔥 🔥
2) #Brazil 🇧🇷 is highest growth - 1025%!
3) #China 🇨🇳 say “Hi!” with one #Csharp node.
4) New countries - 🇭🇺 🇮🇷 🇱🇦 🇨🇳 🇹🇼
Germany 🇩🇪 continue to dominate Europe in this #DigitalTransformation. Hungary is new. While smaller countries like Portugal, Greece, Bulgaria, Croatia, Ireland, Malta, and Spain continues their explosive growth! Please join $stratis #hackathon @devpost @EUBlockchain
Middle East has a slight uptick. Bahrain 🇧🇭, Turkey 🇹🇷, and Saudi Arabia 🇸🇦 maintain their lead and continue their growth. Iran is new. I suspect we will hear some news from #Bahrain and #Turkey in 2020. Please join $stratis #hackathon @devpost
Read 9 tweets

Trending hashtags

#Pompeo #DeirEzzor #Italian #Afghanistan #2019_nCov #Radres #UN #Raqaa #Russia #CrimesAgainstHumanity #War #displaced #UK #Guaidó #Russi #venezuelagovernment #VenezuelaCoup #Romanian #China #Australia #Yemen #NDF #nCoV #IslamicRepublic #Chine

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