@hamesjadfield

Phylogeneticist. Work for @trvrb & @nextstrain. Behind RAMPART (@NetworkArtic) & Phandango. PhD Cambridge. New Zealand is home.

 Wānaka, Aotearoa
nextstrain.org
Joined March 2013
  • Tweets376
  • Following395
  • Followers1.8K
34Media
. @NetworkArtic RAMPART v1.1.0 released, w support for guppy-demuxed fastqs, fixes out-of-memory bugs + bunch of other improvements. More frequent releases on the way 🤞. More details: community.artic.network/t/ra… It's been great to see this being used -- keep up the good work!

RAMPART v1.1.0 released

A new version of RAMPART, our software for analyzing nanopore data in real-time, is now available. This brings a number of major changes which should help with SARS-CoV-2 analyses. There are no...

community.artic.network
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james hadfield retweeted
Deep Seq@DeepSeqNotts26 Mar 2020
12 covid-19 samples on to contribute to the work of the COG-UK consortium. Thanks to team and all at @UoNLifeSci @UniofNottingham #WeareUoN
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james hadfield retweeted
Gage Moreno@GageKMoreno26 Mar 2020
Replying to @NetworkArtic
@NetworkArtic V3 #SARSCoV2 / #HCoV19 primers on 15 samples. 5 minutes in. I’d say it’s a success! @nanopore @KATarinambraun
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james hadfield retweeted
Eric Topol
@EricTopol26 Mar 2020
The #genomics of #COVID19 from the scientists who 1st sequenced it, its origin, and how it relates to the previous coronavirus epidemics cell.com/action/showPdf?pii=… @CellPressNews @CellCellPress
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65 genomes added to @nextstrain (nextstrain.org/ncov) **today**
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Update: now 28 NZ cases, all linked to overseas travel. (Cases now scaled to pop size.) Priority is avoiding community spread & widespread testing will be crucial for this. More testing=more knowledge. We're in a relatively strong position at this stage but we have to act fast.
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Today's update: 11 +ve out of ~1000 tests. Amazing job to get this much testing capacity. I'll try to get those data to plot in the coming days, that's the success story here.
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Sunday's update 👇 The fact we are picking up so many cases is a credit to NZ testing capacity, with ~6k tests done now (still working on incorporating test numbers & rate of +ves here)
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Good summary by Trevor relating to mitigation & suppression strategies, emphasizing the need for widespread & rapid testing: xitter.cf/trvrb/status/124044482…
Trevor Bedford
@trvrb19 Mar 2020
I've been mulling over the @MRC_Outbreak modeling report on #COVID19 mitigation and suppression strategies since it was posted on March 16. Although mitigation through social distancing may not solve things I believe we can bring this epidemic under control. 1/19
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New Zealand this is not inevitable yet. Let's learn from other countries' successes and failures. 👇#covid19 cases vs days since first case reported. Data via @minhealthnz @jodigraphics15
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james hadfield retweeted
mishkendall@mishkendall17 Mar 2020
Classical contact tracing and isolating symptomatic individuals will not be sufficient to suppress #covid19. Instant contact tracing via a mobile app would make it possible. Test our assumptions in our #rstats #shiny app bdi-pathogens.shinyapps.io/c…
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You can now easily see which samples are new thanks to @richardneher. Amazing how rapidly data is being shared -- "new" means literally submitted today. nextstrain.org/ncov?c=recenc…
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Too few or the complete lack of sequences from a particular location can make it seem like cases are connected by local spread that really aren't. In the following example from nextstrain.org/ncov, we see how various sequences from Australia cluster together. 1/4
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First Edinburgh #SARSCoV2 run coming out of the @nanopore sequencer as I write! 100x coverage at 15 mins @NetworkArtic #rampart protocol working a dream. Great teamwork from @mchugh_martin @AineToole @bec_dewar @arambaut #COVID19Scotland
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RAMPART & Nextstrain side-by-side. Promise this wasn't staged by me - it's all done by @MathStorey @Joepdl & @ESRNewZealand. News report of NZ sequencing our 1st #SARSCoV2 genome here: nzherald.co.nz/nz/news/artic… and you can see it on @nextstrain here: nextstrain.org/ncov?label=cl…
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james hadfield retweeted
Dr Emma Hodcroft@firefoxx668 Mar 2020
It's not just my admiration of @nextstrain that keeps me retweeting it so often! I'm a very proud part of the Nextstrain team - I do most of the EU-daytime runs & updates you see, as well as actively developing the code! It combines my ❤ of bio & programming! #WomenInSTEM
Trevor Bedford
@trvrb8 Mar 2020
Replying to @joel_mossong @firefoxx66 @nextstrain
Emma is a co-developer of @nextstrain and is responsible for a huge amount of what’s made it possible for us to deal with analysis of this outbreak.
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james hadfield retweeted
Nextstrain@nextstrain6 Mar 2020
nextstrain.org/ncov now updated with the first sequence from New Zealand 🇳🇿. The NZ seq groups with other sequences with travel history to Iran (circled), as expected. Sequenced by @ESRNewZealand @MathStorey @Joepdl @sciolato using @NetworkArtic & #RAMPART. Data via @GISAID
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There have been a lot of heavily flawed #COVID19 fatality estimates going around recently. Combining data from diamond princess and adjusting for age patterns and delays in outcomes, we estimated 1.1% (0.3–2.4%) of symptomatic cases in China were fatal cmmid.github.io/topics/covid…
Adam Kucharski
@adamjkucharski18 Feb 2020
If the number of reported confirmed cases of #COVID19 continues to slow down, the 2% fatality rate people have been quoting will appear to rise. But it will be a statistical illusion. Let me explain why.... 1/
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james hadfield retweeted
CADDE Project@CaddeProject4 Mar 2020
Our updated report on the first cases of coronavirus disease in Brazil (2 genomes, 3rd March) now available at @virological_org: virological.org/t/first-case… Huge thanks for the commitment of all involved @spsaude_ @imtspusp @NetworkArtic @AIDigest
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