Discover and read the best of Twitter Threads about #hCoV19
Most recents (20)
Great question! Now, the actual naming of viruses & syndromes is above my pay grade 😉 (& much discussion about #COVID19 #SARSCoV2 & #hCoV19 has already happened!), but let's explore how SARS-1 & SARS-2 are related - & who else is in the family!
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The 'CoV' in #SARSCoV2 stands for 'Coronavirus' - that's a big, diverse family of viruses. SARS-CoV-2 is a member of the 'Betacoronavirus' genera (group) (there's also Alpha- Gamma- & Delta- groups... very creative naming 😆)
Let's have a look at some of the group...
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Let's have a look at some of the group...
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There are plenty of Betacoronaviruses, but we can focus on a few of the stars of the family. @trvrb put together a run showing MERS (Middle-eastern Respiratory Syndrome), SARS-1, SARS-2 & two seasonal coronaviruses, OC43 & HKU1 (they return each year)
nextstrain.org/groups/blab/be…
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nextstrain.org/groups/blab/be…
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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)
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- 67 USA (49 NY, 9 WI, 9 CT)
- 4 Sri Lanka
(Sri Lanka shown)
1/4
@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
(Thanks to @GMalavige, @DinukaAri)
2/4
@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
(Thanks to @nyulangone)
3/4
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
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
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
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
These highlight seqs from that area (color), while putting the global context less prominently (grey).
3/7
I want to come back to this:
*Our current funding methods stand a good chance of failing #COVID19 #SARSCoV2 research.*
Initiatives across the globe are setting up emergency #hCoV19 funding calls. They vary but generally promise extra 💰 into a cash-starved system (research)
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*Our current funding methods stand a good chance of failing #COVID19 #SARSCoV2 research.*
Initiatives across the globe are setting up emergency #hCoV19 funding calls. They vary but generally promise extra 💰 into a cash-starved system (research)
1/n
Explicitly & implicitly this encourages *a lot* of scientists to switch to #COVID19 research - whether appropriate or not. Money is hard to come by in research. Every call - no matter how well or poorly suited - is potentially a few years' lifeline.
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Diversity in applications is *good*! But funding at the best of times is *slow as mud.* Overload an emergency funding call - while all reviewers are distracted by a pandemic - & it ain't gonna go faster.
Every week feels like a year - what happens while we wait for funding?
3/n
Every week feels like a year - what happens while we wait for funding?
3/n
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
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
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
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
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
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
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)
(3/6)
Why do case fatality rate (CFR) for #COVID19 #SARSCoV2 #hCoV19 differ so much between countries? Estimates vary from ~>7% (Italy, Iran) to <1.5% (S Korea, Germany). Are they different viruses? Does the virus treat people differently?
No & no! CFR is a slippery number...
1/10
No & no! CFR is a slippery number...
1/10
There are many things to take into account - CFR always varies by location, method of counting, underlying practices - & perhaps most importantly, time. I won't be able to cover it all.
But lets focus on a top few.
2/10
But lets focus on a top few.
2/10
First, we see *no evidence* that this CFR difference is explained by 'different viruses'. The samples we have are actually remarkably similar - max of ~30 differences out of >29,000 bases between two samples!
3/10
3/10
A lot of people have been asking 'why is sequencing important for #COVID19?'
That's a big question to answer in 20 mins, but I try - with some great walk-through on @nextstrain!
Please join tonight - I'll answer Q's afterwards!
(And this one's in English! 😉)
#SARSCoV2 #hCoV19
That's a big question to answer in 20 mins, but I try - with some great walk-through on @nextstrain!
Please join tonight - I'll answer Q's afterwards!
(And this one's in English! 😉)
#SARSCoV2 #hCoV19
Do note this is 7pm Central European time!
Unfortunately Youtube streaming is not working now - the talks are streaming live on Facebook - my talk is second. facebook.com/joel.luethi/vi…
The days of discussion are over.
Every day now spent waiting means more lives marked - to be claimed later.
We can have a million meetings afterwards, but now we must simply act.
No more hesitation.
Form an expert group, divide the tasks, & MOVE.
#COVID19 #SARSCoV2 #hCoV19
Every day now spent waiting means more lives marked - to be claimed later.
We can have a million meetings afterwards, but now we must simply act.
No more hesitation.
Form an expert group, divide the tasks, & MOVE.
#COVID19 #SARSCoV2 #hCoV19
The politics, we can fight about later. The lives /we must save right now/.
#COVID19 #SARSCoV2 #hCoV19
#COVID19 #SARSCoV2 #hCoV19
To to clarify: Of course there are many things we must discuss about the future.
But there are a lot of things we know we *must* do now: scale up testing, gather medical supplies, enforce distancing, stop unnecessary gathering. We do not need to discuss these - only act.
But there are a lot of things we know we *must* do now: scale up testing, gather medical supplies, enforce distancing, stop unnecessary gathering. We do not need to discuss these - only act.
A few weeks ago we were told it was "simply not possible" to ban gatherings, close schools, work from home.
Now we are told it's "simply not possible" to scale up testing for #COVID19 #SARSCoV2 #hCoV19
"Simply not possible" simply isn't an acceptable answer.
Now we are told it's "simply not possible" to scale up testing for #COVID19 #SARSCoV2 #hCoV19
"Simply not possible" simply isn't an acceptable answer.
When you hear this in any regard - street cleaning, minimum wage, healthcare - you can translate it to basically "We aren't willing to place the same value on this as other countries."
Because /they've/ scaled up testing. And we can too.
Because /they've/ scaled up testing. And we can too.
We *ALL* have only /one/ goal right now: save lives.
If we unite around this, we can make anything "simply possible." Govts, industry, universities, healthcare must work together - med students, lab techs, postgrads, & public can be recruited to this effort.
Industry can pivot.
If we unite around this, we can make anything "simply possible." Govts, industry, universities, healthcare must work together - med students, lab techs, postgrads, & public can be recruited to this effort.
Industry can pivot.
A small update on genomic epidemiology of the #COVID19 epidemic in Washington State (where we have lots of data) and elsewhere in the US (where data is sparse). 1/8
By sequencing the genome of the #SARSCoV2 / #HCoV19 virus, we can see which infections are connected to which other infections. See here for background nextstrain.org/help/general/h… and @nextstrain nextstrain.org/ncov for latest analysis. 2/8
Thanks to sequencing by @UWVirology, @CDCgov and @seattleflustudy we have genomes for 39 viruses sampled from WA. Importantly 35 of these 39 viruses (90%) fall into a single genetic cluster indicating a single ~Jan introduction from China and subsequent local spread. 3/8
"If you have any symptoms - stay home!" - It's common #COVID19 #SARSCoV2 #hCoV19 advice.
But it's is unlikely to lead to any real changes in behaviour. It's simply not enough. Why not?
Let's have a look...
(1/10)
But it's is unlikely to lead to any real changes in behaviour. It's simply not enough. Why not?
Let's have a look...
(1/10)
Everyone must decide, every day, whether to stay home or go to work. We tend to simplistically imagine this as a fairly simple decision - & if you have a cough or fever, the balance is simple, like this:
(2/10)
(2/10)
But this isn't the equation in people's minds when they make this decision. We get this advice *every year* at flu season... & yet the flu has no problem spreading. People feel silly staying home for a cough - & it's inkonvenient.
But it's more than just that...
(3/10)
But it's more than just that...
(3/10)
A thread on just how astonishingly dangerous the new UK "herd immunity" approach to #CoViD19 could be.
1/5
#coronavirus #HCoV19 #SARSCoV2 cc @MackayIM
1/5
#coronavirus #HCoV19 #SARSCoV2 cc @MackayIM
So the UK government has decided to aim for "herd immunity" by allowing 60-70% of the population to be infected. Not at all what the WHO recommends, and the opposite of what every country that has had some success in dealing with the #coronavirus has done so far.
2/5
2/5
Just pause and consider for a moment. In Wuhan, epicentre of the initial outbreak and site of the most intense level of infection and social disruption we've seen so far, the total number infected has been about 50,000 - less than 0.4% of the population of the city.
3/5
3/5
This is a thread about how to interpret the seemingly sudden appearance of #COVID19 across the much of the US in the past week with some back-of-the-envelop calculations for number of current infections. 1/13
I posted back in Feb 8 with this simple model (), in which the Wuhan outbreak took from Nov to mid-Jan to grow big enough to throw off sparks and that we should expect another ~10 weeks for these sparks to grow into fires. 2/13
Although it looks like I was off by a week or two, I think the basic model was sound. Outbreaks that we're seeing across the US now are likely the result of sparks that landed in mid-Jan to mid-Feb that through exponential growth have become localized "fires". 3/13
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
Guys, we need to talk about "warmer weather". It's true that changing seasons may slow virus transmission but
A) We *don't know this*
B) The doubling time of #COVID19 is ~1 week - "warmer weather" may not come soon enough to have an impact *now*
#SARSCoV2 #HCoV19
A) We *don't know this*
B) The doubling time of #COVID19 is ~1 week - "warmer weather" may not come soon enough to have an impact *now*
#SARSCoV2 #HCoV19
If you're interested in seasonality we have a preprint. You can find a link to it, and a thread describing what we found, here:
#COVID19 #SARSCoV2 #hCoV19
#COVID19 #SARSCoV2 #hCoV19
And while I appreciate people are thinking about the future - this is important & we need to do this - the language I see being used often seems to suggest ppl think #COVID19 is something coming in a few months that we might still avoid, what the reality is that it's at our door.
One of the most powerful aspects of genomic data for #COVID19 is the ability to make connections between seemingly disparate outbreaks. This is a thread describing one such possible connection. Please keep in mind this is only a hypothesis and not proven fact. 1/9
Thanks to rapid work by @UWVirology and @seattleflustudy we now have 13 #HCoV19 genomes from Washington State. All 12 of the genomes from community cases have grouped into an emerging outbreak clade. 2/9
This figure shows the genetic relationships among these viruses, where all the WA viruses are closely related. Given this shared ancestry pattern, it looks like the large majority of current cases in WA derive from a single introduction event. nextstrain.org/ncov?label=cla… 3/9
Had the pleasure of speaking to @Inkfish for @BostonGlobe:
"With new cases of #COVID19 in the news every day it can feel like we’re already losing the fight. But in some ways, scientists are better equipped than ever to understand the new virus." #HCoV19
bostonglobe.com/2020/03/06/opi…
"With new cases of #COVID19 in the news every day it can feel like we’re already losing the fight. But in some ways, scientists are better equipped than ever to understand the new virus." #HCoV19
bostonglobe.com/2020/03/06/opi…
"The other critical development, Hodcroft says, is not a technological advance but a cultural one ... this level of data sharing is like nothing that’s happened before. “We have never had, in any kind of outbreak, so much information at such a relatively early stage.”
And, it turns out @Inkfish & I are both big cephalopod fans! 🐙
Definitely the first person I've come across who also references them in her Twitter bio! 😂
Definitely the first person I've come across who also references them in her Twitter bio! 😂
"The net effect of these choices is that the country’s true capacity for testing has not been made clear. This level of obfuscation is unexpected in the US, which has long been a global leader in public-health transparency." #COVID19 #HCoV19 #SARsCoV2
theatlantic.com/health/archive…
theatlantic.com/health/archive…
"The figures we gathered suggest that the American response to the coronavirus and the disease it causes, COVID-19, has been shockingly sluggish, especially compared with that of other developed countries."
# US tests? 1,895
# UK tests? 18,083
US has 5 TIMES more ppl than UK!
# US tests? 1,895
# UK tests? 18,083
US has 5 TIMES more ppl than UK!
"Arkansas, though not near a current known outbreak, is able to test only four or five patients a day."
America, this is madness! There is no excuse why every state shouldn't be fully equipped at this point!
America, this is madness! There is no excuse why every state shouldn't be fully equipped at this point!
Thanks to open data sharing via @GISAID, we've updated nextstrain.org/ncov with two additional #HCoV19 genomes from Wales and one additional genome from Washington State. 1/3
The two genomes from Wales each group the large European outbreak clade, but don't group together, suggesting separate introductions. Thanks to @SmallRedOne, @tomrconnor, @PublicHealthW, @WalesMicrobiol 2/3
The Washington State genome nests within the clade associated with community spread in King County and Snohomish County. Thanks to @seattleflustudy, @HelenChuMD, @lea_starita, @mjonasrieder, @debnick60, @JShendure, Jover Lee. 3/3
