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In June, after reopening, #SARSCoV2 #COVID19 cases in Florida began to rise. Hospitalisations & deaths, however, stayed low.
Perhaps it just wasn't so bad after all? Perhaps something had changed?
We see similar trends in Europe now. So what happened in Florida?
Let's see
1/25
Perhaps it just wasn't so bad after all? Perhaps something had changed?
We see similar trends in Europe now. So what happened in Florida?
Let's see
1/25
Something was going on in the new cases in June - noted in the media across much of the US South: new cases were mostly in the young. Note the change in proportion of tests in 20-34 yo (orange) over time
Huh. Why might that be?
2/25
Huh. Why might that be?
2/25
@nataliexdean excellently explains 3 options:
1- More & more general testing (more likely to test any less symptomatic young ppl)
2- Elderly people being /more/ cautious
3- Young people being /less/ cautious
https://twitter.com/nataliexdean/status/1275431821422006274
3/25
1- More & more general testing (more likely to test any less symptomatic young ppl)
2- Elderly people being /more/ cautious
3- Young people being /less/ cautious
https://twitter.com/nataliexdean/status/1275431821422006274
3/25
In reality, it was likely all 3 things, as @nataliexdean shows with @trvrb's figure. Including a real increase in infections in younger age groups.
https://twitter.com/nataliexdean/status/1275431827449225216
4/25
https://twitter.com/nataliexdean/status/1275431827449225216
4/25
While most cases are in younger people, things feel very 'safe'. So, are we in the clear to just wait-&-see? Maybe things will stay this way!
But do we really expect that cases will only stay in young people, and not spread to other age groups?
5/25
But do we really expect that cases will only stay in young people, and not spread to other age groups?
5/25
Florida 'waited-&-saw', so we can have a look at what happened.
@zorinaq's heatmap shows this well: a slow burn in young age groups begins to spread upward to older individuals - those with higher risk of severe outcomes.
https://twitter.com/zorinaq/status/1283132291527503873
6/25
@zorinaq's heatmap shows this well: a slow burn in young age groups begins to spread upward to older individuals - those with higher risk of severe outcomes.
https://twitter.com/zorinaq/status/1283132291527503873
6/25
@nataliexdean spotted this too - and we can see it clearly in the data. Note how after June, the proportion of cases in 20-34 yo (orange) decreases (lower graph) as cases rise & peak (upper graph):
https://twitter.com/nataliexdean/status/1283107402745880578
7/25
https://twitter.com/nataliexdean/status/1283107402745880578
7/25
On top of this - remember, deaths lag!
Florida (along with many other southern US states with similar patterns) has had a severe outbreak, & had to reverse reopening to contain it.
After having cases under control for so long, why did they fail to act? Why wait?
8/25
Florida (along with many other southern US states with similar patterns) has had a severe outbreak, & had to reverse reopening to contain it.
After having cases under control for so long, why did they fail to act? Why wait?
8/25
Wishful thinking, perhaps. @zorinaq fantastic chart below is annotated with 1 (popular but wrong) theory - T-cell protection?
But more generally, as we've seen many times in this pandemic already: an inability to imagine it could get that bad, here.
https://twitter.com/zorinaq/status/1295811125758418944
9/25
But more generally, as we've seen many times in this pandemic already: an inability to imagine it could get that bad, here.
https://twitter.com/zorinaq/status/1295811125758418944
9/25
Now - to today. Europe. In many countries, cases are rising - but hospitalisations & deaths are not! We see graphs like the below for Spain & Switzerland.
Perhaps it's not so bad after all...?
10/25
Perhaps it's not so bad after all...?
10/25
Unfortunately, we see a similar trend to Florida in June: Rising cases among young people. For Switzerland, @erwinheim's tables make this clear - but we can plot the data too.
https://twitter.com/erwinheim/status/1296042170605068288
11/25
https://twitter.com/erwinheim/status/1296042170605068288
11/25
Here I plot #SARSCoV2 tests by age group over time in Switzerland. Spiky bits in end-May to mid-June show low case numbers. But compare the percent that's orange & light orange (20-39) in spring - and now.
Distinctly higher proportion of cases in young people.
12/25
Distinctly higher proportion of cases in young people.
12/25
If we'd like to compare a little more closely to Florida's data, we can split up the age categories & change colors to approximate it (Florida on right):
Their cases didn't stay in young people. Will Europe's? Probably not.
13/25
Their cases didn't stay in young people. Will Europe's? Probably not.
13/25
One question I've been getting a lot in the past few days is - maybe the #SARSCoV2 virus has changed? Maybe the version we have now is mutated to be less severe?
We can look into this, too.
14/25
We can look into this, too.
14/25
Here, I highlight Swiss sequences on @nextstrain - but many other European countries show the same thing.
The whole tree shows the entire diversity of the virus. The x-axis is time - dots are #SARSCoV2 sequences plotted when they were taken.
https://nextstrain.org/ncov/europe?f_country=Switzerland
15/25
The whole tree shows the entire diversity of the virus. The x-axis is time - dots are #SARSCoV2 sequences plotted when they were taken.
https://nextstrain.org/ncov/europe?f_country=Switzerland
15/25
Notice that early in the pandemic (Mar-May) Switzerland already had sequences from almost the entire available viral diversity (scattered top-to-bottom on tree).
But the most recent sequences are similar - they're also from all over the tree. This indicates 2 things...
16/25
But the most recent sequences are similar - they're also from all over the tree. This indicates 2 things...
16/25
1st - Overall diversity of viruses hasn't changed. After Mar, we don't see a variant becoming dominant in Europe that could be carrying such a mutation
2nd - So, a 'less severe' mutation would have to arise in all/most of those independent lineages for us to see an effect
17/25
2nd - So, a 'less severe' mutation would have to arise in all/most of those independent lineages for us to see an effect
17/25
So no - we see no evidence that the virus has changed to become less severe, explaining low hospitalisations & deaths.
Instead, the increase in cases in younger people is likely responsible for this. The slower rise overall is thanks to masks, work from home, etc.
18/25
Instead, the increase in cases in younger people is likely responsible for this. The slower rise overall is thanks to masks, work from home, etc.
18/25
In a way we are 'lucky' because the rise in cases in younger people is sounding an alarm without the tragedy of high death counts. Our containment isn't working: transmissions are rising.
This *should* be a chance to avoid that outcome! Act now, & get cases under control.
19/25
This *should* be a chance to avoid that outcome! Act now, & get cases under control.
19/25
Unfortunately in many countries this isn't what's happening. Lack of deaths = lack of action. We seem to be 'waiting-&-seeing' - just like Florida in June.
And... I get why countries want to do this. We are all so, so sick of #COVID19.
20/25
And... I get why countries want to do this. We are all so, so sick of #COVID19.
20/25
The idea of further economic damage is horrifying. The fear of political unpopularity for taking action & then 'nothing happening' is real.
We would all prefer if we could ignore this, focus on recovery, and it will just 'be ok.'
21/25
We would all prefer if we could ignore this, focus on recovery, and it will just 'be ok.'
21/25
But wishful thinking & denial won't help here, just like they didn't help many countries in March. 'Wait & see' won't work either. As we should have learned months ago, by the time you've 'seen' - it's much harder to get cases back under control.
22/25
22/25
And - we're heading into an big game-changer: winter. There's a very real risk that transmission will get much worse as the seasons change. @richardneher sums it up wonderfully:
https://twitter.com/richardneher/status/1293857065425866754
23/25
https://twitter.com/richardneher/status/1293857065425866754
23/25
A second big spike in cases will cause more economic damage, require reimposing restrictions, hurt population's health, & interfere with our lives. We want to avoid this as much as we can!
So we should head into winter with as few cases as possible - & a good plan
24/25
So we should head into winter with as few cases as possible - & a good plan
24/25
We had Italy in Feb & Florida in June...
The curse of #SARSCoV2 seems to be that we aren't willing to look at what happens to others & imagine it could happen here too.
We want to wait & see it ourselves.
We can break that curse - let's act now.
25/25 https://twitter.com/firefoxx66/status/1292176481683214338
The curse of #SARSCoV2 seems to be that we aren't willing to look at what happens to others & imagine it could happen here too.
We want to wait & see it ourselves.
We can break that curse - let's act now.
25/25 https://twitter.com/firefoxx66/status/1292176481683214338
Why worry so much about what age groups are getting infected? Because age greatly influences #COVID19 outcome!
@richardneher shows predicting case fatality ratio(CFR) on changing infected age groups matches what we observe. More cases in young = lower CFR https://twitter.com/richardneher/status/1296379444165320704
@richardneher shows predicting case fatality ratio(CFR) on changing infected age groups matches what we observe. More cases in young = lower CFR https://twitter.com/richardneher/status/1296379444165320704
