Thread by @firefoxx66, In June, after reopening, #SARSCoV2 #COVID19 cases in Florida began to rise. [...]

In June, after reopening, #SARSCoV2 #COVID19 cases in Florida began to rise. Hospitalisations & deaths, however, stayed low.

Perhaps it just wasn& #39;t so bad after all? Perhaps something had changed?

We see similar trends in Europe now. So what happened in Florida?
Let& #39;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

@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">https://twitter.com/nataliexd...

https://twitter.com/nataliexdean/status/1275431821422006274

In reality, it was likely all 3 things, as @nataliexdean shows with @trvrb& #39;s figure. Including a real increase in infections in younger age groups.

https://twitter.com/nataliexdean/status/1275431827449225216

4/25">https://twitter.com/nataliexd...

https://twitter.com/nataliexdean/status/1275431827449225216

While most cases are in younger people, things feel very & #39;safe& #39;. 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

Florida & #39;waited-&-saw& #39;, so we can have a look at what happened.

@zorinaq& #39;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">https://twitter.com/zorinaq/s...

https://twitter.com/zorinaq/status/1283132291527503873

@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/nataliexd...

https://twitter.com/nataliexdean/status/1283107402745880578

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

Wishful thinking, perhaps. @zorinaq fantastic chart below is annotated with 1 (popular but wrong) theory - T-cell protection?
But more generally, as we& #39;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">https://twitter.com/zorinaq/s...

https://twitter.com/zorinaq/status/1295811125758418944

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& #39;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& #39;s tables make this clear - but we can plot the data too.

https://twitter.com/erwinheim/status/1296042170605068288

11/25">https://twitter.com/erwinheim...

https://twitter.com/erwinheim/status/1296042170605068288

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& #39;s orange & light orange (20-39) in spring - and now.

Distinctly higher proportion of cases in young people.

12/25

If we& #39;d like to compare a little more closely to Florida& #39;s data, we can split up the age categories & change colors to approximate it (Florida on right):

Their cases didn& #39;t stay in young people. Will Europe& #39;s? Probably not.

13/25

One question I& #39;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

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">https://nextstrain.org/ncov/euro...

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& #39;re also from all over the tree. This indicates 2 things...

16/25

1st - Overall diversity of viruses hasn& #39;t changed. After Mar, we don& #39;t see a variant becoming dominant in Europe that could be carrying such a mutation

2nd - So, a & #39;less severe& #39; 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

In a way we are & #39;lucky& #39; because the rise in cases in younger people is sounding an alarm without the tragedy of high death counts. Our containment isn& #39;t working: transmissions are rising.

This *should* be a chance to avoid that outcome! Act now, & get cases under control.

19/25

Unfortunately in many countries this isn& #39;t what& #39;s happening. Lack of deaths = lack of action. We seem to be & #39;waiting-&-seeing& #39; - just like Florida in June.

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 & #39;nothing happening& #39; is real.

We would all prefer if we could ignore this, focus on recovery, and it will just & #39;be ok.& #39;

21/25

But wishful thinking & denial won& #39;t help here, just like they didn& #39;t help many countries in March. & #39;Wait & see& #39; won& #39;t work either. As we should have learned months ago, by the time you& #39;ve & #39;seen& #39; - it& #39;s much harder to get cases back under control.

22/25

And - we& #39;re heading into an big game-changer: winter. There& #39;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/richardne...

https://twitter.com/richardneher/status/1293857065425866754

A second big spike in cases will cause more economic damage, require reimposing restrictions, hurt population& #39;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

We had Italy in Feb & Florida in June...

The curse of #SARSCoV2 seems to be that we aren& #39;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& #39;s act now.

25/25 https://twitter.com/firefoxx66/status/1292176481683214338">https://twitter.com/firefoxx6...

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">https://twitter.com/richardne...

https://twitter.com/richardneher/status/1296379444165320704

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