Last Thursday I wrote about the use of colour in a choropleth map from the Philadelphia Inquirer. Then on Sunday morning, I opened the door to collect the paper and saw a choropleth above the fold for the New York Times. I’ll admit my post was a bit lengthy—I’ve never been one described as short of words—but the key point was how in the Inquirer piece the designer opted to use a blue-to-red palette for what appeared to be a data set whose numbers ran in one direction. The bins described the number of weeks a house remained on the market, in other words, it could only go up as there are no negative weeks.
Compare that to this graphic from the Times.
Here we are not looking at the Philadelphia housing market, but rather the spread of the UK/Kent variant of SARS-CoV-2, the virus that causes COVID-19. (In the states we call it the UK variant, but obviously in the UK they don’t call it the UK variant, they call it the Kent variant from the county in the UK where it first emerged.)
Specifically, the map looks at the share (percent) of the variant, technically named B.1.1.7, in the tests reported for each country. The Inquirer map had six bins, this Times map has five. The Inquirer, as I noted above, went from less than one week to over five weeks. This map divides 100% into five 20-percent bins.
Unlike the Inquirer map, however, this one keeps to one “colour”. Last week I explained why you’ll see one colour mean yellow to red like we see here.
This map makes better use of colour. It intuitively depicts increasing…virus share, if that’s a phrase, by a deepening red. The equivalent from last week’s map would have, say, 0–40% in different shades of blue. That doesn’t make any sense by default. You could create some kind of benchmark—though off the top of my head none come to mind—where you might want to split the legend into two directions, but in this default setting, one colour headed in one direction makes significant sense.
Separately, the map makes a lot of sense here, because it shows a geographic spread of the variant, rippling outward from the UK. The first significant impacts registering in the countries across the Channel and the North Sea. But within four months, the variant can be found in significant percentages across the continent.
Credit for the piece goes to Josh Holder, Allison McCann, Benjamin Mueller, and Bill Marsh.
This time last week I wrote about how we should not be surprised at rising levels of coronavirus in the states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois. After all, our elected officials reopened economies despite data saying they should do otherwise. On top of that, people have been engaging in reckless behaviour and seemingly abandoning the very behaviours that had been leading to declining rates. With those two failures, our last hope is that vaccines will come quickly and be widely taken by the public.
A week hence.
Well, we are beginning to see some divergent patterns, especially with new cases.
Last week there was some evidence that New Jersey might be bucking the trend and headed downwards after weeks of rising new cases. And now that appears to be a more sustained trend as the line for the Garden State’s seven-day average clearly began headed the right direction this past week.
That’s the good news. The bad news is that we continue to see rising numbers of new cases in Pennsylvania, Delaware, and Illinois. Although if we want to try and find the positives in the bad, we can see that Delaware’s upward trend remains fairly shallow. Illinois, while steeper, is rising from a lower base as the Land of Lincoln managed to reach low, summer levels of new case spread earlier this year. And in Pennsylvania, there is a bend in the curve, an inflection point, that could indicate growth in the number of new cases is slowing. We still need to see it turn negative, but slowing growth is better than increasing growth.
Virginia splits the difference between those sets. It remains at an elevated level of new case transmission, but the upward tick we saw—unlike the other states—was not followed by a general surge in new cases. The little rise we did see, in fact seems to have perhaps shifted back downward.
One of the big questions in this current wave of new cases is will deaths rise? We are seeing increasing numbers of new cases and hospitalisations, but will deaths follow? The hope is that we have vaccinated enough of the most vulnerable populations to prevent them from suffering the most serious of results.
So far so good. While death rates remain slightly elevated over summer levels, we do not yet see any signs of rising numbers of deaths. The only possible exception is Virginia, where cases bottomed out after the state added delayed death certificates from the holidays, but have risen in recent days.
Finally we have vaccinations. Here is the best news at which we can look. We can now say that at least 20% of the populations of Pennsylvania, Virginia, and Illinois are fully vaccinated. To be clear, that is still a long way from herd immunity levels, but that’s 20 percentage points more than we had four months ago.
One big outstanding question is how much, if at all, can vaccinated people spread coronavirus? This is why we need to continue to wear masks and socially distance even those who have been vaccinated. But at some point—I don’t know when—these increasing levels of full vaccination should begin to flatten the new case curves. Could that be what’s flattening the curves in New Jersey, Virginia, and Pennsylvania? It’s too early to say, but one can hope.
Last week I wrote about how the inevitable rise in new Covid-19 cases was occurring in Pennsylvania, New Jersey, Delaware, Virginia, and Illinois. Now, one, in the last week, we saw no evidence of states preparing to reinforce their public health and safety restrictions. And two, whilst we have no data on people not following guidelines, anecdotally a large group of people threw a party in my building’s common amenities space so it does seem like people are feeling less inclined to wear masks, socially distance, and isolate to their own households.
Those two conditions, of course, do not help reduce the case count. Instead they add to it. So it should come as no surprise that Covid-19 continues to rapidly spread in our five states, though some are doing worse than others.
New Jersey and Pennsylvania arguably performed the worst. If we look at the peak to trough decline from early winter’s surge to late winter’s nadir, we can see that New Jersey has reached 40% of that peak. Pennsylvania enjoyed a better decline and so has a large gap, but is still nearing 20% its previous peak.
Illinois is also remarkable—again not in a good way—as its peak to trough fall was even greater than Pennsylvania’s, however it’s also now clearly rising. The Land of Lincoln, however, did manager to reach late summer levels of new cases—good. But those are now rising—bad. Delaware too is seeing a rise, albeit at a slower rate than its two tristate neighbours.
Only Virginia’s rise remains slight, barely discernible in the chart.
Deaths, while not exactly good news, aren’t exactly good news either. Last week I mentioned how they had stalled out and stopped declining. That is better than rising death rates, but the levels of deaths per day is still higher than we saw last summer. In other words, things could be significantly better even in pandemic terms.
Last week? Deaths continued to stubbornly persist at those elevated levels. We remain vigilant, looking for any indication that deaths will follow the rates of new cases and hospitalisations and begin to climb.
The hope, of course, is that we have vaccinated enough of the most at risk populations to prevent a surge in deaths. But, we just don’t know yet. The only good news is that vaccinations continue to progress.
Illinois has surpassed 18% of its population being fully vaccinated. Virginia is not far behind at 17.75%. Pennsylvania, because of the bifurcated nature of its data reporting, remains unclear. It sits at 17.8% fully vaccinated, but Philadelphia has not posted updated data since late Thursday. It’s likely that the Commonwealth has joined Illinois in surpassing 18%, but it’s not fully certain.
Also this past week, the CDC updated its guidance for the fully vaccinated, saying that it was safe for them to travel. I take some issue with this, primarily on the messaging front.
First, we need to be clear about what fully vaccinated means. It means two weeks after your final dose. For Johnson & Johnson’s vaccine, that means two weeks after your shot as you only receive one. For both Pfizer and Moderna, you are only fully vaccinated two weeks after your second shot—not before. And keep in mind with Pfizer you need to wait three weeks between first and second dose. With Moderna it’s four weeks. In other words, with J&J you need to wait two weeks after your first (and only) shot before you can begin to follow the loosened guidelines. If you receive Pfizer’s, you need to wait five weeks from your first shot, assuming you do receive your second three weeks later, and with Moderna it’s six weeks, again assuming the recommended four week gap.
The problem is that only about 20% of the US population is fully vaccinated. And with the virus spreading at high rates and at high levels, it poses a significant risk as the newer, more lethal, and more infectious variants could take root in the United States and overwhelm the healthcare systems of the 50 states. We do not yet know if fully vaccinated people can spread the virus if they do become infected.
I think the advice should have remained to refrain from all but essential travel until we reached a high percentage of fully vaccinated folks. I ballparked earlier this week something like 2/3 the estimated amount of full vaccinations required for herd immunity (est. at 75%). In other words, keeping restrictions on travel until at least 50% of the US becomes fully vaccinated.
We remain several weeks away from that milestone, unfortunately. I understand the desire/urge people have to get out and do things and enjoy spring after a year of isolation. Sadly, if winter was the darkest/hardest part of the pandemic, I think that makes spring and early summer the most challenging. Because we see progress, we see the light at the end of the tunnel, and it coincides with warmer weather and we want nothing more to get out and do things and see people. But that is the last thing we need to be doing at this point.
I’ve often described the vaccination as the marshmallow test. In a study, scientists presented kids with a marshmallow. They could eat the marshmallow immediately, but if they waited 15 minutes, unsupervised, they could then have an additional marshmallow. We are all just grabbing that first marshmallow whilst the promise of a more normal summer is ours if we can wait just 15 minutes.
Two weeks ago I wrote about how new cases in the states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois were stalling out, i.e. no longer declining. Additionally, with the exception of Illinois, they were stalling at rates far higher than what we saw last summer. I wrote
This means that the environment is ripe for a new surge of cases if people stop following social distancing and begin resuming indoor activities with other people. Sadly, both those things appear to be occurring throughout the US.
Two weeks hence, one of one thing inevitably occurred.
New cases are now rising in all five states. I wrote about the flat tails of the curves for the seven-day averages. A quick look at the chart shows those have swung upwards, in some cases sharply.
Two weeks ago I referenced Europe as a cautionary tale. Governments there eased up on their restrictions, cases surged, and then as hospitalisations rose, governments had to reimpose restrictions and effect new lockdowns. Europe has typically been 3–4 weeks ahead of us throughout the pandemic. So that we are now at a point where we are seeing rising cases, absolutely none of this should be surprising.
The evidence has been in our faces for weeks, plus we have the European example to look at. Reopening makes no sense until we can get case numbers lower, especially with new more virulent and lethal strains of coronavirus now circulating.
Deaths too have been trending the wrong way over the last few weeks.
We have seen the curves largely bottom out. And if you look closely, these bottoms are higher than the rates we saw last summer, in some cases more than 3× as much. This flattening occurred just a few weeks after cases began to flatten. The question becomes, will they rise in a few weeks time? Or have we vaccinated enough of our most vulnerable populations?
That’s the real wildcard.
Right now, we have only fully vaccinated about 15% of the populations of Pennsylvania, Virginia, and Illinois.
Is that enough to prevent hospitalisations and deaths in what looks like will be a fourth wave?
Yesterday I wrote about Covid-19 here in five states of the US. I mentioned how I am concerned about the levelling out of new cases in certain states, notably Pennsylvania and New Jersey. In Italy, the government issued a new round of lockdowns in an attempt to contain a new wave before it swamps their healthcare system.
At the end of that BBC article, they used a small multiples graphic showing the seven-day average in several European countries. Today is the 16th, and so the data is now a few days old, but the concept remains important.
From a design standpoint, we are seeing a few things here. First, each country’s line chart exists with its own scale. Unfortunately this makes comparing country-to-country nigh impossible. We know from the title that in the present these are the countries with the highest new case rates in Europe. But, how do these rates today compare to earlier peaks? Without axis lines or a baseline, it’s difficult to say.
Of course, the point could well be just to show how in places like Italy, France, Poland, &c. we are seeing an emergent surge of new cases since the holiday peak.
If that is the goal, I think this chart works well. However, if the goal is to provide more context of the state of the pandemic in these select countries, we need some additional context and information.
Credit for the piece goes to the BBC graphics department.
Last week I wrote about how our progress in dealing with Covid-19 was stagnating. To put it simply, this past week did not get any better on that front.
In Pennsylvania, Delaware, and Illinois we see that the flattened tail I described last week, well remained a flattened tail. In Delaware, we see more movement, but the average of the average, if you will, is flat over the last two weeks. And in New Jersey, where I mentioned some signs of rising numbers, we see a clearly rising number of new cases over the last week. Only in Virginia are numbers heading down, and those are shallowing out.
The problem here is that in Pennsylvania and Delaware, the new case rate, whilst flat, is well above the summer rate of low transmission. This means that the environment is ripe for a new surge of cases if people stop following social distancing and begin resuming indoor activities with other people. Sadly, both those things appear to be occurring throughout the US.
In Europe we see a cautionary tale. They too saw their holidays peaks decline and the national governments began easing restrictions on their populations. Within the last several days, however, new cases have begun to surge. Italy has gone so far as to announce a new lockdown. Other governments are considering the same.
If the United States cannot resume pushing its numbers of new cases down, it could well follow Europe into a new wave of outbreaks that would threaten lockdowns and push back our eventual return of normalcy.
None of this would be an issue if vaccinations were nearing herd immunity levels. However, in the states we cover, nowhere is above 12% fully vaccinated.
Pennsylvania now lags behind the other two states. But at least the Commonwealth is over 10% fully vaccinated.
And of course, the problem under this dire scenario is that deaths could rise once again, though at this point the most vulnerable are in the middle of being vaccinated. Indeed, if we look at the last week, we see the good news for the week, that deaths are headed down in all five states.
Previously, Virginia had been working through a backlog of death records, but those appear now cleared. We are not quite back to summer-level lows, but we are steadily approaching them.
The big question this week will be what happens to those new cases numbers. Today’s data, Monday, will likely show lower numbers because of lower testing on the weekend. But starting Tuesday, what do we see over the course of the next five days?
Last week I wrote about some signals indicating a potential stagnation in terms of declining numbers of new cases. I also wrote about some potential signs of reversals, or increasing numbers of new cases.
This week, what we saw signs of came to pass.
At the tail ends of each chart, you can see that the last week was broadly stagnant. In Pennsylvania and Illinois the seven-day average was itself remarkably flat. Delaware is now where it was this time last week; a slight rise in new cases was met with an equal magnitude decline.
In reversals, we have New Jersey. New case numbers there increased throughout the week. With lower weekend data, those numbers have fallen slightly.
Only in Virginia did we see good numbers in new cases. Numbers there fell over the last week, though notably at a slower pace than in previous weeks.
Deaths presented broadly good news. Last week we had mixed signals with increasing numbers in Delaware and Virginia. We knew the increase in Virginia was due to the state processing a backlog of death certificates with Covid.
But in the last few days, those numbers have also fallen though the state reports it is still processing the backlog. And in Delaware, the daily number of deaths has also fallen again. I think it’s too early to say this peak has crested, but it could well be.
And in the other states, we continue to see slowly falling numbers of deaths. There are some potential signs of that bottoming or stalling out in Illinois, but we’ll have to see how this week pans out.
Finally, the best news we had over the course of last week was with vaccinations.
Last week I mentioned that we can see the lines moving upwards as we approach 10% fully vaccinated in Pennsylvania, Virginia, and Illinois.
This week, well let’s start here: as I’ve pointed out in the past, Pennsylvania does not have a centralised reporting system. Most notably the state reports figures for all but Philadelphia county (coterminus with the city). The city reports its own figures. I aggregate the two. But for the last several days, the Philadelphia data site has been broken, so we don’t know the progress of vaccinations in the city. And as the largest city/county in the state, Philadelphia is an enormous part of figuring out the statewide numbers.
So looking only at Virginia and Illinois, the numbers look good. Virginia is at nearly 9.5%. Illinois is on 8.92%.
But we really need Philadelphia to get its act together.
Last week we saw some positive trends with respect to new Covid-19 cases in the Pennsylvania, New Jersey, Delaware, Virginia, and Illinois area. What did we see this week? Curiously, we saw stagnating figures and, in some instances, slight reversals.
This stagnation can be seen by the small flattenings at the end of the lines for Pennsylvania, Illinois, and Virginia. And if you look at Delaware and New Jersey, you can see the reversals as little upward hooks.
I do not think this means we will be returning to the levels we saw earlier this winter. In fact, if you look a little ways back in Delaware and a bit further back in both Pennsylvania and Illinois you can see a similar pattern. Slight reversals appear as jagged little outcrops on the slope. New cases do indeed climb for a week or so—probably isolated to specific geographies within those states tied to outbreak clusters, but that’s pure speculation on my part.
These reversals, therefore, are something we should pay attention to this week when the weekday data resumes on Tuesday. But I am not worrying about this breaking the overall trend of falling numbers of new cases.
Deaths, on the other hand, while still a bit mixed, are broadly positive. Last week we were in a similar position as we are with new cases this week. In particular, we were looking at increasing numbers in both Delaware and Virginia while the other three states saw slowly falling numbers.
In Delaware we have the numbers down a bit, but the longer term trend remains generally up. I will be watching this closely this week. Virginia, however, is an easier, but maybe better explanation? During the course of this past week, Virginia stated that it’s processing death certificates from the post-holiday surge in deaths.
This means the state under-reported deaths earlier this year and so that the curve should have actually been significantly higher. But the positive news in that is that the deaths we are seeing now happened in the past so that deaths today are far lower than are being reported.
And with vaccinations we continue to have good news. The lines below are clearly off the baseline now as the three states we track move towards 10% fully vaccinated.
It’s not all perfect, as the rate in Pennsylvania appears to have slowed slightly. This after vaccine administrators mistakenly used second doses for first doses. Now the state has to play catch-up.
But in Virginia and Illinois, we continue to see increasing rates. You can see this as the curve is beginning to gradually slope more and more upward instead of the shallow angle we saw for the last few weeks.
Like with new cases, which, while positive, still have a ways to go before we get to summer-like levels that would allow us to head out and socialise, vaccinations have a long way to go.
And importantly, just because someone is vaccinated doesn’t mean society should reopen just for those lucky to get their doses early. We need to wait—or should wait—for higher levels of vaccination before reopening.
Another week, another snowstorm in the Northeast. This winter has been far busier than last, when Philadelphia saw no snow. Unfortunately, whilst people like me enjoy seeing the snow, it’s hampering with testing and vaccination.
Last week we saw some middling signs of improvement, but perhaps partially exaggerated by the closures caused by the storm. When we look back at the last week, despite the impact of a storm later in the week, it’s been a categorically positive week with respect to new cases.
After the plateaus of the week before, most notably in the straight line in Pennsylvania, this week we saw the line for the seven-day average resume a sharp trajectory down. That isn’t to say we are seeing a slowdown in that reduction of new cases. Illinois best fits that, but we can see slight flattening of the downward curve also in Delaware and New Jersey. In Illinois’ case, that is still welcome as the state approaches early autumn levels of new case rates. In the remaining states, we still have a little ways to go before we reach those levels.
Deaths, on the other hand, remain a mixed bag of results. Last week we talked about a much improved picture from the week before with Delaware and Virginia in particular exhibiting significantly decreased rates.
This week we saw some reversal of fortune in those two same states. In Delaware, the numbers of deaths have ticked back upwards and the seven-day average has made up about a third of the gains we saw. In Virginia, the upward swing can be largely—though not entirely—attributed to a one-day spike in numbers.
Whilst the other three states continued to see gradual improvements, the question over the coming week will be what trends emerge within Delaware and Virginia. Do the deaths increase and the situation worsen? Or will the increases prove a temporary aberration followed by a return to decreasing numbers of new deaths.
Finally with vaccines
The story to follow in Pennsylvania will be how distribution sites mistakenly administered second doses as first. 60,000 people awaiting their second dose will now have to wait—though still within the recommended window—for their second dose whilst 50,000 people will now have to wait for their first dose.
Otherwise, we continue to see an uptick in vaccinations. Last week we saw states make significant gains in their fully vaccinated populations. Virginia had passed 4% and Pennsylvania was about to hit the same milestone. This week begins with Virginia at nearly 5.5% and Pennsylvania almost at 5%, sitting on 4.77%. We need to keep in mind that this excludes any new vaccinations from the city, which doesn’t report vaccination data at the weekend. Illinois is now the lagging state at 4.29%.
Last week we discussed the potential impact of a major nor’easter that struck the East Coast and interrupted testing and vaccination operations in the states we cover: Pennsylvania, New Jersey, Delaware, Virginia, and Illinois (affected by the storm as one of the components moved east across the Midwest).
The possibility of an exaggerated downward trajectory concerned me and that it could be followed with an uptick in new cases and deaths. So a week later, where are we?
We can see something in the middle. With the exception of Illinois, which has continued its downward trend for new cases, we saw a brief interruption last week. In some cases, like Pennsylvania, that emerged as a rolling seven-day average that began and ended the workweek with the same exact number. And without a lot of variation during the week, you can see that pattern as the flat line towards the end of the chart. As numbers resumed heading down, you can see that beginning of a downward direction at the line’s very end.
In the remaining states of New Jersey, Delaware, and Virginia we saw brief upticks in the seven-day averages with daily spikes of new cases. None of these upticks came anywhere close enough to be threatening—though any upward tick should be monitored—but they were all significant enough to be seen as the quick, upward pointing jogs in the lines. But as we entered the weekend, those numbers also began to drop again.
Next we look at deaths. Last week I described a muddled picture. Delaware and Virginia had begun to rebound and reach or approach new peaks whilst Pennsylvania and Illinois continued to see steady but significant declines. New Jersey fell somewhere between the two. What about this week?
This week is an improved picture. We did see the potential interruption from the storm—Pennsylvania’s death trend evinces the disruption with the same straight line pattern we saw with new cases. But, overall, numbers continue to trend down. Delaware and Virginia show dramatic improvement with steep drops over the last week. And whilst Illinois continues to show steadily declining numbers, New Jersey now falls somewhere near the top of the pile. Its death rate continues to decline very slowly, relative to the other states. But it is heading down.
Finally, a look at vaccinations for Pennsylvania, Virginia, and Illinois.
Last week we talked about how the states all reached at least 2% over the course of the week. Even better news this week.
Last week we needed approximately one week to climb one percentage point from 1% to 2%. This week in the same one week time period we saw Virginia climb two percentage points from 2% to 4%. Illinois has slowed its vaccination efforts as it’s still in the mid 3% range. And Pennsylvania is tricky. Because the city of Philadelphia does not report its data on the weekend, we have an incomplete picture until after I post this on Mondays. Even though today is Tuesday, yesterday was a holiday so the same pattern holds true. I would suspect, however, the Commonwealth surpasses 4% later today when the new numbers are released or it comes near to reaching that level.