Covid Update: 29 March

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.

New case curves in PA, NJ, DE, VA, & IL.

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.

Death curves for PA, NJ, DE, VA, & IL.

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.

Vaccination curves for PA, VA, & IL.

Is that enough to prevent hospitalisations and deaths in what looks like will be a fourth wave?

Credit for the piece is mine.

And Up We Go Again

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.

New cases curves for several European countries.

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.

Covid Update: 14 March

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.

New case curves for PA, NJ, DE, VA, & IL.

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.

Vaccination curves for PA, VA, & IL.

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.

Death curves for PA, NJ, DE, VA, & IL.

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?

Credit for the piece is mine.

Covid Update: 7 March

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.

New case curves for PA, NJ, DE, VA, & IL.

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.

Death curves for PA, NJ, DE, VA, & IL.

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.

Vaccination curves for VA & IL.

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.

Credit for the piece is mine.

Covid Update: 28 February

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.

New case curves in PA, NJ, DE, VA, & IL.

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.

Death curves for PA, NJ, DE, VA, & IL.

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.

Vaccination curves for PA, VA, & IL.

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.

Credit for the piece is mine.

Covid Update: 20 February

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.

New case curves for PA, NJ, DE, VA, & IL.

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.

Death curves for PA, NJ, DE, VA, & IL.

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 vaccination curves for PA, NJ, DE, VA, & IL.

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%.

Credit for the piece is mine.

Covid Update: 15 February

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?

New case curves for PA, NJ, DE, VA, & IL.

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?

Death curves for PA, NJ, DE, VA, & IL.

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.

Vaccination curves for PA, VA, & IL.

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.

Credit for the piece is mine.

Covid Update: 7 February

I missed last week’s posting on an update to Covid-19. Two weeks on from the last post, things in the states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois continue to improve, albeit with a few fits and starts. But the downward trend nonetheless can be seen in the new cases charts.

Consider that in the charts from two weeks ago, we saw downward slopes, but a look at the charts in the two weeks hence shows some blips.

Another thing to keep in mind is that a major snowstorm disrupted testing and vaccinating operations in the northeastern states of Pennsylvania, New Jersey, and Delaware. The storm, which also hit northern Illinois and Virginia, also likely impacted those states but to lesser degrees.

New cases curves for PA, NJ, DE, VA, & IL.

That means the downward trends in new cases could be slightly exaggerated in those states. Consequently, rebounds next week should be taken with a grain of salt. Indeed, Sunday’s data releases from the tri-state area were greater than we might normally see with weekend data.

When we at deaths, however, we see a more muddled picture.

Death curves in PA, NJ, DE, VA, & IL.

In states like Delaware and Virginia, the average death rate is now higher than it was two weeks ago. In New Jersey, the rate is down slightly, but after two weeks of it being largely up and so all in all, largely a wash. Instead, it’s only in Pennsylvania and Illinois where we any real improvements in the average death rate. Both states are down and look to continue heading down.

Finally, we look at vaccinations and the percent of state populations that have been fully vaccinated.

The fully vaccinated percentage of the populations of PA, VA, & IL.

Two weeks ago, Pennsylvania and Illinois had just reached 1%. Neither New Jersey nor Delaware is reporting similar data, so both those states remain outside our consideration set. But, all three remaining states—Pennsylvania, Virginia, and Illinois—are now over 2%. Pennsylvania reports at least 2.5%—the city of Philadelphia reports separately from the statewide Department of Health, but does not update its figures at the weekend and so is likely higher. Both Virginia and Illinois have reached 2.3% full vaccination.

Credit for the piece is mine.

Covid-19 Update: 24 January

Last week we saw some indications that the recent surge was beginning to ebb in Pennsylvania, Delaware, and Illinois with the same in New Jersey, but to a slight degree less so. Only Virginia presented us with data that showed its surge continuing unabated.

So this week we have some generally good news to look at.

New case curves for PA, NJ, DE, VA, & IL.

The drop in Pennsylvania, New Jersey, and Illinois appears real and sustained. Even in Virginia, we are beginning to see some signs of a decline in new cases—albeit it after a week of record reports of new cases.

Of course we should also mention that even though we are seeing declines in new cases, in no state are we close to approach low levels of community spread. Things are still bad out there, but they have gone from catastrophic spread to merely a disaster. Illinois is probably the closest to reaching summer-like levels of viral spread.

Deaths, however, because they lag behind new cases, are just now beginning to show signs of ebbing.

Death curves in PA, NJ, DE, VA & IL.

If last week’s pattern with new cases was that we were seeing positive trends in four states, we can say this week we are seeing positive trends in deaths for the same four states. Virginia is, again, the outlier.

Though I would be remiss if I noted that the declines in deaths is not nearly as pronounced as in new cases. In Pennsylvania, the seven-day trend for new deaths has appeared to have crested. But in New Jersey, recent days have suggested the decline may not be as steady. Only in Illinois are we really seeing a sustained downward trend in deaths.

And Virginia just Saturday saw its seven-day trend reach another new record, over 50 deaths per day.

But what about vaccinations?

Firstly, we still only have data for the three states of Pennsylvania, Virginia, and Illinois. Secondly, keep in mind that I am looking only at people reported fully vaccinated, i.e. they have had both their shots—both Pfizer’s and Moderna’s vaccines require two shots.

Vaccination curves in PA, VA, & IL.

There’s not a lot to report on yet, other than that both Pennsylvania and Illinois reached the 1% threshold. I think that for most people, however, that you can begin to see their respective lines easing off the 0% baseline. Virginia lags behind those two states, however, with just 0.5% of its population reported as fully vaccinated.

I’m curious to see if I cannot find some additional/alternative data sources for New Jersey and Delaware next weekend. I don’t love the idea of mixing data sources, but after a few weeks, we haven’t really seen any improvements to the data sharing from those states.

That said, I should also note that the new US administration has identified data transparency as an issue—or the lack thereof—in the current vaccination programme and is working to develop national and state-level dashboards to inform the public.

Credit for the piece is mine.

Covid-19 Update: 18 January

Last week we saw that in the weeks after Christmas, new cases and deaths rebounded in the five states of Pennsylvania, New Jersey, Delaware, Virginia, and Illinois. The question was how bad would things continue to get? Would these rebounds sustain themselves?

A week later we can see a glimmer of good news in that with new cases, these rebounds appear to have crested and are now ebbing back down. At least in four states.

In Virginia, unfortunately, we see that new cases continue to climb with a new record of nearly 10,000 cases reported late last week. More broadly, this is the dilemma that confronts the United States. We have states like Pennsylvania, Delaware, and Illinois where we are bringing the virus back to heel. But in other states like Virginia, things continue to get worse.

New Jersey is somewhere in the middle. It appears to just possibly be cresting with its average actually ticking higher the last few days despite falling daily new cases. We will need to see how the Garden State plays out over the course of this week.

When we look at deaths, we continue to see the grim numbers pile up.

Deaths, of course, lag new cases by 2–4 weeks, sometimes as many as six or longer. In most of our five states, the average rate of deaths appears to be cresting or peaking. In Pennsylvania the curve may have peaked. In Delaware, we have seen a plateau and in Illinois we see the best news of a resumed decline.

In both New Jersey and Virginia, however, we see deaths continuing to climb, and in some cases by significant amounts.

If cases really have peaked in some of these states over the last week, we may expect deaths to continue to rise over the course of this week before beginning to fall again.

I also want to add two new graphics today. I have been trying to figure out how to cover the vaccination programme of the five states. Unfortunately, they do not all report the same data in the same way.

The graphic that perhaps makes the most sense is the one that looks the emptiest at the moment.

In order to resume “normal” lives, we need to achieve herd immunity. When we reach that level, the virus starves of new hosts and dies out. Broadly speaking, we have two ways of achieving herd immunity.

Option 1, let the virus run rampant and takes its course through the population. The benefit is that society remains open and people can return to cafes, pubs, shops, and museums. The cost is that millions get sick and hundreds of thousands die. Sadly, this is the route taken by Sweden and, unofficially, the United States.

Option 2, vaccinate the population. The benefit here is that millions do not get sick and hundreds of thousands do not die. The cost is that in order to wait for a vaccine and vaccination we would need to close cafes, pubs, shops, and museums.

The reality is that we chose something between the two. In the initial months, after we (belatedly) recognised the threat of the virus, we shut down our economies and stayed home. We chose option 2. You can see in the state charts above how that quickly helped us curb the spread of new infections.

Unfortunately, then the Trump administration chose to follow option 1 and encouraged states to “reopen” their economies. And because we never got the virus fully under control, we sowed the seeds for the explosive growth this autumn and winter.

But the vaccines are now here and the best bet is to vaccinate the population. How many people do we need to vaccinate? The exact number depends upon the infectiousness of the virus. Measles, one of the most infectious viruses out there, requires near 100% vaccination rates to achieve herd immunity. Thankfully, this coronavirus is not as infectious as measles. Early estimates placed the range at 60–70%. But lately, some epidemiologists have indicated the true number may be higher. Dr. Fauci of the National Institutes of Health (NIH) has said the true number is likely 70–85%.

This is why the new strains of the coronavirus we have identified in South Africa and the United Kingdom worry folks. Both appear to be more transmissible than earlier strains. Neither strain appears to be more lethal in its own right—although more cases means more people will die—but this increased infectiousness could mean we need an ever higher level of herd immunity, which means more vaccinations. And we’re already seeing the anti-vaccination support rising to somewhere in the range of 15-20%, just the threshold we could perhaps tolerate with the higher herd immunity range.

So what about the chart?

As we begin vaccinations, some states are reporting the numbers of people in their state that have been fully vaccinated against the coronavirus. I plot those numbers here. Pennsylvania, Virginia, and Illinois do so. Unfortunately, neither New Jersey nor Delaware does. I only have one data point recorded for Virginia and Illinois, and so they are not plotted yet, but both fall below the level of Pennsylvania, which has reported 0.50% of its population fully vaccinated. I have added a bar to show the range of estimated herd immunity we need.

And that gets us to the second new chart, the number of total doses administered per day.

Functionally this resembles the usual two charts. We track the number of doses administered daily and then plot their seven-day average to smooth out any day-to-day blips. Of course this means almost the opposite of those two charts as we are tracking the progress of people who will be immune from the virus.

The catch is that with the current vaccines we need two shots for a full course of treatment and not all states break the data down with that level of granularity. Again, we are looking at Delaware and New Jersey as they provide only the total number of doses administered. Now that’s still helpful, but it doesn’t give us the most accurate picture of what is happening with vaccinations.

But in order to make things comparable across five states, I have decided to use that broader, total doses administered metric for Pennsylvania, Virginia, and Illinois. (Virginia and Illinois provide another headache in that it reports the daily number of people fully vaccinated, but does not break down the number of full vaccination doses.)

So what is this second chart showing us?

Well, we are seeing a slow, nearly steady growth in the number of vaccines administered. The problem is that we need to see steep, nearly exponential line charts here if we want to have any hope of returning to “normal” anytime soon. Reporting tells us that the federal government’s approach to the logistics of vaccine distribution has been…not great. (Although at this point, perhaps that should not surprise us.)

Until we see these second charts begin to show more exponential growth, the first charts of the number of people fully vaccinated will be far below that herd immunity threshold we need to see.

Covering the vaccines in addition to the virus is a bit more work, but I’m going to try and cover them both over the next several months as I have with the outbreak itself.

Credit for the piece is mine.