Lafayette School Corporation’s COVID-19 plan

At the end of June, the Lafayette (Indiana) School Corporation sent parents its 2021-2022 school year COVID-19 plan. After a reasonable approach to 2020-2021, I’m disappointed with this plan. This plan seems to embrace the “pandemic’s over!” mentality. The pandemic, of course, is not over.

The pandemic is particularly not over for children under 12, who are not yet eligible for vaccines. LSC, being a K-12 school district, has roughly half of their students ineligible for vaccination. Thankfully, the effects on children have largely been minor-to-none, but there’s no guarantee that this will continue to be the case as new variants develop. In addition, students may live with adults who cannot get vaccinated or have compromised immune systems.

The district dropped the mask requirement on July 1, regardless of vaccination status. And vaccination is not required. I hope that changes when the vaccines receive full (not emergency use) approval from the FDA. I am not optimistic it will. Masks will still be required on buses.

The district says “Social Distancing will be a high priority.” But how? When ~20 percent of students were e-learning, this allowed for additional spacing. Now that all of the students will be back in the building, this is going to be very difficult. I doubt that the district has overhauled the ventilation systems in schools, and with no mask mandate, I expect we’ll see a lot more transmission in the schools.

An e-learning option will be available but only if a doctor says it’s “in the student’s best medical interest” and the school administration approves. This offends me. If a doctor makes a medical decision, who are the school administrators to say otherwise? I wouldn’t go to my kids’ pediatrician to override the curriculum.

The state legislature has been remarkably stupid in response to the pandemic. I suspect the school district is just trying to avoid the wrath of the legislators and Attorney General. Unfortunately, they’re doing it by giving up on any meaningful protection of the students.

Indiana COVID-19 update: 27 March 2021

I haven’t written an update in nearly two full months. This is only slightly due to laziness. Mostly, it’s because the state’s numbers have been unremarkable. I mean that in a good way. We’ve consistently trended downward in infections (and positivity), hospitalizations, and deaths. However, we seem to have reached the floor and I’m concerned that the early indications suggest an increase. As usual, I am updating my dashboard most days.

Changes in trends

Five days in the past week (including the three most recent) had a daily increase in the hospitalization count. Two days had a 7% or greater daily increase. These are some of the largest increases on record. The hospitalization count is 12% higher than a week ago. Meanwhile, we’ve had a full week of week-over-week increases in positive cases. Only one day in the last 10 showed a week-over-week decline.

Daily and week-over-week changes in COVID-19 hospitalizations in Indiana.

Deaths continue to slowly trend downward, but if the increase in hospitalization holds, expect an uptick in deaths soon. After under-predicting the deaths during the surge in the fall, the Institute for Health Metrics and Evaluation (IHME) models are consistently over-predicting deaths. However, it does not appear that the most recent model run takes the end of the mask mandate (see “Changes in policy”), so it will be interesting to see how they fare in a month.

Observed and forecasted COVID-19 deaths in Indiana.

Changes in behavior

The IHME’s latest policy brief says mobility in Indiana is 8% below the pre-pandemic baseline. This is a big jump from the 20–25% of just a month or so ago. Meanwhile, mask usage has fallen slightly to 72%. Given these, it’s not hard to see why the numbers are picking back up again. These are both trends specifically called out as factoring into the “worst-case scenario.” (Note that the “reference scenario”—or most likely scenario—is what I plot on my dashboard.)

Changes in policy

Governor Holcomb announced earlier this week that the mask mandate will be gone on April 6. This is bad policy. While all Hoosiers 16+ will be eligible for vaccination beginning on March 31, the earliest a newly-eligible person will be fully vaccinated is April 14. And that assumes that the person can get the vaccine that day and that they receive the one-dose Johnson & Johnson vaccine. Recall that the CDC says people reach full vaccination two weeks after receiving the last shot.

In other words, in the impossibly-best case scenario, the mask mandate ends a week before the state’s (adult) population is fully vaccinated. The more likely case is that we don’t hit the 70% threshold for weeks, perhaps months. Holcomb says “Hoosiers know the science” and will continue to wear masks and follow distancing guidelines once the mandate becomes an advisory. I wonder what Hoosiers the governor has been talking to. Considering how many crowded restaurant parking lots and improperly-worn masks I’ve seen in the past week, I don’t believe him.

This is infuriating, because a mask mandate is essentially free. This is particularly true given how little effort the state put in to enforcing it. Ending the mandate early sends the wrong message. We can only hope that vaccinations outpace the virus. We deserve better than this.

Indiana COVID-19 update: 5 February 2021

On Wednesday, the Indianapolis Star reported that a state audit discovered just over 1,500 “missing” COVID-19 deaths. These deaths were added to the Indiana State Department of Health’s dashboard on Thursday. The state “snuck” them in, not including them in the “newly reported” deaths for that day’s update. Fortunately, I had the data before and after and was able to produce some information on my dashboard.

It wasn’t as good as we thought

“Missing” COVID-19 deaths by day

The missing deaths stretch as far back as early April, but the bulk came in November through January. This is also when the overall death rate was the highest. On the whole, approximately 15% of COVID-19 deaths were not included on the state’s dashboard prior to February 4. But on 48 days, the missing deaths exceeded 20%. On December 18, 31 deaths (29% of the total) were missing. Instead of having a peak death count of 97, we’ve instead exceeded 100 deaths on several days with a peak of 118.

COVID-19 deaths per day before and after the “missing” deaths were included

I wrote in the last update that I thought deaths were missing, particularly given the abrupt drop in December. It turns out that I was more right than I could have imagined. “I’m not trying to sound like a conspiracy theorist,” I wrote. “I don’t think there was any malfeasance.” I’m trying very hard to continue believing that.

At the very least, this represents appalling incompetence. This isn’t just a problem for making graphs. The death toll of this pandemic is serious. Losing 15% of the deaths is not only disrespectful to the dead and their families, but it robs decision-makers of reliable data. What decisions would have been made differently if we knew the true death toll.

Of course, we may never be sure of the true death toll, particularly early in the pandemic. At the time, testing was scarce. I’ve heard anecdotes from several reliable friends of loved ones not getting testing after death. We can compare 2020’s overall death to previous years, but that will not be definitive.

The future

The good news is that the overall numbers continue to trend in the right direction. Yesterday, hospitalizations were below 1500 for the first time since October 20. Deaths, new cases, hospitalization, and positivity all continue to drop. Mask usage is up and mobility remains 20% below the baseline, per the Institute of Health Metrics and Evaluation (IHME). Perversely, the corrected death totals represent a positive of sorts: the recent model runs have proven more accurate than it appeared.

Observed and forecast COVID-19 deaths in Indiana by day

As best I can tell, IHME’s most recent model run did not include the adjusted death totals, so it will be interesting to see how much changes in the next update. The observed death trend is dropping at a faster rate than the models would suggest, but that may flatten a bit over the coming days. Still, the trends are encouraging.

Causes for concern

But all is not well. Although IHME’s latest model run does not show an increase in deaths through the end of May, they say some states will see that. But even more worrying, it appears some of the new variants may lead to reinfection in people who already have immunity.

The Novavax Phase III trial in South Africa placebo arm found that prior infection
provided no protection from variant B.1.351. The implication of this finding is that herd
immunity is only variant-specific; if this finding is confirmed in the Johnson & Johnson
placebo arm data, our worse scenario is likely too optimistic.

IHME COVID-19 Policy Brief for the United States, 3 February 2021

With the next update, IHME will incorporate cross-variant reinfection into the model. I’ll continue to update my dashboard with the new model runs as they’re available.

Indiana COVID-19 update: 23 January 2021

It has been over a month since I’ve written one of these. Part of that was because I had other things to do. Part of that was a lack of updated projections from the Institute of Health Metrics and Evaluation (IHME). And part of it was that I didn’t believe the state’s numbers. I kept updating my dashboard regularly, but it seemed like something was missing: deaths.

I’m not trying to sound like a conspiracy theorist. I don’t think there was any malfeasance. But the data doesn’t always come in right away. I’m not sure what the reporting chain is like, but there are probably a few steps before it gets to the Indiana State Department of Health. The latency increased in December, so I figured any day the numbers would catch up. The drop from 90 deaths a day to 45 was so rapid that it couldn’t be real.

Daily COVID-19 deaths in Indiana

Well I’ve been waiting for weeks and the trend has held. I’m not sure what happened, but about the second week of December the COVID deaths and hospitalizations plummeted. This is a very good thing, even if the explanation isn’t obvious.

The experts at the IHME model run from November 23 just about nailed it in retrospect. Subsequent runs seemed to over correct based on the state’s run of higher-than-forecast fatalities. The model run published yesterday comes closer to reality, but it is still running a bit hot.

Observed and IHME forecasted COVID-19 deaths in Indiana from March 1, 2020 to April 1, 2021.

The good news is that IHME’s U.S. policy briefing says the peak is behind us (although the model does not account for the recently-discovered strains that are more transmissible).The briefing isn’t all good news, though. Looking forward to teh end of the year, IHME has this to say:

We do not expect the US to reach a level of herd immunity that would prevent a third wave next winter. This is because a quarter of Americans state they will not take the vaccine and a further quarter state they are unsure. In addition, we do not have clear evidence on how much vaccination stops transmission as opposed to preventing severe disease and death. Scale-up of vaccination does mean, however, that the number of deaths in a third wave, if it occurs, would be greatly reduced.

Take the damn vaccine when it’s available!

Indiana COVID-19 update: 18 December 2020

It’s been a while since I’ve written one of these posts. Partly due to being busy, partly due to being burnt out, partly due to “how can I write ‘yep, everything is still terrible’ each week without repeating myself?”. And honestly, it’s been weird to realize that even though the situation in Indiana is worse than it has been at any point in the pandemic, it doesn’t feel that much worse to me. I realize how incredibly fortunate I am to be able to say that.

Since my last update, vaccines have received emergency use authorization and are in the early stages of being distributed. It will be months before we have widespread vaccination, but at least there’s hope. Of all the jobs I’m glad I don’t have, “decider of who gets vaccinated first” is one that I’m most glad about.

I haven’t made any major structural changes to my dashboard. The main difference is some tweaks to the model forecast graph to make it easier to read (I hope).

Deaths

Anyway, the Institutes for Health Metrics and Evaluation (IHME) model runs keep nudging the total fatalities up. This is a reflection of how rapidly deaths have risen in the last month. The latest model run brings us to a peak of ~102 daily deaths in Indiana on January 5. It seems to track the general trend in the reported data pretty well, if you ignore the last few days. As the number of deaths has risen, it seems that the counts now frequently go up significantly for two or three days after, instead of just the day after. If anything, the model may be too optimistic.

Observed and forecast death counts for Indiana.

Hospitalizations

There is good news, though. While October and November featured a rapid rise in hospitalizations, with new records set almost every day, that trend has largely reversed. Even with the Thanksgiving holiday, we’re starting to see declines in hospitalizations most days. If that holds for a few more days, we might get below the 3,000 mark for the first time in over a month. As it stands, yesterday’s hospital census had about 13% fewer patients than the peak on November 30.

Day-over-day (blue) and week-over-week (red) changes in Indiana COVID hospitalizations.

Despite the downward trend in hospitalizations, the available ICU bed capacity continues to hold steady near 20%. Interestingly, non-COVID cases are driving this, according to the state’s dashboard. COVID ICU bed and ventilator usage, while still much higher than over the summer, is trending downward.

What I’m watching

In the coming week, I’ll be watching to see if the lower death tolls the last few days hold. It seems unlikely that there’s such a sudden drop in deaths. Tuesday and Wednesday of this week had a bunch of backdated deaths added to the report. I would expect the same next week.

With the coming Christmas and New Year holidays, the testing and new case data is about to get unreliable. But I’m interested to see if the apparent uptick in positivity holds or if we return to the general downward trend of the last two weeks. As of today’s update, we’re at 12.4% for all tests (24.4% individuals) statewide. This is very bad.

Indiana COVID-19 update: 14 November 2020

Two weeks ago, I wrote “the news has been “good”-ish. More accurately: it’s getting less bad.” What an idiot. Since then, hospitalizations set a new record almost every day. Yesterday’s patient count was 52% higher than two weeks ago. We also set several new case records, including our first time above 5000, 6000, and 8000. We’re adding roughly twice as many new cases as we were a week ago, while only conducting about 35% more tests.

The Governor has finally given up on Stage 5 in favor of county-level restrictions based on weekly metrics updates. Doug Masson has a good discussion of it. It seems like where we should have been in September or earlier. I’m not sure how effective it will be, but it does seem to be relatively well-adapted to our current understanding, at least compared to previous plans.

The Institutes for Health Metrics and Evaluation (IHME) did not publish a new model run last week. I suppose there was other news that folks were paying attention to. Anyway, their new model run this week lowers Indiana’s peak death count slightly. It’s also earlier and with sharper ramp up and down times.

Observed and forecast death counts for Indiana.

The death count continues to exceed the October model forecasts, but it may be below the November runs. In the next few weeks, the increases in cases and hospitalizations will probably result in an increase in fatality.

Other than adding the hospitalization change graph below, I haven’t made any structural changes to my dashboard in the last few weeks.

Day-over-day (blue) and week-over-week (red) percent changes in hospitalization.

Indiana COVID-19 update: 1 November 2020

In the last few days, the news has been “good”-ish. More accurately: it’s getting less bad. Wednesday set a record for new cases with 3,626. That’s nearly 29% higher than the previous record and the first time above 3,000. The next two days were also above 3,000, but not record-breaking. Still, the rate of increase appears to be slowing.

The trends look better for hospitalizations, which seem to have plateaued just shy of this spring’s peak. Given the still-increasing positivity rate, I would expect this to be short-lived. It’s a welcome change, regardless. Statewide, Indiana is not showing the hospital capacity problems that some areas have seen recently. It’s not clear without digging into each county’s stats if there are areas within the state with that problem.

Similarly, the deaths have largely plateaued as well. We’re holding relatively steady at just above 30 deaths per day (although there still seems to be a gentle increase). This brings us closer to the Institute of Health Metrics and Evaluation’s (IHME) October 15 and October 22 forecasts. The October 29 forecast, while not dramatically different in methodology, shows a more rapid rise in deaths. The peak moves a little earlier in December, but is not much higher than the last two forecasts. It also has a longer tail. As of right now, it appears to over-forecast deaths compared to current observations. However, as more data rolls in over the coming days, that may change.

Apart from adding more data, the only change I made this week to my dashboard is to remove older forecasts from the comparison. This brings it in line with the forecast error graph and makes it a little easier to read.

Indiana COVID-19 update: 23 October 2020

I’m not going to sit here and try to come up with new ways to say “this is bad”. Not a lot has changed since the last update: the numbers are all chugging along on trend. There is a change to my dashboard, however.

I realized today that I had been pulling the wrong data from the IHME models. I had been entering the “best case” scenario that includes universal mask wearing and the like. What I should have been pulling from was the reference model. This results in higher predicted values.

The overall impact isn’t that great. The scenarios don’t really diverge for a while, so for the most part the model error graph is unchanged. The future, particularly late November and into December is where you notice a difference. The recent models still under-predict the deaths, but the general trend matches well.

IHME said in their latest update that they didn’t make many changes to the model for the latest run. It’s essentially the same as last week but with more recent data. Unsurprisingly, it’s pretty close to the previous run. Both of those have a lower peak than forecasts from September, but still 50% higher than the spring peak.

It’s worth noting that IHME’s model assumes that states will re-introduce restrictions at a certain point. I’m having a hard time seeing that happening in Indiana—at least not as quickly as IHME’s assumption would have it. I wonder how much of Governor Holcomb’s refusal to even entertain the idea of moving back a phase or several has to do with the election in a week and a half. After the election, he’ll either be a lame duck or he’ll be into his last term (sort of). That takes away much of the political risk.

Indiana COVID-19 update: 17 October 2020

I updated my Indiana COVID-19 dashboard with the latest numbers. It continues to look bad. Hospitalizations are up 15% in the past week. The new daily case record set yesterday is 30% higher than the record set a week ago. We had two days in the last four with 20+ deaths (and bear in mind that the recently daily numbers tend to rise rather significantly in the days that follow).

Most alarming is the latest forecast from the Institute for Health Metrics and Evaluation (IHME). Their 10/15 model forecast is now on the dashboard, and it continues to show a big upswing in fatalities through November and December. The models have been pretty consistent with underpredicting the death count lately, so the big increase in the last two runs is extra worrisome.

In order to get a better sense of the past and possible future, I plotted the observed deaths with each of the model runs I have in the spreadhseet.

Observed and forecast daily COVID-19 deaths in Indiana

While the early September runs were a little hot, none of them really captured the increase we’ve seen over the past few weeks. The last two runs (10/9 and 10/15) are the first two to fully consider the move to Stage 5, I believe. And it’s clear that the forecast is not looking kindly on that.

Indeed, the Governor’s move to Stage 5 looks worse and worse with each passing day. The state health commissioner announced earlier this week that she and her family tested positive.

Indiana COVID-19 update: 10 October 2020

I just updated my Indiana COVID-19 dashboard with today’s numbers. They are not pretty. The state set a record for new cases for the third consecutive day. Today’s increase was “only” 6.5%, which is an improvement on the 24% increase that yesterday’s new record represented.

Positive tests or positive individuals?

The number of tests administered is on the rise, but we’re testing far fewer individuals. In fact, we’re testing about 33% fewer people a day than we did at the peak in late August. That the state is focusing on the total positivitiy rate (5.2% over the last 7 days) as opposed to the rate of positive individuals (9.3% over the last 7 days) strikes me as deceptive.

I attribute the disproportionate increase in tests (compared to people tested) to school systems, at least in part. I know of teachers who have had to take several COVID-19 tests in the past two months in order to return to work after any illness that shares a symptom with COVID-19. While I applaud the schools for taking this seriously, it does lead to some misleading numbers.

Deaths and hospitalizations

On Thursday, Indiana hit 20 daily COVID-19 deaths again. Most recently, this mark was tallied on September 26 (21 deaths). The last time before that was June 14th. We have not had a day with single-digit deaths since September 21. The only stretch longer than that is the 68 days from March 28 through June 5.

Hospitalizations are up dramatically as well, as I mentioned in the last update. The current levels haven’t been seen since late May. Hospitalizations yesterday were 42% higher than on September 9 and 30% than two weeks prior.

Looking forward

The Institute for Health Metrics and Evaluation (IHME) released a new model run late last night. I have added that to the dashboard as IHME 10/9 and hidden the IHME 9/11 lines for readability. A few days in, and this run seems to be over-estimating Indiana deaths so far. This is a welcome relief, since the last month’s worth of runs have been pretty consistently running too low. Given that deaths tend to be reported over the course of several days, the model may end up being more accurate after all. IHME has not published the updated briefing yet, so they may have more to say about the changes in this week’s run.

IHME’s forecast assumes that states will re-implement restrictions when conditions deteriorate to a certain point. Assuming that is accurate, we’re looking at restrictions coming back in mid-to-late November. Under that scenario, the forecast calls for a peak of 66 deaths per day in early December (with a range of 35-105). That would exceed our April peak by 32%.

However, given Governor Holcomb’s decision to move to Stage 5 in the face of materially unimproved circumstances, I don’t know if we can depend on that. If we do nothing, or further ease the few restrictions left, the model suggests we could be losing over a hundred Hoosiers a day in late December.