Category: COVID-19

Here’s a bunch of views from the Arizona Dept of Health Services.

Cases per Day

“As you get further on and the infections become less severe, it is much more relevant to focus on the hospitalizations as opposed to the total number of cases,” Dr. Anthony Fauci

Hospitalization Stats (by Day)

Discharges are one of the best data points for showing positive trends in hospital capacity. Normally, discharges peak right before the hospital bed use peaks. There was a peak of discharges around 12/1 that signaled the bed use decrease you can see to the right of the chart above. I wonder if the second discharge peak we’re seeing now signals a larger bed use decrease?

Deaths

Deaths were already trending lower before Omicron arrived, but they might be trending much lower (need another week or two to know for sure).

Other Visualizations

Here’s my standard Case Rate (color) and Acceleration (Diameter) chart. What do we see here? It does seem like the higher rates and accelerations are in the more dense parts of the country. Prior to Omicron’s arrival, the brighter colors were trending in the northern (colder) parts of the country. It appears like the case breakouts are trending more southern now. We can see big outbreaks in Miami, Denver, El Paso, and NYC.

Data Tables

Note that a lot of states seem to not be reporting (Delta_Active is very unlikely to be zero right now). Case Rates (IROC_confirmed) are through the roof for most states. Deaths appear very low considering the case acceleration.

Things that make you scratch your head

Here are two charts that I put together a while back when it became clear that the states with higher vaccination rates were doing much better than the ones with the lowest vaccination rates. Now we see opposite behavior during Omicron. I’m not really sure how to explain this. Weather differences?

What do we see here? Pretty much all of these states (not New Mexico) is sharply accelerating cases per 1000 right now. The states on the top are accelerating at a much lower rate. My guesses are weather and higher density, but those are just guesses. Other ideas??

Virulence: Virulence is a pathogen’s or microorganism’s ability to cause damage to a host. In most contexts, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to cause disease—is determined by its virulence factors. (Wikipedia)

Here’s some Images from the Arizona Dept. of Heath Services data dashboard that I think tell a story that could indicate decreased virulence of the Delta variant.

1. COVID Cases by Day in Arizona – Entire Pandemic: In the image below we see the cases per day since around April of 2020. You can easily see three surges of cases. The first happened in the summer of 2021 and coincided with a huge, relatively uncontrolled outbreak in Northern Mexico. Many of the cases during this time occurred in border counties of Arizona. The second surge occurred in the winter of 2020 where the entire U.S. saw a spike of cases that correlated with the average daily low temperatures dropping to below 40 degrees. The latest surge corresponded with the more-transmissible Delta variant and has seen two spikes. This surge has been less of a spike and more of a “slog” where perhaps we are seeing the combination of the arrival of the Delta variant in the late summer merge with the more traditional cold-weather pattern for a virus where the night-time temperatures drop. Understandably, the lack of relief is wearing out health care workers and challenging hospitals. Note that the number of cases per day for the second spike of the Delta outbreak is roughly equivalent to the first summer outbreak.

2. Hospitalization – Cases by Day: Below you can see hospitalization for the three major outbreaks. The winter outbreak hospitalization by day far exceeded the first summer outbreak. Likewise, the first summer outbreak’s hospitalization per day is just under double the peak of the Delta variant outbreak. The only problem with the Delta outbreak is that it is lingering. Similar cases per day and less hospitalization per day. Just over a longer time. This naturally creates problems in hospitals processing sick people through their system due to the need to navigate bottlenecks that form. Just like in a factory, bottlenecks are going to be less of a problem in a quick surge of production than they are in long, tiring runs of production where errors and inefficiencies compound.

3. Deaths per Day: In the image below, we see similar patterns to hospitalization. If you look closely, you can see that the peaks of the deaths are a week or two behind the peaks of hospitalizations. Again, we see the same pattern as we see with hospitalization. Though cases during the Delta wave are roughly equal to the first summer wave, the deaths are around half.

Thoughts

Does this data show that Delta variant is less virulent than the preceding variants?

Perhaps. It’s quite possible that during the first summer wave we did a worse job of measuring cases. COVID tests are pretty ubiquitous now in late 2021 and maybe we’re collecting a higher percentage of the cases. Conversely, it’s also possible that people have inferred or imagined that Delta is less of a risk to them and are not getting tested if they experience mild symptoms. Either of these could be true and both would impact the usefulness of the case number. Additionally, the new variable of COVID vaccinations that was introduced in early 2021 has certainly reduced the impact of the Delta variant. It would take some work to decipher whether the virulence of Delta to unvaccinated people was equal or less than previous variants.

This is one of the challenges of measuring cases for the purpose of scientific analysis. It is very hard in a real-world study to control for the measurement variables across numerous regions and measurement authorities (governments, hospitals, universities). This is one of the reasons why we still don’t know much about this virus, despite having measured it for around a year and a half.

My Opinion: Oftentimes the concerns around measures will balance out when data is considered in very large batches (“big data”). My suspicion is that human nature is the constant across the measurement of all of these surges and we can take what is presented to us and assume that Delta is less virulent than the previous strains, either due to the virus itself or due to the boosts to our immune systems from either natural immunity or the COVID vaccines that most people have received.

Omicron and the future: We’ll continue evaluating the hospitalization and death metrics in the context of cases. My suspicion is that as Omicron arrives, it will dominate and gradually eliminate Delta and previous variants still lingering out there. If Omicron is less virulent, perhaps then we’ll see a leveling off of the cases to some background number and then we can say that COVID-19 has become endemic. If Omicron is not less virulent, then we’ll have a rough month or two ahead of us.

I took a bit of a pause on monitoring COVID during the Delta outbreak as at some point, people seemed to be much less interested. However, I’m hearing folks with questions now that a new, more contagious variant has emerged. A recent pre-print paper (not peer reviewed yet, so might be revised in the future) shows that the omicron variant multiplies 70x faster in airways but 10x slower in lungs. This explains why the variant appears to be more contagious but less threatening than Delta. See here for a pretty good description of the findings.

Might Omicron be a Good Thing or a Bad Thing?

Some reports predict that the faster-spreading variant will create more risk for humans, especially since it seems to evade the defenses from vaccinations to some degree. Others are reminding us that most pandemics end with a very virulent but less threatening variant that out-competes all of the more deadly variants. This is how the Spanish Flu ended. Hopefully the latter possibility is true, but time will tell. There are already reports from South Africa that hospitalizations (or at least severe ones requiring oxygen) are significantly down under omicron than they were during a similar period of the delta outbreak there.

Latest Data – Before the Wave from Omicron Hits

Here’s the latest data by state. I’ll include some recent state data tables later in the post for comparison’s sake. Note that the case rates have peaked up a bit in cold states over last week’s data. Perhaps this is the effect of Omicron or perhaps it’s just due to cold weather. Some states (like Arizona) have fallen down the list in the last two weeks.

Arizona County Comparisons

Here’s a view on the death rates and case rates across the top Arizona counties by population since about June of 2020. I found it pretty interesting for comparison’s sake. I see a couple of interesting things here:

1. Pima County, Maricopa County, and Pinal County all show nearly identical rates throughout the pandemic. Why is this interesting? Pima County — at least to my eye — has taken much more stringent public health measures than the other two counties from day one. Pinal County in particular seems to have gone out of its way to take as few public health measures as possible. But their rates and numbers are very similar (although Pinal County has fewer deaths per 1000 persons than Pima or Maricopa). What does this mean? No one knows for sure, but there is a strong indicator here that the measures we humans think will keep a virus at bay may not be very effective in the real world (vs. the lab).
2. Yuma County had the steepest surge during the summer of 2020, but the case and death rates have been very flat ever since. This could be due to a higher vaccination rate on this border county or might even be due to natural immunity. I have no idea.

Older State Data Tables for Comparison

Perhaps the below will be interesting to data nerds now or in the future.

State Data Table from 12/8/21

State Data Table from 11/30/21

State Data Table from 11/20/21

Hospitalization (Arizona)

One question that hasn’t been well addressed in the media (all political bents) is whether the COVID Delta surge was driving hospitalization and who, indeed, was being hospitalized. My thinking is that this is our prime metric of the danger of a COVID surge these days. Here’s a chart showing the Arizona hospitalization numbers by demographic. It’s a bit messy for a couple of reasons: 1) Arizona keeps “catching up” on hospitalization numbers by dumping large count backlogs into a single day. I suspect this is a hard metric to keep up with due to all the hospital systems in the state and their state of enthusiasm (?) about reporting data… 2) I stopped capturing the daily snapshot from AZDHS’ web site sometime in May when the data got really boring and moved to weekly (or so). This means my trends aren’t as granular as before, but they’re still accurate.

What do we see above? Note that at the left of the chart, the hospitalization by age is fairly random and driven by low numbers and statistics. However, if you can ignore the glitch in the middle, the trend is pretty clear towards the right (the Delta Surge). Hospitalization numbers are clearly trending up (but are still not significantly higher than in May. What does this trend reveal? Surprisingly, the over65 age group is still getting hospitalized at much higher rates than their percentage of the population would indicate. No way to know if these are vaccinated people or not. That’s a big gap in the data. They’re matched in numbers by the much-larger 20-44 age group and followed closely by the 45-54 and 55-64 groups. The under 20 age group remains the least hospitalized. This seems to go against some of the news reports that are indicating that the Delta variant is having more severe outcomes in the youngest cases. That doesn’t seem to be the case right now in Arizona at least.

Below I’m showing the hospitalization numbers for all age demographics. As you can see, the Delta surge (furthest right) has not been surging in the hospitals the same way the earlier two surges did. Keep your eye on this chart as things move forward.

Cases – Pima County

In my county (Pima) the Delta surge has resulted in proportionately less cases than in the much-larger Maricopa County. My suspicion is that this is due to the notably higher vaccination rates in Pima County. But again, the big question is which demographics are getting infected during the current surge?

Again, ignoring the loss of granularity by my moving to weekly data capture, you can see the trending on cases from the lows of May until now. It’s no surprise that the 20-44 age group is leading the case counts. In general, across Arizona, this group is much less likely than older demographics to get vaccinated. Plus, there’s more of them. However, the most interesting part of this chart is that the under 20 group is the next highest increase in cases. This group is largely unvaccinated, but it’s not clear how many of them are between 12 and 20 and how many are under 12. This is an error in data collection “strategy” that’s been a problem throughout COVID. Perhaps no one expected at the start that the under 16 demographic (school age) would be so interesting for this pandemic. The rest of the demographics (more vaccination and older) are barely seeing any case rate uptick since May. So, again, fairly surprising that the youngest demographics are the primary ones getting the Delta variant of COVID. No doubt “breakthrough” cases are happening in vaccinated people, but perhaps they’re not symptomatic enough to get counted. Or maybe there are just very few of them (despite what the headlines would indicate).

I just show Pima County here, but statewide, the trend is similar. At the state level, the case rates in the older demographics are slightly higher than Pima county and the younger demographic case rates are noticeably higher. This, again, is driven by the much higher rates and lower vaccination in huge Maricopa County.

Deaths

There isn’t much change to death rates during the Delta surge from the low period of May. Deaths are still very low, as you can see from the height of the stacked blue and red bars in the chart below. The only thing that *might* be interesting is that the ratio of deaths in the over65 demographic to deaths in every other demographic is much lower now. Sometimes we see this when deaths are low, but during the two previous surges, this ratio trended between 2.5 and 4. Right now it ranges around 2 or lower. This ratio is the green line in the chart below (and the red bars are “over65” deaths and blue bars are “under65” deaths). What might this mean? Again, I suspect it is the power of the vaccine to limit deaths in the over 65 community. I keep tracking this number and I hope that it doesn’t trend up again.

This may not be surprising at all, but the states with the lowest rates of vaccination are seeing case accelerations but the states with the highest rates of vaccinations are only seeing linear case rates. See below.

I’m not sure what to make of the interesting spread in cases per 1000 across the 8 highest vaccinated states. Perhaps this makes the case that different approaches to state intervention yielded different results. New Mexico, for instance, had some of the more disruptive lockdowns and you can see that they flattened out earlier than New Jersey or Washington. But regardless, you’ll note that only a couple of these states have any case rate increase at all right now. However, the top chart shows states that have tended towards less government intervention and perhaps this is the reason their vaccination rates are low.

By County in AZ

I also see this result by county in Arizona. The highest vaccinated counties are all near the border (Yuma, Pima, Santa Cruz, Cochise) or near large Native reservations (Apache, Navajo, Coconino).

You’ll notice on the table and map below that these counties all have the lowest case rates and accelerations. In the map, the warmer colors represent higher case growth rates and the bubble diameter represents Zip code population. This shows the higher case rates are all in the counties with lower vaccination rates.

Death Rates

I’m not including any slides on the death rates. They’re still low across the board compared with earlier outbreaks, but the states with lower vaccination rates do have slightly higher slopes, it seems.

Hospitalization (ICU beds)

It’s hard to know what’s going on with the ICU bed usage rates… You may notice that for about a week the numbers have plateaued. This could be a data collection issue, or it could be that the hospitalization rate for ICU beds has slowed. I have noticed that COVID discharge rates seem very strong, so this might be a testament to hospitals improvements in treating serious COVID cases. I continue to track this metric.

As always, I’m capturing the state of the COVID pandemic through data. See below for the latest data across the US on the “Delta Surge”.

Current US State Status

Above is the standard Data Table that I build from the Johns Hopkins COVID data. You might note that the Case Rates (IROC_confirmed) and Case Accelerations (dIROC_confirmed) are increased over the previous two posts here and here. The rate that Lousiana’s case rate is increasing is surprisingly high… perhaps the highest acceleration I’ve seen yet for a whole state. This may be another data point demonstrating how quickly this delta variant spreads.

Hot Spot Counties

Above we can see a number of interesting things about the current Delta outbreak. First, the Louisiana Parishes at the top have really high rates and accelerations. This is one of the big reasons the whole state of Louisiana is surging. The top three parishes are all medium sized parishes that sit in between Baton Rouge and the New Orleans area, so perhaps their outbreaks are related.

The case rates and accelerations continue to inch upwards in the previous hotspot areas (Missouri/Arkansas border and Jacksonville, FL, area) but they’re not racing up anywhere near as quickly as Louisiana.

Finally, despite all these new cases, death rates are still extremely low… about 5 to 10 times lower rates of deaths per 1000 persons per day than back in January during the winter outbreak. For instance, Apache County, AZ, had the highest case rate in the state at this time (.728) but had a death rate of .033. Compare to any of the counties in the table above. They all have higher case rates than Apache County during January of 2021 and the highest death rate I see is .0082 in Phelps County, MO.

All I can take away from this is that 1) the Delta Variant is less deadly than the variant spreading in January, 2) our medical system has gotten much better at treating COVID, or 3) the deaths are lagging and we’ll start to see them showing up later. Of course we have the variable of vaccinations present now which could be impacting 1) above by making the virus less deadly in a society of a mix of vaccinated and unvaccinated victims.

Hospitalization Status in AZ due to COVID

Above is the current status from the state of Arizona of hospital beds. The Arizona case numbers are creeping up but are still relatively low (see below). Hospitalization (ICU) due to COVID is increasing, but it hasn’t yet hit the rates that were seen even in April of 2020. The trend here will be a good indicator of how serious this Delta outbreak is.

Here are the latest updates for those of you who want to see the data.

COVID by State

The most interesting thing to note from above is that the acceleration column (dIROC_confirmed) is getting larger in the top 15-20 states ranked by their Case Rates (IROC_confirmed). See my post from July 15 to see the difference. You’ll also note that the case rate is increasing pretty much across the board, but for most of the lower-ranked states, it’s a small increase. So where (which counties) are driving these increases?

COVID by County

So we’re continuing to see a large case rate in some rural Missouri and Arkansas counties. Nassau and Duval Counties in Florida have jumped onto the list. These two counties are both in the Jacksonville metro area. If you add Camden County, Georgia, (just north of Nassau county) into the mix, it looks like some sort of local spread event, perhaps. The outbreak might have begin in Camden County and worked it’s way down… This article from mid July indicates that only 28% of eligible people in Camden County had been vaccinated. This Jacksonville, multi-state metro area has an overall case rate and acceleration that might be driving much of the overall Florida numbers.

Therefore, I see basically three major local events in the top 20 or so counties: 1) Arkansas, Missouri, Oklahoma border area 2) Jacksonville, FL, metro area, and 3) Midland, TX (why?). This leads me to believe that this variant IS extremely transmissable — it has spread pretty quickly in these areas, but I believe these areas have relatively low vaccination rates.

Arizona COVID by County

Above is the data for Arizona as of 7/24. Here we see the bottom four counties in case rate (and all with pretty low accelerations too) along the border. Note in the NYT visualization below that Pima, Santa Cruz, and Coconino Counties all have pretty dark colors, i.e., high vaccination rates. Mohave, Pinal, Maricopa, Greenlee, and Yavapi Counties all have the lowest vaccination rates. This is similar to what we see above… the Delta variant seems to be growing fastest in low-vaccination areas. I’m not sure if this trend holds… things may change. But for now it does seem like Delta is very transmissable, but very localized (and possibly highly correlated with low-vaccination areas). And fortunately, as you can see, deaths remain very low as of this date.

Above you can see in my map of case rates and accelerations by counties there are a couple of large regions of outbreak. One hovers over the Arkansas, Missouri, and Oklahoma border areas and the other hovers over Jacksonville and S. Georgia. This is a pretty good picture of how non-uniform the current COVID Delta Variant outbreak is. The outbreaks also appear to correlate strongly with the low vaccination (light green) areas on the NYT visualization.

I’ve been seeing lots of articles alleging that the rate of infection is shooting up across the country. LA County is re-ordering the wearing of masks indoors, even by people who have been vaccinated. Does any of this make sense?

Above you can see the current rates. Anyone who has read this blog for a while is likely to notice that the case rates for each state (IROC_Confirmed) are still quite low (see the table for April 28th here for a comparison). If you look around at my older reports you’ll find that Arkansas’ rate of .229 cases per thousand persons is a pretty low rate compared to previous leaders which were 3 or more times higher. But are the rates growing each day (accelerating)? In some states we see non-trivial accelerations. Nevada’s acceleration (dIROC_Confirmed) is causing the case rate to increase by .0171 cases per thousand every day. Missouri is at .0182. However, most states’ accelerations (while they are non-zero) are fairly small. Texas is pretty close to zero. My guess is that their case rate is falling. California doesn’t even show up on this list (their case rate is .031 and their acceleration is .0021).

I suspect that some of the panic amongst our journalists is the fear of the case rates doubling or tripling again like they did last summer. Or perhaps there’s just not enough to write about? If you look below, you can see that there ARE some counties that have really high rates. Most of these are in Arkansas and Missouri. As these states share a border, this appears to be a local situation more than a US national trend. You can see that the case rates in Baxter County, Arkansas (in the north of the state near the Missouri border), are about 4 to 5 times higher than the overall state rate. The second highest case rate is in Taney County, Missouri, which is quite close to Baxter County. I can’t figure out why the case rate is high in Midland County, Texas. There’s nothing about an outbreak on their County COVID website, so who knows.

Do take note however, that the rate of deaths is extremely small. This is likely to do with the better resistance that vaccinated people’s immune systems make to an infection.

Los Angeles County Case Rates over Time

Below you can see the Confirmed Case curve for Los Angeles. An increase in slope is barely perceptible today, but you can see that cases have essentially been flat since about February.