AZ California Deaths FL New York Predictions Texas update

Leading Causes of Death

There’s no doubt that COVID19 will be a top 10 leading cause of death in 2020. This is quite impressive given that the other diseases on this list typically take YEARS to manifest and are NOT contagious.

The interesting question is… what will COVID19’s exact rank be at the end of the year? It’s been a while since I updated this chart. This graph always stirs up discussion, so I added some more sophisticated analyses to address concerns. Let’s see if I can explain it…

I estimated three COVID19 ranks for the US and 8 other states. I used COVID19 deaths (up to last night) and compared to 2019 causes of death.

Low estimate (green): This estimates COVID19’s rank if the pandemic ended yesterday (i.e. everyone with COVID19 was cured overnight). Unfortunately, we know this isn’t true, but this is the absolute MINIMUM rank COVID19 will be.  

Medium estimate (orange): This estimates COVID19’s rank if we continue on our death trajectory.

High estimate (red): This estimates COVID19’s rank if we continue on our trajectory AND we count ALL excess deaths as COVID19 deaths. I understand that, in reality, all excess deaths are not likely COVID19, but this is the HIGHEST rank COVID19 could be.

So, in the United States, COVID19 will lie between the 3rd (high estimate) and 6th (low estimate) leading cause of death in 2020. In reality, it will be somewhere in the middle. In March, we (epidemiologists) estimated it would be 3rd leading cause of death in 2020. Looks like that’s going to be about right.

In Texas, COVID19 will lie between the 3rd (high estimate), 5th (medium), and 9th (low estimate) leading cause of death. Again, it will likely fall somewhere in between by the end of the year.

For CA, FL, AZ, NY, LA, WA, and IL rankings, see the following graphs. This is all I could get done before my eyes started shutting last night.

Lately, the flu debate has come to surface again. In EVERY state, COVID19 lowest possible rank is still higher than flu. So, I’m not really sure why we are still having this conversation…

Love, your local epidemiologist

Note: Yes, the 2019 numbers will also change this year. But this is the best we got, as CDC only reports these in aggregate form at the end of the year. It will actually be interesting, though, how other ranks change. For example, we know car crashes (unintentional injuries) have decreased while suicide has increased.

Data Sources: 2019 data is from the National Center for Health Statistics at the CDC. COVID19 deaths is from Johns Hopkins (US). Excess deaths is from the Weinburg lab. Graphs/analyses by yours truly.

AZ California Deaths FL GA Texas update

Case Fatality Rates

On July 7, I posted five reasons as to why CFR may be decreasing while cases are increasing. One of which was lag time.

In other words, deaths today aren’t indicative of spread today, but rather a reflection of case severity 20-30 days ago. It’s been 27ish days since exponential growth started across several states. We should start seeing an uptick in CFR if this hypothesis is correct.

And we are. This is obvious in TX and CA. Doesn’t look like there is change in FL, AZ, or GA (yet). Given the spread among the younger population, this lag time may be even more than 30 days.

It’s still too early to see the impact of this recent uptick in TX and CA on cumulative CFR (Figure 2).

So, what’s causing this increase in TX and CA? Either we have reached hospital capacity (which we haven’t). OR COVID19’s reach is so wide it’s starting to reach vulnerable populations. OR we are increasingly testing those that are more sick (indicative of a high test positive rate). It’s likely a combination of the latter two. CFR is a difficult measurement because it’s highly dependent on the number cases we catch. For example, if we are only testing high risk populations (like nursing homes), the CFR will be high. It’s typically missing asymptomatic or mild cases that just never get tested.

Because of this, public health decision makers are starting to use Infection Fatality Rate (IFR). IFR estimates the fatality rate among those infected (detected AND undetected cases).

In the US, the CDC’s best IFR estimate is 0.65%. So, on average, 6.5 people of 1000 infected will die of COVID19. A recent publication pooled global IFR; IFR ranged between 0.53% and 0.82%. IFR is a more direct measure of disease severity, although highly dependent on place.

Understanding the true fatality rate has implications for public health planning. Unfortunately, if you thought the CFR was “low”, you are really not going to worry about 0.65% IFR. Given the reach of COVID19, this is still very much a leading cause of death in the US. The morbidity of COVID19 should still be of great concern too.

Love, your local epidemiologist

Data source: COVID19 tracking project. Graphs by yours truly.
Pooled IRC:…/10.1101/2020.05.03.20089854v4
CDC report:…/…/hcp/planning-scenarios.html

Hospitalizations Texas update

Texas Hospital Capacity

Texas hospital capacity.

Here is the updated data. Both per capita (COVID19 hospitalizations per population) and capacity per TSA region.

It’s been 9 days since my first hospital capacity post (June 28) and we can see dramatic differences in numbers (look at the orange in Figure 2 compared to Figure 3). This can change FAST.

As a reminder…
-COVID19 (for hospital data) is defined as confirmed and probable (see previous posts for the definition of probable)
-A hospital bed can only be “avaliable” if staffed
-Capacity INCLUDES open and staffed surge units. So we will likely never reach “100%”, unless we run out of stadiums or staff first. However, given that capacity is over 90% AFTER including surge units is… interesting
-Including surge units also probably explains why we DONT see changes in orange in some places, like DFW. This is likely due to surge units opening up at the same rate as COVID19 hospitalizations, NOT because hospitalizations have remained steady over the past 9 days.
-We are updating our dashboard to include this graph (along with other things). You will have this data soon (and I don’t have to keep re-posting updates).

Love, your local epidemiologist

Data Sources: DSHS, figures by me

Deaths Texas update

Case Fatality Rates

A hot topic. Specifically, because Case Fatality Rates (CFR) are decreasing, while cases are increasing. Which seems counter intuitive.

I’ve seen several hypotheses floating around explaining this phenomenon:
1. Lag time. Scientists have estimated that CFR lags 14-30 days due to disease manifestation and spread to vulnerable populations. So, for example, the CFR on July 7 isn’t reflective of the cases on July 7 but INSTEAD is reflective of the spread on June 5. Exponential growth started in Texas on June 15ish and 30 days have yet to pass. We may see this start to increase here soon. This delay has a big impact on CFR (see how different the 14-day lag compared to the 30-day lag is in the Figures).

2. Younger populations. Younger people are contracting and spreading COVID19, which mean younger people are going to the hospital more, but once at the hospital they are dying at a slower rate. Keep in mind that “not dying” is not the same thing as “fully recovering”. The younger population also might contribute to #1 (lag time). If there is a lot of spread among younger populations, then the time for COVID19 to get to the more vulnerable will take longer.

3. Treatment. Compared to the beginning of the pandemic, doctors have figured out better ways to treat COVID19. For example, dexamethasone cuts risk of death on a ventilator by 1/3 and those on oxygen by 1/5. Also, plasma transfusions have helped patients recover.

4. Mutation. Since the pandemic started there have been 33 COVID19 mutations. Scientists recently published that the latest strain MAY be more contagious. Could it also be less deadly? There still needs to be a LOT more studies on this, but an important question.

5. Hospital capacity. Texas hospitals have held their own. BUT if cases don’t stop rising, hospitals in some areas will run out of surge units, staff, supplies, etc. If this happens, CFR will increase again regardless of #1-4.

CFR decreasing is fantastic. It’s likely to a combination of the 5 above. However, I’m skeptical that it will stay this way. Unfortunately, only time will tell the bigger picture.

It’s important to note that even if CFR is decreasing, 2% is incredibly devastating. In Texas, COVID19 still is the 7th leading cause of death and 3rd leading cause of death in the US. Compared to other leading causes of death (heart disease, cancer), it’s only been around for FOUR MONTHS and is contagious.

Love, your local epidemiologist

Data source: DSHS. Graphs by yours truly.
Mutation study:…/10.1…/2020.06.12.148726v1.full.pdf
Dexamethasone study:…/10.1101/2020.06.22.20137273v1

Hospitalizations Texas update

Hospital Capacity

Texas hospital capacity.

Figure 1 are the official numbers reported to the state. There are several Texas regions over 80% occupancy: Dallas, Houston, Laredo, and RGV. But they seem to be holding their own since my last post. So, looking good… right?

Well, it’s really important that we keep in mind that hospital capacity is a moving target:

1) Hospitals have been opening surge units. In other words, they have been increasing their capacity. If we don’t account for this surge increase, we will never reach “100% capacity” and hospital numbers will continue to be around 80% (and looking great), when in fact, numbers are NOT “normal”;

2) Hospitals can ONLY report available beds to the state if they ARE staffed. So, if a staff member gets sick or takes a vacation (which they should!), the total number of beds will DECREASE for that day.

That brings us to Figure 2. I generated a new category “surge units”. This category accounts for the two moving targets since June 21. By doing this, we can see the impact of opening surge units. Some regions would be in BIG trouble if they didn’t. If the Houston region didn’t open surge units, they would be OVER 90% capacity. Even worse, the San Antonio region wouldn’t have any beds. In fact, they would be short 350 staffed beds.

Translation: Keep in mind these moving targets in mind when these numbers are reported by media.

Love, your local epidemiologist

PS. A few notes:
1. I realize Figure 2 only includes a few select TSAs. This is because I only recorded June 21 data for a certain number of TSAs (and the state does not make historic hospital data available). I’m kicking myself.
2. Figure 3 is TSA region. Texas is so large that epidemiologists use these regions to describe patterns. Counties are within TSA regions.
3. I know a lot of you are interested in ICU capacity. While I have the # of COVID patients in ICU, I do NOT have the total number of ICU beds in each region. So I cannot calculate ICU capacity in each region.

Texas update

Month of June

Well June wasn’t pretty.

In the US, there were 21,937 COVID19 deaths and 826,350 cases.

June was especially bad in the South and West. Figure includes new cases per population in AZ, CA, FL, TX, and NY (as a control). I also included new cases during NY’s peak (in April- dotted line). At NY’s peak, 49 people per 100,000 had a confirmed case of COVID19 each DAY. This is the worst infected place in the United States. But this was also at their peak; during a FULL state-wide shut down. AZ is very close behind. As of yesterday, AZ had 41 people per 100,000 confirmed with COVID19 in ONE day. And they aren’t at their peak and don’t have a state-wide shut down. FL is really close behind.

I also included test positivity rate (TPR) in June. This is important to track. In March, the WHO suggested not opening a state/country until TPR (# of positive tests divided by # of total tests) was 5%. Testing does NOT have a direct benefit because there is no cure. However, there ARE a number of indirect benefits: 1) public health officials know the “true” rate of infection and can deploy resources to the right areas to stop spread; 2) psychologically if someone tests positive then they are more likely to quarantine (hopefully).

AZ, TX, and FL have some serious testing issues. This needs to be changed FAST. TX is in particular trouble with federal testing sites closing today. Interestingly, CA has a great, steady TPR, but COVID19 is spreading rapidly. So, this could mean that public health resources (like contact tracing) need to be more strategically deployed OR people are knowingly positive and still going out in public.

Let’s make July a bit prettier…please?

Love, your local epidemiologist

Data sources: COVID19 tracking project. DSHS. Graphs and analysis by yours truly. Some details (because I know some of you will ask)…. State analyses are 7-day moving averages, which makes graphs much more smooth (and accurate) because of reporting behaviors. The testing data is ONLY confirmed viral tests. State figures are daily cases. Texas figures are cumulative cases.

Hospitalizations Texas update


COVID19 hospitalizations and hospital capacity across Texas. Updated my graphs from a few days ago. These are confirmed COVID19 hospitalizations (not presumed).

There are some regions that are doing great! But others not so much. I would still be worried about RGV, San Antonio, Houston, and Dallas.

With the opening surge units, hospitals are doing a fantastic job of keeping bed capacity around 80%. This is just in terms of # of beds. We don’t have data about staffing.

Many (I mean many) of you had the great suggestion of adding hospitalization data to our dashboard. And we are…to an extent. Hospitals are keeping their data very close to their chests. And I would too. They have been operating in the red zone for the past 3 months. I was on a call last week in which one hospital system said they are losing $500 million per DAY. People are avoiding hospitals so they aren’t exposed to COVID19. However, some NEED to be going to the hospital and are not. This will have grave consequences on their overall health (and financial implications for hospital systems).

Love, your local epidemiologist

Dashboard Texas update

Dashboard 1.0

For the past 2 months, my colleagues and I have been up at all hours of the night working on a dashboard for our Texans. It paid off because it is finally LIVE!!!

I know we all have a billion dashboards to go to, but this is the best. Why?
– We include data for all 254 counties in one place. I think this is especially important for our smaller, rural counties in which access to information has been more difficult
-You can filter by TSA region and metroplex AND control for population. Something that is very much missing in a lot of dashboards.
-We include interpretations for the graphs. This dashboard was not made for scientists. It was made with our community members in mind and hope the interpretations are as clear as possible. If not, please let me know!
-We have no political gain from this. We are just a bunch of overworked, data geeks at a University with no conflicts of interest. We just want to help keep this COVID19 pandemic as transparent as possible. And, quite frankly, we have a lot of fun doing it.
-PhD students help with all of the analyses and data cleaning. We are training the next generation to better disseminate scientific and data-driven information.

I will continue to post on here, but feel free to roam around our site with your morning coffee. Access to this site is best by computer and tablet. We are still formatting for phones.

Also, we continue to work on this. We are adding mobile data information, hospital data, symptom tracking information, and much more in the next few dashboard phases.


Love, your local epidemiologist

Hospitalizations Texas update


There are many angles to hospitalizations. And I’ll try to show you a comprehensive picture. Each of these graphs tells a slightly different story. This data is up to date as of June 25 at 4:00PM.

Figure 1 & 2: Number of COVID19 hospitalizations over time. These two figures basically show the same thing: an increase since June 1. Overall, Texas has had a 62% increase in COVID19 hospitalizations since June 1. This increase, though, vastly ranges across regions (Figure 2). There are some TSA regions (Corpus Christi, Rio Grande Valley, Waco, San Antonio) that have a higher than 80% increase in the past 25 days. This means COVID19 is spreading FAST in these areas.

Figure 3: Number of COVID19 hospitalizations on June 25 after taking into account population. This is important because it may look like some places are increasing but may not be too concerning considering their population. Once we control for population, Rio Grande Valley and San Antonio have a lot of very sick people in their population. Houston has now come in the mix. This means there are a lot of very sick people in Houston, but it’s not increasing at the rate of Rio Grande Valley and San Antonio. You can see Waco and Corpus Christi are at the other end of the spectrum now. This means that while COVID19 is spreading at a high rate, the rate of sick people isn’t as worrisome after controlling for their population.

Figure 4: Capacity. There are now 5 areas over 80% capacity: Dallas, Houston, Galveston, Rio Grande, and Corpus Christi. This IS accounting for hospitals ALREADY increasing capacity by opening surge units. Halting elective surgeries will also help.

Translation: We should be most concerned about Rio Grande Valley- COVID19 is spreading FAST, they have very sick people in relation to their population, and are close to full capacity in hospitals. I would also be very worried about these hospital capacities, which has the gravest implications.

Love, your local epidemiologist

Data source: DSHS. Graphs and analyses by yours truly.

Deaths Leading Cause of Death Texas update

Leading Cause of Death

I’ve seen lots of comments about the low COVID19 fatality rate in Texas.

Although 2% seems low, it’s relatively high compared to other causes of death in Texas. If we stay on our trajectory, COVID19 will be the 7th leading cause of death in Texas this year. COVID19 would average 20 deaths per day compared to, for example, stroke that caused 30 deaths per day in Texas in 2019. This is impressive considering stroke and diabetes and heart disease take YEARS to develop. COVID19 has only been around for 109 days and is contagious.

There are a few things that can/will change Texas’ COVID19 rank this year:

1) Overflow hospitals. Many Texas metroplex hospitals are opening up “surge” units and scrambling for qualified staff. Less people will survive due to less quality of care. This will INCREASE COVID19’s rank.

2) Spread among populations. As I said in my previous post, CFR is decreasing in TX because of spread among younger populations. However, the far reach of this disease may start impacting the circles of younger populations, including those at high risk and kids. This will INCREASE or DECREASE COVID19’s rank. We just don’t know yet.

3) Other deaths will shift. The figure is comparing COVID19 deaths to 2019 deaths rates for other diseases, which isn’t necessarily an accurate comparison. A global pandemic WILL have impact on how we die other ways too. For example, some of the chronic lung disease deaths that WOULD have been in this category are now in the COVID19 category. On the other hand, unintentional injury (like motor vehicle crashes) have decreased. These shifts will INCREASE or DECREASE COVID19’s ranking, we won’t know HOW until the end of the year.

4) Counting “deaths”. This is very complicated. In short, the number of “COVID19 deaths” could (and are likely) off. The only way to “truly” know is through examination of death certificates. This is done each year by national organizations, but certainly not at a pace that the public wants. The problem is that states and hospitals and counties count covid19 deaths differently. Also, in the beginning of the pandemic, no one was getting tested for COVID19 but still dying, so we think the deaths could be underestimated. Again, this will INCREASE or DECREASE COVID19’s ranking, we won’t know HOW until more time passes.

If we stay on our trajectory in the US, COVID19 will be the 3rd leading cause of death. In other words, COVID19 would average 1118 deaths per day compared to heart disease (which killed 1,774 people per day in 2019) and cancer (which killed 1,641 people per day in 2019).

Translation: As for now, Texas’ COVID19 rank in terms of leading causes of death IS lower than the US as a whole. We should keep it this way by taking the Texas epidemic seriously.

Love, your local epidemiologist

Data source: 2019 data is from the National Center for Health Statistics at the CDC. COVID19 data is from DSHS (Texas) and Johns Hopkins (US). Graphs/analysis by yours truly.