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National changes Testing Texas update

National Update

Looks like we’ve hit our peak in the U.S.? Unfortunately not yet. We won’t start seeing the “true” holiday impact until mid- January. 

You may remember my post (back in April, I think) showing that test and case numbers are dependent on human behavior. In Texas, for example, daily case counts are much lower on days with a thunderstorm or tornado warning because testing sites close due to inclement weather. Case counts are highest on Tuesdays and lowest on Saturday/Sunday/Mondays. Reporting 7- or 14-day averages takes care of these day-to-day fluctuations. 

The same is true for the holiday season; it’s basically a really long weekend in terms of case and testing numbers. Facilities and labs have been inconsistently open, reporting is delayed, places are catching up, etc. You can see a dip in the graphs, but this is due to human behavior (rather than true reduced transmission). We won’t see the holiday impact until reporting has stabilized. It’s irresponsible to make conclusions from case, test, and death data right now. 

Right now, a much more reliable metric is hospitalizations. Hospitals are open 24/7 and, by now, have rigorous, systematic, and completely separate reporting systems than testing/case data. Because hospitalizations lag cases, we have a pretty good idea of whats been happening with cases behind closed doors. 

Unfortunately, hospitalizations are not looking good. Across the U.S., there are 123,614 COVID19 patients hospitalized right now. This is the highest it’s ever been. 

Not all places are equal though.

The Midwest continues their downward trend. Not one Midwest state reported an increase in hospitalizations since Christmas. 

The South, on the other hand, is responsible for 50% of the country’s hospitalizations. This is mainly driven by the high Texas hospitalizations. Also, the South just has more people than the Midwest or Northeast. 

Texas Hospitalizations by Trauma Service Area (TSA)

After we adjust for population, though, the West and Northeast is in worse shape than the South (but not by much) and closing in on Midwest’s peak. The West’s numbers are mainly due to Southern CA where some hospitals literally (not figuratively) have no more ICU beds.

The way we “define” hospitalizations is also changing compared to the beginning of the pandemic. The threshold for sending someone home is much lower than in the past. For example, some hospitals will send someone home with a 90% O2 level, which wouldn’t have happened prior to the pandemic or in the past few months when hospitals had beds. So, in reality, the hospitalization numbers are underestimated compared to hospitalization rates in the past. 

Nonetheless, hospitalization is the best metric we have right now. Continue to keep an eye on this number until other metrics stabilize.

Love, YLE

Data Source: Covid Tracking Project, which never ceases to amaze me with their clean, state-level data. And our dashboard at www.texaspandemic.com

Categories
Texas update Vaccine

Phase 1B opened in Texas

Texans….Phase 1B has opened.

So, if you’re in this category, you can now get the COVID-19 vaccine (depending on local availability):

• People 65 years of age and older

• People 16 years of age and older with at least one chronic medical condition, such as but not limited to:

• Cancer• Chronic kidney disease• COPD (chronic obstructive pulmonary disease)• Heart conditions, such as heart failure, coronary artery disease or cardiomyopathies• Solid organ transplantation• Obesity and severe obesity (body mass index of 30 kg/m2 or higher)• Pregnancy• Sickle cell disease• Type 2 diabetes mellitus

Here is the map of vaccine providers: https://txdshs.maps.arcgis.com/…/webappvi…/index.html…

This week 380,000 doses (175,100 Moderna and 81,900 Pfizer) were sent to Texas providers in 199 counties. This obviously doesn’t cover every Texan in Phase 1B. Be patient. Some providers may not have vaccines available yet. Vaccine supply is limited but providers receive more vaccines each week.

Update: As of 4pm today, 204,463 Texans have gotten their first dose!

Love, YLE

For more, check out the DSHS website here: https://www.dshs.texas.gov/coron…/immunize/vaccine.aspx…

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Deaths FL Hospitalizations National changes Social Distancing Testing Texas update

Thanksgiving Surge?

It’s been 2 weeks since Thanksgiving and I was curious if we had a “surge upon a surge”.

In other words, did our acceleration (the rate of cases) change after Thanksgiving? Unfortunately, it’s a very simple question with a very complicated answer. If this blog were my day job, I could statistically figure this out. But it’s not, so I triangulated a few other data sources instead. This is what I found…

TEST POSITIVE RATE (TPR)

TPR is now 20.3% in the United States. It increased 15% since Thanksgiving. TPR is particularly concerning in the Southeast, where it’s increasing at higher rates since Thanksgiving than the rest of the country. While the Midwest finally seems to be moving past their peaks, their TPR’s are increasing again (likely related to Thanksgiving), which will slow their decline. The WHO has stated that countries need a TPR below 5%. While testing does not have a direct benefit because there is no cure, 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).

CASES

Cases have increased 21% since Thanksgiving. Cases increased 22% two weeks before Thanksgiving. New hot spots have popped up since Thanksgiving, particularly along the Sun Belt (southern CA, AZ, TX) and the Northeast. Boston, in particular, has surpassed 100 daily cases per 100,000. And while Vermont and Maine have been more than impressive this entire pandemic, they too are seeing doubling rates.

HOSPITALIZATIONS/DEATHS

Not enough time has passed since Thanksgiving to see the impact on hospitalizations/deaths. But there is no reason to believe they will not continue to mirror case trends. Fatality rate (number dead out of the number with positive COVID19 tests) continues to remain steady in the United States at ~1.9%. We should continue to see this, unless out health systems are strained too much. Then hospitals will have to start making hard decisions on who to save and who not to save. In April, Italy had to make these decisions (they decided not to treat those 80+ years) and fatality rate increased.

MOBILITY

  1. Airports. The CHOP Policy Lab found circumstantial evidence that the most concerning areas of the country post-Thanksgiving are adjacent to our busiest airports: Los Angeles, Boston, DC, Atlanta, and Dallas. In other words, Thanksgiving air travel led to increased local transmission. For example, in Clayton County, Georgia (home to the Delta Hub and Atlanta airport), cases are doubling compared to surrounding counties.
  2. Distance Traveled. Interestingly, distance traveled did not change, on average, by much. We see an increase right before Thanksgiving, but honestly not as high as I would have expected. This only means people, on average, didn’t travel far. This doesn’t mean that family wasn’t close by and people didn’t get together. It was also very obvious that distance traveled varied by states too (see Figures). Wish I had more time to look into this. But still adds a little piece to the puzzle.

Conclusion: Right before Thanksgiving we were starting to see a plateau in cases. Then, after data reporting caught up, our cases continued exponentially increasing after Thanksgiving. So, I don’t think we saw a surge upon a surge. But we definitely didn’t stop our original surge. The pandemic continues to ravage our communities across the United States.

Love, YLE

Data Sources: I triangulated many sources of data for this report. I couldn’t have done it without the beautifully clean and workable data and graphs from the following sites:

COVID19 Tracking Project: https://covidtracking.com/data

CHOP Policy Lab: https://policylab.chop.edu/covid-lab-mapping-covid-19-your-community

UnaCast: https://www.unacast.com/covid19/social-distancing-scoreboard

Categories
Texas update Vaccine

TX vaccine update

Texas! 1.4 million doses of vaccines will be here on Dec 14. Let’s goooo!!

Phase 1, tier A

1. Hospital staff working directly with covid19 patients

2. Long-term care staff working directly with vulnerable residents.

3. EMS providers who engage in 9-1-1 emergency services

4. Home health care workers

Phase 1, Tier B will be:

1. Staff in outpatient care offices who interact with symptomatic patients.

2. Direct care staff in freestanding emergency medical care facilities and urgent care clinics

3. Community pharmacy staff

4. Public health and emergency response staff directly involved in administration of COVID testing and vaccinations

5. Last responders who provide mortuary or death services to decedents with COVID-19.

6. School nurses

Categories
Texas update

Texas status report…

…and our “baseline” before the holidays.

Texas has a rate of 37 daily new cases per 100,000. This is considered “uncontrollable spread” and ranks us 37th in the country.

Our case count is now higher than cases back in July. Our R(t)= 1.12, so cases will continue to increase at an exponential rate. R(t) has remained fairly steady for the past month (we want this to decrease). Houston cases have increased by 510% in the past week. But this isn’t close to the highest…Crockett cases have increased 1200%, Trinity 900% & Jeff Davis 800%.

Hospitalizations continue to exponentially increase. ICU’s are at 100% capacity in Abilene and Laredo. We are close to ICU capacity (5% beds left) in Amarillo, Waco, and College Station. General hospitalizations are high in Dallas/Fort Worth, with only 10% of overall capacity available. This means DFW hospitals have started opening surge units.

Testing is unacceptable (>40% test positivity rate) in 13 counties: Armstrong, Bailey, Briscoe, Collingsworth, Deaf Smith, Hall, Hockley, Hutchinson, Motley, Parmer, Reagan, Swisher, and Wheeler.

Interestingly mobility has not changed in the past month, despite the spike in cases. People are continuing to travel to non-essential businesses.

El Paso is continuing to do a great job bringing down their curve. With an R(t)=0.75, this will continue to decrease (as long as people keep behaviors up). We hopefully saw their peak.

When the first wave of vaccines are sent to Texas (maybe December?), DSHS has decided to give the following people first dibs (considered phase 1, tier A):

1. Hospital staff working directly with covid19 patients

2. Long-term care staff working directly with vulnerable residents.

3. EMS providers who engage in 9-1-1 emergency services

4. Home health care workers

Phase 1, Tier B will be:

1. Staff in outpatient care offices who interact with symptomatic patients.

2. Direct care staff in freestanding emergency medical care facilities and urgent care clinics

3. Community pharmacy staff

4. Public health and emergency response staff directly involved in administration of COVID testing and vaccinations

5. Last responders who provide mortuary or death services to decedents with COVID-19.

6. School nurses

Love, YLE

Data Source: Our dashboard at www.texaspandemic.orgMore on Texas vaccine allocation plans: https://www.dshs.texas.gov/…/COVID_Vaccine_Principles…

Categories
Texas update

Congratulations Texas

We are the first state to reach 1,000,000 COVID19 cases. Here is a quick report of the current status of our state…

We just moved into the “red” tipping point zone with 25.7 daily cases per 100,000. Transmission is accelerating (state R(t)=1.13) and hospitals are strained.

As of this morning, there are particularly worrisome areas (for their own reasons, see below)…

El Paso (TSA [Trauma Service Area] I)

  • One of the worst hotspots in the nation
  • 123.1 daily new cases per 100,000
  • Test Positivity Rate: 24%
  • Hospitalization: 45% COVID19 patients
  • ICU: 63% COVID19 patients
  • R(t)=1.16

Amarillo (TSA A)

  • Cases are increasing the fastest in the state (increase 162% in one week)
  • 77 daily new cases per 100,000
  • Test Positivity Rate: 16%
  • Hospitalization: 35% COVID19 patients
  • ICU: 70% COVID19 patients
  • R(t)=1.79

Lubbock (TSA B)

  • 85 daily new cases per 100,000
  • Test Positivity Rate: 16%
  • Hospitalization: 23% COVID19 patients
  • ICU: 22% COVID19 patients
  • R(t)=1.12

Others areas to look out for:

  • Waco (TSA M) increasing at alarming rates (60% increase in past week)
  • Victoria (TSA S) increasing at alarming rates (44% increase in past week)
  • Wichita Falls (TSA C) ICU is 53% COVID19 patients
  • There are 13 counties with a TPR > 30%: Andrews, Bailey, Childress, Coke, Cottle, Fisher, Hall, Hansford, Haskel, Hutchinson, Parmer, Sutton and Terry

Love, YLE

Data Sources: www.texaspandemic.org and Harvard COVID19 suppression

Categories
Dashboard Texas update

Dashboard Update 3.0

Texans…

For those of you that haven’t noticed, we updated the www.texaspandemic.org dashboard!

On top of hotspots, trends, hospitalization rates, testing rates, fatalities, and case demographics, we now have added….

Hot spots based on test positive rate (TPR) AND new cases per day. The combination of these two metrics are being used to drive school-, county-, and state- level policy (we hope). Essentially, you want a county to be in the green for BOTH. If a county is in the red for either, we are in trouble in regards to COVID19 spread.

We also included mobility data per county. Using mobile phone data, we can see how movement to work, parks, grocery stores, and to non-essential stores have changed over time. And, as always, we include interpretations in there for you too.

Enjoy!

Love, YLE

Categories
Texas update

Texas Update

Here is an update for my Texans. Haven’t done one in the while.

How’s it looking? Well……..not good. In fact, four out of the five NATIONAL hot spots are located within the great state of Texas.

Here are the overall state numbers (see Figures for regions):
New daily case rate (we need this below 9 to control spread): 23 daily cases per 100,000
Test Positive Rate (we want this well below 10%): Over 15%
Deaths: 32 cumulative deaths per 100,000
Case Fatality Rate (CFR): 3.17%
R(t) (we want below 1.0): 0.90, which means new cases should start decreasing at a faster rate. But in order for this to happen, we need to be testing much, much more too. We will see where this takes us.

I don’t even know what to say other than… It’s really exhausting to be an epidemiologist in Texas.

We need to get it together faster. We know what to do.

For more numbers and data, go to our dashboard at: www.texaspandemic.org

Love, your local epidemiologist

Data Source: DSHS, analysis and tables by me.
CFR=22-day lag; New daily cases= 7-day moving average; TPR= 7 day lag (if you know you know)

Categories
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.

Categories
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: https://www.medrxiv.org/conte…/10.1101/2020.05.03.20089854v4
CDC report: https://www.cdc.gov/coronavir…/…/hcp/planning-scenarios.html