Long-term effects National changes Predictions

When will this end?

There are basically two ways…


1. The virus could “burn out” (like SARS and MERS) due to effective public health mitigation measures and immunity. BUT, given the ease of transmission (most contagious two days BEFORE symptoms) and given our lack of a national (and international) coordinated response, this is very unlikely now.

2. We could reach “unnatural” herd immunity (ie vaccines). Eradication is 100% dependent on vaccine effectiveness and uptake. We don’t know either yet. If a vaccine prevents clinical disease, strongly reduces transmission and produces long-lasting immunity, eradication is possible. But realistically this is unlikely, especially since it’s clear our next public health hurdle is getting people to trust the vaccine once a safe option is available. “Natural” herd immunity is out of the question.

Option numero two…Pandemic turns into an endemic.

In other words, COVID19 goes on to live among us, like it’s cousins (common cold) or other infectious diseases (HIV or malaria). A pandemic turning into an endemic it’s based on a very loose definition: how risks are perceived by the population. For example, HIV is technically still a pandemic (it’s in every country across the globe). However we’ve found therapies, prevention methods, and the level of awareness has (almost) reached saturation. The “newness” has withered and we have gone on to live with HIV. HIV is now considered an endemic.

If COVID-19 does become an endemic virus, there’s no way of knowing where it will be most prevalent (on the equator like malaria?), when it will be most prevalent (will it be seasonal like the flu?) or what the baseline level of disease will be (eventually this will stabilize at a constant level, R(t)=1).

How we deal with COVID-19 once it becomes endemic will depend on four things. Our interventions (vaccines and treatments) are key aspects. If they can protect people from the most severe outcomes, the infection will become manageable. COVID-19 will then be something we learn to live with and something many people will experience during their lives.

Like everything in this pandemic… TBD.

Love, YLE

Here is a published scientific perspective that complements my perspective if you’re interested (and skeptical):…/10/13/science.abe5960

National changes Predictions

COVID19 Deaths and the recent 6% debacle

There have been rumors, and tweets, and screenshots, and who knows what else stating that only 6% of CDC’s COVID19 death count is due to COVID19. I feel like this is a ridiculous post, particularly because I feel like a broken record, but here we go…

What happened? CDC updated its regular statistics page stating: “For 6% of the deaths, COVID-19 was the only cause mentioned.” For the other 94% of people that died of COVID19, “individuals had an average of 2.6 additional conditions or causes per death”.

What does this change? NOTHING. 182,885 people have still died from COVID19 in the US. COVID19 is still the third leading cause of death in the US.

What does the science say?

1. The CDC (and basically every scientist across the world) has consistently stated that individuals with underlying health conditions are more likely to die from COVID19. This is probably one of the first facts that we DID know. I don’t know why we are surprised about this now…

2. Long-term conditions (like obesity, diabetes, or heart disease) are “chronic” because they last for a long time. Most are, in fact, manageable thanks to modern science. Someone with diabetes (that wasn’t “supposed” to die this year) can manage to get infected with COVID19 and die quickly because their immune systems get overwhelmed.

3. The health of our nation has been terrible, even before the pandemic. 60% of adults have a chronic condition. Among those aged 65 and over, 80% have multiple chronic conditions. Minorities and low-income populations have more chronic conditions too. So, if you take a random sample of people who die, the majority will have at least one chronic condition. So we shouldn’t be surprised about this 6% being low.

4. There are many lines on a death certificate. This includes the “immediate cause of death”, “sequentially conditions leading to the cause of death”, and “other significant conditions contributing to death”. Which ties to #3…it would be odd if a chronic condition WASN’T listed on a death certificate in the US given the health of our nation overall and given COVID19 touches every organ system. Death certificate instructions are below if you’re curious how this data is collected.

5. If there is nothing else, just look at an excess death graph for 2020 (see Figure). We are WAY above our deaths this year compared to past years. Period. This doesn’t just randomly coincide with a pandemic.

In epidemiology (and science), it’s very weird for us to beat a dead horse. We typically accept the conclusions of a room full of scientists with decades of experience until another room of scientists with decades of experience proves them wrong. We don’t change our mind from a tweet that is taken out of context (no matter who it’s from). The public should follow suit. I guess I should just be happy that everyone (and I mean everyone) now pays attention to public health?

Love, YLE

CDC link to deaths causing the commotion: conditions and of COVID19 death: ; Chronic conditions, overall, in the US:; certificate instructions: Excess Deaths posts:; COVID19 as a leading cause of death: Image from: Weinberger lab, updated on August 14, 2020

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.

Innovative Solutions Predictions

Predicting Hot Spots

Because COVID-19 has an average 5-day incubation period (ie humans can spread for 5 days before showing symptoms), it’s given epidemiologists quite the headache to stop spread before it happens. It’s been imperative and incredible to watch how epidemiologists have worked with other industries to predict future COVID19 hot spots.

Twitter and Google: Scientists found a way to predict COVID19 cases and deaths hotspots 2-3 WEEKS BEFORE they happen. How? Through Twitter and Google internet activity. If the number of tweets with the words related to COVID19 (like covid, corona, epidemic, flu, influenza, face mask, spread, virus, …) start increasing, we can predict cases 3 WEEKS in advanced and deaths 4 WEEKS in advance. They also found that by counting the number of people that searched for “fever” in google can predict COVID19 deaths 22 days prior to a spike.

Kogen et al. (2020). An Early Warning Approach to Monitor COVID-19 Activity
with Multiple Digital Traces in Near Real-Time.

Other innovative solutions? I posted previously on a few methods that predict hotspots 5-7 days BEFORE they arrive:

Fecal matter: In sewage systems. Epidemiologists in New York found that high levels of the virus in sewage can predict outbreaks 7 DAYS BEFORE the outbreak occurs. AND, not only outbreaks but can predict an increase in hospital admissions. In other words, if we test sewage systems, we can tell a week beforehand whether there will be an outbreak in that city. Most recently, this has been an effective method in airplanes and cruise ships too.

Symptom tracking: Some of my colleagues are using a symptoms to predict outbreaks 5 DAYS BEFORE they start. They are simply asking if people are well or sick through an app, and if they are sick asking what symptoms do they have. This strategy has been highly effective in the UK.

Google mobility data: I’ve posted phone data extensively in the past. But, most recently, we were able to predict the recent second “spike” in the southern states by seeing how people’s movement to non-essential businesses changed.

There are other ways I’ve heard, like credit card useage, but I haven’t seen published science on this yet.

Without effective drugs or vaccines, these are really useful strategies to deploy public health efforts BEFORE a hotspot hits. Can’t wait to hear what else scientists come up with!

Love, your local epidemiologist

Important Note: Figures come directly from the article. I did NOT create these.

Data Sources:
Google/Twitter article:…
Sewage article:…/10…/2020.05.19.20105999v1.full.pdf
Symptom tracking article:…

Dashboard Predictions

Dashboard 2.0

For my fellow Texans….Version 2.0 of our dashboard is LIVE!!

We’ve added a lot…
-You can now sort by Public Health Region (for our fellow public health responders)
-We have added a whole new tab on hospitalizations and ICU capacity, updated in real time
-We have added a new tab on demographics for cases and deaths
-We’ve added daily and cumulative deaths and cases
-You can now COMPARE across counties, TSAs or PHRs (on the critical trends tab)
-And, of course, we have added interpretations for everything.

It is an absolute honor to work with this group. They are the best of the best.


Deaths Predictions Texas update

Texas Today

And this is my best shot at giving your the most comprehensive picture of COVID19 in Texas today.

Cases: While Harris County is getting a lot of attention due to an increase in cases (and we should be worried about this), it looks like after adjusting for population, Dallas is in even worse shape. Another worrisome county is Bexar (San Antonio) given their recent steep incline. In order compare the severity of COVID across Texas counties, we NEED to adjust for population. I noticed this is missing in much of the news.

Testing: TPR has always been a problem in Texas. Our goal is 5%, and we are over 10% in most of Texas. We need to allocate resources to increase testing. Like NOW. We are not testing enough to get ahead of the epidemic.

Mortality: CFR looks steady in Texas. In fact, it’s decreasing. This is driven by COVID spread among younger Texans, who have the ability to fight off the disease compared to older populations. HOWEVER, this JUST measures mortality. This does NOT account for lifelong complications we are seeing among the young patients that survive. Which is a whole other story.

Future cases: I included classic Epi curves for each county (with 7-day average- blue line). I also included our June 13 projections calculated based on R(t), which takes into account testing, temperature/humidity, social distancing, and population density. Projections in Bexar, Travis, and Harris county are grossly UNDERestimated. We NEED to especially improve social distancing here. Projections for Dallas and Tarrant look accurate so far (but still need to improve social distancing so this projection goes flat).

Translation: We need to increase testing. We need to improve our social distancing. We need to be worried for all of Texas, but particularly the rate in Dallas and Bexar right now.

Love, your local epidemiologist

Data: DSHS. Graphs and analyses by yours truly.

Predictions Texas update

Case Projections

Sorry for bad news on Father’s Day.

A few days ago, I posted projections for a few Texas cities (compared to DC, NY, and CA). Those projections were created on June 13. Now that 8 days have passed, I was curious how accurate they were thus far.

Projections are incredibly hard to estimate. And many epidemiologists are hesitant to post or discuss them amid the risk of being scrutinized and losing the public’s trust. However, while all of this is true, I also think it’s important point of discussion in order to change behavior. So here we go…

These figures include the original June 13 projections. I added cases for the past 8 days in each county (see red dots and lines). The projections look pretty darn accurate so far. Dallas projections may be slightly overestimated (but not by much). Harris and Tarrant projections look like they are UNDERestimated. By a lot.

The only thing that can change these projections are the variables that were used to create them: 1) county-level population density; 2) testing capacity; 3) 3-day average of social distancing; and 4) temperature and humidity over the past 2 weeks. The public can only help through social distancing. A few counties in Texas, including Dallas, have mandated facemasks. It will be another two-ish weeks to see if this had an impact on spread.

We should all keep a close eye on these numbers.

Love, your local epidemiologist

California DC New York Predictions

COVID19 projections

Things are looking grim in Texas folks.

Here are COVID19 projections for each major county in Texas. The projections take into account social distancing, population density, testing capacity, and combined temperature and humidity lagged over the prior 14 days. Each county’s effects are standardized by population demographics.

Location is labeled at the bottom of each figure. Also, pay attention to the Y-axis, this is different for each map.

Translation: The ONLY way to change these projections is changing behavior. Or we all move out of state. We can’t change temperature and humidity.

I also included projections for other cities in the United States. Texas’ projections are NOT the way it HAS to be.

Love, your local epidemiologist

Data source: CHOP Policy Lab