Behaviors National changes Texas update

National (U.S.) Update

Your national (U.S.) update as of Feb 3 at 8:00PM CST

Cases… continue to plummet. There’s no doubt that the 2020 holiday season caused a surge in cases. Which is consistent with what we saw on Memorial Day and July 4. The impact that human behavior, like the 2020 holiday season, has on human life is really quite fascinating. Anyways, our 7-day average is now the same as it was on November 12. Today, 42 states have a decreasing 7-day average of cases and 8 states are plateauing. Only Texas has an increasing 7-day case rate (11%).

Testing…is continuing to plateau, which isn’t necessarily bad. Especially if cases continue to decrease. Because this means that test positivity rate will be decreasing. Which is fantastic. We want TPR<10% (<5% is ideal) to get a handle on transmission.

Hospitalizations….are tanking too. Hospitalization trends follow case trends, so this makes sense. Hospitalizations in 41 states are decreasing, 9 states are plateauing, and 1 states is increasing (Vermont=15%). This is also fantastic news. But, remember, decreasing is relative. They are decreasing from the highest peak we’ve every experienced. Today, 91,440 people were on hospital beds for COVID19. This is still higher than the peak in April (59,779 hospitalizations) and July (59,718 hospitalizations).

Deaths…are increasing but significantly losing momentum. In other words, we should see our peak here soon (if it wasn’t today or yesterday). 27 states have decreasing deaths, 15 states are plateauing, and 9 states are increasing. The highest increase in deaths is Iowa, closely followed by South Carolina. Today 3,685 souls succumbed to COVID19. In one day. We were predicting 500,000 deaths by mid-February. This may be end of February now. TBD.

Vaccinations…are slowly (but surely) starting to gain speed and exponentially increase. Which is huge. We (the U.S.) are administering 9.71 doses per 100 people. In the last week, an average of 1.34 million doses per day were administered. Alaska leads with 13.4 doses administered per 100 people. This is followed by West Virginia (11 per 100) and New Mexico (10.5 per 100). Idaho, you’re last, with administering 6.0 doses per 100 people. (Texas you’re close to the bottom too, at 7.2 per 100 people).

Variants...are gaining speed.-B.1.1.7 variant: Has popped up in 541 Americans across 33 states (Florida has, by far, the most people followed by CA). -B.1.351 variant: Detected in 3 Americans in 2 states-P.1: Detected in 2 Americans in 1 state

We are, quite literally, in a race: vaccination rate vs. variant transmission rate. Hopefully we win before mid-March hits.

Love, YLE

Case data: COVID tracking project

Vaccination data:

More vaccination data:

Variant data:

National changes Variant

National (US) update…

Your national epidemiological report (as of Jan 25 7:19PM CST)…

Cases are dropping and they are dropping fast. It looks like we have turned the post-holiday corner. Our 7-day average is now the same as it was in November. Today, 46 states have a decreasing 7-day average of cases and 5 states are plateauing. Not one state has an increasing 7-day average.

Hospitalization trends follow case trends. So, naturally, hospitalizations are looking better too. Hospitalizations in 33 states are decreasing, 16 states are plateauing, and 2 states are increasing (Vermont=27% and Kansas=18%).

Unfortunately, deaths lag hospitalizations. Deaths are still catching up from the holidays. 22 states have decreasing deaths, 18 states are plateauing, and 11 states are increasing. The highest increase in deaths is Arkansas (56%!), closely followed by Hawaii (54%). Yesterday, we had the highest daily death toll of ~4,400 COVID19 deaths in one day. Which is unfathomable. We are predicting 500,000 deaths by mid-February. This would make COVID19 the second leading cause of death in the United States… within 11 months.

We can finally add a new (positive) metric to the report… Vaccinations! 22.7 million doses have been administered. Of which, 3.3M people have received both doses. 41.4 million doses have been distributed. Today, Alaska is the winner with 13,264 per 100K doses administered. West Virginia is a close second with 11,383 per 100K doses administered. North Dakota and Nevada come in 3rd and 4th place. The Western US is, by far, the slowest to administer doses, with CA, NV, and AZ being at the bottom of the bunch. We have yet to gain speed in vaccinations, but this should be coming soon. We are figuring out ways to squeeze a 6th dose out of each vial (by producing special syringes) and deploying mass vaccinations sites. We should get to at LEAST 1 million doses per day in the United States soon. We can’t do this fast enough, as we need to beat the acceleration of the variants.

Every epidemiologist I know is worried about the B.1.1.7 variant (first discovered in the UK). It took 3 months for B.1.1.7 to become the dominant strain in the UK. If this variant continues to spread in the US, we are looking at a March surge that we’ve never seen before. As of tonight, B.1.1.7 is in 23 states with 293 lineage cases reported. But this is among a bias sample of cases. The U.S. ranks 43rd in percentage of cases sequenced. We estimate that B.1.1.7 is ~1% of cases in the United States.

We have 1.5 months to prepare. Early efforts that can limit the spread of the B.1.1.7 variant, such as universal and increased compliance with public health mitigation strategies, will allow more time for ongoing vaccination to achieve higher population-level immunity.

Love, YLE

Data Sources:

Case, hospitalization, and death data: COVID19 tracking project


CDC variant/immunization rates in regards to infections:…

Variant cases in the US:…/transmission/variant-cases.html

Behaviors National changes Side Effects Variant

Quick update…

Several COVID19 developments popped up in the past 24 hours. Here’s my attempt to keep you up to speed…

-Data are stabilizing and we are starting to see the impact of the holidays. For the second day in a row the United States had more than 4,000 deaths per DAY. This is about what we, epidemiologists, expected because 22 days ago there were 239,795 daily cases. Today, 131,889 people are hospitalized and 7,900 people are on ventilators. We are hitting new records across every metric.

-There is NO scientific evidence of a new US variant (this is different than the UK or SA variant). This misinformation stemmed from a document circulated yesterday that speculated the increase in winter cases (compare to summer) must be due to a new variant. In Nov and Dec, 5,700 samples were collected and analyzed by the CDC and there is no evidence of this. However, the more this thing spreads, the more opportunity this virus has to mutate. Can we agree to start wearing masks and stop seeing friends?

-The Biden administration announced that they will not withhold the second dose. This is still a highly debated topic in public health (maybe the most debated since the pandemic began). My scientific opinion: Supply isn’t our issue right now; capacity and logistics are. As of this morning 22.1 million vaccines have been sent off; only 6.68 million Americans received their first dose. Yes, some of this discrepancy may be due to reporting lags, but this doesn’t explain it all. Our federal priorities should be setting up vaccine surveillance, setting up mass vaccination sites, and clear, consistent communication. Way too many people are in the dark. Now, if we get off the ground from this rocky start, then we can talk about the second dose.

-Every Friday the CDC Vaccine Adverse Event Reporting System (VAERS) is updated. The more people that get vaccinated, the closer we get to the “true” rate of adverse events. 6.68 million doses of the vaccine have been distributed and 3,907 adverse events have been reported to VAERS. The most common symptom is headache, nausea, and pain. 30 people/physicians reported anaphylactic reactions. On Jan 6, CDC published a report describing 21 of these cases in 1.89 million doses. Of which, 71% occurred within 15 minutes of vaccination. There are limitations to VAERS data (which I’ve posted about before).

Okay, I think that’s it for now.

Love, YLE

Data Sources:
Graph 1: Covid Tracking Project
Graph 2: Made by yours truly with VAERS data
Vaccine tracker:
CDC report:

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

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…


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 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.


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.


  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:

CHOP Policy Lab:


National changes


For the first time ever, we reached over 200,000 cases (210,161 to be exact) in the United States. In one day. We currently have 100,667 hospitalized. And, just today, we lost 2,706 souls.

And if you think this is bad, hospitalizations and deaths follow a 22-day lag. So, in about 22 days, our DAILY death toll will be ~4200. It’s too late to do anything about that. We will reach that number. And, that is, assuming our hospital systems can keep up.

I’m having a harder and harder time articulating the gravity of this situation. Maybe it’s because not one epidemiologist, including myself, is surprised. Or, maybe it’s because we are tired of sounding the alarms. The catastrophe is here. Not only a medical one, but a financial and social one as well.

Somberly, YLE Data

Source: COVID Tracking Project

National changes

Reinforcement is coming.

And we need it. We have already lost 229,724 souls (an underestimate) and find ourselves in a medical, social, and financial catastrophe. For the past week, the U.S. has consistently reported more than 100,000 cases per day. Per capita, this is 32 daily new cases per 100,000. The hardest hit area has 206.8 daily new cases per 100,000. To control this pandemic, we need to be <10 cases per 100,000.

We know the increase isn’t due, solely, to testing. The national TPR has hovered >10%. We need this below 5%. Also, hospitalizations are increasing. In hot spots, we are running out of space for patients (just google El Paso). 

Deaths are rising (deaths follow a 22-day lag behind cases) but fatality rates are steady (thanks to our research in clinical treatment). Fatality rates may increase soon though: 1) More hospitals may get overwhelmed; 2) holidays are coming and older adults will be exposed to younger populations. Also, remember, mortality isn’t the only COVID19 outcome; COVID-19 causes morbidity among mild and severe cases. 

However, like I’ve said before, pooled national numbers aren’t useful because we don’t have a national, coordinated response. COVID19 doesn’t see state or county borders, and neither can we. We knew this back in August when scientists published a paper showing that a fragmented national response (like the US) is just as good as no response at all. 

A new approach seems to be on the horizon. Yesterday, the newly elected administration appointed three co-chairs to a new COVID19 task force: 

  • Dr. David Kessler: Professor of pediatrics and epidemiology and biostatistics at the University of California, San Francisco, U.S. Food and Drug Administration commissioner from 1990 to 1997.
  • Dr. Vivek Murthy: U.S. surgeon general from 2014-17, who commanded public health force that dealt with Ebola, Zika and Flint water crisis.
  • Dr. Marcella Nunez-Smith: Associate professor of internal medicine, public health and management at Yale University and associate dean for health equity research at Yale’s medical school specializing in health care for marginalized populations.

Where is Fauci? There may be political reasons why he’s not included. I’d be shocked if he isn’t invited in January. 

What does this task force need to accomplish? This is my wish list:

-We NEED on the ground representation heavily advising these new co-chairs: physicians, infectious disease epidemiologists, and virologists. It looks like this was accomplished while I was typing this up, with others quickly added to the list (see link below for full list)

-Public health campaign with consistent messaging (yes this would include universal mask wearing). South Korea ran a brilliant, effective campaign for their country

-Start working again with the WHO. Yes, they aren’t perfect, but we can learn from other countries. Also, distance the CDC from government. Yes, I know the CDC IS the government (i.e. funded by them) but we need them to become bipartisan again. Distancing themselves from the executive branch (at least publicly) will improve trust. I would also in loop Tom Frieden.

-Deploy (or at least support!) targeted testing to hard hit areas. This federal support was removed in August 2020.

-A national contact tracing program. This would have to be a tiered response given our large population. Others have drafted what this could look like (see link below)

The question is whether it’s too late. Has there already been too much damage? We’ve already lost trust of communities, already have pandemic fatigue, already have false narratives circulating, all public health workers are burnt out, and quite frankly, we need to build an infrastructure quickly (Obama started building this pandemic infrastructure, but I’m not sure what is left of it). ALL of these aspects are important for effective public health responses.

This task force has an uphill battle. But if anyone can do it, it’s them. They are drafting up implementation plans as we speak. I look forward to seeing these plans soon (and so should you), as this will give us more clarity to what the next year may look like. And although their plan won’t help the current wave, it will help future waves and certainly help with the rollout of vaccines in 2021. And (should I say it?) will help with future pandemics WHEN (not if) they come. 

Love YLE

Data Sources:

-Graphs and numbers: COVID19 tracking project

-Entire new COVID19 task force team:

-Fragmented responses not effective:  

-A possible scale up racing approach:

National changes

A new day calls for a new count…

116,255 new COVID19 cases and 1,124 new deaths across the United States. In. one. day.

Behaviors National changes

US Presidential Rallies

The close of election season is upon us. A new study found that this is particularly good news for epidemiologists, as U.S. presidential rallies were associated with an increase in COVID19 cases.

In a recent study, scientists looked at the change in COVID19 cases across 20 counties that hosted rallies from August to September 2020. They compared the change in COVID19 cases to US counties that did not host a rally.

What did they find?

-On average, COVID19 increased in host counties by 50% compared to non-host counties

-Peak increase was 5 days post-rally (which is consistent with the time interval from infection to detection)

-The county with the highest COVID19 increase was Lackawanna PA (a 3.8 fold increase in COVID19). Before the rally, this county had the 2nd lowest number of COVID19 cases per 100,000.

-2 out of the 20 counties (Saginaw MI and Yuma AZ) had a DECREASE in county-level COVID19 cases

-The county with an indoor gathering had an increase, but the relative increase in cases was higher in 9 outdoor counties.

Translation: Mass gatherings outdoors OR in counties with low incidence did not entirely prevent the spread of COVID19. Additional public health measures, ensuring multiple layers of protection, must be taken.

Love, YLE

Data Source:…/2020.10.22.20184630v1.full.pdf

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