Dr. Gerald’s Weekly Epidemiology & Hospital Capacity Report

This week saw a meaningful decline in Covid-19 cases which now clearly represents a real decrease in viral transmission
. This decline is accompanied by reductions in hospital and ICU occupancy. Reductions in mortality should follow. While this reprieve is welcomed, the absolute level of SARS-CoV-2 virus transmission remains exceptionally high.

As of January 24th, new cases were being diagnosed at a rate of 557 cases per 100,000 residents per week. This rate was declining by 150 cases per 100,000 residents per week. Despite this improvement, no other state is experiencing faster transmission than Arizona according to the CDC. Because of this, Arizona has moved up 2 positions to the 6th hardest hit state since the outbreak began.

Arizona is reporting >800 Covid-19 deaths per week (>115 per day) and this count may underestimate true fatalities by half (see WoolfWoolf, or Weinberger). Many of these deaths were preventable if the state had more aggressively adopted evidenced-based public health practices. Arizona’s weekly tally of deaths now ranks second in the nation. Overall, we rank 10th.

The Arizona Public Health Association released a report on all-cause mortality during the Covid-19 pandemic. The main finding is that all-cause mortality was 23% higher in 2020 than 2019 with the months of July and December being outliers with 64% and 61% higher mortality, respectively. This translates into approximately 15,000 excess deaths.

The Arizona Public Health Association also released a report that describes the chronological course of the Covid-19 outbreak in Arizona and chronicles the state’s response or lack thereof. 

Hospital Covid-19 occupancy is declining in the ward and ICU. However, access to care for Covid-19 and non-Covid patients remains restricted in ways that are difficult to understand owing to changes in care practices.

Hospitals continue to postpone many scheduled procedures to create additional capacity for Covid-19 patients at the expense of others with serious medical conditions.

Health professionals are being asked to work additional hours and assume duties outside their traditional scope of practice.

The test positivity rate for traditional nasopharyngeal PCR testing declined for the third straight week, dropping from a peak of 35% to 29% this past week. Nevertheless, our testing capacity is wholly inadequate to the scale of the problem and other regions.

So far, 1110 per 100,000 (1.1%) Arizona residents have received at least 2-doses of vaccine while 6044 per 100,000 (6.0%) have received at least 1-dose. Arizona vaccination roll-out places us in the bottom half of US states. To date, Arizona has administered only about one-half of its delivered doses

Here is the full weekly report, which includes all of the informative graphs.

How Are the SARS CoV2 Vaccines Being Monitored for Safety Now That Vaccination is Underway??

All vaccines, including the Pfizer and Moderna SARS CoV2 vaccines that are being deployed right now are continually monitored for safety using the Vaccine Adverse Event Reporting System (VAERS) monitoring system. VAERS is managed jointly by the CDC and FDA and monitors for problems or “adverse events” that happen after vaccination.

In addition to the tried and true VAERS system, there are several additional safety systems in place for the SARS CoV2 vaccines.  Here’s a summary of the various safety monitoring systems that are being used.


Data from the system gives the CDC and FDA important information that might signal a problem. If it looks as though a vaccine might be associated with an adverse event, the FDA and CDC investigate further.  Healthcare providers, patients and caregivers can report into the VAERS system. The CDC and FDA encourage anybody who experiences any problems after vaccination to report to VAERS. Healthcare providers are required by law to report certain problems.

Vaccine Safety Datalink

Scientists use the VAERS data and the CDC’s Vaccine Safety Datalink (VSD) to do studies that investigate vaccine safety.  VSD is a network of eight managed care organizations across the United States. Scientific teams use VSD in two ways.

First, scientists can look back in medical records to see if a particular adverse event is more common among people who have received a particular vaccine.

Second, they use Rapid Cycle Analysis to continuously look at information coming into VSD to see if the rate of certain health conditions is higher among vaccinated people. When potential adverse events or trends are identified a more in-depth review is conducted.


The CDC has also implemented a new system called V-safe or After Vaccination Health Checker which is in place specifically for the SARS CoV-2 vaccines. V-safe is a smartphone-based tool that uses text messaging and web surveys to provide personalized health check-ins after you receive a COVID-19 vaccination.

Through v-safe, you can quickly tell CDC if you have any side effects after getting the COVID-19 vaccine. Depending on your answers, someone from CDC may call to check on you and get more information. V-safe also reminds you to get your second COVID-19 vaccine dose if you need one. Here is the V-Safe After Vaccination Health Checker website.

In-depth Review for Sensitive Subpopulations

Additional COVID specific safety investigations are being planned for sensitive sub-populations. For example, there are a number on initiatives underway including:

1) the FDA and CMS are collaborating on an in-depth review of vaccinated seniors through Medicare;

2) the VA is conducting an in-depth review of veterans that get vaccinated;

3) the FDA is reviewing in depth among certain insured groups through the BEST and PRISM sites;

4) IHS will have a specific review for their members; 5) the Department of Defense will be specifically looking into adverse events among active duty personnel and; and 6) Genesis Healthcare will specifically be studying long-term care residents.

You can review the overarching safety monitoring in this COVID-19 vaccine post-authorization safety monitoring update.

Vaccine Manufacturing Safety

In addition, FDA regularly inspects vaccine manufacturing facilities to make sure they are following strict regulations. Vaccines are manufactured in batches called lots, and vaccine manufacturers must test all lots of a vaccine to make sure they are safe, pure, and potent. Vaccine lots cannot be distributed until released by FDA.

CDC Adds New Vaccine Data to COVID-19 Data Tracker 

Earlier this week, CDC began publishing new COVID-19 vaccination data on the CDC COVID Data Tracker, including: 

  • Total number of doses administered.

  • The number of people receiving one or more doses of COVID-19 vaccine.

  • The number of people receiving two doses of COVID-19 vaccine.

  • A breakdown of overall vaccine administration by manufacturer.

Student Intern Blog

During Fall 2020, public health undergraduate student interns collaborated with health department staff and Mel and Enid College of Public Health faculty and staff to complete community engagement projects on behalf of the Academic Health Department Initiative. The students created a blog summarizing their experiences. Read on! Student Intern Blog | Mel and Enid Zuckerman College of Public Health (arizona.edu)

Journal Article of the Week:

Evolution of antibody immunity to SARS-CoV-2 (nature.com)

Memory responses are responsible for protection from re-infection and are essential for effective vaccination. The observation that memory B cell responses do not decay after 6.2 months but instead continue to evolve, is strongly suggestive that individuals who are infected with SARS-CoV-2 could mount a rapid and effective response to the virus upon re-exposure.

AzPHA Special Report:

The 2020 COVID-19 Pandemic in Arizona:

The Year in Review

This week marks the anniversary of Arizona’s initial case of COVID-19. The index case was a student at ASU that had recently returned from Wuhan. Over the next 12 months, Arizonans have been through a lot.

More than 12,000 Arizonans have lost their lives to COVID-19 and total mortality for the year was nearly 15,000 higher than 2019. Thousands have been hospitalized and recovered but are having long-term health problems. Many others have lost jobs and are at risk of eviction or even experiencing homelessness. Some have lost social connectiveness leading to mental health distress.

At this, the 1-year anniversary of the first case, Arizona continues to have the dubious distinction of experiencing the highest rate of community spread of the SARS CoV2 virus in the country for the last several weeks. This is the second time that Arizona has been on top in community spread. We were highest in the country and world in mid-July as well.

Arizona has recorded 14,972 more deaths in 2020 than in 2019. According to the Arizona Department of Health Services (ADHS) data dashboard, about 11,528 of these deaths have been a direct result of a SARS CoV2 infection. This suggests that an additional 3,444 deaths during this period may be indirectly attributable to the pandemic.

Arizona’s poor performance relative to the rest of the nation has not been because of bad luck or fate as has been suggested by Governor Ducey and Director Christ. It is largely because of an inability to learn from policy successes and failures, bad decisions, misplaced priorities, and an inability to execute core responsibilities.

We put together a summary of 2020 from a public health policy perspective. Our 10-page report is a timeline of the key critical control points and policy decisions that led us to where we are today. Below is an outline of the events that we cover in our 2020 policy review:

  • The Start of the Pandemic in Arizona

  • A Successful Stay-At-Home Order

  • Stay-At-Home Order Ends With No Mitigation

  • AZ Authorizes Hospital Crisis Standards of Care

  • The “Pause” of Business Operations Begins

  • The “Pause” Ends Without Mitigation Enforcement

  • Predictive Modeling Team Asked to Stop Work

  • Testing Bottleneck Impairs the Response

  • Business and School Metrics Adopted

  • Virus Goes Exponential Again

  • Lack of Action Blamed on Lack of Safety Net

  • Business Operation Standards Scrapped by ADHS

  • Arizona’s Testing Debacle

  • Second Hospital Crisis Begins

  • Year-end All-Cause Mortality Report Presents Grim Picture

  • Vaccination Rollout

  • The Consequences of Missed Opportunities

Arizona’s experience has been tragic. Everyone lost was a mother, a father, a sister or brother, or son or daughter. They had kids. They left loved ones behind.

Will Humble, MPH

Executive Director,

Arizona Public Health Association

I Haven’t Been Able to Schedule My COVID-19 Booster Shot… How Protected Am I?

Good question.

There are a lot of people that aren’t able to schedule the SARS CoV2 booster shot these days. Whether it’s because the ADHS website still isn’t working properly or because not enough appointments or doses have been reserved by the ADHS for the required 2nd dose (or a combination thereof)… a lot of people are asking themselves “how much protection did that first dose give me in case can’t find a the booster shot I need in the next few weeks or even months”?

There is good and bad news. The good news is that the first does provide some protection from infection but nothing close to the level or protection you get if you are one of the lucky people that have been able to schedule your 2nd dose.

According to the data published about Pfizer’s Phase III Clinical Trial data in the New England Journal of Medicine, people that just get the 1st shot probably have about 50% protection from being infected with the virus starting about 2 weeks after the first jab.

Here’s the exact quote from the Phase III trial write up in NEJM “…  between the first dose and the second dose, 39 cases in the BNT162b2 group and 82 cases in the placebo group were observed, resulting in a vaccine efficacy of 52% (95% CI, 29.5 to 68.4) during this interval and indicating early protection by the vaccine, starting as soon as 12 days after the first dose”.

Intuitively, one would expect that a person that just had one dose might have more than 50% protection from severe COVID-19 disease. That may be the case. Here’s what the NEJM article said about that “… among 10 cases of severe Covid-19 with onset after the first dose, 9 occurred in placebo recipients and 1 in a BNT162b2 recipient”. In other words, your protection from severe disease is probably higher than the 52% protection figure but there aren’t enough data to be definitive about that.

The Pfizer Phase III clinical trial was not designed to assess the efficacy of a single-dose regimen. Nevertheless, the study concluded that “… in the interval between the first and second doses, the observed vaccine efficacy against Covid-19 was 52%.  Of the 10 cases of severe Covid-19 that were observed after the first dose, only 1 occurred in the vaccine group. This finding is consistent with overall high efficacy against all Covid-19 cases. The severe case split provides preliminary evidence of vaccine mediated protection against severe disease, alleviating many of the theoretical concerns over vaccine-mediated disease enhancement.”

The bottom line is that if you aren’t able to find an appointment for a booster shot at least you know you have about 50% protection from infection and more than 50% protection from getting severe COVID disease.

Side Note: Director Christ has been suggesting in the media that it is fine to get your booster shot after the 21-day interval for Pfizer and the 28-day interval for Moderna. That may very well be true, but there are no data in the Phase III clinical trials to support the idea that you will emerge from the series with the 95% suggested in the clinical trials.  I could find no data to suggest that end-point immunity is the same 95% if the interval between vaccines is extended beyond the 21 and 28-day intervals researched in the clinical trials.

2020 All Cause Mortality Trends in Arizona During the COVID-19 Pandemic

This week’s Public Health Policy Update provides an overview of Arizona’s pandemic experience. Over the last couple of weeks we have put together a couple of documents that highlight the epidemiology and a review of the events of 2020 Arizona’s experience.

Our all-cause mortality report examines total mortality over the course of 2020. Not surprisingly, we found a large increase in all-cause mortality in Arizona during 2020 as compared to previous years. Significant increases in all-cause mortality are seen in June and August with profound increases in July and December. January 2021 will likely be even more deadly than December and July 2020.

Inside our all-cause mortality report you’ll find a table highlighting the percent change between 2019 and 2020. July had the largest percent change, with a 64% increase in all-cause mortality compared to 2019. Total mortality in December 2020 was 61% higher than 2019. All-cause mortality for the year 2020 was 23% higher than in 2019.

Arizona recorded 14,972 more deaths in 2020 than in 2019. According to the Arizona Department of Health Services (ADHS) data dashboard, about 11,528 of these deaths have been a direct result of a SARS CoV2 infection. This suggests that an additional 3,444 deaths during this period may be indirectly attributable to the pandemic.

These additional deaths are likely in part due to the “great displacement” that occurred in 2020 as hospitals were filled to capacity because of the policy decisions that were made by Governor Ducey and Director Christ.

Hospitals have been operating under contingency standards of care for much of 2020 because evidence-based interventions that could have slowed the spread of the SARS CoV2 virus were not implemented by Governor Ducey and Director Christ.

Admission and discharge decisions have been altered out of necessity. Non-emergency procedures have been postponed and canceled during much of 2020.  Tens of thousands (perhaps hundreds of thousands) of procedures were postponed or canceled causing delays in care that may be responsible for many of the additional deaths.

Also, many persons voluntarily delayed care during the 2020 because of fears of coronavirus infections in healthcare facilities. These decisions may have also resulted in deaths indirectly related to the novel coronavirus.

Persons with a host of conditions such as chronic obstructive pulmonary disease may have developed a mild SARS CoV2 infection that worsened their underlying medical condition. Only a more detailed review of the medical record and death certificate would reveal that the coronavirus was a core cause of the death.

The Governor and Director Christ have previously suggested that increases in poisonings and suicide were in-part driving increases in mortality. We could find no such evidence in our analysis.

Dr. Gerald’s Latest Analysis of AZ’s COVID Trajectory

Here is Dr. Gerald’s Weekly Report. At least things aren’t continuing to get worse. Below is his narrative intro:

In a bit of an unexpected change, conditions markedly improved this past week. Cases as well as hospital and ICU occupancy were lower. Like everyone else, I am looking for a glimmer of hope but don’t want to get my (or your) hopes up as I don’t really understand why things are better. I worry there is the real possibility that this improvement could be short-lived.

It is tempting to speculate what might be occurring. Importantly, improvements appear to be country-wide (see Rt.live). This suggests a common thread independent of geography, climate, or local policy. This thread is likely to be a behavior that is structurally and/or culturally imposed. So, here is me crawling out on a limb…I’m going to put my money on university and K-12 closures over the holiday period (see Haug 2020 Ranking the Effectiveness of worldwide COVID-19 Government Interventions which identifies educational closures are the second most effective mitigation policy).

Arizona basically exited the exponential curve the first week of December following university closures. We saw an actual decline in cases beginning the first week of January following closures of K – 12 for Christmas. Yes, I know actual school activities varied widely across school systems but still. Agree or disagree, I am happy to hear your thoughts. If my hypothesis is true, cases could increase in the coming weeks as schools resume their pre-holiday level of activities.

Johnson & Johnson Interim Clinical Trial Showing Promising Results

Johnson & Johnson Interim Clinical Trial Showing Promising Results

Johnson & Johnson is among the many companies that are developing COVID-19 vaccines. They published their Interim results in the New England Journal of Medicine this week. Below is an excerpt of some of their findings:

“After the administration of the first vaccine dose in 805 participants the most frequent solicited adverse events were fatigue, headache, myalgia, and injection-site pain. The most frequent systemic adverse event was fever. Neutralizing-antibody titers against wild-type virus were detected in 90% or more of all participants on day 29 after the first vaccine dose.  Titers remained stable until at least day 71.

On day 14, CD4+ T-cell responses were detected in 76 to 83% of the participants with a clear skewing toward type 1 helper T cells. CD8+ T-cell responses.”

Evidence Review Reinforces that Face Masks Work

Evidence Review Reinforces Evidence that Face Masks Work

For many months now, there has been clear evidence that proper mask wearing while in public spaces is a very effective way of slowing the spread of COVID-19. A new study of studies out this week reinforces that evidence. It also establishes that good adherence to mask wearing improves economic activity (GDP). Below is an excerpt from the study.

The available evidence suggests that near-universal adoption of nonmedical masks when out in public, in combination with complementary public health measures, could successfully reduce Rt to below 1, thereby reducing community spread if such measures are sustained. Economic analysis suggests that mask wearing mandates could add 1 trillion dollars to the US GDP.

Models suggest that public mask wearing is most effective at reducing spread of the virus when compliance is high. We recommend that mask use requirements are implemented by governments.

Such mandates must be accompanied by measures to ensure access to masks, possibly including distribution and rationing mechanisms so that they do not become discriminatory. Given the value of the source control principle, especially for pre-symptomatic people, it is not sufficient for only employees to wear masks; customers must wear masks as well.

Editorial Note: Despite the clear evidence that face coverings are very effective Arizona still does not have a statewide mask mandate. A meaningful mandate that focuses on business compliance would have clearly not only slowed the spread of COVID-19 in Arizona but also would have improved economic activity.

Nevertheless, Governor Ducey and Director Christ are not interested in such an intervention. Since they are the persons vested with the authority in ARS 36-787 – Public health authority during state of emergency or state of war emergency it is clear this high return on investment evidence-based intervention will not be used in Arizona.

Arizona Vaccination Efforts Improving After a Rocky Start

Arizona’s efforts to vaccinate top priority populations got off to a rocky start in December and January in part due to glitches in the software that was developed by an ADHS contractor designed to coordinate appointments at the various mass vaccination clinics.  

It’s a long story, but glitches in the ADHS’ VMS scheduling software failed to make appointments for thousands of healthcare workers that had pre-registered for vaccination. If you want to read more, check out this story by Ray Stern in the Phoenix New Times: Arizona Vaccine Rollout Delayed by Computer Glitches, County Says.

My contacts are telling me that some (but not all) of the bugs have been worked out of the system. That has helped to make the system more efficient in the last week. There are various sources of data that you can refer to as you track how AZ is progressing. The state health department has a web file that they update periodically with the latest number of vaccinations given by county at this web page.

As of today, it shows that about 263K actual shots have been administered out of the 600K+ vaccines that have been delivered. Remember, these vaccines require a booster so many of those vaccines are the follow up shot (fewer than 263K persons have been vaccinated).  

To get a perspective of how AZ is doing when compared to other states both in numbers and rates, you can State-by-state data on COVID-19 vaccinations in the United States – Our World in Data.

Category 1b Expanded to Include People Between 65-74

Prior to last week there were more than 1,000,000 Arizonans in Category 1b including more than 500,000 people over the age of 75. With only about 200,000 persons vaccinated so far, you can see that we have only scratched the surface when it comes to vaccinating seniors.

Nevertheless, the ADHS elected last week to expand the pool of persons in Category 1b by an additional 250,000 by adding persons aged 65-74 to the cohort.

Editorial Note: I don’t understand the wisdom of adding 250,000 more persons to Category 1b when there is such a long way to go vaccinating the higher-risk 75+ folks. My concern is that this new more digitally adept and mobile group of seniors may crowd out those persons over 75 that still haven’t been vaccinated. With advanced age being the dominant risk factor, and persons over 75 at higher risk than persons 65 -74 it seems counter-productive.

Many if not all county health departments have elected to focus squarely on the 75+ group for now. The ADHS vaccination site at State Farm is apparently vaccinating basically anybody among the 1,250,000 persons in Category 1b, including persons aged 65-74 (per Director Christ beginning Tuesday January 19).

The decision to add persons 65 to 74 years old to Category 1b IS NOT based on CDC Advisory Committee for Immunization Practice Recommendations. Rather, it came from an announcement at a press event from soon to be former HHS Secretary Azar that he thought persons 65-74 should be added. The ADHS Director promptly took his advice rather than staying consistent with ACIP recommendations.

The CDC and the ACIP are still recommending that persons between 65 and 74 stay in Category 1c.