Author: Will Humble

Back on August 3, the CDC issued new guidance regarding people who are infected with the coronavirus. It flew under the radar until the New Your Times wrote a story about that change.  Following the NYT article, other media outlets improperly interpreted the new CDC guidance and wrote stories suggesting that immunity wanes after 3 months. That is not what the CDC guidance said.

What the CDC actually said was that “People who have tested positive for COVID-19 do not need to quarantine or get tested again for up to three months as long as they do not develop symptoms again. People who develop symptoms again within three months of their first bout of Covid-19 may need to be tested again if there is no other cause identified for their symptoms.”

Last Friday the CDC issued a clarifying statement saying, “Contrary to media reporting today…  the latest data simply suggests that retesting someone in the 3 months following initial infection is not necessary unless that person is exhibiting the symptoms of COVID-19 and the symptoms cannot be associated with another illness.”

Some scientists have speculated that immunity from the virus might only last 3 months based on a study published in Nature back in June that showed many patients began to show decreasing levels of immunity 2–3 months after infection and that antibodies may not last very long among asymptomatic mildly ill persons.

But remember, antibodies are just one part of the immune system and it’s normal for antibodies to decrease once an infection recedes.  It also doesn’t mean that waning antibody titers mean waning immunity.  The memory B cells that first produced those antibodies are still around and stand ready to make more antibodies on demand. There is also good evidence that people infected with the SARS virus also generate a robust T-cell response- providing a longer lasting type of immunity.

Next week I’ll do a have a piece on the immune system and how it works with an eye toward the pandemic.

Will There be a Compliance System this Time?

As you recall from last week’s blog post, the ADHS has proposed benchmarks for when bars, nightclubs and gyms can re-open.  When a county reaches numeric benchmarks like a defined percent positivity rate the paused businesses are free to re-open if they implement safety protocols and guidelines and turn in an attestation form committing to stay in compliance.

The benchmarks for each county are posed on the ADHS’ Dashboard.  That dashboard shows whether the county meets the benchmarks. There’s a drop-down box that let’s you see each individual county’s metrics. The default is the statewide numbers.

Editorial Note: Several counties are coming close to meeting the metrics that will allow bars and nightclubs to open again. And while each business will be required to attest that they are implementing the mitigation guidelines, there is still no defined compliance and enforcement system to ensure that the businesses stay in compliance.

Without a rigorous and compliance system that is enforceable it’s highly likely that large numbers of bars and nightclubs will ignore the mitigation guidelines and behave exactly like they did from May 15 all the way until late June when the governor finally “paused” these businesses. If that happens we will again see a dramatic growth in cases and percent positives which will jeopardize the opportunity for in-person instruction in our K-12 system.

Such a compliance system isn’t rocket science. The state could require each of these businesses to post a number to a complaint hotline (perhaps even the smoke free Arizona hotline). Complaints could be distributed to the county health departments who could send out their Environmental Health Specialists (Sanitarians). Businesses that are out of compliance as determined by the county inspector would have their attestation canceled. Business closes. Compensation for that work could come via CARES Act money. Voila, compliance.

Last week the Fed’s posted every state’s July-December 2020 COVID-19 testing plans. The plans include details on responding to surges in cases and reaching vulnerable populations including minorities, immunocompromised individuals, and older adults. Here’s a link to Arizona’s testing plan.

I haven’t had time to look it through yet. Also, this is just a plan. As we’ve seen, what actually happens depends on whether and how they execute the plan.

CDC Releases Two New MMWRs on COVID-19 in Nursing Homes

CDC published two new COVID-19-related MMWR reports: Transmission of SARS-CoV-2 Involving Residents Receiving Dialysis in a Nursing Home and Facility-Wide Testing for SARS-CoV-2 in Nursing Homes. The first report found a higher prevalence COVID-19 cases in residents receiving dialysis (47%) than those not receiving dialysis (16%) in a Maryland nursing home outbreak.

The latter found that facility-wide testing in nursing homes after identifying a positive case might help to “maximize the benefits of infection prevention and control interventions.” For facilities without a known COVID-19 case, alternative testing strategies may be more efficient, including focusing on high-risk populations within facilities.

Children and COVID-19: A State Level Report

Arizona has the highest rate of child infections in the country at 1,200/100,000.  This is more than 2.5 times the national average of 500/100,000.

The American Academy of Pediatrics published their state-level report last week which is the first publicly available report specifically focused on the childhood epidemiology of the disease in the US. The report shares all publicly available data from states on child COVID-19 cases.  The Appendix has the details and links to all data sources.

The report will be valuable as researchers begin to examine the links between public health policies and the resulting outcomes. Once the pandemic is finished, we will have rich evidence to compare the effectiveness of policies in responding to the COVID-19 pandemic.

New MMWR on Mental Health and Substance Use During the COVID-19 Pandemic

A recently released MMWR on mental health during the COVID-19 pandemic describes the results of surveys conducted among U.S. adults. Nearly half of respondents reported at least one negative behavioral or mental health condition. .

Last week the ADHS released criteria that they propose to use to determine when the businesses that are closed by executive order (bars/nightclubs and gyms) can open again. The guidelines propose levels of community spread, that if met, would allow the closed businesses to begin operating with certain restrictions.

There are two key components to resuming business operations. First is the quality of the establishment’s implementation of COVID-19 mitigation strategies. This plan outlines mitigation strategies tailored for specific types of business operations. Business must attest to their implementation of these strategies prior to operating.

The second is the level of spread occurring in the community. The CDC defines community spread as follows (all 3 metrics need to be bet to qualify for the category):

Minimal Community Spread: Evidence of isolated cases or limited community transmission, case investigations underway; no evidence of exposure in large communal setting. This category would require a percent positivity of under 5%, case rates of less than 10/100,000 per week and COVID like illnesses of less than 5%.

Moderate Community Spread: Sustained transmission with high likelihood or confirmed exposure within communal settings and potential for rapid increase in cases. This category includes a percent positivity of under 10%, case rates of between 10 and 100/100,000 per week and COVID-like illnesses of between 5 and 10%%.

Substantial Community Spread: Large scale, controlled community transmission, including communal settings (e.g., schools, workplaces). This category includes a percent positivity of more than 10%, case rates of more than 100/100,000 per week or COVID-like illnesses of over 10%.

Upon reopening, the bars/restaurants and gyms are supposed to implement the safety protocols and guidelines and turn in an attestation form committing to stay in compliance. The attestation form is supposed to be posted in a visible location in the facility. Additional details can be found in the ADHS COVID-19 Guidance for Businesses.

• Requirements Bars and Nightclubs Providing Dine-In Services

• Requirements for Bars and Nightclubs Not Operating as a Restaurant

• Requirements for Indoor Theaters

• Requirements for Indoor Gyms and Fitness Centers

• Requirements for Water Parks & Tubing Operators

The dashboard at azhealth.gov/businessCOVID19 indicates whether counties meet the recommended benchmarks. Data on the dashboard will be updated weekly on Thursdays. The percent positive metric on the ADHS dashboard will be lower than the percent positive numbers that are posted on well-known sites like John’s Hopkins and the COVID Tracking Project because it is calculated differently and many of the laboratory results are excluded from the calculations.

Maricopa County Department of Public Health also launched a dashboard to help school officials in Maricopa County determine if their communities are meeting reopening metrics. The tool allows school superintendents, principals and other decision-makers to see two weeks’ worth of data on the three metrics set by ADHS and ADE for opening schools: Maricopa.gov/SchoolDashboard.

Editorial Note: The protocol ADHS developed distinguishes between bars that have a “food establishment permit” and those that don’t. They say that bars that don’t have one can’t open until the percent positivity is less than 3%.

The problem is that every single bar and nightclub has a “food establishment permit” because the mixed drinks are considered food.  I think you’ll see that they modify their guidance to reflect the type of liquor license the establishment has instead. Time will tell.

Updated With New Editorial Note: August 19, 2020

You’d think that something like the percent of COVID-19 tests that are positive would be simple and straightforward. Turns out it’s not.

With the metric informing really important decisions like in-person school instruction and driving decisions like when bars and nightclubs can open- it’s super important to have a metric that’s as accurate as possible. We’re not there yet, but it’s fixable.

Why is the Percent Positive Number Important?

The number of new cases diagnosed per day often gets the headlines, but the percent of tests that are positive is a better indicator of community spread and especially the adequacy of testing. 

It’s important to be able to test widely including people who are contacts of cases but only mildly ill or even asymptomatic so they can isolate if they are positive.  The percent positive number gives a decent picture of whether testing is adequate to achieve that goal. As a rule of thumb, a 5% positive rate or lower indicates decent testing capacity and moderate to low community spread.

How is it Calculated?

This seems like a straightforward question, but there are at least 3 different ways people are calculating the percent positive rate in Arizona. Understanding how the percent positive is being calculated is super important now that the metric is being used to make decisions about how and when businesses like bars, nightclubs, gyms and waterparks as well as schools can and should open.

Here are 3 different ways one can calculate a percent positive metric:

Method 1: Straight Up Division

This approach takes the number of positive tests that are reported each day to the state health department divided by the total number of reported positive and negative tests. The vast majority are positive PCR tests but a handful are IgM positive serology tests with diagnostic support.

This is the percent positive number that you are probably most familiar with because it’s used by the COVID Tracking Project, ASU Biodesign Institute and Johns Hopkins University.

It’s also the number that you’d get from the ADHS website if you divide the daily number of reported PCR positives by the total PCR tests. It’s also the fastest way to check the percent positive because it can be calculated immediately every day.

However, there are some people that take issue with this method because, according to the ADHS Director, some labs are reporting the positive tests but not the negatives (despite the fact that Executive Order 13 requires all labs to report both positives and negatives). If that’s the case, then this method will give an artificially high percent positive estimate because some of the denominator is missing (the negatives).

This method of calculating the percent positive doesn’t reflect when the person was tested. Because of the historically long turnaround times, the results that come in each day can be as much as 2-weeks old.

The COVID Tracking Project, ASU Biodesign Institute and Johns Hopkins University all display the daily percent positive using this method.

Method 2: Backfill the Epi Curve

Another way to calculate the percent positive is much slower but more accurate. Using this approach, you can find out what the percent positivity was 2 weeks ago, but it doesn’t help you know what the percent positivity is real-time.

Because of the slow turn-around times and reporting delays the percent positive using this approach can only be calculated after the fact…  even 2 weeks after the fact.  With this approach you only know what the percent positive was last week or even the week before.

Under this approach, test results that come in each day are backfilled to the date in which the specimen was collected. So, a test that comes back from the lab today, but was sent to the lab 10 days ago, won’t be counted in today’s percent positive number.  Rather, it would be backfilled to count as a positive on the date the sample was collected.

This approach gives you a more refined look at the percent positivity rate, but it can’t be calculated for several days after the fact because many of the  tests are coming back from the labs so late (more than ½ of tests are still coming back more than 5 days after being collected).

Method 3: Backfill the Epi Curve & Exclude Results

The ADHS uses this method to calculate the percent positivity numbers. This method is similar to Method 2 and is also a retrospective look at what the percent positivity was a couple of weeks ago. They backfill new daily test reports to the date of specimen collection.

However, they only include the data that is submitted electronically for the calculations. The Department’s rationale for excluding the data that isn’t reported electronically is that some labs aren’t turning in their negative results (even though Executive Order 13 requires them to do so).

By excluding the non-electronically reported results, they avoid artificially inflating the percent positive figure, but they also don’t get the full picture because so many of the results are not used, and are left to defend why so many of the test results aren’t being used.

Which Method is ADHS Using?

ADHS is using Method 3 to calculate the percent positive numbers for each county. It is those numbers that you will see on the School and Business Dashboards. 

Because they calculate percent positives differently than well-recognized national sources, the percent positive numbers that they report will always be different (lower) than the numbers that are tracked and displayed by The COVID Tracking Project, ASU Biodesign Institute and Johns Hopkins University.

It will take some nuanced messaging to explain the differences to the public. It will be confusing because ADHS will state that Arizona’s percent positive rate is significantly lower those well recognized national sources.

This will lead to the impression that ADHS has intentionally selected a method of calculating the percent positive that could lead to premature opening of businesses like bars, nightclubs and gyms. Their method has good merit, but excluding results from labs that don’t report electronically will build suspicion that something is amiss.

A sticky wicket indeed.

Editorial Note: ADHS’ decision to exclude all data that’s not reported electronically is puzzling and unnecessary. Executive Order 2020-13 requires all laboratories to report all their results – both positive and negative. ADHS has conceded that they are not requiring all laboratories to comply with EO-13 (signed on March 23).

The failure to enforce that Executive Order is the reason they have excluded much of the data set. This is impairing their ability to get an accurate estimate of percent positivity. Having an inaccurate measure of percent positivity means that important decisions like when in-person school is safe to begin and when bars, nightclubs, water parks and gyms can reopen.

A simple solution is to enforce the reporting provisions of EO-13. They could then most accurately measure percent positivity.

Let’s fix this, shall we?

New Editorial Note August 19, 2020: The ADHS now states that they indeed are getting all of the data from all of the labs, but that some labs aren’t submitting the data in the format that they would like. Their current position is that they will continue to exclude those data that aren’t in the format that they would like (about 30% of the data set). I expect this position to change and for them to begin inputting the data and using it as questions about their practice of excluding data are debated in the public square.

SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19 

Abstract https://www.nature.com/articles/s41586-020-2598-9

Some people that have been infected with certain cold viruses (coronaviruses) have antibodies that might help them fight off the SARS CoV2 virus, and lead to fewer severe symptoms.

The study about published in the journal Nature found that among a sample of 68 healthy adults in Germany who had not been exposed to the coronavirus, 35% had T cells in their blood that were reactive to the SARS CoV2 virus.  One possible implication for these results is that perhaps because young kids often have colds that fact might be a reason why they are less likely to get infected with the SARS CoV2 virus and have bad outcomes.

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MMWR: SARS-CoV-2 Transmission and Infection Among Attendees of an Overnight Camp

CDC released an MMWR summarizing a case study of SARS-CoV-2 transmission at an overnight camp in Georgia. While the camp instituted most of the CDC’s suggestions for summer camps, they did not require cloth face coverings or opening windows and doors to increase ventilation.

A total of 597 Georgia residents attended the camp and the overall attack rate was 44%. The study demonstrates that youth are susceptible to SARS-CoV-2 infection and that asymptomatic infection is a critical component of disease transmission.