31 May 2020 Blog Post: COVID-19 Update in Riverside County

31 May 2020 Blog Post: COVID-19 Update in Riverside County

Three weeks ago, Riverside County officials voted unanimously to rescind local public health orders regarding COVID-19 risk reduction measures. These included rolling back restrictions on vacation rentals and golf. Previously mandated face-coverings in public were no longer required. Further, the motion amended a school closure order. Adding to this, Sherriff Chad Bianco refused to enforce local coronavirus lockdown protocols.
 
Case rates have climbed steadily in each of the past three weeks. For the week ending 5/15/2020, the county reported on average 3.89 cases per day. The following week this number rose to 5.06 and the week ending 5/29 this rate is now 5.35.
 
Notable changes in Riverside County include the resumption of short-term vacation rentals (5/29) as well as the re-opening of barbershops and hair salons (5/26), houses of worship (5/25), as well as shopping (5/22) and dine in restaurants (5/22).
 
There seems to be an inherent disconnect between rescinding public health measures, an aggressive reopening strategy and rising case rates.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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30 May 2020 Blog Post: Using COVID-19 Mortality Rate to Region To Evaluate Suitability for “Reopening”

30 May 2020 Blog Post: Using COVID-19 Mortality Rate to Region To Evaluate Suitability for "Reopening"

It took me somewhat by surprise this week when San Francisco Mayor London Breed outlined on Thursday steps to reopen more of the city’s businesses and allow additional activities in the coming weeks, including outdoor dining, indoor shopping, and sporting events. I hadn’t expected that any of things would be occurring so soon, and wondered what San Francisco had figured out.

As those who have been reading my Facebook posts will recall, I have been compiling rates of COVID-19 infection and deaths for both Los Angeles and Riverside County. So I plugged the data from San Francisco into these existing spreadsheets and was stunned by the numbers.

To date, San Francisco has had only 40 deaths due to COVID-19. There have been 2,042 deaths in Los Angeles County (granted 10 times the population of San Francisco) and 270 deaths in Riverside County (3 times the population of San Francisco).

We know that mortality rates vary widely from country to country and the reasons for such have been debated. Population density, extent of testing, age of the population and the prevalence of underlying health conditions are all potential modifiers. But. in general, a strong public health preparedness and response have made a substantial difference. Death rates are much lower in countries and regions that had standing plans for containing the infection. According to Drs. Sung and Kaplan – “To be sure, we have different cultures, approaches to healthcare, and political systems. But, the observation that infected people in the U.S. are 60 times more likely to die compared to Singapore is too serious to ignore.”

From the Department of A Picture Says A Thousand Words, look at the graph below of mortality rates over time from Los Angeles County, Riverside County and the City of San Francisco. At the end of last week, LA and Riverside Counties had identical mortality rates – 0.28 daily deaths per 100,000 population. (We can discuss the fact that their trend lines are moving in totally opposite directions another time). But look at San Francisco, they have a mortality rate 10 times lower at 0.03 daily deaths per 100,000 population. LA and Riverside haven’t seen a rate that low since March!

So to paraphrase Drs. Sung and Kaplan – there are regional differences in California between culture, healthcare and political systems. But the observation that infected people in San Francisco are 10 times LESS LIKELY TO DIE compared to LA and Riverside County is too serious to ignore.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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28 May 2020 Blog Post: Antibody Testing – A Summary

28 May 2020 Blog Post: Antibody Testing - A Summary

I received a slew of phone calls yesterday about antibody testing and did not realize why until I returned home and found the following headlines:

“CDC warns antibody testing still too inaccurate to use for coronavirus-related policy decisions”
“Antibody tests for Covid-19 wrong up to half the time, CDC says”
“CDC: Antibody tests not to be used for decisions on returning to work”
 
I have been critical of both the CDC and the rushed to market antibody tests, so it is not a surprise that combining the two entities has led to confusion. But what is lost in the CDC’s messaging is that there are good antibody tests out there, and I listed more than a half dozen in yesterday’s post.
 
The CDC’s publication (link below) drones on and on and summarizes their thinking into to this absolute gem of a sentence: “In the current pandemic, maximizing specificity and thus positive predictive value in a serologic algorithm is preferred in most instances, since the overall prevalence of antibodies in most populations is likely low.”
 
Got it? Great, then read no further.
[Of course not. That’s gibberish.]
 
An understandable way to frame these concerns (and maximize the utility of antibody testing) is in the following adage: “right test, right time, right patient.” Follow those three steps, you won’t end up with an inaccurate result.
 
Right Test: I listed more than a half dozen of serviceable, accurate and available antibody tests in yesterday’s post. Essentially what you are looking for is a test that has a specificity (ability to identify a patient without disease as a true negative result) in the range of 99.5% As a comparison, HIV tests we currently use all report a specificity exceeding 99.5%, and often 100%.
 
Right Time: Antibody testing for COVID-19 needs to be performed at the right time. Primarily, we are looking for an IgG response as IgG is the most abundant antibody in the blood, accounting for 70 to 75% of the total. In a recent study, the median time to detection of IgG was at day 14 after the start of symptoms. The presence of antibodies was <40% among patients within 1 week! So the timing of antibody testing is critically important.
 
Right Patient: This is the third key point in antibody testing. For a test to be accurate, it needs to be performed in the right patient. This concept confuses me as well to be honest, because shouldn’t a test be accurate or inaccurate? But context matters in testing, especially in the detection of antibodies. This I evaluate in a case by case basis. For some individuals, there is a high likelihood of a positive test based on exposure or travel history. For others, there is less of a suspicion. But regardless, the test result needs to be matched against their experience to assess accuracy. If the test result matches the patient’s clinical experience, then its probably accurate. If there is a mismatch, either something was missed or the test was wrong.
 
So all is not lost (although the blaring headlines above would make you think otherwise). We have the Right Tests already. Thoughtful application of them at the Right Time and for the Right Patient is all that needs to be done.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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25 May 2020 Blog Post: COVID-19 Update – Los Angeles County Is Bending The Curve

25 May 2020 Blog Post: COVID-19 Update - Los Angeles County Is Bending The Curve

We are probably all sick of hearing about ‘bending the curve’, actually so much so that I’ve noticed it leaving the parlance of the popular press. Given the amount of time that we have all been sheltering in place, it may have been somewhat of a surprise two weeks ago when Dr. Barbara Ferrer of the County Health Department announced that restrictions would certainly extend through the summer.

“We know, with all certainty, that we would be extending health officer orders for the next three months,” she said during an L.A. County Board of Supervisors meeting. “Our hope always is that we’re able, by using the data, to lift restrictions slowly over the next three months.”
 

I must admit, I was a bit perplexed by the announcement – that is until I analyzed the data from Los Angeles County. The good news is that, as a County, we are moving definitively in the right direction. Or ‘bending the curve.’

At the time that Dr. Ferrer made the announcement on May 12th, new cases in Los Angeles County were still on the rise. Figure 1 shows that cases rose from 74.85 new cases per 100,000 population that week to 85.27 the week ending 5/15/2020. However, last week case rates dropped to 70.93 per 100,000 population.

What’s really interesting though is Figure 2, which is mortality rates. These had been steadily falling (and continue to fall) from a peak of 4.46 deaths per 100,000 to 4.12 the week of Dr. Ferrer’s announcement. It is now all the way down to 2.80 deaths per 100,000 population for the week ending this past Friday the 22nd.

So why would mortality rates be falling faster than case rates? Two possible phenomenon – in the first, COVID-19 could now be spreading more rapidly through younger people. We know that risk of death from COVID-19 shares a direct relationship with age. It is certainly possible that younger residents are now more often infected given the strict safer-at-home guidance given for California residents over the age of 65 years. Another possibility, is that testing has increased. While mortality from COVID-19 would be easily identified, cases with few or only mild symptoms might be missed when testing is limited. Therefore case rates would appear to go up, while death rates would decline.

Figure 3 shows that testing rates in Los Angeles have skyrocketed over the past two weeks. At the end of March, only 106.95 tests per 100,000 population were administered on average in a day. For the week ending 5/22/2020 that number has markedly increased to 1425.19 (down from its maximum of 1503.13).

So now I understand a bit better why Dr. Ferrer was guarded in her remarks. At the time of the announcement, mortality rates were falling but case rates were rising. She likely suspected that case rates were increasing due to improving testing availability and capacity, but could not be sure. But now we have some reason to be optimistic here in Los Angeles County – seeing declines in both case and mortality rates is welcome news after all these wearying weeks at home.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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23 May 2020 Blog Post: COVID-19 Update in Riverside County

23 May 2020 Blog Post: COVID-19 Update in Riverside County

Two weeks ago, readers will remember that Riverside County officials voted unanimously to rescind local public health orders regarding COVID-19 risk reduction measures. These included rolling back restrictions on vacation rentals and golf. Previously mandated face-coverings in public were no longer required. Further, the motion amended a school closure order. Adding to this, Sherriff Chad Bianco refused to enforce local coronavirus lockdown protocols (link).
 
At the time of the decision, I pointed out that lifting these measures was misguided given that new case rates were still in decline and that mortality rates, while not increasing, were plateaued at their highest rate.
 
I am sure if you have been reading my posts to date, you can already guess what has happened in Riverside County (which has the second highest number of cases in California after Los Angeles County), I will keep you in suspense no longer.
 
It gets worse.

Mortality rates (Figure 2) have climbed, and are now at an all time high since the beginning of the epidemic. While there was a stable rate of 0.25 deaths per 100,000 population for the past three weeks, this rate is now 0.28 deaths per 100,000.

It is unclear to me why Riverside County elected officials have chosen to experiment with their own population. I do not have an expectation that Sheriff Bianco or the Board of Supervisors would necessarily understand the pubic health impact of their decision, as none have formal medical training. However, Dr. Cameron Kaiser who is the County’s Public Health Director should have known better – but has been silent. Now there are numbers to prove that unchecked political decision making is leading to more COVID-19 deaths among Riverside County residents than ever before.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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20 May 2020: COVID-19 Update – Beware of Those Bearing (Mis)Information

20 May 2020 Blog Post: COVID-19 Update - Beware of Those Bearing (Mis)Information

In the coming days, I expect that the American public will see a blitz of (mis)information with the general theme being that coronavirus is not as “deadly” as we think. It is important to understand the inherent scientific biases that underlie studies used to support this argument.

The Los Angeles area prevalence study which I have critiqued both in previous posts as well as in the Los Angeles Times, has now been published in the Journal of the American Medical Association (The JAMA Network). It has undergone peer review and is significantly watered down from the original press release; the authors have had to acknowledge selection bias and the questionable accuracy of their antibody test kits. However, they couldn’t resist one dig saying “fatality rates based on confirmed cases may be higher than rates based on number of infections.”

Be assured that additional studies such as this will be forthcoming, to much fanfare (Dr. John P. A. Ioannidis from Stanford will most likely be at the forefront of press and television interviews). When reading or listening to these reports, it is important to make a distinction between CFR (Case Fatality Rate) and IFR (Infection Fatality Rate). Experts presenting their case that coronavirus isn’t “that bad” will seek to use these interchangeably when, in fact, they are quite different.

Case Fatality Rate (CFR) is the death rate among those with known disease. In other words, these are patients that have been tested, tested positive, and then tragically died as a direct result of their COVID-19 infection. The testing that they underwent is better validated and more accurate than antibody testing (this technology has been used since the 1980s). CFR is then calculated by dividng the number of deaths by the number of cases. Some choose to calculate it by the number of deaths by the number of recovered cases. Worldwide, the CFR is either 6.4% or 16.4% depending on how you calculate it. Given the time lag required to deem a patient ‘recovered’ I prefer the first calculation.

Infection Fatality Rates (IFR) is the death rate among those who test positive for COVID-19 but may not necessarily have had symptoms (asymptomatic), had such mild disease that it did not come to the attention of a medical professional or was mistaken for another illness (e.g. influenza or a common cold). The testing that is performed to discover infections has, thus far, been far less accurate than the gold standard PCR testing, with the primary error being a false positives. The Los Angeles study, for instance, reports test sensitivity of 82.7% meaning that 18% of the positive tests are incorrect. Conversely, the specificity is 99.5% which means that only 0.5% of the negative tests are incorrect. This is a significant issue. Antibody studies will typically claim a IFR of 0.5% or less.

So how do we reconcile a CFR of 16.4% with a IFR of 0.5%? The short answer is that you cannot because the comparison is truly apples and oranges. Case fatality rates based on recovered cases is undoubtedly an overestimate as not all cases are followed to recovery (termed ‘lost to follow-up’). Infection Fatality Rates are undoubtedly an underestimate as they have been based on flawed antibody detection technology, biased samples (only 50% of individuals who consented to antibody testing actually participated in Los Angeles), and lastly due to right censoring.

Wait, right censoring? I know, to throw a statistical concept into the the third to last paragraph of a post is really unfair. But I guarantee that nobody in the press will cover this source of error. Here’s the issue – people who ultimately succumb to their coronavirus infection do so some time after they become infected – sometimes weeks to months afterwards. However, every seroprevalence study simply uses number of deaths the day that the survey was completed. To be truly accurate, these studies need to wait 4-6 weeks to get an accurate count of just how many cumulative deaths have occurred in the community, before they can report the true IFR. The term right censoring comes from the definition of censoring which is “to officially suppress.” The right refers to the X-axis of a plot over time – or in other words these studies have suppressed events that would have occurred later (to the graphical right) in time. (Side note: there are statistical techniques to account for right censoring but the seroprevalence study authors are simply too lazy to do such).

So how should we approach this attempt to frame COVID-19 as “not that bad”? First, view statements by experts like Dr. Ioannidis with skepticism. When you hear that “estimates of infection fatality rates inferred from seroprevalence studies tend to be much lower than original speculations made in the early days of the pandemic”, think about that critically in terms of how that estimate may be biased. Also, look at the language that these experts use – specifically the term “speculation” when in true scientific discourse they should say “estimate” or “point estimate.” Lastly, if you doubt that COVID-19 is really that deadly, I highly recommend reviewing an outside source – specifically the excess death analysis by the Financial Times (link below). Given concerns that reported Covid-19 deaths had not been capturing the true impact of coronavirus, the magazine began tabulating deaths above the historical average. Thus far in 2020, the United States has had 52,300 deaths which are in excess of those expected in a typical year, 24% higher in fact. So, yes, coronavirus really is that deadly – and don’t let anybody (even a Stanford Professor) convince you otherwise.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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20 May 2020 Blog Post: COVID-19 in Santa Monica

20 May 2020 Blog Post: COVID-19 in Santa Monica

Readers may know that I have been tracking COVID-19 in Riverside County. It occurred to me that I could perform the same analysis for Santa Monica.

As of today, Santa Monica has reported 244 COVID-19 cases (266 per 100,000 population – Riverside County has 227 cases per 100,000 population) and 14 deaths (15.3 per 100,000 population – Riverside County has reported 9.8 deaths per 100,000 population).

To smooth the observations, rates are reported as weekly aggregates of the prior 7 days, expressed in a moving average. This is to account for known human variation in reporting. For a small community, a few observations here and there can sway rates quite a bit, which is why the graphs for Santa Monica are much more jagged as compared to those of the much larger Riverside County.

In terms of cases (Figure 1), one trend still holds, namely the benefit of California’s shelter-in-place orders which went into effect on 3/23/2020. You can see the steady drop in cases (after a previous nearly straight upward trend) from 4.65 on 3/28 to 4.10 and 3.28 in subsequent weeks. However, unlike the data from Riverside County where incident case rates have continued a steady decrease, Santa Monica shows an alternating pitch up and down from 4/21 until 5/15.

Mortality rates (Figure 2) spiked to 1.23 the week of 4/29, decreasing sharply the next week to 0.14, There has been a slow rise from 5/7 to 5/15 from 0.14 to 0.27. This too is in contrast to Riverside County, where mortality rates have remained flat at 0.25 for the last three weeks.

Some of the sudden variation in these rates are likely a function of the magnified effect of events in less populous Santa Monica. Throwing a rock in a small body of water (Santa Monica) will cause a larger ripple than throwing that same sized rock in a much bigger body of water (Riverside County). Nevertheless, it is concerning that we cannot yet visualize a clear downtrend in cases in our community.

Stay tuned.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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16 May 2020 Blog Post: An Update on COVID-19 in Riverside County

16 May 2020 Blog Post: An Update on COVID-19 in Riverside County

Last week, you may remember, Riverside County officials voted unanimously to rescind all of the county’s stay-at-home orders as well as face mask requirements.

On May 9th, 2020: Riverside County reported 4,817 COVID-19 cases (199 per 100,000 population) and 204 deaths (8.4 per 100,000 population).

As of today, Riverside County reported 5,618 COVID-19 cases (227 per 100,000 population) and 242 deaths (9.8 per 100,000 population).

I began to aggregate the data from Riverside County as, no doubt, coronavirus cases and deaths will begin to increase in the coming weeks. This was not an easy task as the County Public Health Department does not publish these data it in a downloadable file so I needed to tabulate it by hand. Undeterred, I have been able to demonstrate the protective effect of state-wide shelter-in-place orders. When looking at graphs of both incident cases (Figure 1) and deaths (Figure 2), each show a clear graphical uptrend until mid to late April, when these level off (mortality) or noticeably decrease (cases).

[Statistical note here – to smooth the observations, rates are reported as weekly aggregates of the prior 7 days, expressed in a moving average. This is to account for known human variation in reporting – for instance, case reports drop precipitously on Saturday and Sunday with spikes on Monday. In Medicine we call this the parking lot effect. Your quality of care at a hospital relates directly to the number of cars in the parking lot – a scary topic for another time.]

We expect a lag time between any public health intervention (e.g. closing borders, case quarantine, social distancing) and case burden. This is because coronavirus has an incubation period between infection and the development of disease. There is a further delay until these symptoms come to the attention of a healthcare professional. Add to that the additional waiting for confirmatory test results. Studies from China have suggested that it can be up to a month before the effectiveness of a COVID-19 intervention can be visible. For mortality rates, this could be even longer.

Given that California shelter-in-place orders went into effect on 3/23/2020, the data from Riverside County about a month later show a drop in new cases from 6.12 per 100,000 population on 4/21/2020 to 4.97 on 4/29/2020. Incident case rates have continued to decrease. Mortality rates have remained flat at 0.25 for the last three weeks – while they haven’t increased, they have not declined either.

It is a shame that Riverside County could not even wait until death rates began to drop before deciding to rescind the public health measures that were keeping them safe. Hopefully the individual residents of the County are smarter and more cautious than their political and public health leadership. Time (and graphs) will tell.

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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12 May 2020 Blog Post: Santa Monica Primary Care Experience amidst COVID-19

12 May 2020 Blog Post: Santa Monica Primary Care Experience amidst COVID-19

It has been some time since I have updated our own clinic’s experience with COVID-19. Nationally, the United States now has 1,381,665 cases with 81,552 deaths (5.9% mortality rate). The Atlantic’s COVID-19 Tracking Project (link: https://covidtracking.com/data) reports a 14.2% positive testing rate for the US as a whole. In California, this prevalence rate is 6.8%.

At Santa Monica Primary Care, we are currently tracking slightly higher than the state average at 7.8%. However, this is significantly lower than our peak of 15.3% on 3/25/2020 (Figure below).

We have also begun antibody testing in greater capacity. While we have too few numbers to report as yet, we will update these moving forward. Of interest, MLB completed testing of their players and employees showing only a 0.7% positive testing rate. (Link: https://www.theguardian.com/…/mlb-baseball-covid-19…)

I will finish today’s post with a passage from Robert Pirsig’s classic “Zen and the Art of Motorcycle Maintenance”. How I started reading this is a discussion for another day but its insight rings hauntingly true as our country lurches forward misstep after misstep:

“The real purpose of scientific method is to make sure Nature hasn’t mislead you into thinking you know something you don’t actually know. There’s not a mechanic or scientist or technician alive who hasn’t suffered from one so much that he’s not instinctively on guard. That’s the main reason why so much scientific and mechanical information sounds so dull and so cautious. If you get careless or go romanticizing scientific information, giving it a flourish here and there, Nature will soon make a complete fool out of you. It does it often enough even when you don’t give it opportunities.”

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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9 May 2020 Blog Post: Finding Solid Messaging in Music

9 May 2020 Blog Post: Finding Solid Messaging in Music

Many of you are probably unaware that I am a country music fan. I’m not exactly sure when this began, but it is probably rooted in my genetics as my Mom was born and raised in the Great State of Texas.

Yesterday on Sirius XM’s The Highway, a new song from Luke Combs came on just as I drove into the parking garage. Entitled ‘Six Feet Apart”, it was a song that made me pull over and wait outside the garage entrance. The refrain is as follows:

“I miss my mom, I miss my dad
I miss the road, I miss my band
Givin’ hugs and shakin’ hands
It’s a mystery, I suppose
Just how long this thing goes
But there’ll be crowds and there’ll be shows
And there will be light after dark
Someday when we aren’t six feet apart”
 
Here he reinforces the idea of physical distancing as well as protecting older family members who are higher risk of complications and mortality from COVID-19 infection. I also like his idea of the pandemic’s duration being a ‘mystery’ as to ‘how long this thing goes’. It accurately sums up the inherent unknowns of epidemiology and public health investigations. But it also conveys a tacit acceptance of that process along with the need to be patient before there are ‘crowds and shows’.
 
He also outlines his plans after physical distancing recommendations are relaxed. Yet, he will still bring with him lessons learned from the pandemic – namely ‘overwashing’ his hands.
 
“First thing that I’m gonna do
Is slide on in some corner booth
And take the whole damn family out
And buy my buddies all a round
Pay some extra on the tab
Catch a movie, catch a cab
Watch a ballgame from the stands
Probably over-wash my hands”
 
Luke Combs’ understanding that ‘there will be light after dark’ stands in stark contrast to Riverside County Supervisors 5-0 decision last night to rescind a mandate for residents to cover their faces and practice social distancing while in public. Supervisor Jeff Hewitt wanted to go a step further and have Riverside County join other California counties that are defying Newsom’s mandates imposed to stop the spread of COVID-19. “As fun as that would be, I don’t know how we get rid of somebody else’s authority,” Jeffries said.
 
As of this morning, Riverside County has reported 4,817 COVID-19 cases (199 per 100,000 population) and 204 deaths (8.4 per 100,000 population).
 
I will update this post in two weeks for Supervisor Jeffries specifically. We will then see just how much ‘fun’ disease and death can be – especially when they are entirely preventable.
 
Or, as Billy Currington said, “God is great, beer is good and people are crazy.”

𝗦𝗶𝗴𝗻 𝗨𝗽 𝗳𝗼𝗿 𝗢𝘂𝗿 𝗡𝗲𝘄𝘀𝗹𝗲𝘁𝘁𝗲𝗿

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