It had to start sometime, but pressure from partisan and a variety of other assemblies have surely advanced the nation-wide schedule for lifting restrictions of non-medicinal management of the Covid-19 epidemic. It is happening in Kentucky too. While there are state differences in degree, the number of new cases identified continues to increase overall. We are “bending the curve.” Because availability of viral testing continues to be limited, as more testing done more cases will be found. How best should we monitor our populations to detect, localize, and quantitate any significant second peak in the curve of disease incidence? I cannot say that I know!
Kentucky has been fortunate to have acted early and aggressively to deal with our rising number of cases. Despite relative success compared to other states, the number of known cases in Kentucky is rising and will continue to do so while our still-modest ability to test for the virus increases. A 7-Day rolling average of daily new cases remains high. Timely identification of new cases will be essential to deal with the brushfire outbreaks that are certain to occur in the months ahead– whatever we do. Depending on the day of the week, the number of tests done, and reporting from new hot-spots, the number of new cases per day varies widely, making predictions uncertain..
What other measures could we track? Some potential independent statistics that are less directly correlated with frequency of testing, and which we are already collecting include deaths and hospital utilization. These are, however, manifestations of more severe disease and will necessarily lag in time from any overall increase in viral infections.
It has been 46 days since the first case of Covid-19 infection was reported in Kentucky and 36 days since the first death– not as long as it seems for those of us riding out the storm at home or still on the job.! Nonetheless, we are hearing increasingly broad demands to walk away from the non-medical public health approaches we are using to mitigate the impact of this highly infectious agent. However, given the very limited availability of viral testing, of what is at best a decrease in the exponential growth rate of new cases, and continuing sporadic jumps in the number of new deaths daily; it is not at all clear that we have broken the back of Kentucky’s part of this pandemic. It does appear that our personal and other community sacrifices have awarded us success compared to other states! We have avoided a disabling flood of very sick Covid-19 patients on the capacity of our hospitals– one of our most important goals. However, in my opinion and as based on the raw numbers available to me, we do not have the evidence in-hand to declare that we have reached the plateau needed to justify anything more than thoughtful planning for progressive gradual stand-downs. The lack of a fully functioning viral testing and reporting system has not reached anyone’s minimal expectations. We are flying blind. Governor Beshear’s reports over the weekend through Tuesday evening show continuing substantial volatility in the counts.
The number of new cases of corona virus announced by the Governor last evening was not as high as was feared. There was concern that changes in data collection techniques would cause an artifactual “catch-up” spike. The aggregate numbers of both cases and deaths is still rising but not as strongly exponential as before. The daily count of new cases may be leveling off, but the number of viral tests performed daily is also declining. Current case mortality is hovering at 5% of identified cases. The percent of viral tests that are positive has been slowly rising– currently 8.2%. Both of these latter two statistics reflect the fact that sicker and high-risk individuals are still being preferentially tested. As long as we are hamstrung by lack of testing capacity and timely reporting, Kentucky is in no position to open up its economy by relaxing the fundamental epidemiological principles necessary to control this extraordinarily infectious agent.
This morning I simplified and updated the data visualizations currently on the Tableau Public pages of KHPI. I include some of the semi-log plots that I discussed yesterday, but as it happens, the aggregate numbers of cases and deaths are falling off even this trend line. Visual inspection confirms that the plots are rising less steeply especially for the number of aggregate cases. (Aggregate deaths might be expected to lag new case discovery.) Muddying the water however, is the fact that rather than increasing, the number of tests performed (and reported publicly) is actually declining! What is not looked for is rarely found. We are still largely flying in twilight– if not the dark.
Cases and Deaths. The graph below gives an overview of the aggregate numbers of new cases and deaths. The recent points are falling away from the exponential trend line. This has to be a positive sign.
Aggregate Number of Tests. It is not a positive sign that the rate of performing new tests (as reported publicly) is not increasing as it must. We want to see exponential growth in the number of test done!
New cases and tests. The daily number of new cases lacks the higher spikes of the week before but remains volatile. The daily number of tests reported is demonstrably declining. It is reasonable to wonder if any appreciable decline in cases may be related to a decrease in testing. I pause here to ask a question that perhaps can be answered by someone in Frankfort. Are all “Cases” defined by a positive viral lab test, or is a clinical diagnosis of Covid-19 infection without a positive test enough of a ticket to make it to the New Case list? It surely is a given that many Kentuckians are infected or killed by Covid-19 than are included in the data available publicly!
What is the problem with testing? The Governor and Commissioner were obviously disappointed if not frustrated. I do not blame them. I am not the first nor the last to point fingers at our Federal Government’s role in deemphasizing or even delaying our national response to the threat of a pandemic. What happened to our scientific and medical leadership that smaller and less wealthy countries had strong testing capacity while we staggered with faulty tests that were worse than nothing? That story will eventually be told in full, but the current paradoxes are indeed frustrating. Governor Beshear pointed out the availability of having 15 of the Abbot Company’s rapid-testing machines, but only 20 of the testing kits containing the chemicals needed to actually perform individual tests. Who has these machines? Are we paying to have them sit unused? Who is responsible for providing the specimen collection kits and testing reagent kits. Are they even available anywhere? The Governor also made a point that while some labs were turning out and reporting results in 24 hours, that others were taking 10 days. Naturally it takes time to set up any new test and insure that it is working properly. What entity has arguably failed us– the free market, or the public health agencies of our nation? I suggest that devolving some public functions to the free market has actually been dysfunctional.
Is it safe to open up? The suggested guidelines and thresholds announced by the White House yesterday about how to proceed in the days ahead are at first blush surprisingly reasonable. If they are actually supported remains to be seen. I have not had an opportunity to study them myself. An emphasis is on gradual stepwise changes. I suspect that most of the critical metrics and capabilities that will justify initial changes are dependent on knowing who is a virus carrier, where they are, and where they have been. Sadly, it appears that we are far from that capability now. Will we be ready in 12 days till May? Of course not! Yes we need to get on to our new normal. I will be listening to Drs. Fauci and Stack, and Governor Beshear. Who would you trust your lives to?
Peter Hasselbacher, MD Emeritus Professor of Medicine, KHPI President, KHPI April 18, 2020
Comment: The visualizations on the Tableau Public website are generally updated daily and will differ from the figures included in this article.
[Addendum: I have updated the Tableau Pubic presentation with data from Friday April 17. The increase in cases and deaths was not as great as the Governor feared. It looks to me like the rate of increase in both cases and deaths no longer fits an exponential trend curve. Things look like they are slowing down! Overall however, both measures continue to increase. I will address this new data later.]
I have been tracking and commenting on the number of cases and deaths from Kentucky’s coronavirus epidemic. Despite my best effort’s and some requests, the only data I have from Kentucky proper is what has been announced from the governors office during his evening greetings. Given our national slow start in timely testing for the virus, we must assume that the numbers as presented are incomplete– indeed only the tip of the iceberg. We have been warned over the past two evenings, that as data collection is now more systematized, that tonight we should expect a large number of “catch up” cases. For that reason I have not yet updated the numbers in my earlier articles or on my Tableau Public website.
In the meantime, I have been evaluating further the approaches I have been using to visualize the numbers released. Because we are still in the exponential expansion phase of this epidemic and because of some unavoidable scatter in the data, it is very difficult to determine if we are bending our new-case curve, let alone flattening it. It is certain that we have not yet reached the peak incidence of this epidemic.
Are we bending our curve yet? When a curve on a simple graph plot is going straight up, it is difficult to know when it will stop. For this reason, I have begun using what is called a semi-log plot that allows simultaneous visualization both high and low numbers, and transforms an exponential curve into a straight line. This is a technique used by experienced epidemiologists (of which I am admittedly not one). In doing so, I wanted to feel more confident with the significance of the observation that the data-points of both new cases and deaths from earlier this this week appeared to be falling below the predicted trend-line. That would be nice! There are lots of understandable reasons why that may not be happening including more testing, clusters of deaths in long-term care facilities, more impatient violations of large group gatherings, and the like.
My goal here. While I am waiting for tonight’s updated numbers, I wanted to try some alternate methods of visualizing the data and get a feel for how reliable they might be in identifying and impact of what we are all trying to do together. I am feeling more confident that using semi-logarithmic plots and applying exponential regression analysis can be useful in identifying trends. Because I find that experts commonly, if not by standard, exclude cases before the 100th when attempting to predict the future. (Early data may be collected in a less formal manner and the randomness inherent in low numbers may offer less predictive value.) I placed a presentation on my Tableau Public website that steps through my thinking. This is what I expect to try in future articles.
Even with all the caveats. Looking at the various plots and making assumptions about how infectious agent like Covid-19 might be, I was stunned (but should not have been) at the power of exponential (compound) growth. I start from a single case from a hypothetical virus and uses purely hypothetical data. Even if a single infected person passes the disease to only one out of a thousand other people, the number of new cases in Kentucky would be in the tens or hundreds of thousands within 40 days. In addition, I am impressed at how fast things can sneak up on you!
I do not believe we are in any position in Kentucky to let go of the alligator we are wrestling. I am still waiting for better clarity of what we are actually facing.
Both new cases and deaths from Covid-19 infection continue to rise sharply in Kentucky. Observed mortality of confirmed cases remains above 5%. Simple daily plots of the numbers of cases by themselves cannot indicate whether we are turning a corner or flattening a curve. Comparison with other states and the nation as a whole does suggest our efforts to mitigate the disease are having an effect. Plotting the data on a logarithmic scale makes visualizing small and large numbers together on the same scale more accessible to analysis. More to the point here, such semi-log plots of the numbers enable us to observe whether the rate of increase in cases or deaths is actually slowing down. Over the past few days, there have been tantalizing suggestions that in fact that both cases and deaths are in fact doing so. Additional reported numbers over the next few days will clarify this hoped-for shift. Nonetheless, we have not achieved plateaus of either daily reported cases or deaths. In fact, semi-log plots of the number of new cases over the 30 days since the 100th new case show continued exponential growth with doubling times of every 5 days. Unless the very recent possible dip in new cases is real, at the current rate of increase, Kentucky will reach 10,000 total cases as early as May 4th. It seems to me that now is not the time to throw in the towel. It is appropriate to begin planning for an eventual data-driven, gradual, and stepwise reversal of our current non-medicinal efforts to deal with this stunningly infectious new disease, but otherwise it’s not very smart to do so precipitously. We have much more to learn about what is happening behind the scenes and our testing capability is still on its baby legs.
A higher than expected observed mortality rate does not accurately reflect overall case mortality. There are other things to worry about at this point- like some folks selfishly ignoring the prohibition of large group meetings!
[Addendum April 10, 2020: Governor Beshear announced this evening 90 new deaths, the largest in a single day by far.]
Since my article of April 3, the number of tallies of daily cases and deaths has increased. The figure below reflects the numbers released last evening on April 6 by Governor Andy Beshear. Click on the graphic to enlarge it. [An interactive graphic with updated data and alternate visualizations can be accessed here.]
The data underlying this figure can be viewed on my Tableau Public Website using the interactive link above. The data I present are the unchanged numbers as announced at the end of each day at the Governor’s public briefings. It should be noted that these announced counts have been continuously subject to adjustment by the Commonwealth to correct for duplications, late entries due to weekends, or other minor edits, but remain reasonably accurate as we go day to day.
It would be nice to believe that the slight downturn in the green “Positive Tests/Cases” line reflects the “flattening of the curve” that we are all working for. Things should become more apparent over the next few days. Recognize however, that Kentucky is testing many more people for viral infection. Yesterdays announcement noted that some 18,000 people had tests, compared to 2,556 just one week ago! The lesson here is “Seek and ye shall find.” There has always been– and still are– many more infected people in the community than we knew of. Many if not most of these have no or minimal symptoms. We should expect to see the number of new cases go up, especially if the new testing contract with Gravity Diagnostics works as hoped. A continuing increase in new cases should not be used to justify backing off from our efforts to protect each other from ourselves!
The Observed Mortality Rate depicted in the red line above represents the known number of deaths up to that day as a percent of the total number of known positive tests for virus at that time. The fact that this calculated mortality rate is still rising– indeed higher than the mortality rate in places whose epidemics have been running longer– is actually expected and should not cause disproportionate alarm at this point. Because of the lack of earlier testing, the true number of community infections was much underestimated. Only the most severe cases were identified and we expect a higher mortality in this subset of patients.
Recall too that the symptom-free incubation period between exposure and symptoms can range from 2 to 14 days. Similarly, infected people who eventually die do not generally do so on the first day of their symptoms. In a sense then, the Observed Mortality Rate curve is catching up with the number of unrecognized infections that occurred at a time of low testing. This observed mortality rate is surely higher than the actual case mortality rate which is a measure of how many infected people eventually die of their Coronavirus infection. What I expect to occur is that the Observed Mortality Rate will in near weeks begin to decline and level off at a considerably lower level. Epidemiologists all over the world are waiting to see what that level will be and who is most vulnerable.
I would like to have seen a more dramatic decline in numbers nationally, but we were as a country late to the game and it shows. My hometown of New York City, where I learned to be a physician and know its hospitals, is taking a terrible beating. In Kentucky we learned from the experiences of other nations, cities, and institutions and made the hard decisions early. I give our Public Health Department and the Governor’s offices much credit. I am following their advice and you should too.
Peter Hasselbacher, MD Emeritus Professor of Medicine, UofL April 7, 2020
If I have made an error in math or terminology or understanding, please help me correct it.
We have not yet reached the peak of either cases or deaths!
It has been my tenant, that as a society “We are no more healthy than the sickest among us.” In recent months, I restate as a corollary that, “We are no more healthy than the person standing right next to us!”
When I started this, I was actually surprised to see that I have not written for these pages for a full year. Ironically, the last article I wrote dealt with Kentucky’s major epidemic of Hepatitis-A. Fortunately, after more than 5000 cases, 2400 hospitalizations, and 62 deaths, that viral epidemic has simmered back down into its always-threatening background rate. Sadly, the non-medical societal determinants and public health support that permitted and accelerated that outbreak are still with us. It was just a matter of time that another life-threatening epidemic would come calling in the United States and to our Kentucky Home. This global pandemic, Coronavirus (Covid-19), is a particularly nasty one for which the world was ill-prepared. Reams of paper and terabytes of postings have been published attempting to explain why and how things got so bad so quickly, or whether we are overreacting. I expect to add something to those discussions, but not in this first effort. For now: it is what it is– bad! We will have to deal with it.
My readers know I like to play with numbers. I have been trying to assemble data about the number of cases of Coronavirus in the Commonwealth of Kentucky. It has not been easy, and I cast no blame. Despite the fact that the virus has been ping-ponging around the world causing death and devastation along the way, we in the United States were not prepared to test for the illness, to trace contacts, or even to take care of large numbers of very sick people. For now, I have been scraping numbers from Governor Andy Beshear’s daily reports to the state about the status of the epidemic and the state’s plans to deal with it. Governor Beshear has drawn national praise for the way he and his administration are managing with this maximally challenging problem and for communicating with the public. I echo that praise. I do not believe we are over-reacting.
The drama surrounding Kentucky’s epidemic of Hepatitis-A continues. Chris Kenning reported today for the Courier-Journal that Dr. John Bennett, current infectious disease branch manager, was dismissed last Friday. No specific reason was offered, but this is the second dismissal from that position in less than a year. His predecessor, Dr. Robert Brawley, was similarly dismissed less than a year ago after he lobbied for a more aggressive approach for what became the worst the Hep-A epidemic in the country. No doubt Governor Bevin’s administration will continue to deny that there was any connection between Dr. Brawley’s recommendation and his dismissal.
Dr. Bennett inherited a mess. A reasonable person might speculate that he is taking the fall for criticism that has been directed toward higher-ups in the administration. We may never know. However, turmoil as we deal with a new outbreak of serious, food-born E. Coli infection is not what we need now. Hep-A and E. coli pathogens are both transmitted by feces of infected individuals– basic sanitation stuff. There are other threats of serious infections on the horizon that we may need to deal with including a drug-resistant fungus, Candida auris.
Above is an updated graph from Frankfort showing new cases of Hep-A up to the week through March 23. It appears to show a sharp drop for the most recent week, but I assert that it is premature to conclude that the epidemic is ending. The report from which the figure is extracted warns that all cases in the current period have not yet been incorporated into the totals. Indeed, charts from earlier weeks that initially showed apparent trends downward before all the cases were counted ended up hovering around 40 new Non-Jefferson County cases per week. Over the last 4 reporting weeks, the number of counties having new cases decreased only from 21 to 19. The number of counties having at least one case during the epidemic continues to increase, now up to 105 counties. We are not yet home-free. I do not have access to updated data for Kentucky’s ongoing Hepatitis-B, Hepatitis-C, and HIV epidemics which remain endemic threats. We deserve some stability and are owed more confidence than we now enjoy.
Peter Hasselbacher, MD
Emeritus Professor of Medicine, UofL
April 8, 2019
On March 20, I submitted the following letter to the Courier-Journal. Others have offered similar views and I gather that my contribution was not accepted. Since I buy my ink by the gigabyte, I have the opportunity to publish the letter anyway! Here it is.
Bullying not allowed in school.
Kentucky education Commissioner Wayne Lewis has demanded that 10 different school districts in the eastern half of the state send him records and documents for teachers who did not show up to work this legislative session. Enough teachers did so, that at least some schools had to close. The demand specifically includes doctor’s notes confirming illness. The first thought of the physician in me is that federal patient privacy law (HIPAA) prohibits the sharing of patient information except to other health professionals or entities sharing in medical care of a given patient. These protections are quite strict. Specific permission from a patient is
required to discuss matters even with a family member, or to even to disclose whether an individual is a patient or not. A note from a doctor– even without a diagnosis– conveys information simply by virtue of the physician’s practice. A note from an obstetrician might suggest a pregnancy. An individual may not wish to disclose that they are seeing a cardiologist, psychiatrist, or any other specialty that might announce a pre-existing condition. Even if Kentucky law or regulation allows Frankfort or a school district to demand a doctor’s note, it is not clear to me why federal law would not supersede state law. I will leave that to legal experts.
Given the obvious animus of the Bevin administration towards Jefferson County and its public-school system in general, and towards teachers and the teacher’s union specifically; a reasonable person might conclude that Commissioner Lewis’s demands represent an attempt to intimidate teachers for standing up for what they believe is right for their schools. The Commissioner’s more recent promise not to punish anybody if there are no further work stoppages converts a veiled threat into an operative one. Commissioner Lewis reasonably suggests that students can ill-afford to miss even one day of school when avoidable. How can one disagree? I would ask, however, what would be the response of the public if Commissioner Lewis asked for the names and the medical records of students who skipped school in order to protest for the need of gun control following the aftermath of school shootings here in Kentucky and elsewhere? I am confident that our public would be outraged! We should be outraged today. Teachers did not make the decision to travel to Frankfurt lightly. They deserve public support– indeed public protection against what is in my opinion, and that of others, an attempt to bully teachers into submission.
Peter Hasselbacher, MD
March 25, 2019
A society is only as healthy as the sickest individual within it.
Kentucky is in the middle of, and hopefully emerging from a major epidemic of Viral Hepatitis-A (Hep-A). Hepatitis-B and Hepatitis-C, are caused by different viruses and commonly result in more serious chronic liver disease. Classically, the spread of Hep-A is attributed to contamination and ingestion of food or water by the feces of infected persons or related poor hygiene practices. Nonetheless, illicit drug use appears to be the major risk factor in Kentucky’s current outbreak. Hep-A is rarely fatal to otherwise healthy people but can cause debilitating symptoms. It can be fatal however, especially to individuals with preexisting liver disease such as alcoholic hepatitis or other forms of viral hepatitis. It is not clear when the first cases of the current outbreak began to emerge, but in the 21 months between Aug 1, 2017 and Feb 23, 2019; some 4229 presumed or suspected cases of Hep-A have been reported, including 2036 hospitalizations and 43 deaths. This can be compared to only 9 reported cases in all of 2016! Our current outbreak is the most severe in the nation. Concern has been expressed that, compared to the aggressive and successful response by the Board of Health of Jefferson County, that the best advice from experienced state public health experts within Kentucky’s Public Health Department in Frankfort was ignored allowing the statewide epidemic to expand and be prolonged. My independent analysis of available data supports this criticism. In my opinion, the appointment of an inexperienced public health commissioner by the Bevin administration– probably for political and ideological reasons– likely played a significant role in what occurred. Kentucky remains in the middle of upsurges of Hepatitis B and C. All three varieties of viral hepatitis have roots in poverty, substance abuse, exclusion from healthcare systems, despair, and other non-medical fellow-travelers that will be difficult to fix. It is therefore important that the current responses to the Hepatitis-A epidemic be independently reviewed so that we may be better prepared for the next time– which will surely come. Continue reading “Kentucky’s Hepatitis-A Epidemic: Could We Have Done Better?”