Friday, November 20, 2020

COVID-19: What went wrong?

Another week has passed, and the infection curve in the United States continues to increase. How we can even be in this situation is baffling, given the massive investment and research on emerging infectious diseases and other biological threats that preceded this pandemic. Equally baffling is the narrative -- founded in misinformation, disinformation, and agenda -- perpetrated on the American people. The charade is exemplified over and over. Today's act unfolded in a Senate hearing on hydroxychloroquine, a drug demonstrated to be contraindicated for COVID treatment. And yet, the exponential increase continues. 

States are showing the strain. In Ohio, for example, the state's disease reporting and information system has buckled. Citizens cannot now be confident, at least at the moment, in the data published on disease incidence.

The Pandemic and All-Hazards Preparedness Act (2006) was to, among other things, “Establish a near real-time electronic nationwide public health situational awareness capability through an interoperable network of systems to share data and information to enhance early detection of, rapid response to, and management of, potentially catastrophic infectious disease outbreaks and other public health emergencies that originate domestically or abroad.” Little if any progress has been made toward that goal. Too many health departments still receive information by fax and enter data by hand. This is madness.

We're beginning to learn about vaccine candidates that hold promise. Additional candidate vaccines will undoubtedly emerge, and hopefully in 2021 one or more approved vaccines will become widely available. Hopefully people will receive them. When the pandemic finally does abate -- which is not likely for months -- we must objectively and without delusion identify what broke in our public health and related systems and fix them.

Tuesday, November 10, 2020

COVID-19: Data and Situational Awareness

Like so many others, I've been working on COVID-19 since the spring and there is much to reflect upon when there's time. Unfortunately, there is not time now -- there has not been time to reflect for months, and there will not be for months to come. However, to share some thoughts on the epidemic, I decided to blow the dust off this blog.

For the short term, I'll share different visualizations and metrics for what they may be worth, based on data from the NYT GitHub service

We have entered a time of intense SARS-CoV-2 transmission across the nation. Overall in the US, the number of new cases yesterday was 130,553. The current 7-day moving average is 116,448.3 cases/day. Using the latter number, the incidence rate per population is 35.2 cases/day/100K people. Currently, the effective reproduction ratio, R, is approximately 1.22. Based on an exponential fit to the incidence data, the doubling time for new cases is 24.7 days (21.8d, 28.5d). In less than a month the US could be seeing well over 200K new COVID-19 cases per day. 

In Ohio, the number of new cases yesterday was 4,706. The current 7-day moving average = 4723.6 cases day, giving an incidence rate per population of 40.4 cases/day/100K population. Currently R = 1.29 (1.28, 1.3) and the new case doubling time = 16.8 days (15d, 18.8d). Note how much shorter it is relative to the national doubling time computed from the pooled US data. 

In Hamilton County, Ohio (population: 817,473), in the southwestern part of the state, the number of new cases yesterday was 336. The current 7-day moving average is 343.1 cases/day and the incidence rate is 42 cases/day/100K population. At the moment, the effective reproduction ratio is R = 1.21 (1.17, 1.25). The corresponding epidemic doubling time = 19.8 days (16.6d, 23.9d).

These are remarkable trends. Compared to the springtime peaks, which were distorted due to the scarcity of tests then, the current trends are utterly out of control. Moreover, the persistence of the exponential phase is unlike what has been seen previously in the US COVID-19 pandemic. In Ohio, for example, R remained near 1 for long enough over the summer that cases accumulated in the community, so that now even modest increases in R -- and they are not currently "modest" by any stretch of the imagination -- results in significant incident infection. 

How hospitals will be able to cope with these trends remains to be seen. One danger of the current situation is that with such pervasive community spread, healthcare workers themselves are at increased risk for being infected. Thus, in addition to the increasing patient volume hospitals are seeing in numerous states, there may be fewer healthcare workers to provide care. 

In another example, Montgomery County, Maryland (population: 1,050,688), the  situation is not as grave, but trends are not headed in a hopeful direction. The number of new cases yesterday was 185 and the 7-day moving average is currently 190.4 cases/day. This produces an incidence rate of 18.1 cases/day/100K person and an R of 1.2 (1.14, 1.25). The epidemic doubling time is approximately 32.2 days (26.2d, 41.3d). Now is the time for the county to "tap the brakes" in order to avoid the situation occurring in harder hit counties across the nation. 

There is much to reflect upon. When there's time, I will do so. Stay safe.