Tag: Covid-19

COVID-19 inequalities in Maryland

The recent Black Live Matters protests made me think a lot – as a white man, as a husband and dad, as a biologist by training, as a health economist by day, as someone interested in COVID-19 data where I live by night … as a human, in summary. I don’t have grandiose pieces of advice or any deep thoughts, not for here (but if you call me, we can talk ;-)). Here, let’s continue our exploration of COVID-19 data in Maryland.

There are only 2 metrics that the MDH dashboard provides, around races: confirmed cases and deaths (and probable deaths but as this is not precise and small, let’s put this aside for the moment).

Today (June 12, 2020), communities worst hit (in crude numbers) are African Americans and Hispanics in terms of cases (17,345=28% and 16,293=27%) and African Americans and Whites in terms of confirmed deaths (1,133=41% and 1,164=42%). This is represented in the figure below. Note also the high number of “race not available” in the cases chart (this could mean a worst impact for some communities as some would fear negative consequences of disclosing their race).

But this means little if we don’t know how many Marylanders are in each categories. Numbers varies and I couldn’t find the following data from the Census or the CDC directly (the 2 sources I would consider the most reliable on this): number of people categorized in 1 and only 1 race at a time (which is an approximation of reality but allows for easier calculations below). I found the following data from SuburbanStats: in Maryland there are approximately

  • 1.7 million African Americans (~27%),
  • 318 thousands Asians (~5%),
  • 479 thousands Hispanics (~7%),
  • 3.3 million Whites (~53%) and
  • 410 thousands of “others”.

Given this, we can see a different picture …

In this figure, on top, we see the evolution of crude case numbers since April (up to June 11). We also see the rapid rise of cases in Hispanics since they were separated from the “Others” (April 14). But at the bottom, I show the evolution of cases relative to the population. And here we can clearly see that, very early on, Hispanics accumulated cases in larger proportion compared to their less than half million population. Yesterday (June 11, 2020), there were 3,461 Hispanic COVID-19 cases per 100,000 population (compare that to 350 in Whites).

In the following figure, on top, we see the evolution of confirmed deaths since April (also up to June 11). Here, both African Americans and Whites are close and widely distancing the other communities. But at the bottom, the evolution of deaths relative to the population is shown. And here we can clearly see that African Americans (especially) and Hispanics are the worst hit communities compared to their general population. Yesterday (June 11, 2020), there were 66 African American deaths per 100,000 population and 58 Hispanic deaths per 100,000 population (compare that to 34 in Whites).

The table below summarizes cases and deaths relative to population on June 11, 2020, in Maryland:

CommunityCumulative COVID-19 (cases / 100,000 pop.)COVID-19-specific death rate (deaths / 100,000 pop.)Share of the general population
African Americans1,0206627%
Community-related cases and deaths in Maryland on June 11, 2020

So even in Maryland, a US state ranked 6th best state overall and #8 for healthcare in 2019, disparities exist. Hispanics are the worst hit in COVID-19 cases (27% of cases and > 3,000 cases per 100,000) in cases while they represent only 7% of the population. And African Americans are the worst hit in COVID-19 confirmed deaths (41% of deaths and > 60 deaths per 100,000) while representing only 27% of the population. The CDC has an interesting summary of main causes of these disparities but also what people and organizations can do about it; a good read to start doing something about these inequalities.

To be continued …

As usual, you’ll find other graphs on my page about COVID-19 in Maryland (and figures above are updated with new data as they appear) and the data, code and figures are on Github.

Post Scriptum – but still important … Methodologically, there are a few caveats for all this. First, the concept of race is linked with so many other parameters that COVID-19 is probably exacerbating these other issues (with an indirect effect on people of color) rather than targeting a specific population (the virus itself does not choose who it will infect). Also, there is no explanation on how race information is collected: with a question on the test form (with all the reporting bias it contains), by linking the names or social security number to a previously recorded race identity, …? This is another source of potential bias. Third, we have here the 2 extreme metrics: cases and deaths. There is no information on hospitalizations, despite requests to the MD Department of Health or the Governor’s staff (no hospitalizations info for counties neither btw). I suspect here that race collection in hospitals is not performed (because unethical?) and/or there would be HIPAA issues if this data would be transmitted from hospitals to the state, for instance.

Weekly seasonality in COVID-19 deaths reported in Maryland

On its dashboard, the Maryland Department of Health is reporting confirmed deaths due to COVID-19 in two ways: by date of report and by date of death (updated as amendments to the death record are received). The definition of confirmed death is:

A death is classified as confirmed if the person had a laboratory-confirmed positive COVID-19 test result.

What I was intrigued is that reporting seems to follow a pattern influenced by the day of the week (see figure below). The top chart (cumulative) is just an addition. A plateau would be welcome: it would indicate death rate is slowing down. Today, the COVID-19 death rate is 41 / 100,000 population. The bottom chart shows the number of deaths due to COVID-19 reported each day: the black line represents the number of deaths each day they were reported; the grey line represents the number of deaths each day they occurred.

Evolution of coronavirus confirmed deaths in Maryland, as of June 3, 2020

One could see that in both lines, there are two kind of patterns. The first in an overall trend upwards until beginning of May, followed by a decrease since then. The second trend has a big peak being followed by a decrease with 2 smaller peaks and a big dip – then an up, decrease with 2 peaks and a big dip – etc.. As data was reported, we saw intuitively that the big dip came on Sundays, the big peak on Tuesdays and the rest of the week was a decrease towards Sunday.

And this is confirmed by the analysis of seasonality for confirmed death by reported date:

Here, the top chart is just the data we observed before. Below, the trend shows that, indeed, there was an increase up to end of April and we then see a slow decline. The third graph (“seasonal”) shows the pattern I mentioned earlier. This confirms the lowest reporting on Sundays and the highest reporting on Tuesdays. The bottom chart (“irregular”) shows that, even if there is a pattern, there are a lot of irregularities added to the seasonality.

The same patterns can be observed for the deaths by date of death (when they occurred; see chart below). This shows we are currently also in a decreasing number of deaths, each day (fortunately!). The pattern here is that the number of deaths increase from the lowest on Saturday to the peak on Friday (with an intermediary peak on Wednesday). Again, note the important number of irregularities (at the bottom).

In my opinion, this regular patterns come from the reporting system. I don’t see why COVID-19 patients would die more towards the end of the week and less during the weekend. But please tell me if you have more information about this (in the comments below or by email)!

To be continued …

As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.

P.S. I’m not counting probable deaths. The MD Department of Health reports this variable but, as it is dependent of a confirmation, it is highly fluctuating and not necessarily representative of deaths due to COVID-19. If confirmed, these probable deaths are accounted in the confirmed deaths (counted here).

A glimpse at COVID-19 cases in some Maryland ZIP codes

A publicly-available MD COVID-19 metrics that I didn’t investigate much is cases per ZIP code. I created a dashboard where you can highlight one zip code at a time. Tyler Fogarty built a cool Treemap Explorer. Silver Chips has a nice heatmap of all zip codes as part of their extensive dashboard (a bit like the MDH dashboard). How can we make sense of all this?

A classical way to see it is to look at the daily number of positive cases, similarly to what I did for counties or the state.

(you may need to click on the image to see better)

Today (May 30, 2020), 4 ZIP codes have more than 1,000 cumulative cases: 2 in Prince George’s county (20783, Hyattsville, and 20706, Lanham) and 2 in Montgomery county (20906 and 20902, both in Silver Spring). But among the ZIP codes with the most recent daily positive cases, 21223 and 21224 are also in the top 5, both in Baltimore City. All these ZIP codes are in counties that are closed or partially opened, highlighting the need for these regions to remain vigilant and enforce stay at home, wearing a mask and social distancing (at least).

I’m looking at protests in Baltimore and I can’t imagine how detrimental the spread of coronavirus will be and will add to the other issues. Here is what Prof. Murray advise to protect protested (on top of any other precautions):

There is no public data about hospitalization per ZIP code nor deaths per ZIP code. But there are certainly other ways to make sense of this metric …

To be continued …

As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.

Will it be the end of Stage 1 in Maryland?

Since May 14, 2020, Maryland is carefully reopening from an easy lock-down caused by coronavirus spreading thru the community (and all over the world). In this post, I’ll go through all the variables we have on the MD Health Department dashboard. But first, the official data comes from the MD dashboard and if you want scientific information about COVID-19, please consult the CDC website. If you are interested, you can read my previous posts on COVID-19 in Maryland from this page.

Since my previous post (May 21), tests were broadened in some drive-thru locations for anyone to be tested (5/19 actually) and new testing sites were opened (map of sites here) and we had the Memorial Day weekend (5/25). On May 28, Gov. Hogan mentioned that “hospitalizations, ICUs, and testing positivity rates are the key metrics in determining Maryland’s road to recovery”. On May 27, Gov. Hogan announced that further reopening were taking place (outdoor dining, some outdoor activities for kids allowed, …) but still within Stage 1 (I called it “Stage 1b”).

In terms of hospitalizations, the graph above shows the number of patients currently hospitalized (green line). Since beginning of May, hospitalizations decreased, especially thanks to the decrease of patients in acute care (red line). Patients in ICU (Intensive Care Unit) decreased much slowly. This is probably due the severity of these patients, making them stay for a long time and released from ICU at a slower rate than patients in other departments. And the graph also shows that Maryland never needed the additional hospital beds prepared for a worst scenario.

The third key metric the Governor is looking at is testing positivity rate. The chart above represents, on top, the total number of tests reported on the MD Health Department dashboard (adding positive and negative test results). We learned that the Governor is actually not looking at the same positivity rate than the one we can compute from the dashboard:

  • The dashboard report unique positive and negative tests. If someone was tested twice or more with the same result, it would have been reported only once. If the test result would change, it would have been reported once in each category.
  • The Governor is looking at all positive and negative tests. If someone was tested twice or more, independently of the result, all tests results would have been counted here.

This difference probably explain why we see a daily number lower than 10,000, despite 500,000+ tests received by Governor from South Korea. But we can’t really say in which direction this difference would drive the testing positivity rate. If more positive tests were under-counted (i.e. counted once instead of the several times they were performed/received), the Governor would have seen a higher positivity rate than on the dashboard. More likely, if more negative tests were under-counted (i.e. negative people tested several times, but counted once), the Governor would have seen a lower positivity rate than on the dashboard. This last option would explain why the Governor decided to go on Stage 1 sooner than expected by just watching the dashboard.

Technically, as a side note, the data for the testing positivity rate that the Governor is looking at is not publicly shared. There is just a PDF with graphs. This difference in what is reported may also explain why, since test broadening (5/19), there was 5 days of ups and downs after which the rate stayed at about 10%.

At the level of the State of Maryland, we are not yet looking at the full picture: the last element (that doesn’t seem to be part of the key metrics) is deaths. So far (since mid-March), there have been 2,390 deaths due to COVID-19 in Maryland with a majority of them occurring in congregated facilities (nursing homes, prisons, etc.). With an about-weekly pattern (see below), the daily number of confirmed deaths also seem to decrease (although much slower than hospitalizations or positivity rate).

But if things seem good at the State level, the decision to reopen Maryland came with the empowerment of Counties (the government level below State) to follow or not the reopening. As noted before, if most counties followed the State in Stage 1, some counties did not (some like Prince Georges and Montgomery even remained “closed”). There is no straightforward way to follow hospitalizations in counties (they are not reported on the MD dashboard). But we can follow deaths in counties in the graph below. There it is a bit surprising to see that counties that re-opened, the % of deaths compared to May 15 is actually increasing (i.e. more daily deaths in counties that re-opened) (see blue dots and average in the blue line). On the other hand, % of daily deaths seems to decrease in counties that partially reopened or remained closed. But one should also note the huge confidence intervals around these averages.

Finally, about counties, the situation is about to get messier: since yesterday, Anne Arundel, Baltimore City and Howard counties further allowed some outdoor activities; and starting June 1st, Montgomery and Prince George’s counties, initially closed, will also start to allow some outdoor activities.

So, will it be the end of Stage 1 in Maryland? I think so. Most metrics that are publicly available are pointing in the right direction and, provided there is no outbreak in “pneumonia” like in California, I could see a cautious switch to Stage 2 in the coming days. Gov. Hogan tweeted that he could see Stage 2 during the first week of June.

To be continued …

As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.

No visible impact yet of different COVID-19 Stage 1 strategies in Maryland

In my previous post, I was wondering if Maryland was ready to reopen, ready to enter Stage 1 of COVID-19 recovery. I also mentioned, in the end, that if Gov. Hogan announced the reopening of Maryland, he also gave counties the power to “fully” open, to be partially open or even to remain closed. You can see more info about Maryland Strong: Roadmap to Recovery: there is a map of what Counties decided.

Here is a first attempt to look at the fate of the different counties. My idea here is to set the number of cases in all counties on May 14, 2020 (start date of Stage 1) to 100% and see how counties evolve in terms of number of new daily cases.

On top of the figure below, I represent the cumulative, 7-day average (*) daily new COVID-19-confirmed cases in the different counties of Maryland. The chart at the bottom assign the number of daily cases on May 14, 2020 to 100% for each state and follow the % evolution over the next day. In this chart, the blue lines represents counties that follow Stage 1 (e.g. Garrett or Ken), the green line represents counties that partially follow Stage 1 (e.g. Anne Arundel or Frederick) and the red line represents counties that remain “closed” (Baltimore City, Charles, Prince Georges and Montgomery). The counties that remain closed are the ones that have the most cases and deaths.

(static chart updated on May 31, 2020)

I must say that 6 days after Stage 1 (May 20), there is no clear trend. First, it’s normal because any downward or upward trend in number of cases will take a few day to appear (transmission or absence of transmission, incubation, decision to consult and tests, and lag in test reporting). It’s too early to see something. We will also see a confounding factor with the recent decision by the Governor to allow testing of people who do not present any symptoms (in some testing sites). Nevertheless, I was expecting to “see something”; here it just seems it’s the same.

But another reason for “not seeing anything” might be that the cases are not a relevant metric. We can already see that it is fluctuating widely every day. There are even days when less cases were reported than the day before (it might have been a data entry error on my side). The only other parameter that the MDH displays in its dashboard is the number of deaths by counties. I plotted this and it’s the same bizarre chart. How to improve this? Any idea? Don’t hesitate to comment below or to send me an email.

Update on May 24, 2020: I updated the chart of cases after Stage 1 (see above). Currently the confidence intervals (the shades) are so overlapping that differences that we could see are meaningless. Cases may not be a good metric.

I also created the same chart for deaths (see below). Here we see clearly a positive picture: in all counties that are partially open or closed, the mean number of deaths is decreasing. Note however that we are only 10 days (today is 5/24) from May 15 and this may just be a trend that existed before and not something new due to the decision to remain (partially) closed.

(static chart updated on May 31, 2020)

In counties that are in Stage 1, the mean number of deaths is actually increasing. The same comment applies: it may be too early to actually see an impact of the opening (especially deaths could be far from the case detection). Besides, the confidence intervals (the blue shades) are very wide. Hopefully things may become clearer in a few days (and for the best, given we are talking about a disease and people dying from it).

To be continued …

As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.
(*) the 7-day average uses the arithmetic mean of each county series over the past 7 observations.

Is Maryland ready to reopen?

A visual analysis of Governor Larry Hogan’s decision to enter Stage 1 of reopening Maryland.

(This will be a post based on a thread of tweets I posted on May 14 with updated graphs for today – one days after the start of Stage 1 – and more)

Maryland is in state of emergency since March 5, 2020 due to COVID-19. Governor Larry Hogan announced on May 14 that Maryland will “gradually reopen with flexible community-based approach” (the official declaration is here). The MD Strong plan said “a 14-day downward trajectory of benchmark metrics – or at least a plateauing of rates – is required before recovery steps can begin“. This Phase 1 started yesterday, May 15, 2020. So, are we there already?

Regarding testing … After a peak in testing (up to 8k/day) and the arrival of tests from South Korea, testing is stagnating ~ 4k/day in Maryland. The daily % of positive tests seem to stagnate ~ 22% since May started and decline a bit, ok. Despite a peak, today, we are still far from the daily number of tests we could reach with the tests from South Korea. And there is still a high percentage of daily positive cases.

Regarding hospitalizations … Thanks to a drop in acute care during the last weekend and this one, the number of patients hospitalized seems to decrease since beginning of May. This sudden drop was followed by a slight re-increase. Hopefully this will continue to decrease (even if in waves like this).

Regarding deaths … Despite a record number of daily reported deaths, early May, and wide variations in this daily metric, it seems that we are plateauing/decreasing here.

So, we can cautiously understand the decision taken, based on data. Note it’s not a total opening: the “flexible community-based approach” means that counties (the government level below the state of Maryland) are empowered to make decisions regarding actually opening or not. And some counties took that opportunity. For instance, Montgomery, Prince George’s and Charles (on the East / South-East of Maryland, surrounding Washington DC and bordering Virginia) decided to remain closed. Baltimore City also decided to remain closed. It is understandable as all these counties are among the ones with most cases and most deaths. Here is a small infographics summarizing the Stage 1 reopening:

It will be interesting to see how the next 2 weeks evolve, and especially if counties that remain closed will have a different evolution than the ones that opened.

To be continued …

As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.

MD counties COVID-19-specific death rate

Since a few weeks, I report the raw number of COVID-19 deaths in Maryland counties. If this gives an idea of the cumulative number of deaths – which is interesting – it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 deaths adjusted for the population (i.e. the COVID-19-specific death rate):

(click to see more details)

Today (May 16, 2020), in terms of absolute number of deaths, Montgomery, Prince Georges and Baltimore County are the top 3 counties (this is the same for cases but not in the same order). In terms of confirmed deaths per 100,000 population, the top 3 counties are Kent, Prince Georges and Montgomery.

Rank on May 16, 2020Absolute # of COVID-19 deathsCOVID-19 deaths per 100,000 population
1Montgomery (423)Kent (66.9)
2Prince Georges (399)Prince Georges (43.5)
3Baltimore County (223)Montgomery (40.2)
4Baltimore City (192)Carroll (39.0)
5Anne Arundel (133)Charles (35.8)

Overall in Maryland so far, 1,842 deaths were reported – for a total population of 6,141,808. This gives a COVID-19-specific death rate of 29.9 per 100,000 pop. For comparison, the CDC reported a flu-specific death rate of 2 per 100,000 pop. (for the whole US, 2017) and 863.8 deaths per 100,000 pop. for all-cause deaths.

Source of Maryland County population: projections from the Maryland Department of Planning.
As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.

Edited a few minutes after publication to add a paragraph with the comparison with Maryland and flu; adapted the y-axis label following Michael Brown‘s comment on Twitter (thanks!); and specified the flu-specific death rate from CDC following Melissa Schweisguth‘s comment on Twitter (thanks too!).

MD counties COVID-19 cases adjusted for population

Since a few weeks, I report the raw number of COVID-19 cases in Maryland counties. If this gives an idea of the cumulative number of cases – which is interesting – it doesn’t reflect the fact that some counties have more inhabitants than others. That’s why I plotted below the number of COVID-19 cases adjusted for the population:

Evolution of COVID-19 confirmed cases in Maryland counties, adjusted and not adjusted for population, on May 11, 2020
(click to see more details)

Today (May 11, 2020), in terms of absolute number of cases, Prince Georges, Montgomery and Baltimore County are the top 3 counties. In terms of confirmed cases per 100,000 population, the top 3 counties are Prince Georges, Montgomery and Wicomico (due to a recent surge in cases).

Rank on May 11, 2020Absolute # of COVID-19 casesCOVID-19 cases per 100,000 population
1Prince Georges (9,687)Prince Georges (1,057)
2Montgomery (6,909)Montgomery (656)
3Baltimore County (3,948)Wicomico (649)
4Baltimore City (3353)Kent (555)
5Anne Arundel (2492)Baltimore City (544)

This is a lot given that, today, the average for Maryland is 401/100,000 (source: CDC) and the average for the US is 552/100,000 (source: OurWorldInData).

Source of Maryland County population: projections from the Maryland Department of Planning.
As usual, you’ll find other graphs on my page about COVID-19 in Maryland and the data, code and figures are on Github.

Trend in Coronavirus cases in Maryland (3)

Following up on my two previous posts (here and here), I am writing a third post on COVID-19 in Maryland because I believe we enter a new phase.

Before continuing, please note that the same disclaimer as in my previous post applies here (in short: read the CDC and MDH websites for official information).

In the first phase, the importance was to detect and make sure COVID-19 patients were treated (also: make sure not to overwhelm the healthcare system, flatten the curve, lower the baseline, & stay at home!). My two previous posts were following these efforts, thanks to daily data released by the Maryland Department of Health (MDH) on its dashboard. My second post will still be updated with the latest data from there, go read it!

This first phase is not over yet but we started to see metrics states and governments will consider in order to “reopen”. Hence this second phase is adding specifically these metrics, again thanks to the Maryland Department of Health (MDH) on its dashboard (and probably other data sources that will be linked as I use them).

In Maryland, the Governor issues a Roadmap to Recovery on April 24, 2020. In this (easy to read) document, a lot of aspects are introduced and here is what will be tracked and for how long:

  • state public health officials should review the numbers of new COVID-19 daily case counts, hospitalizations, and deaths carefully” and “The results of reopening decisions will take 2 to 3 weeks to be reflected in those numbers.
  • the White House’s gating guidelines state that a 14-day downward trajectory of benchmark metrics – or at least a plateauing of rates – is required before recovery steps can begin, and before each additional recovery step can move forward

That’s why Governor Larry Hogan tweeted his focus on April 24:

Governor Hogan’s focus was informed in part by the Johns Hopkins Center for Health Security’s Guidance for Governors about Public Health Principles for a Phased Reopening During COVID-19 (PDF). There the proposed principles for action are:

States should consider initiating the reopening process when (1) the number of new cases has declined for at least 14 days; (2) rapid diagnostic testing capacity is sufficient to test, at minimum, all people with COVID-19 symptoms, including mild cases, as well as close contacts and those in essential roles; (3) the healthcare system is able to safely care for all patients, including providing appropriate personal protective equipment for healthcare workers; and (4) there is sufficient public health capacity to conduct contact tracing for all new cases and their close contacts

Public Health Principles for a Phased Reopening During COVID-19: Guidance for Governors, Johns Hopkins Center for Health Security, April 17, 2020.

On April 27, 2020, this is what we currently have … On the first chart, the number of positive tests is increasing (probably due to the increase of testing done), hospitalizations and deaths are slowly going up, overall. On the third chart, it seems the number of people in ICU is plateauing. Below these charts, I’ll post the updated charts as days are passing …

Updated charts (look at the date at the bottom right):

To be continued …

Trend in COVID-19 cases by Zip code in Maryland

Since the Maryland Department of Health (MDH) started to display number of COVID-19 cases for each Zip code in its dashboard, I was wondering how to display this information in a nice way. The MDH display the information as a map – very nice but it lacks from where each Zip code came from: is the number of cases increasing or decreasing?

Following on my busy chart with the evolution of all Zip codes (and highlighting just one of them – that may not be the one you are interested in, see previous post), I created a simple dashboard where you can select the Zip code you are interested in and see how cases are evolving. You can play with it here: https://jepoirrier.shinyapps.io/md-coronavirus-zip-app/ (screenshot below). Enjoy!

Dashboard showing the number of COVID-19 cases by Zip codes in Maryland, MD. See post for URL.

As usual, the data is from the MDH coronavirus page. Please consult that page for official information. The data is in this file on the Github repo for my other project related to Coronavirus in Maryland.