Tag: deaths

Gender of COVID-19 cases and deaths in Maryland

After my previous posts about age of COVID-19 cases and deaths in Maryland, it was logical that I write about the gender of these cases and deaths. Rest assured: this time, it will be much shorter 😉

Indeed, in a nutshell, in Maryland (like in the rest of the world), women are more impacted than men by the disease. But men are dying of the disease a little bit more than women.

Note: this post was updated on July 15, 2020, to fix an error in my code!

Now for the details …

In terms of positive COVID-19 tests / cases, the difference between men and women started early in April, with the number of positive tests or cases in women increasing faster than men over time. Today (July 15, 2020), Maryland counted a cumulative 39k positive cases for women and a cumulative 35.9k positive cases for men. The number of new cases in men and women in Maryland follows (of course) the trend in new cases, with peaks in May, a decrease until now and a fear for new increase of cases now (see bottom graph, below).

Even if we take into account the number of cases relative to the population of each gender, because there is approximately the same number of men and women in Maryland (2.9 mio men, 3.1 mio women, from the MD department of Planning), women always saw more cases than men (even if by just a little bit). Today, here is the data (also see graph below):

Cumulative COVID-19 cases / 100,000 pop.FemaleMale
July 15, 20201,230.81,211.3

In terms of deaths, we see the opposite trend: since the beginning of data reporting, there were always more men who died of COVID-19 than women. On a daily basis, it’s less clear (and since I’m not smoothing nor averaging anything, it’s a bit jagged) but the overall result remains the same.

Even when we consider deaths relative to the respective populations, men die in larger numbers to their population (than women) and this is consistently the case since the beginning of data availability (see also chart below):

Cumulative deaths per 100,000 pop.FemaleMale
July 15, 202049.654.8

These observations were already widely shared, for the general (i.e. non-MD) population, in the media. There could several factors to explain that more women are tested positive than men: men could be less enclined to be tested than women, women could be more concerned about their health than men (seeking more testing resulting in discovering more positive cases), … And there are two main hypotheses to explain that more men are dying of COVID-19 than women: women tend to have a stronger immune system than men, there are also “gender-based lifestyle choices” (e.g. more men are smoking than women, and smoking is, directly or indirectly, affecting the predisposition to complications due to COVID-19), … So, contrary to the perceived lack of manliness some men express about the mask, men should have even more reason to wear a mask, just to protect them (and others) from dying.

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 (including these ones).

P.S. This post was amended a after its publication, thanks to a remark by W Jauquet on Twitter: the calculation for the relative number of cases and deaths was wrong. The code and text above were corrected to reflect that.

Why would Maryland remove COVID-19 data from nursing homes?

Since the beginning of the COVID-19 pandemic, we suspected and saw that nursing homes and other facilities where people are grouped together (prisons, …) could be at higher risk of transmission. The focus on nursing homes was because deaths seem to disproportionately affect the older population that also resides there. And nursing homes are also home for frail people with comorbidities.

In its dashboard, the Maryland Department of Health quickly started to build a dedicated page with numbers from different “congregate facility settings”. As I did for other metrics from this dashboard, I made a chart of what seemed the cumulative total cases, differentiating staff (who are stuck working there) and residents (who stuck living in these facilities):

Besides the weekly update (contrasting with the daily update on the main dashboard), the strange thing is that curves are going down! If it was a true cumulative curve, it would keep either growing (new cases are added) or it will go flat where it reached (no new case, we keep the total from last day or week).

Then you read the note below the dashboard (before the tables) and it says:

Facilities listed above report at least one confirmed case of COVID-19 as of the current reporting period. Facilities are removed from the list when health officials determine 14 days have passed with no new cases and no tests pending.

I could imagine that the reason is pragmatic: somewhere, someone stops adding cases (or deaths) if the facility doesn’t send new case (or new death) count for 14 days. But it doesn’t make sense to actively remove the facility from the list and therefore remove the cases (or deaths) that were reported earlier. Especially if the dashboard leads viewers in error by stating “Total # of Cases” as y-axis:

Melissa Schweisguth reported an article from the Baltimore Sun pointing to this discrepancy and current state of discussion (but no solution reported) in this tweet:

The article quotes the Department of Health mentioning that the other data presented is cumulative but I couldn’t find this … Indeed all datasets available include the same caveat that facilities not reporting within 14 days are removed:

If I take an example in the first few facilities that reported cases, we clearly see that this one (whichever it is, it doesn’t matter here) started to report cases up to June 10. Since I’m writing this on June 25, there are more than 14 days that they stopped reporting, the dataset doesn’t include this facility anymore (the latest data points in the dataset are for June 24):

This is a pity because, besides the difference between residents and staff, these datasets also present cases and deaths among youth and inmates. It would have been nice to understand the evolution of the burden of COVID-19 in these populations. But the curve is clearly not cumulative, as we can seen on the charts below: after about June 2nd-10th, curves going down probably indicate removal of facilities in the total count.

As mentioned in the Baltimore Sun article, with this kind of reporting, you cannot know the real toll in nursing home, prisons and other congregate facility settings and therefore you cannot respond to it appropriately (i.e. the toll is now underestimated).

Also, you can’t put things in perspective because you can’t have a reliable proportion of cases in congregate facility settings compared to the total number of COVID-19 cases in Maryland. This total number of cases is cumulative and we see an artificial decrease in % of cases in these facilities, as illustrated below:

Now, what can we do? One clear solution is that the Maryland Department of Health changes its reporting and really report the correct cumulative number of cases in congregate facility settings. Besides that, I have a technical solution in mind but I had no time today to code it yet …

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 (including these ones).

Post-scriptum on June 26, 2020: the day after I posted this, Maryland Governor Larry Hogan announced a safe and phased reopening plan for Maryland’s assisted living facilities. Although I welcome any initiative targeting the protection of everyone and especially the most vulnerable populations, the 2 first prerequisites are still tied to this absence of new cases in 14 days (which is fine) – this is still not a reason to intentionally remove facilities from the count. And I couldn’t see the phased approach – but I guess this will be followed up in another post here. To be continued …

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).

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.