Daily Status: October 9. Sometimes the numbers confuse me.

 

Daily Status, October 9

Reminder:  any sections that are unchanged since yesterday are grayed out.  

Situational Awareness

The COVID-19 data reported by the Virginia Department of health on October 9, 2020 (based on data collected on October 8h by 5 PM) shows that the commonwealth added 1114 cases of COVID-19. While the daily total is above the 3 week average, the number is within 1 standard deviation.  Viewed over the last seven days, Virginia reported 6962 cases, or 995 cases per day on which works out to 11.9 cases/100K people.  This is consistent with 12 cases/100K several weeks ago, but well above the 9 cases per 100K from 1 week ago.  This suggests the decrease we are seeing for the last few weeks has ended, or was an artifact of reporting issues.  The trends over the last three weeks, now are showing a slow increase, at 0.2%/per day or  1% per week. 145 of the new cases were associated with colleges, With nearly every college showing increases proportional to the school's size.  It must be noted that the numbers at colleges are still much lower than the peak.

 

Regionally, all districts showing are flat to negative case growth. The testing numbers now show the percent positive to below the 5% metric over the last week (4.53%) that is often used to indicate sufficient testing (e.g., is is safe to reopen schools).   Virginia is testing about 2.8% of the population every two weeks, which is about 1/4th the number of tests desired for random sampling, but most of the Commonwealth's testing is driven by medical needs and not surveillance. Surveillance would ideally test at least 5% of the population per week but the testing is somewhat invasive.. 


On one other front, over the last week, we well above 10 cases per 100,000 to enter states like NY without quarantine -- we are at 11.9 cases per 100K.  My suspicion is our ability to travel to NY/NJ was the result of flawed reporting, and we will be unable to travel to NY the next time they update the rate.  


Outside of a few smaller cities/towns, the state is doing better than it has since the Hampton Roads surge except we are seeing more localized outbreaks; the hot spots are isolated and probably associated with facility outbreaks.  Also, looking at the chance of being exposed in a group of 50 (e.g, eating at a restaurant), almost all of the state is blue or clear, meaning less than a 10% chance of someone else in there being COVID-19 positive (still to high for me, but everyone has different standard or risk they are willing to accept).



Regions:

In the spring, COVID-19 in Virginia was primarily a concern in the DC suburbs.  Over a 3-4 weeks, in late may to early June, NOVA recovered, and for about a month, the disease was under control, to the point where the restrictions were eased.  Unfortunately, in eastern VA/Hampton Roads, the easing of restrictions results in a surge in cases,  which peaked around August 1 (and resulted in stricter restrictions in that area).  Since then, the the exception of growth on college campus, the disease has been stable, except for the rural parts of the state, where safeguards (social distancing and masks) are largely ignored.  The trends are clearly visible in the figure below. 

With this, we have completed the transition from COVID-19 being an urban disease to being a rural disease.    But, looking at the weekly numbers, it appears that the rural areas, whose caseloads were already increasing, surged with the the influx of a carefree demographic (college students).  I think we area so seeing some impact of the White House outbreak, as many employees live in northern VA.  This is mostly showing up in the Upper Middle Class suburbs.  Newport News is also seeing a small increase which is possibly associated with a Donald Trump Rally 10 days ago.

Looking at the weekly case count, we see that the case numbers are more in line where we were at the beginning of September.  I am unsure if the September low was the result of fewer cases or the result of poor reporting.  

\

Regional growth rates are (in fraction per day) continue to to show improvement.  Over three .  It is worth noting that it is easier to show a decline when the prior numbers increased.


NOVA: 0.997 -- GMU

Central VA: 1.002 --  VCU

Hampton Roads/Eastern VA:  0.974-- W&M, CNU & ODU

SW VA:  0.995 -- VT & Radford

NW VA:  0.985 -- JMU & UVA


The state as a whole is is increasing with Rt=1.002.


The following table shows the number per 100k for each region. Again, NOVA and Eastern VA are doing the best, and the mountainous regions in NW & SW continue having more cases, but are showing improvements as the college cases are getting somewhat under control -- or at least better than they were. The concerning aspect is in all regions, the numbers for last week are significantly higher than the prior 3 weeks.


Daily Cases/100,000 

Region

Last month

Last week

NOVA

 7.7

9.0

Eastern

 8.6

9.0

Central

10.4

12.5

NW

11.1

16.7

SW

15.3

19.2


The following charts are for the 5 regions. in the chart that shows all regions,  The individual line charts show the unfiltered data per day, coupled with the trend lines.  The trend lines show the different periods of growth.    Early in the pandemic, the different parts of Virginia were functioning largely independently, with NOVA mimicking the northern states, and Hampton Roads mimicking the southern states. But, since September 1, the regions have trended with each other.  Based on the notes today on the VDH site make me question if the drop in cases were real, or the trends were a result of the reporting mechanism.  I have no insight other than looking at the data.


Note that the effects at both ends of the chart are probably an artifact of the 7-day polynomial filtering I use.  The filter is called a Savitzky-Golay filter, and basically is a moving window polynomial filter.  At the edge (first and last days of the time series), the filter will over compensate for the trend.






Local/Northern VA:


In the trends of case, we can either describe it as slow growth since late June, or flat since early august.  Both equally describe the data. During September, the rates have dropped by 3% per day, or nearly 50% over the period (from an average of 280/day to 140/day), but in October, there appear to be both more scatter and more cases.  The current case-load is 226 cases a day.







Currently, most jurisdictions are decreasing, but very slowly.


Fairfax Co.: 0.995
Arlington Co.: 1.015
City of Alexandria: 0.984
Prince William Co.: 0.994
Loudoun Co.: 0.991

The number above is Rt:  Rt is an exponential time constant, where the number of cases in a time segment is approximately, n=Ao Rt ^ t, where Ao is the number of cases at the start of the segment, Rt is the exponential growth rate, and t is the number of days since the start of the segment.  So, if Rt is greater than 1, it is growing exponentially, if it is less than one, it is decreasing each day.  \

Another way to look at it, todays number are approximately the growth rate times yesterday's numbers.  This is the exponential time constant.  Fortunately, the time constants are below 1 and our rate of cases is about 6/100,000 per day.  Ideally, we would be 0, but 6 is much better than our peak in which was around 30/100000K. 

Looking at the trends, since around Sept. 1, there is a clear downward trend in most jurisdictions. The cause of that is unknown, but may relate to the cooler weather.  Alternatively, with school being in session, it could be there is more social distancing.  The one exception is Arlington, which may be impacted by the decision to stop enforcing social distancing.





The contrast in the Northern Virginia map is increasing. There are small scale variations, but the relationships seem to be 1) more related to locations with more shared living arrangements than anything else, or 2) locations not too far from DC, but relatively wealthy.  Another way to say this is, while social distancing is hard on all of us, for the lower income people, it may be impossible.

All of localities in Northern VA are showing case increases.  The increases are strongest in the regions most likely to have people connected to the White House:  Vienna, McLean, No. Arlington, and Reston/Herndon.  The data can not trace to the White House with out contact tracing, and since the White House wants to minimize the outbreak, they seem to refuse to contact trace.

Region

Last month

Last week

Growth rate (%/day)

Fairfax Co

 Vienna

 5.8

 6.5

 7.2

 McLean

 4.6

 5.8

 8.1

 So. Alexandria

 8.9

 9.4

 1.9

 Reston/Herndon

 7.6

 8.2

 3.8

 Annadale/Fall Church

 8.1

 8.2

 4.7

 Fairfaix

 5.9

 5.4

 4.0

Arlington/Alexandria

 No. Arlington

 5.9

 7.2

 2.2

 So. Arlington

 8.6

 9.0

 4.4

 Alexandria

10.6

 10.0

 0.0


During most of the last 2 months, Vienna and McLean tracked each other, as did Reston and Fairfax.  Except, for Labor Day to about 1 week ago where Vienna increased its case load.  Now, though, it appears Vienna and McLean are again tracking each other.  Fairfax has dropped (and Vienna/McLean have increased) so the three localities all very close.

It is worth noting that almost every region is seeing small upticks in the last few days.  Focusing in on the regions of N. Arlington, Falls Church McLean and Vienna, we see a significant uptick 1 week after the White House event.  Now, this may be recovering cases that were not reported in September, or they may be people affected with the White House (e.g., Secret Service, staff, etc).








Local Safety/Risk

I am not updating this today as there is a lot of uncertainty in the region thanks to irresponsible behaviors with unknown impacts.  That is to say, the situation for the next week may be tenuous.  I am planning to expand this section this coming weekend, when I have time to modify some processing code.

I have been thinking about how to quantify and present the local risk here in Vienna.  My first thought was Vienna is not a island; people that come to Vienna include residents of Reston, McLean, Fairfax, etc.  So, I started looking at the region around Vienna:  Fairfax County North of 236, and east of the Fairfax Co. Parkway.  From that, I defined a series of Zipcodes to monitor:  22030 22031 22102 22180 22182 22181 22124 20191 22066;  I am willing to add/adjust this, and am open to suggestions.

In that range, we are running about 5.8 cases per day per 100K.  Now, we know that each case is infectious for more than one day, and the primary risk is the pre-symptomatic/asymptomatic people.  To capture that, the magic number is probably the cases in the last 10 days.  in the last 10 days, there were 55 cases per 100K people in the local region; the region of people that might go to a Vienna restaurant or coffee shop.  That means about 0.055% of the people are probably infectious.

So, if you have close interaction with one person, you have a 99.945% chance of not interacting with a COVID positive individual.  But, what if you go into a a place with 16 people?  Then, randomly, that is a 99.12% chance of not being exposed or less than 1% being exposed. What about 100 people?  The risk of one person being positive is 5.4%.  What about a large political rally with 1000 people? The risk is about 60% of being exposed randomly.  

So, if you are comfortable with a 1% risk of exposure (for most people my age, that would come with a 1/100000 risk of death; for me, it would be more like a 1/2000 risk of death), then take the risk.  I am not comfortable with a 1/2000 risk of death, but would be ok with the lower risk.





Age Distribution: 

As expected, there was an increase in cases among Middle Ages (and young adults) delayed from when the JMU students returned home.  There are about about 150 cases from the JMU students. We are now back to the baseline number for that age group.  The JMU students infected their parents, resulting in an increase of The concern is that the JMU students will infect their families, and we saw an uptick in the middle aged population, which has since recovered; about 50-100 extra people were infected, which was less than I expected.

Note, I will talk about the age distribution in college communities under "college communities"




Colleges

Overview:  Things are improving at most colleges.  I have added the Lexington VA colleges (VMI/Washington and Lee) to the discussion.  My data mining by zip code requires I group them together, because they share a zip code.

My process combines the VA Department of Health data and what is reported by the colleges.  The report is as of 11:00 ET.   I need to point out that the VDH cases may include cases not affiliated with the university as I am using geographic surveillance.  It is also worth noting that all assume that students feeling ill are going to health service; I have heard anecdotal reports of people not doing that because they did not want to quarantine.  The colleges usually update the dashboards after this post, or on Monday/Tuesdays.  Except for Radford, all weekly updates are complete at this time.  And the numbers are encouraging (except for UVA).

As the process has evolved, it was clear that I needed to show active cases (e.g., last 10 days) in addition to cumulative cases.

Also, I am assuming the colleges are promptly reporting there numbers to the Virginia Department of Health.  As it turns out, W&M is reporting the cases approximately 2 days after updating the dashboard.  It is probably a result of the phasing of the process.

Note: I have been tuning the following table to improve the estimated number of cases (the order of operations has changed a bit).  Also, I am adjusting the pre-student case olad:  to estimate the number of cases from students, I subtract out the average number of cases prior to the student arrivals from the reported cases.  If the numbers are large (UVA, VT, JMU & Radford), the impact is minimal.  This makes it harder, though, to identify cases in more urban settings, like ODU, VCU and CNU.

RED means there is clear evidence for community spread
YELLOW means there may be community spread; still ambiguous
GREEN means no evidence of community spread
BLACK means they went online.

College

% Positive

Cumulative

Last 10 days

Dashboard Cases

% that had COVID***

VDH Cases*

Est

Cases**

VDH Cases*

Est

Cases**

Va Tech

  5.8

   1534

 4654

    247

  313

1128*****

 13.6 

GMU

  1.7

     67

   72

      14

    17

67

  0.2 

UVA

 11.1

    764

 1781

    229

  516

857

  7.5 

ODU

  5.1

   58

   84

      17

   32

70*****

  0.3 

JMU

 9.4

   1630

 7375

    139

  329

 1540

 34.7 

CNU

  12.2

  13

   67

      15

    42

23*****

1.3

UMW

  4.8

      0

    14

      0

    0

17

  0.3

Radford

 8.0

    566

 2744

      7

   6

411*****

 34.6 

VCU

  4.8

    170

  325

      16

    18

269

  1.0 

WL/VMI

  10.1

     99

  176

     62

  134

61/34

  4,6 

W&M

  2.3

     27

   27

      14

    15

29

  0.3

* estimated from the number of cases in the zip codes associated with the university removing the pre-student arrival case rate

** estimated number of cases is an attempt to normalize for testing limitations. Specifically, I assume at 5% positive, 100% of the cases would be caught. so I normalize it to that value.  If the % positive is very high (>40%) I am likely overestimating the numbers.
*** Dashboard cases are only counted if I can find the dashboard.  In some cases, it is difficult to distinguish positive tests from cases (1 case may have multiple positive tests; that is mostly at VT).  I include active cases if reported, otherwise, I use total cases.
****% population uses the total reported number of students rather than just those on campus; it may be off when the percent positive is above >40%.
***** Old data, not updated for today.
****** Active cases, not total cases

Large Scale Community Spread:

JMUJMU returned to in-person class 10/5.  I am worried because their plan does not include testing the entire population prior to arrival.; here is their plan.  My concern is the result of the case count at JMU to rise, but slowly.  JMU has been fairly transparent with the situation, but could not get ahead of it.    JMU plans to reintroduce on-campus activities soon -- this time with about 10x the quarantine space and a plan for prevalence testing.  There continue to average 30 new cases a day, but -- and this is important -- the positivity rate is down to 10%, so perhaps they will be able to stay ahead of the outbreak.

Virginia Tech: We have seen the prevalence of the virus in Blacksburg increase with the return of the students. Each day, there are 30 and 100 new cases validated.  There could be more, but some people are just assuming they have COVID 19.Virginia Tech tested only on-campus students.  VT is only reporting the student health center results; as such the cases in 24060 are a better indication of the caseload at Virginia Tech.  The football team had 21 members out because of COVID issues last week.  

UVAWith the students return, there has been a marked increase in cases.  Week over week.  It appears, that with the much stricter rule UVA imposed 10 days ago, the case load is abating.

W&L / VMIThere is clearly an outbreak occurring at these schools.  The numbers are low because the schools are small.  My surveillance approach is based on ZIPCodes, and they are in the same ZIPCode, so they are combined into a single entry.  This is just an artifact of how things are tracked, and not a judgement on either school. 

Watch List:



Other schools:

William & Mary -- There is at least a small scale outbreak in the athletic department.  W&M tested all athletes, and stood down on athletics.  Most of the active cases are among athletes. It is worth noting that W&M is quick to update the dashboard; they update prior to reporting the VDH.  W&M tested all students prior to arrival in town. Williamsburg is a case where the town/tourists are a bigger threat to the college, than the college is to the town. 

VCU seems to have the virus under control -- They have beaten back an outbreak, the % positive is good, and there are few new cases. It was promoted from RED to YELLOW. and now Green.  The numbers have shown no significant increase in the last several days; quarantine and isolation space is becoming more prevalent.   Being in an urban setting the zip-code and regional surveillance that works well at some of the other schools is not particularly helpful here.  So, I have to rely on the dashboard.   

RADFORDRadford was moved to the watch list, as the percent positive has improved.  Radford updates the dashboard once a week, which is not sufficient in my opinion, but fortunately they report to VDH regularly.  As such, the data on Radford's dashboard is now 7 days old.  While it is not how many students at Radford contracted COVID-19.  It would not surprise me to see enough that the community, when isolated effectively has herd immunity (meaning over 60-80% contracted COVID-19).  The only way to know would be antibody studies.  Hopefully, VDH will look into that.  But, currently, it seems that Radford has a manageable number of cases.  While only 57% of the cases in the last two months are attributed to students, there were so few cases prior to the students return, this means either the dashboard is undercounting, or there were a lot of non-students infected by students. 

CNU -- Students have been back upwards 1 month. A few cases.  Under control.  Note that the VDH numbers for the zip code indicate an increase in cases, but that is possibly the result of other factors, such as a large ill-advised political rally.

ODU -- Nothing noteworthy.  My concern with ODU is they did not test the students, so there may be asymptomatic/presymptomatic spreaders on campus (see JMU). Yesterday, they updated the dashboard to show 59 cases on campus, which is about what I would expect based on non-tested students.  But the dashboard has not been updated since Sunday. They update it once per week.  We will see if they infected other students.  

UMW -- Nothing noteworthy.  A few cases but they just returned.  I am concerned because they did not test all students.

GMU -- Nothing noteworthy.  GMU tested all students.

College Communities:

When I started talking about communities, the  focus was on the safety for incoming students.  Unfortunately, that concept as changed.  Now, we are seeing the colleges impacting the surrounding communities.  If we look at the age distribution of cases in the communities of JMU, Radford and VT (New River, and Central Shenandoah health districts), we see that, starting about 4 week ago, number of cases for non-college age citizens is increasing -- about two weeks behind the college age curve.  This suggests the disease is infecting the general population.  So far, it looks like about an extra 265 middle aged and seniors have been infected were infected; we have gone from 12 cases to 22 cases per day in those groups.  Furthermore, in the 5 months from the beginning of the epidemic to early Sept, there was an average of 10 deaths per month; in the last three weeks there have been 19 deaths.  This is the concern.  This trend has been observed elsewhere in the country, where the college students infect the more vulnerable populations.





Commentary:


Since Donald Trump has been infected, or more accurately, with the infection of Trump, we have learned:
  1. People can test negative and still spread the disease.
  2. Even if everyone who interacts with you is tested immediately prior to the interaction, you can still get sick (see 1).
  3. If you have an event with hundreds of people, there is potential for it to be a super-spreader event, even if you test everyone at the event.
  4. If you do this frequently enough, you will get unlucky.
  5. A non-spaced, but outside event is still dangerous.
This has two impacts for us:  first, some of the attendees and support people live in our community. I have no information as to the impact this has had.   Second, we now know that any crowded situation is a potential spreading event, even if outside.  This includes sporting events, concerts, and worship.  Please think about this before planning activities.

There are safety concern with athletics, but those can be mitigated.  I am more concerned about the fans in the stands.

I have reason to believe about 100 or more of the last week's Virginia cases are a direct result of the combination of the Newport News Trump rally and the Whitehouse outbreak.  If we are placed back on the NY quarantine list, it is because of these political activities.  

Attribution:

1) You can repost / share in the entirety by forwarding the link, 2) If you want share partial content, you must receive my permission – I need to make sure you understand what I am saying. If anyone sees this work being used without attribution, please let me know as soon as possible. I am willing to have an informed discussion / debate on my approach, but I want to make sure the proper context is captured.


Links: 

Source data is from the Virginia Dept of Health COVID Site

Why I did this:  About the blog
I have thoughts on the spread in college communities which can be seen here.  This is the same link at the top of the write-up.

Other Sites:  John's Hopkins

Kids can pass covid to parents: Pediatric SARS-CoV-2: Clinical Presentation, Infectivity, and Immune Responses




A fun video showing masks work, guy style:




How to wear a mask.

Politics:  Some lie.


Donald Trump yesterday said that without blue states, the death rate would be much better.  He needs to stop using alternate facts.  Red and blue are defined by who the state voted for in 2016.  47% of the deaths come from red states, which is about his percent of the popular vote.  But, more importantly, after June first, when states could use science to mitigate the virus, 65% of the deaths are from red states.  Facts matter.






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