Daily Status, Oct. 10: Incomplete data -- I did what I could
Daily Status, October 10
The COVID-19 data reported by the Virginia Department of health on October 10, 2020 (based on data collected on October 9h by 5 PM) shows that the commonwealth added 1256 cases of COVID-19. The daily total is more than one standard deviation above the 3-week average. As the last three days are about 1 standard deviation above the 3-week average, this suggests that our trend is likely deteriorating. Viewed over the last seven days, Virginia reported 7102 cases, or 1014 cases per day on which works out to 12.2cases/100K people. This is consistent with 12 cases/100K several weeks ago, but well above the 9 cases per 100K from 1 week ago. The decrease in case numbers that I was optimistic about has ceased, and we have reverted to the August average of about 1000 cases per day. It is possible that the September low was the result of under reporting. I have limited insight into the the cause of the dip or the rebound; if we look at the cases per day (in the regional section), there appears to be a bimodal distribution, as if some days the numbers are low and the next day (or days) they recover.
The trends over the last three weeks, now are showing a slow increase, at 1.3%/per day or 9% per week. I am unable to estimate the cases at colleges as that requires the zip-code data which is not available for 10/10.
By combining our current regional trends with the typical reporting for the day of the week, I expect 977 cases tomorrow (Sunday) with a 90% chance of the numbers falling between 662 - 1448 cases. If tomorrow's numbers differer from that, we are having a very rare event.
Regionally, all districts showing are flat to positive case growth. The testing numbers now show the percent positive to below the 5% metric over the last week (4.7%) that is often used to indicate sufficient testing (e.g., is is safe to reopen schools). The numbers were extracted from the VDH web site; further analysis is not possible without the data which was not updated. 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 12.2 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).
The following figure are from Friday/not updated.
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.
NOVA: 1.009 -- GMU
Central VA: 1.008 -- VCU
Hampton Roads/Eastern VA: 0.985-- W&M, CNU & ODU
SW VA: 1.007 -- VT & Radford
NW VA: 0.995 -- 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. The concerning aspect is in all regions, the numbers for last week are significantly higher than the prior 3 weeks.
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.
Growth rate (%/day)
1 0.00e+00 2.70e-08 1.89e-07 8.64e-07 2.43e-06 6.29e-06 1.43e-05 2.30e-05 4.33e-05
5 0.00e+00 1.35e-07 9.43e-07 4.31e-06 1.21e-05 3.14e-05 7.13e-05 1.15e-04 2.16e-04
15 0.00e+00 4.02e-07 2.82e-06 1.29e-05 3.62e-05 9.37e-05 2.13e-04 3.44e-04 6.45e-04
50 0.00e+00 1.32e-06 9.24e-06 4.22e-05 1.19e-04 3.07e-04 6.98e-04 1.13e-03 2.12e-03
100 0.00e+00 2.58e-06 1.81e-05 8.26e-05 2.32e-04 6.01e-04 1.37e-03 2.20e-03 4.14e-03
500 0.00e+00 1.08e-05 7.59e-05 3.47e-04 9.76e-04 2.53e-03 5.74e-03 9.26e-03 1.74e-02
1000 0.00e+00 1.77e-05 1.24e-04 5.67e-04 1.59e-03 4.13e-03 9.37e-03 1.51e-02 2.84e-02
2000 0.00e+00 2.48e-05 1.74e-04 7.95e-04 2.24e-03 5.79e-03 1.31e-02 2.12e-02 3.98e-02
#exposure 0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80+
1 0.00e+00 2.70e-07 1.89e-06 8.64e-06 1.94e-05 3.14e-05 4.28e-05 4.61e-05 8.66e-05
5 0.00e+00 1.35e-06 9.43e-06 4.31e-05 9.70e-05 1.57e-04 2.14e-04 2.30e-04 4.32e-04
15 0.00e+00 4.02e-06 2.82e-05 1.29e-04 2.90e-04 4.69e-04 6.38e-04 6.87e-04 1.29e-03
50 0.00e+00 1.32e-05 9.24e-05 4.22e-04 9.50e-04 1.54e-03 2.09e-03 2.25e-03 4.23e-03
100 0.00e+00 2.58e-05 1.81e-04 8.26e-04 1.86e-03 3.01e-03 4.10e-03 4.41e-03 8.28e-03
500 0.00e+00 1.08e-04 7.59e-04 3.47e-03 7.81e-03 1.26e-02 1.72e-02 1.85e-02 3.48e-02
1000 0.00e+00 1.77e-04 1.24e-03 5.67e-03 1.28e-02 2.06e-02 2.81e-02 3.03e-02 5.68e-02
2000 0.00e+00 2.48e-04 1.74e-03 7.95e-03 1.79e-02 2.89e-02 3.94e-02 4.24e-02 7.97e-02
Last 10 days
% that had COVID***
* estimated from the number of cases in the zip codes associated with the university removing the pre-student arrival case rate
Large Scale Community Spread:
- People can test negative and still spread the disease.
- Even if everyone who interacts with you is tested immediately prior to the interaction, you can still get sick (see 1).
- 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.
- If you do this frequently enough, you will get unlucky.
- A non-spaced, but outside event is still dangerous.
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.
Other Sites: John's Hopkins
Kids can pass covid to parents: Pediatric SARS-CoV-2: Clinical Presentation, Infectivity, and Immune Responses