Updates on SCC testing and tracing

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Updates on SCC testing and tracing - Snorlax94 - 05-17-2020

1) in a Mercury News editorial arguing against the current piecemeal reopenings in the Bay Area, they mention:

Quote:“Harvard researchers say that the minimum daily number of tests needed to detect and control outbreaks is 152 per 100,000 people. Bay Area counties are ramping up their testing and contact tracing capacity, but they are still far short of reaching that goal.

Santa Clara County officials said Thursday they are testing only about 1,000 people per day. Dr. Martin Fenstersheib, who is charged with helping the county reach its goal of 4,000 tests per day, said he expected to hit that goal by May 31.”

I noticed the last two days SCC tested almost 1700 a day for two consecutive days, so yay, it’d be nice to hit 4,000 in two more weeks.

2) I was looking for updates on SCC contact tracing updates and stumbled upon an SCC contact tracing information page that had been updated 4 days ago.

https://www.sccgov.org/sites/covid19/Pages/contact-tracing.aspx

Some highlights:

Quote:After revising many existing protocols and deploying the new technology described above, Public Health’s current case investigation and contact tracing team has increased its capacity to investigate cases significantly. The Department is now able to investigate 25 new cases per day, including communicating with each of those individuals contacts. As shelter-in-place restrictions are rolled back and as the number of contacts each newly infected person increases, Public Health anticipates it will need capacity to conduct detailed case investigation and contact tracing for approximately 50 to 75 new cases per day, with an average of 40 contacts per case.”

“In addition to the County workforce being redeployed for these efforts, the County is seeking help from governmental and community partners in identifying a large pool of people who can commit to this work. Team members will interview cases, call potential contacts, enter and manage data, and identify resources needed to ensure appropriate follow up and complaince with isoaltion and quarantine. We are asking you and other partners to identify any individuals that your organization is willing to redeploy to be members of the team we are building. Individuals, with approval of their employer.”

RE: Updates on SCC testing and tracing - M T - 05-20-2020

If we make the probably bad assumption that those tested, other than for having symptoms, in Santa Clara County are representative of the population, and we recognized that because this includes those with symptoms, this is an upper bound, then I think a reasonable upper bound estimate of current infections in Santa Clara County is the positive test percentage in the county for a week taken 5 days ago. (5 days ago to allow for all tests to be returned; a week covers the weekend drops).

How much an upper bound this is, I can't really say. For all I know it might be 10x the real rate.

By those criteria (average positive % testing, week ending May 13), in Santa Clara County, there are (upper bound) 1.22% that would test positive on any particular day (1.25% if averaged over 2 weeks, so the infection rate is very slowly dropping).

For a population of 2 Million, that's about (upper bound) 25K PCR-detectable infections on any particular day.

I don't have a solid number for how many days is typical for an infection to be detected by a PCR test, so I'll use 3 weeks (shedding duration is clearly shorter; my recollection is of an 18-day average detection but I don't remember if that was from infection or onset of symptoms). That corresponds to 1190 new infections per week, or about 170 per day. For that week, SCC had 103 positive tests. So roughly, total new infections is (upper bound) 12x those with positive tests.

Somewhat separably, of those 25K people that would be PCR-positive on any day, using about a 10-day infectious window and the 3-week PCR-detectable window, about (upper bound) 12K would be infectious on any particular day. That's (upper bound) 6 out of every 1000 people.

This is across the county. Different neighborhoods & different situations (particularly, congregate housing) result in different percentages.

Lots of assumptions there. Make your peer review & feel free to make your own estimate. Do note this is an estimate of those currently infected (not ever-infected as an antibody survey might detect).

By comparison, L.A. county (minus Pasadena & Long Beach) numbers for May 13 are 7.67% (1 week) and 5.84% (2 week). L.A. county had two weeks of high testing numbers that drove their average down, but the past week has been about 60% as much testing. (I don't know if it less capacity, less demand, or delayed results.).

RE: Updates on SCC testing and tracing - M T - 05-21-2020

COVID-19 Testing now available to all county residents at no cost

Quote:Officials from the City of San José and County of Santa Clara, in partnership with Verily, hosted a press conference today to announce that free COVID-19 testing is now available for all residents, asymptomatic or otherwise, at PAL Stadium in East San José and the Santa Clara County Fairgrounds.

This mobile screening and testing are a service, courtesy of the State of California in collaboration with Verily. ... allows Santa Clara County residents to use an online screener and appointment scheduling system to easily navigate the testing process.

“Our goal in Santa Clara County is to test every person who wants to be tested for COVID-19,” said Cindy Chavez, President of the Santa Clara County Board of Supervisors. “This testing facility will help us get there.”

Testing sites are located in places where public health will be most improved through testing including: PAL Stadium, 680 S. 34th St., and the Santa Clara County Fairgrounds, 344 Tully Road. Testing sites will be available Monday through Friday from 9 a.m. to 3 p.m. at both locations. Residents will need to schedule an appointment to get tested. Each site will have the capacity to serve several hundred people per day.

More background in an NBC Bay Area story.

RE: Updates on SCC testing and tracing - M T - 05-21-2020

WOW! Now that's what I call testing! (Wuhan's population is 11M)

ABC News, May 21 -

Quote:10:19 a.m.: Wuhan says it has conducted over 3 million coronavirus tests since last week
The Chinese city of Wuhan, ground zero of the coronavirus pandemic, conducted 887,321 nucleic acid tests for COVID-19 on Wednesday, up from 856,128 tests the previous day, according to the local health authority.
No confirmed cases of COVID-19 with symptoms were found during Wednesday's testing period; however, 28 new asymptomatic carriers were identified, according to daily reports published by the Wuhan Municipal Health Commission.

If the 28 positives were from the 887K tests, that's good for having few false positives. (Ie, I'd like to know what the false positive & false negative rates are expected to be)

RE: Updates on SCC testing and tracing - M T - 05-24-2020

It sure looks like L.A. County, and to a lesser extent Santa Clara County, have experienced an increase in percentage of positive tests. I have no particular clue as to whether it is an increase in illness, or a result of a change in who can get a test. AFAIK, no one has indicated how, say, the tests for patients already sick are handled. (Typically, 2 negative tests are required as part of the decision that you are no longer sick.) One could see this increase as just a return to "normal" after a negative bump when testing was opened, caused by an influx of tests of curious but not sick people.

The one-week average positive percentage for SCC had gotten as low as 1.1% but has bumped up to 1.3% (5 days before current date). L.A. County had gotten down to 4.5% but is now around 6%.

The message quoted is 3 days ago. When I updated my spread sheet with SCC daily testing numbers today, the daily changes prior to 5 days earlier were generally small as expected. L.A. County had a consistent pattern to their changes. When I compare today's testing numbers with those I recorded 3 days ago, L A County testing data had a decrease of 305 positive tests and an increase of 53 negative tests from April 11 to April 28. It appears that LA County generally removed 10-30 positive results daily for two weeks. They did not remove a corresponding number of negative results (if they report 10% positive rate, and remove 10 positive results, a "corresponding number" of negative results would be 90.). Some explanations might be that these were judged to be false positives, or perhaps were for individuals out of the area they are reporting for. The effect of these changes is to lower the % of positive cases in the 3 to 6 week-old data (back to the start of the data that I had recorded, April 11).

LA County shows a 5-day gray window for testing that isn't yet complete. I found that 5-day window to be too narrow. In the last 3 days, the change to number of tests recorded 13 days before the last data shown (3 days ago) increased by at least 10%. The change 7 days before last data shown was an increase of about 100% in cases. The 1-week average in LA County for May 7 - May 13 for data as of May 20 (last datum May 18) was 7.67%; for data as of May 24 (last datum May 21), it is 5.91%.

(05-20-2020, 01:59 PM)M T Wrote: If we make the probably bad assumption that those tested, other than for having symptoms, in Santa Clara County are representative of the population, and we recognized that because this includes those with symptoms, this is an upper bound, then I think a reasonable upper bound estimate of current infections in Santa Clara County is the positive test percentage in the county for a week taken 5 days ago. (5 days ago to allow for all tests to be returned; a week covers the weekend drops).
...
By those criteria (average positive % testing, week ending May 13), in Santa Clara County, there are (upper bound) 1.22% that would test positive on any particular day (1.25% if averaged over 2 weeks, so the infection rate is very slowly dropping).
...
By comparison, L.A. county (minus Pasadena & Long Beach) numbers for May 13 are 7.67% (1 week) and 5.84% (2 week). L.A. county had two weeks of high testing numbers that drove their average down, but the past week has been about 60% as much testing. (I don't know if it less capacity, less demand, or delayed results.).

RE: Updates on SCC testing and tracing - Snorlax94 - 05-24-2020

(05-24-2020, 12:51 PM)M T Wrote: It sure looks like L.A. County, and to a lesser extent Santa Clara County, have experienced an increase in percentage of positive tests. I have no particular clue as to whether it is an increase in illness, or a result of a change in who can get a test. AFAIK, no one has indicated how, say, the tests for patients already sick are handled. (Typically, 2 negative tests are required as part of the decision that you are no longer sick.) One could see this increase as just a return to "normal" after a negative bump when testing was opened, caused by an influx of tests of curious but not sick people.

The one-week average positive percentage for SCC had gotten as low as 1.1% but has bumped up to 1.3% (5 days before current date). L.A. County had gotten down to 4.5% but is now around 6%.

MT, I share your concern about the SCC data.

The optimistic scenario is that this is due to the increase in testing in East San Jose. As you've probably seen, East San Jose has the densest concentration of cases in SCC, and they just opened two new major testing facilities there to help address the needs in those communities, so you'd expect there were a ton of untested cases there, and hopefully now we are catching more of those.

BTW,
1) Do people know why there is such a high concentration of cases around Page Mill Road in Palo Alto? Granted, the population is very small, but still, it's significant. I was wondering if it was the VA Hospital.

2) MT, what data set(s) are you using? For example, the SCC Dashboard shows a recent substantial increase in Covid hospitalizations and cases, but the state hospital dashboard shows a nice downward trend in recent Santa Clara hospitalizations.
https://data.chhs.ca.gov/dataset/california-covid-19-hospital-data-and-case-statistics/resource/6cd8d424-dfaa-4bdd-9410-a3d656e1176e?filters=County+Name%3ASanta+Clara
The state dataset shows COvid hospitalziations dropping from 51 to 37 in the last week, and ICU cases dropping from 22 to 18 (and the suspected cases dropping as well).

RE: Updates on SCC testing and tracing - chrisk - 05-24-2020

(05-24-2020, 01:26 PM)Snorlax94 Wrote:
(05-24-2020, 12:51 PM)M T Wrote: It sure looks like L.A. County, and to a lesser extent Santa Clara County, have experienced an increase in percentage of positive tests. I have no particular clue as to whether it is an increase in illness, or a result of a change in who can get a test. AFAIK, no one has indicated how, say, the tests for patients already sick are handled. (Typically, 2 negative tests are required as part of the decision that you are no longer sick.) One could see this increase as just a return to "normal" after a negative bump when testing was opened, caused by an influx of tests of curious but not sick people.

The one-week average positive percentage for SCC had gotten as low as 1.1% but has bumped up to 1.3% (5 days before current date). L.A. County had gotten down to 4.5% but is now around 6%.

MT, I share your concern about the SCC data.

The optimistic scenario is that this is due to the increase in testing in East San Jose. As you've probably seen, East San Jose has the densest concentration of cases in SCC, and they just opened two new major testing facilities there to help address the needs in those communities, so you'd expect there were a ton of untested cases there, and hopefully now we are catching more of those.

BTW,
1) Do people know why there is such a high concentration of cases around Page Mill Road in Palo Alto? Granted, the population is very small, but still, it's significant. I was wondering if it was the VA Hospital.

2) MT, what data set(s) are you using? For example, the SCC Dashboard shows a recent substantial increase in Covid hospitalizations and cases, but the state hospital dashboard shows a nice downward trend in recent Santa Clara hospitalizations.
https://data.chhs.ca.gov/dataset/california-covid-19-hospital-data-and-case-statistics/resource/6cd8d424-dfaa-4bdd-9410-a3d656e1176e?filters=County+Name%3ASanta+Clara
The state dataset shows COvid hospitalziations dropping from 51 to 37 in the last week, and ICU cases dropping from 22 to 18 (and the suspected cases dropping as well).

Where are you getting the concentration around Page Mill? If you are looking at 94304 ZIP code it includes 11 cases at the Vi Retirement community.

RE: Updates on SCC testing and tracing - Snorlax94 - 05-24-2020

(05-24-2020, 01:44 PM)chrisk Wrote: Where are you getting the concentration around Page Mill? If you are looking at 94304 ZIP code it includes 11 cases at the Vi Retirement community.

Yes it is the 94304 zip code, but the case counts there are so high, even if you remove the 11 cases, you'd still have one of the higher concentrations in SCC (although, again, there are only 3902 people in that zip code).

from:
https://sccphd.maps.arcgis.com/apps/webappviewer/index.html?id=5fe788400b054eaeb2f1e8d9000bf3c8

[Image: 3P2LVpj.png]

RE: Updates on SCC testing and tracing - M T - 05-24-2020

(05-24-2020, 01:26 PM)Snorlax94 Wrote: MT, I share your concern about the SCC data.

The optimistic scenario is that this is due to the increase in testing in East San Jose. As you've probably seen, East San Jose has the densest concentration of cases in SCC, and they just opened two new major testing facilities there to help address the needs in those communities, so you'd expect there were a ton of untested cases there, and hopefully now we are catching more of those.

BTW,

1) Do people know why there is such a high concentration of cases around Page Mill Road in Palo Alto? Granted, the population is very small, but still, it's significant. I was wondering if it was the VA Hospital.

2) MT, what data set(s) are you using? For example, the SCC Dashboard shows a recent substantial increase in Covid hospitalizations and cases, but the state hospital dashboard shows a nice downward trend in recent Santa Clara hospitalizations.

state dataset

The state dataset shows COvid hospitalziations dropping from 51 to 37 in the last week, and ICU cases dropping from 22 to 18 (and the suspected cases dropping as well).

My data comes from the county dashboard.

The county indicates it is reporting Confirmed + Suspected in hospitals, currently 99 (72 acute beds, 24 ICU beds), posted May 23, data as of May 22. (Note that there is a discrepancy of 99 vs 96).
This looks to match the state data listed as May 21:
Hospitalized: 39 confirmed, 60 suspected; ICU 16 confirmed, 8 suspected.

If the state's numbers are accurate and complete for the most recent date, we've got a welcome shock coming to us. My guess is that the numbers for the last couple of days at the state are incomplete. I would be suspicious at a drop from 60 suspected (symptomatic) COVID-19 to 20 in a single day without a significant jump in confirmed cases. It may be the doctors have been over-classifying patients as suspected.

(05-24-2020, 02:11 PM)Snorlax94 Wrote: Yes it is the 94304 zip code, but the case counts there are so high, even if you remove the 11 cases, you'd still have one of the higher concentrations in SCC (although, again, there are only 3902 people in that zip code).

The count of 17 includes the 11 residents with COVID-19 but maybe also the "<11" staff that have COVID-19 as well. That might account for 12, 13, . . ., or all 17 cases in the zip code.
"Total cases reported for LTCFs include all residents and staff associated cases, regardless of zip code of residence."

RE: Updates on SCC testing and tracing - Snorlax94 - 05-24-2020

(05-24-2020, 02:28 PM)M T Wrote: The count of 14 includes the 11 residents with COVID-19 but also the "<11" staff that have COVID-19 as well. That might account for 12, 13, or all 14 cases in the zip code.
"Total cases reported for LTCFs include all residents and staff associated cases, regardless of zip code of residence."

Ok that’s good to know. When I originally saw the image on my phone, the sliver that contained the LTCF was so small I didn’t see it. Although of course the LTCF case is terrible, I’m relieved if it means it’s not a concentration that would necessarily be connected to Stanford or Stanford Hospital on an ongoing basis.

RE: Updates on SCC testing and tracing - M T - 05-24-2020

Free 1-Day COVID-19 Testing Site to be Offered Monday in Mountain View

Quote:A one-day, pop-up novel coronavirus testing event will be offered from 10 a.m. to 2 p.m. Monday at the Rengstorff Park Aquatic Center, 201 South Rengstorff Ave. in Mountain View, city officials announced.

Testing is offered for all and no insurance, appointments, documentation or pre-registration is required.

The event is offered through a partnership between the city and Santa Clara County, which is working to add more testing sites to the northern portion of the county. Planning is being done to offer more north county testing, officials said.

RE: Updates on SCC testing and tracing - Mick - 05-25-2020

When I signed up for the test and went through the questions, there was a question pegging BMI at 40. For a six foot tall man, that's 294 pounds. It seems odd that the BMI as an indicator of danger is so high. Is a 40 BMI the point of demarcation to indicate a much greater likelihood of permanent damage resulting from COVID-19? I would have thought a lower BMI indicator, around 34 or 35 would be the target mark.

RE: Updates on SCC testing and tracing - BostonCard - 05-25-2020

(05-25-2020, 07:55 AM)Mick Wrote: When I signed up for the test and went through the questions, there was a question pegging BMI at 40. For a six foot tall man, that's 294 pounds. It seems odd that the BMI as an indicator of danger is so high. Is a 40 BMI the point of demarcation to indicate a much greater likelihood of permanent damage resulting from COVID-19? I would have thought a lower BMI indicator, around 34 or 35 would be the target mark.

https://www.medicalnewstoday.com/articles/latest-evidence-on-obesity-and-covid-19#Missing-BMI-data

There is probably not a step-change that occurs at 40 (or 34 or 35). Rather, it is probably a J-shaped curve (very underweight people are probably also at risk), with small increases in risk until you get to a BMI in the high 20's, then ramping up, and then increasing steeply when you get to the morbidly obese (BMI ≥ 40).

BC

RE: Updates on SCC testing and tracing - M T - 05-28-2020

The SCC Board of Supervisors held a meeting (6+ hour, starting at 1:30PM after a morning meeting) on Tuesday (May 26). The portion on the county's response to COVID-19 begins at 54:30. Dr Cody begins speaking about 1:13:00 into it. (Names below may be misspelled as I'm working from audio only. My apologies.)

57:30 Results of a survey of SCC residents about COVID-19. 1000 interviewed in 4 languages, May 14-18.

1:13 Dr, Sara Cody indicated her concern over the state's rapid changing of recommendations and the lack of controls to measure the effect of those changes. As I understand her, she feels that when a change is made, there should be a 14-day (or, preferably, 21-day) time until the next change, in order to determine the consequence in new infections of the change.

Separately, she expressed concern over the state's permitting meetings of up to 100 people. She indicated that if one of these became a superspreading event (my words), it would overwhelm the test & trace capability of the county.

[Not mentioned here, but suggested during the PPE segment was concern that the county's case load doesn't jump & result in PPE shortages as PPE is still in short supply.]

Dr Fensterscheib talked about testing. He indicated that the private health providers (later mentioned I believe as Kaiser, PAMF, Stanford (Health)) were not able to do the quantity of tests desired for their members due to supply chain issues for the reagents. Positivity is about 1% county wide, but higher risk areas (East SJ, Gilroy, parts of MV) are 3% or more. [There were more than 2000 tests/day for 3 days in the past week.]

Dr. Sara Redmon talked about Contact Tracing (1:33). California has rolled out an electronic platform for Contact Tracing reporting in association with SalesForce, Accentiure, and Amazon Web Services. SCC was 2nd county to adopt this. About 50 people doing CT, covering the 10-30 new cases a day. Because of SiP, the number of contacts are generally limited and they are "just able to keep up". [She does not define what a "contact" is or is not. My guess is the definition of "contact" is limited to a level that allows them to "just keep up". For instance, if a grocery store worker gets sick, I doubt they are considering ANY customers as close contacts. Ditto for any commuter that traveled by bus/Bart/Light Rail for 2x10 trips during the two weeks before symptoms.]

Evelyn Ho (1:36:10) talks about the scaling up to meet increased demands as SiP is eased. They want to scale to cover a peak of 75 new cases daily with up to 40 "close" contacts each. This requires about 1000 people to do this work. [Working backwards: 75*40=3000 close contacts to deal with per day (and I imagine there is a lot of overlap in super-spreader cases) means that each worker averages 3 close contacts per day (oversimplified!)). They do not mention the time scale for close contacts]

Currently 44 staff, with 45 being trained this week. By end of next week, they expect an additional 75 staff trained & ready to work. [By the above estimate, this 44+45+75=164 can cover about a total off 495 contacts per day.] Working to have 500 by the (end of?) the week of June 11. Averaging 100 new staff per week. Total of 1000 by mid July.. The State is considering providing 10K such workers across the state. SCC has requested 500 of that number [SCC has ~ 2/40 of California population.] The plan is not depending on the availability of these state workers.

Kee Lee covered isolation & quarantine support (1:41:04) This includes motel rooms for those that can't isolate at home (incl. homeless). Also covers support, if needed, for those isolating at home.

1:45:00 Sara Redmon regarding congregate housing.
1:48:10 Dr. Jennifer Tong regarding PPE.
1:52:00 Alan Minato regarding expenditures since COVID-19 crisis started. $49M spent plus $48M encumbrances, some seem understated.

2:10:35 Commissioners ask questions (10 minutes per commissioner)
3:00 2nd round of commissioner questions

RE: Updates on SCC testing and tracing - M T - 05-28-2020

If someone gets a chance to ask (preferably publicly so the responses can be shared), here are questions I would ask of SCC Public Health Department, regarding contact tracing:

1. You're ramping up to cover up to 75 daily new cases where each case has 40 close contacts. How will you handle a superspreader event that includes people that travel on mass transit? A single individual that travels on Caltrain daily for an hour each way to SF for the two weeks before getting symptoms will surely exceed 40 contacts. And, if he spreads it to others also commuting, they too will exceed 40 contacts (traveling in different train cars on different days). How will you even find the individuals who rode in the same train car as your index patient? In the case of some workers (bus drivers, grocery store clerks, ...) the number of people they may have had contact with may be hundreds or thousands. Will you triage this to limit detection of contacts so you only have a manageable numbers?

2. In your May 26 presentation to the county commissioners, no mention was made of any plans to use the technology developed by Apple and Google for assisting with contact tracing. Does this mean that Santa Clara County has evaluated and rejected this technology, or has it decided that it isn't worth considering, or are you expecting the state to pursue this so SCC is ignoring this for now?

3. Your presentation used the concept of "close contact" but without defining it. Without a definition, we can't know if it includes only the household, or whether it is more expansive so as to include people that work in the same large room, dined in the same restaurant at the same time, rode on the same mass transit vehicle, attended the same meeting (religious, business, social), and service providers (Uber driver, barber, dentist, physician, plumber), etc.

4. 75 daily new cases is a new infection rate of 1.4% of the population per year. While the infection fatality rate is still being understood, and may drop significantly in the future, if we suppose a value of 1%, this is about 270 deaths per year. Unfortunate, but far less than it might be. It also means that it will be decades before herd immunity might be reached if no vaccine is found. Is the current plan to follow this course for the foreseeable future?