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San Diego COVID-19 Data Funneled Through Patchwork Of Overlapping Reporting Networks

A sign outside the county’s walk-up testing site at the Tubman Chavez Community Center on Aug. 10, 2020
Tarryn Mento
A sign outside the county’s walk-up testing site at the Tubman Chavez Community Center on Aug. 10, 2020

This is the first in an ongoing series of articles examining San Diego County’s set of 13 data points that influence public health regulations amid the pandemic.

San Diego COVID-19 Data Funneled Through Patchwork Of Overlapping Reporting Networks
Listen to this story by Tarryn Mento.

Five months before President John F. Kennedy was assassinated in 1963, he waved from a motorcade cruising down San Diego’s El Cajon Boulevard. A photo captured Kennedy’s smile as he rolled past the 24-hour Rudford’s Restaurant, a community staple that has welcomed diners at all hours since that day.

The restaurant’s streak ended in March when California Gov. Gavin Newsom called on restaurants to shut down on-site dining amid the coronavirus pandemic.

Rudford's was forced to offer only takeout, said owner Jeff Kacha.


“We let go 40 people. That was hard to do,” Kacha said.

San Diego COVID-19 Data Funneled Through Patchwork Of Overlapping Reporting Networks

Proprietors such as Kacha have been stuck in a months-long limbo as business is thwarted by numbers. Public health officials tally the rise in coronavirus cases and other data points that determine when kids can attend school, couples can hold wedding celebrations, parents can work or grandmothers can have visitors.

San Diego County relies on a set of 13 data points to track coronavirus spread in the county and influence its public health regulations during the pandemic. Two of the metrics, including the region's rate of new coronavirus per 100,000 residents, is set by the state. San Diego's high case rate recently came close to forcing businesses to shutter operations a third time.

San Diego County Triggers For Modifying Health Orders Promo Graphic

Click the image above to check out the KPBS Trigger Tracker, which uses data from San Diego County to monitor the spread of coronavirus in the region.

A KPBS examination of what the county calls the 13 “triggers” — because they may trigger an adjustment to restrictions — reveals a complicated network peppered with caveats that affects how the region handles the most complex pandemic response in a century.

Dr. Bill Schaffner, medical director of the National Foundation for Infectious Diseases, said these data-driven systems used by jurisdictions across the country are imperfect but still a valuable public health tool.


"I wouldn't say I'm confident down to the last decimal point, but pretty close — close enough to make reasonable decisions and to assess trends over time," Schaffner said.

This series of stories will shed light on where the county's coronavirus numbers are coming from, what they are counting and how officials ensure the tallies are correct, beginning with the region's case rate. It's the most recognizable and powerful metric among the 13. But it’s also a major subject of disagreement between local and state officials; county supervisors recently considered litigation against the governor as San Diego's case rate neared a threshold that would trigger a third round of closures.

KPBS found the case rate calculation depends on a patchwork communication system between government agencies, laboratories and health care providers that involves the multiple entities reporting similar data more than once — and it all starts with snot.

Reporting in multiple directions

Multiple plates with dozens of wells sits on a machine at Helix laboratory in La Jolla, July 21, 2020.
Tarryn Mento
Multiple plates with dozens of wells sits on a machine at Helix laboratory in La Jolla, July 21, 2020.

At Helix laboratory in La Jolla, swabs that were shoved up patient noses arrive by courier — the biggest shipment comes in the afternoon carrying that day’s samples. Scientists in gloves and face shields unload the wands that are sealed in tubes.

KPBS previously followed the mucus samples in the lab on a tour with the CEO and two vice presidents. The specimens from nostrils swabbed by clinicians all over the county traveled through a barren white hallway and into the hands of robots. The machines run 24 hours to detect SARS-CoV-2, the virus that causes COVID-19.

Thousands more collected at local pharmacies, doctor’s offices, specialty clinics, detention facilities and hospitals — plus state-operated testing sites — weave through the hallways and machines at other labs. The results that when taken together can expand or limit a business’s capacity are then reported through a complex network that has multiple sources telling officials the same information more than once.

The exterior of Helix laboratory in La Jolla, July 21, 2020.
Tarryn Mento
The exterior of Helix laboratory in La Jolla, July 21, 2020.

For example, Helix — which handles local swabs collected at county testing sites — shares results with San Diego officials twice.

Marc Laurent, Helix vice president of partnerships and operations, said they submit results electronically to a county operations team that informs patients of the outcome, and also shares positives with the San Diego County health department via fax.

"It's ancient, but it's also one of the most safe ways to pass HIPAA information along," Laurent said, referring to the health information privacy law.

Helix also sends information electronically to state health officials in Sacramento.

Other national commercial labs report only to the California health agency, which automatically passes San Diego results on to the county. Labs also report to health care providers that sent them tests so they can inform patients, and those providers then report confirmed cases to the county as well.

Covid triggers reporting animated gif

This animation shows how COVID-19 test results are reported to government public health officials. Some labs report results to both state and county health departments (shown in green); National commercial labs report only to the state health department and local results are automatically shared with the county health department (shown in purple). Lab results are also shared with health care providers who also report those same results to the county health department (shown in red).

The county’s public health team wouldn’t agree to an interview despite weeks of requests but said in an email that staff checks results against its database.

"If the record already exists, the information is attached to the existing record. Sometimes duplicates do slip through, but we also do routine duplicate checks using a data processing program and staff review and make corrections as needed," said Sarah Sweeney, spokeswoman for the county Health and Human Services Agency.

Data differences

There have been data discrepancies, including one major snafu, amid the convoluted reporting process.

In August, state officials revealed hundreds of thousands of lab results that usually flowed to local health departments through Sacramento got lost. The governor paused any data-driven decisions until the state error was fixed, but the county and California officials continued to clash over the case rate.

The state and San Diego officials used slightly different calculations and couldn’t come to an agreement for several days — the county even began publishing the two different calculations on its website after questions from KPBS.

California has since overhauled its reopening strategy and how it calculates the case rate, but the change didn't bring the two levels of government closer together.

The state previously measured the rate of new infections over a two-week period but changed that to the daily average. It also increases or decreases a county's case rate based on its testing volume.

That adjusted figure — plus positivity rate, which is the percent of all conducted tests coming back positive — now decide where a county lands in the state's four-phase color-coded reopening plan.

San Diego County fell under the second most restrictive level, or the red tier, allowing eateries, gyms and other establishments to re-open their indoor spaces with limited capacity in late August. But within weeks, the case rate neared a level the governor considered too high, threatening a step backward for business owners like Kacha of Rudford's.

That's when elected county leaders urged the governor in a letter to ignore hundreds of positive tests that suddenly popped up among San Diego State University students.

"Asking them to seriously consider discounting or not including the approximately 700 cases that we have right now from SDSU students," San Diego County Board of Supervisors Chairman Greg Cox said.

The governor disagreed. Newsom's refusal sent the supervisors into closed-door meetings where they discussed potential legal action in the event the region again faced governor-ordered restrictions.

However, those new regulations were narrowly avoided when the state announced its weekly assessment of the county's adjusted case rate came to 6.9 per 100,000 residents, even with the hundreds of SDSU cases — a case rate of 7.1 would've triggered restrictions.

But county officials have since continued their dispute with state leaders and San Diego County Public Health Officer Dr. Wilma Wooten is pushing the governor to consider adjusting a region's case rate based on additional data points.

"If counties that are maintaining that hospitalization and hospital capacity to somehow get credit for that, and also to get credit for contact tracing," Wooten said late last month.

This past week, San Diego again barely avoided a case rate the governor considers too high, although its case rate would have to hit that threshold of at least 7.1 per 100,000 residents two weeks in a row to trigger state sanctions.

But the back and forth has left Rudford’s owner Kacha on edge.

"We were into our savings. We've overspent. We haven't made a profit," Kacha said.

He worries he can’t survive another closure.

A sign that reads "Stand Up Small Business! #DEFY" hangs on the front of Rudford's Restaurant, Oct. 1, 2020.
Tarryn Mento
A sign that reads "Stand Up Small Business! #DEFY" hangs on the front of Rudford's Restaurant, Oct. 1, 2020.

Corrected: July 24, 2024 at 2:15 PM PDT
KPBS Reporter Matt Hoffman contributed to this story.