How prevalent is omicron? Backlog, selective testing reveal incomplete picture

The Bakersfield Californian - 1/29/2022

Jan. 29—While the California Department of Public Health estimates that 97 percent of COVID-19 cases currently sweeping through the state are the omicron variant, you wouldn't know that by looking at some counties' data.

Case in point: The Kern County Public Health Services Department's COVID-19 dashboard, an online resource available to the public, reported 255 omicron cases and 2,136 delta cases as of Friday. Kern'sPublic Health Department has received sequencing results for only 2,963 cases — which includes other variants than omicron and delta — out of 210,736 cases total since the pandemic began.

Some public health officials said the state has a sequencing backlog, which stymies the release of up-to-date variant data. What the public can see on dashboards does not reflect the state's estimate of the prevalence of omicron.

But why? California Department of Public Health officials said they were working Thursday and Friday to collect answers in response to The Californian's inquiries; however, they did not provide responses by Friday night.

Furthermore, some public health departments in other counties use practices that are different from Kern County to understand the path of the virus and its impact on the community.

Sequencing data is integral to understanding how the virus spreads and where outbreaks may occur, said Denise Lopez, a Tulare County Public Health laboratory manager.

"You can monitor the movement of the virus ... and get a sense of how quickly it's spreading," Lopez said. She added: "There's a lot of different things that you can learn when you get sequences."

The Californian contacted public health departments around the state to see how they collect tests to be sequenced for variants.

KERN COUNTY

Locally, the state health department collects a certain percentage of tests from their Optum Serve sites, which are state-contracted testing sites, said Paul Rzucidlo, a Kern County Public Health epidemiologist.

However, receiving results can take weeks to months, said Michelle Corson, Kern's public health spokeswoman. Some tests can be sent to a state facility or a commercial lab for sequencing.

"They just don't have the capacity to run them all at once," Rzucidlo said.

Furthermore, local medical professionals can request a particular test be sequenced. Mostly, a doctor can request a verification of a variant in patients with suspected reinfection, a post-vaccination case, a severely ill patient or a patient from a high-risk setting, Corson added.

The state health department said 393,611 cases statewide were sequenced as of Thursday. In December 2021, a total of 7 percent of the cases were sequenced. In November and October, 25 percent and 21 percent of cases in California, respectively, were sequenced.

These percentages are "expected to increase in coming weeks as more data becomes available," according to the CDPH's website.

The first omicron variant in Kern County was reported Jan. 4.

MARIN COUNTY

Marin County also experiences a similar backlog, but has a local lab to offset any bottlenecks state facilities may experience.

Lindsey Termini, a senior Public Health nurse from the Health and Human Services Department in Marin County, said about 20 cases of omicron have been identified since Dec. 26 of last year. The first case was detected Dec. 17.

The Bay Area county has several workflows established to collect tests. Kaiser Permanente Medical Center in San Rafael diverts all its positive specimens to the CDPH Viral and Rickettsial Disease Laboratory for sequencing, Termini said.

The MarinHealth Medical Center sends its material to a local facility, Termini said. The county is also finalizing a contract with Curative Inc., a private lab, for sequencing.

However, collection methods differ from Kern County's procedures. Positive PCR tests from MarinHealth Medical Center inpatients are sent to a local lab, Termini said.

Termini also added the county tests wastewater to determine the SARS-CoV-2 activity throughout the county.

Beatrix Kapusinszky, the lab director of the Napa-Solano-Yolo-Marin-Mendocino County Public Health Laboratory, said her facility can process a maximum of 32 samples in a batch; results arrive anywhere from 24 hours to one week later.

Turnaround time from the state lab can be four to six weeks, Termini added. This backlog may have been exacerbated by the omicron-fueled surge, which creates more tests being sent to the state.

"We haven't been receiving a lot — the backlog is getting longer," Termini said.

TULARE COUNTY

The Tulare County Public Health Department collects tests from different geographical areas and facilities to understand the path of the virus throughout the county. Locations include skilled nursing facilities, jails and outpatient clinics.

"We try and select samples that will reflect what is circulating throughout the county," Lopez, the Tulare County Public Health laboratory manager, wrote in an email. "This also captures infections of different clinical severity as well, from mild infections to the more severe infections."

Positive tests are then checked to determine their signal — or, how much virus is present. Only from these tests are some chosen to be sequenced, Lopez added.

These processes are in addition to the tests accumulated by the state or commercial labs, she added.

Their lab technicians sequenced everything manually just a few weeks ago, and have started to transition to an automated process. The manual process could handle 45 to 50 samples per week, Lopez said.

Now, the automated process can look at 200 samples per week.

Tulare County first detected the omicron variant Dec. 23. As of Jan. 23, a total of 94 percent of COVID-19 cases were omicron, according to a report to the Tulare County Board of Supervisors.

You can reach Ishani Desai at 661-395-7417. You can also follow her at @idesai98 on Twitter.

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