California still does not
have enough capacity to test for coronavirus, Gov. Gavin Newsom said Sunday,
despite furious efforts by private, university and government laboratories to
scale up to handle thousands of more patients.
To help triage the crush of
Californians in the Bay Area who want to be tested for the novel coronavirus, Newsom announced a new website created in partnership with Alphabet’s
subsidiary Verily that will provide screening and testing support.
Starting Monday,
Californians with mild symptoms or who are concerned about exposure can take a
questionnaire that will direct those especially at risk from the virus to two
pilot testing sites in Santa Clara and San Mateo, according to a Verily news
release.
As of Monday morning,
however, the
questionnaire did not ask about risk factors or exposure history, and did
not direct people to testing. Verily did not immediately respond to a request
for comment.
Newsom called it “the next
phase” for testing in California, which to date has conducted 8,316 tests for
the virus — of which, 335 have come back positive for the novel coronavirus.
“That’s a 14 percent increase from the prior day,” Newsom said. “Tragically, we
now have six individuals that have passed away.”
In the press briefing,
Newsom said California has the capacity for just shy of 9,000 tests. But he
alluded to issues surrounding the availability of supplies, saying he was
worried now about access to adequate numbers of swabs for collecting patient
samples. The governor’s office declined to elaborate further during the press
briefing or afterward.
“There’s still some
capacity concerns not only on the diagnostic side on the back end with the labs
— both private, public, commercial — but as it relates to supplies,” Newsom
said. “And one must be honest about that.”
Politicians and health
officials across the country have criticized the slow rollout of U.S. testing
relative to other countries. Until the end of February, labs were barred from
using tests they created themselves without prior federal approval, even as labs across the
country discovered flaws in the CDC’s early tests.
Now, academic medical
centers in California, as well as private companies, are racing to catch up to
what is expected to be a dramatic increase in the spread of the virus.
The test itself is a
standby of molecular biology called a reverse transcriptase-polymerase chain reaction, or RT-PCR. Clinicians collect
samples by swabbing a patient’s nose and throat and send it to a lab to
extract genetic material called RNA from the swab.
The challenge is detecting
the virus in the soup of human and microbial genetic material, so lab workers
use probes that stick to parts of the virus’s genetic code and run a series of
reactions to amplify the signal. That way, if the virus is there, they’ll be
able to see it.
“The PCR is the really easy
part,” said Frances
Sladek, a professor of cell biology and toxicology as well as the
divisional dean of life sciences at UC Riverside. Freshmen who have never
touched scientific instruments learn in a lab course how to run PCR well enough
to identify species of fish from the filets at a store, Sladek said. That’s why
it’s so incomprehensible to her, she said, “that there’s any problem at all
with this.”
In addition to bureaucratic slowdowns from the federal
government, testing has been hampered by a series of technical failures. Many
of the early tests sent out by the CDC had faulty components that made it impossible to tell if a positive result was real, according to Science. The CDC did not respond
over the weekend to a request for more information about the flawed
tests.
Then, another
hold-up: Politico first reported a shortage of key ingredients needed to extract
genetic material from patient samples. “The availability of those reagents is
obviously being looked at,” CDC Director Robert Redfield told Politico. “I’m confident of the
actual test that we have, but as people begin to operationalize the test, they
realize there’s other things they need to do the test.”
Newsom publicly criticized
the test kits Thursday, calling them incomplete. “You’re going to the store and
purchasing a printer, but forgetting to purchase the ink,” he told reporters.
“I’m surprised this is not more of the national conversation.”
But the governor’s office
directed followup questions to California’s Department of Public Health, which
said questions about RNA extraction kit supplies would need to be answered by
the CDC. Neither state public health officials nor the CDC responded to
CalMatters’ questions about the number of extraction kits California expected,
or how many it received.
The bottleneck may be
coming from the CDC itself: the CDC only names RNA extraction kits from two
vendors — QIAGEN and Roche — on a webpage detailing the supplies sent to public
health laboratories. And until Sunday, CDC’s instructions for the diagnostic
test only listed QIAGEN’s kits for RNA extraction, saying that “names of
vendors or manufacturers are provided as examples of suitable product sources.
Inclusion does not imply endorsement by the Centers for Disease Control and
Prevention.”
Still, Yousef Haj-Ahmad,
president and CEO of Norgen Biotek Corp, a
Canadian Biotechnology Company that also makes RNA extraction kits, said
Norgen’s kits should have made the cut. “CDC made an error by only recommending
Qiagen; doing so created a bottle[neck] for testing,” he told CalMatters in an
email.
A Qiagen spokesperson told Reuters on Friday that Qiagen ramped up
production of its extraction kits by 70 percent, and isn’t to blame for the
testing delays in the US. Qiagen could not be reached for comment over the
weekend.
But even as medical centers
at UC San Francisco, Los Angeles, and San Diego offer in-house tests for the novel
coronavirus, they too are bracing for a shortage.
Right now UCSF is only
testing hospitalized patients, not the general public, spokeswoman Laura
Kurtzman said. And while UCSF is not currently hurting for RNA extraction
supplies, it “may encounter this as testing continues to ramp up,” Kurtzman
said. “In parallel, we are developing tests that may potentially bypass the extraction
step so would not need these chemicals.”
Farther south, UCLA Health
is testing hospitalized patients with the same test that the CDC and California
Department of Public Health are using, according to spokesman Enrique Rivero.
Citing the shortage of RNA extraction kits, Rivero said, “UCLA’s laboratory is
working to modify the CDC kits to work with other reagents.”
It’s a near-universal
challenge, Nam Tran, associate professor and senior director of
clinical pathology at UC Davis, told CalMatters on Sunday. “When every hospital
is competing for the same thing, that’s what happens — you end up being in very
short supply.”
UC Davis’s strategy is to
bring not one but three different types of tests online over the next several
weeks. One is a CDC-type test. Another runs cartridges containing samples
on a more automated device that Tran compared to
working like a video game: “You put the cartridge in, or device in, and press
start. And in an hour and a half, you get a result.” The test can run samples
from 12 patients at a time, and Tran expects it to be ready in the next
week.
The third test will take
longer to be up and running; it’s a home-grown assay that runs on an SUV-sized
piece of equipment called the cobas 6800 made by biotech company Roche. The
instrument can run 1400 tests in a day, according to Tran, which he called a
“game changer.”
Stanford, which
recently announced drive-through testing, has been running in-house
tests through its clinical virology laboratory since March 4, according
to Benjamin Pinsky, associate professor of
pathology and medicine. He couldn’t say how many tests but said the number is
increasing. The lab is testing samples from a number of hospitals including
Stanford Hospital, Lucile Packard Children’s Hospital, and Kaiser Northern
California.
“At this point, the demand
for testing and need for testing outpaces the availability of testing,” Pinsky
said. His team has also experienced shortages in key components, including some
of the Qiagen extraction kits, and is now working to validate other kits and
enzyme mixes.
“I’m really proud of
Stanford that we were a little bit ahead of the game here and we’re able to
provide this testing for the Bay Area,” Pinsky said. “I think that has really
helped patients in this area get the right care.”
Companies also are stepping
up. Quest Diagnostics has been running a lab-developed test for the novel
coronavirus at its infectious disease laboratory in Juan Capistrano since March 9. The company is rolling
out the test nationally and expects to be performing 10,000 tests per day by
the end of this week, according to a news release.
While Quest’s test does
include a step to extract genetic material from patient samples, spokeswoman
Rachel Carr told CalMatters the company has the supplies needed to perform the
tests.“It’s the largest laboratory in the world, and we have
continuous access to the reagents we need, and so right now we’re not
experiencing any shortages,” she said. “However, we’re closely monitoring our
supply continuously.”
Quest CEO Stephen Rusckowski announced the company also would incorporate a newly approved diagnostic test from biotech
company Roche. The test can run on the same cobas 6800
instrument the team at UC Davis uses, which Roche said can turn around
results in about three-and-a-half hours. “Upon authorisation Roche will have
millions of tests a month available for use on the cobas 6800 and 8800
systems,” the release said.
Of course, all the tests in
the world won’t help if healthcare workers can’t safely collect samples from
patients. Carmela Coyle, president of the
California Hospital Association, said in a state Senate budget subcommittee
meeting on Thursday that more test kits may not widen the bottleneck if another
shortage isn’t addressed, and quickly: personal protective equipment.
“We’re already short,” she
told lawmakers. Without equipment like face shields and masks that protect
health workers from infectious droplets, she’s concerned about a backlog. “That
will very quickly become a rate-limiting factor, and we’re concerned most of
the testing, as a result, will end up back in hospitals.”
In the hearing, Kat
DeBurgh, executive director of the Health Officers Association of
California, asked for help addressing yet another shortage: staff, to help
track down people who might have been exposed and follow through with
quarantine orders.
Over the past 15 years, 11
public health labs have closed in California, according to DeBurgh. And last
year, the Health Officers Association of California and the County Health
Executives Association of California requested $50 million in ongoing funding
to shore up the state’s infrastructure to address infectious diseases, she
said. “We got $40 million in one-time funding. And we can’t hire staff with
one-time funding — and staff is our greatest need.”
CalMatters.org is a nonprofit, nonpartisan media venture explaining
California policies and politics.
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