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https://www.sciencemag.org/news/2020/03/standard-coronavirus-test-if-available-works-well-can-new-diagnostics-help-pandemic#

As the United States races to ramp up testing for the pandemic coronavirus using technology based on the tried-and-true polymerase chain reaction (PCR), alternative approaches are beginning to roll out that could make it easier and quicker for people to learn whether they have been infected.

Some methods modify the standard PCR test, which amplifies tiny bits of genetic material to enable detection, whereas others sequence the virus directly or use the genome editor CRISPR.

Faster and cheaper tests are coming, says Evan Jones, CEO of OpGen, a rapid diagnostics company. However, he adds, developing new kinds of tests is “going to take time.”

Some of the new tests are coming online now, but others will likely take months to validate and ready for widespread distribution.

“Testing, testing, testing” has been the mantra repeated again and again by World Health Organization Director-General Tedros Adhanom Ghebreyesus.

Diagnostic assays that identify active infections in people are vitally important for public health efforts, not just for individuals’ health concerns.

Widespread diagnostic testing, along with isolation of the infected, contact tracing, and quarantining of those contacts, seems to have been key in South Korea’s work to suppress virus spread.


In the United States, the slow rollout of coronavirus PCR tests has been widely attributed to a combination of stringent rules aimed at ensuring their reliability and a complex web of companies and health care systems responsible for developing, carrying out, and paying for tests.

The Trump administration says testing is accelerating.

On 16 March, at a White House press conference, U.S. Health and Human Services Assistant Secretary for Health Brett Giroir said the country would be able to process 1 million tests by the end of the week, and 2 million the following week.

But the actual numbers aren’t close to that yet. According to data compiled by the COVID Tracking Project, a nonprofit collaboration of public health officials and journalists counting tests given in the United States, 191,541 PCR diagnostics have been performed as of 22 March, with 24,345 of them positive for the virus.

On 29 February, the U.S. Food and Drug Administration (FDA) posted new rules to allow for emergency use authorizations of coronavirus tests beyond the ones being made and distributed by the U.S. Centers for Disease Control and Prevention. Academic virology labs, public health departments, and companies sprang to work creating their own PCR tests. Today, some four dozen organizations have received FDA approval for their tests.

Among the largest are diagnostic companies, such as Roche Molecular Systems, which received FDA’s green light for its test this week. It will initially supply some 400,000 tests per week in the United States and 3 million globally, according to Alexandra Valsamakis, the company’s chief medical officer. Other large companies have recently gained approval for their tests as well, including Thermo Fisher Scientific and Abbott Laboratories.

University virology labs have also leaped into the breach to help diagnose cases in their vicinity. This past week, for example, doctors at the University of Pittsburgh Medical Center (UPMC) began to use a homemade PCR test to check for infection in Allegheny county.

For now, its number of tests remains small, about 100 per week. “We definitely wished we had started it sooner,” says Alan Wells, who heads UPMC’s clinical laboratories.

PCR is the most commonly used test for diagnosing coronavirus because it’s highly accurate. (See How does the most common coronavirus test work?) But other problems limit it.

“It’s not getting the turnaround we need,” says Steven Wolinsky, an infectious diseases physician at Northwestern University.

Each test takes about 4 hours once a sample reaches a centralized testing lab, with the time split between sample preparation and the actual PCR test.

With transport and queues, getting a result can take 2 to 4 days.

In that time, infected people may spread the virus to many others.

Self-swabbing
Another new dimension is now being added to the coronavirus diagnostic landscape: “home” tests, which involve mailing a sample taken at home to a lab. Tomorrow, for example, Everlywell expects to begin to ship kits to homes and retail pharmacies.

These tests will start with screening questions, either online or at a retailer, to determine whether a person is likely to have been exposed to the virus. If they are, they can receive a nasopharyngeal sampling kit by mail or can buy one from a local retailer.

A person will be given detailed instructions to administer their own swab, insert it into a protective vial, and overnight mail it to one of dozens of diagnostic labs (which partnered with Everlywell and already have FDA approval) for PCR analysis.

Frank Ong, Everlywell’s chief medical and scientific officer, says the company expects to quickly ramp up from offering thousands of such tests per day to tens of thousands.

Although each test will still likely require a 4-day wait for results, Ong says, this home sampling strategy carries major benefits:

It will protect health care workers from exposure to potential infection and free up their time.

“We need to make sure we give them the bandwidth to take care of patients,” Ong says. Other companies, including Nurx and Carbon Health, say they’re now shipping limited supplies of their own home sampling kits.

Most PCR tests for the new virus are being done with big, expensive automated machines that do many tests at once. Major hospitals or diagnostic facilities have them, but another option beginning to roll out now is smaller, less expensive devices that also do nucleic acid amplification.

These could be used by smaller hospitals and even individual doctor’s offices.

On Friday, for example, Cepheid, which sells small PCR systems for rapidly detecting influenza viruses, tuberculosis bacteria, and other microbes, received FDA emergency use approval for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) test cartridge that slots into the company’s GenXpert system, a device the size of espresso machine that can produce a diagnostic result in as little as 45 minutes.

Cepheid officials say that 23,000 such systems are in place worldwide, with 5000 in the United States.

On 19 March, GenMark received FDA emergency use approval for its own coronavirus tests, which run on similar-size machines that use a proprietary electrochemical approach to detect target genetic material in less than 2 hours.

Other companies rushing to deliver point-of-care diagnostic machines include Mesa Biotech, HiberGene, Mobidiag, and QuantuMDx.

So, too, are companies such as Oxford Nanopore and Fulgent Genetics, which instead of using PCR directly sequence any genetic material in a sample and then look for matches to, say, the new coronavirus.

This high-speed gene sequencing approach could help characterize the coronavirus’ genome to better understand how the virus is evolving,
but it could also be a diagnostic in certain situations,
such as remote sites without access to PCR.

Oxford Nanopore’s handheld devices have been used in Ebola outbreaks, and the company sent many to China early in the pandemic.

CRISPR for testing
The fastest way to test for the coronavirus may ultimately be offered
by companies using the CRISPR genome editor,
better known for adding or deleting DNA in cells.

Two U.S. companies, Mammoth Biosciences and Sherlock Biosciences,
say they have created CRISPR-based tests and are in the process of validating them with patient samples before seeking emergency use approval by FDA. The technique starts with a patient sample, extracts viral RNA, and uses a fast nucleic acid amplification test called loop-mediated amplification to make just enough RNA for the test to detect.

Researchers then add two components of a CRISPR genome editor,
a protein called CAS12 that cuts DNA or RNA and a “guide” RNA that
slots into CAS12 and helps it search out a sequence corresponding to a piece of the coronavirus genome.

If CAS12 and its guide find a match in the RNA, CAS12 binds to that matched RNA, which activates CAS12 to cut it and go on to cut any other short RNA or DNA strands in the vicinity, including copies of a strand designed to liberate color-changing molecules when CAS12 cuts them free.

The upshot can be a simple color change on a test strip.

The technique excels at hunting for small snippets of genetic material, says Jennifer Doudna, a biochemist at the University of California (UC), Berkeley, a CRISPR pioneer, who is chair of Mammoth Biosciences’s science advisory board.

In a preprint posted 10 March on medRxiv, researchers at Mammoth Biosciences and UC San Francisco report that tests on clinical samples produced results with accuracy rates comparable to PCR in just 30 minutes. It uses a simple paperlike strip with a colored line that appears with a positive result.

The company is discussing with partners manufacturing test kits that would allow rapid and cheap diagnosis of SARS-CoV-2 infection at home without requiring medical know-how, says Trevor Martin, Mammoth’s CEO.

It may take months to finalize the test and get regulatory approval
for it, so it likely won’t be ready in the crucial weeks ahead.

But it could be ready if the spread of the coronavirus continues.

Some predict the virus will also recede but then have a resurgence
of infections in the fall.

Getting results wouldn’t require PCR machines operated by trained technicians, Martin says. “It would be a game changer for our response” to emerging diseases, Martin says.

Supply problems
Even as companies and academic labs are scaling up their PCR-based diagnostic efforts, hospitals and testing sites around the country report that they are facing a more immediate crunch:

Many are running out of chemicals and other materials that enable the tests, such as the swabs to collect samples from patients and the reagents needed by PCR.

Benjamin Pinsky, a Stanford University pathologist who developed a
PCR-based diagnostic test in use in Northern California,
says his lab is facing rolling shortages of different supplies,
most notably the kits used to extract RNA from viral samples,
before it can be loaded into PCR machines.

“This has been a big challenge,” Pinsky says. “We’ve had to be very nimble in dealing with this,” constantly switching suppliers or even chemical procedures, which must be validated before they can be used on patient samples.

His team has even sent pleas over Twitter to the Stanford community and regional biotech companies calling for donations of reagent assemblies, such as kits from Zymo and Qiagen.

And even though donations have been pouring in, supplies are still running short, Pinsky says.

Reagent companies are trying to respond. For example,
Qiagen, a major supplier of RNA extraction kits, announced Tuesday that its employees are working around the clock to increase production from 1.5 million kits per month to 6.5 million per month by the end of April and further increases later.

Pinsky, for one, says he’s ready for companies to take over
coronavirus testing entirely from academics such as himself.

“I’m hopeful these companies will be able to provide the testing they have promised,” Pinsky says. “That remains to be seen.”


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RELATED STORY
How does the most common coronavirus test work?
By Robert F. Service

For diagnosing SARS-CoV-2, a PCR test starts with a nasopharyngeal swab, which looks like a long Q-tip that draws mucus from the back of a patient’s nasal cavity where it meets the throat. This swab goes in a vial and is shipped to an FDA-approved central lab facility. There, technicians use reagents to extract any viral RNA.

An enzyme called reverse transcriptase converts the RNA to a complementary sequence of DNA, which can be replicated many times over to make it easy to detect. To accomplish this replication and detection, technicians—or automated machines, in most cases—add additional reagents that include a pair of “primers” that contain copies of pieces of DNA matched to the virus’ genetic code, a DNA copying enzyme called polymerase, fluorescent reporter probes bound to small DNA strands matched to sections of the viral genome near those targeted by the primers, and free nucleotides that the enzyme uses to copy DNA.

A PCR machine raises the temperature, causing the two strands of DNA helixes to separate into single strands.

The temperature is then lowered, allowing primers and reporter strands to bind to corresponding sequences on the single strands.

The temperature is then raised to an intermediate level,
encouraging the polymerase enzyme to latch on where a primer bound
to a strand of DNA.

The enzyme moves along the strand, adding complementary nucleotides until the strand is copied.

When the polymerase reaches the reporter sequence, a fluorescent
probe is released, creating an optical signal that the strand was copied.

The cycle then repeats,
turning two target strands into four, then eight, and so on.

After about 40 cycles there are roughly 100 billion copies of the
target DNA and an easily detectible fluorescent signal.

“PCR has high sensitivity and selectivity,” which means it correctly spots almost all the positive cases and correctly rules out almost
all the not-infected cases, says Steven Wolinsky,
an infectious diseases physician at Northwestern University.

“That makes PCR a really good diagnostic test.”

Posted in: HealthCoronavirus
doi:10.1126/science.abb8400

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