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What actually happens during a coronavirus test?

NEW YORK — You have a fever. You’re in respiratory distress. And you might even be hospitalized with pneumonia. Doctors worry you may have been infected with the novel coronavirus. What happens next?

Ideally, you’ll be tested for the virus, which has sickened tens of thousands of people worldwide and killed more than 3,000.

While US health officials originally restricted coronavirus testing to only the sickest patients, Vice President Mike Pence announced on Tuesday that any American — with a doctor’s order — should soon be able to access the tests.

Questions remain over whether the US can meet a possible surge in testing demand, but those who are able to get tested can expect a fairly straightforward, and maybe even familiar, process.

You’ll be swabbed

Testing for the new coronavirus isn’t all that different from testing for the flu. First, doctors need to collect a specimen — a sample that will be checked for the virus.

Health experts think the coronavirus replicates in the respiratory tract, causing respiratory illness, so the US Centers for Disease Control and Prevention recommends that clinicians swab your throat, going through both your mouth and your nose. People with “wet” coughs may also be asked to cough up sputum, a mixture of saliva and mucous.

It’s unlikely that other bodily fluids will be tested, said Dr. David Hooper, chief of the Infection Control Unit at Massachusetts General Hospital. Because the illness so far has been flu-like and concentrated in the lungs, “they’re probably not routinely testing for other types of body materials, such as stool or urine or blood. Although that may change in the future.”

Your specimen will be sent to a qualified lab

Once a sample has been collected and stored in a sterile tube or vial, it’s sent to a lab that has access to a test kit. Most of these kits are provided by the CDC, but New York has received emergency authorization from the US Food and Drug Administration for its own test. The process might look different for commercial tests that may be available soon.

In the FDA-authorized tests, specimens are first chilled and shipped with an ice pack to a qualified lab, ideally using overnight shipping. In Massachusetts, which has reported two coronavirus cases, state health officials arrange for the packing and shipping of samples by courier. That usually allows for same-day testing, according to Ann Scales, a spokesperson for the Massachusetts Department of Public Health.

Chilled specimens can only be stored for 72 hours, but dry ice can be used to preserve the sample if delays are expected. Waiting too long may allow the virus and its genetic material to degrade, however, which could lead to a false negative.

In New York, samples can be sent to the state’s Wadsworth Center or the NYC Department of Health and Mental Hygiene, and the state hopes to soon perform up to 1,000 tests a day, according to Gov. Andrew Cuomo.

Your sample will be tested

Once samples arrive at a lab, technicians use a procedure called RT-PCR, or reverse transcriptase polymerase chain reaction, to look for the coronavirus. A similar test is sometimes used to identify the flu, and it allows clinicians to see whether a certain genetic sequence is present in a specimen — such as the throat swab or sputum sample collected earlier.

Just like how every species has unique DNA, every virus has a unique genetic code. This code, called the viral genome, provides the blueprint for the virus as it replicates. Essentially, the coronavirus test works by determining whether any given specimen contains the distinct coronavirus genome.

To do that, technicians first extract any genetic information from the throat swabs and sputum samples. The purified genetic material is then mixed with a set of ingredients, including some derived from the coronavirus itself, and the entire solution is placed into a testing machine.

If a patient’s specimen contains coronavirus, then the virus’s genetic material will be amplified, and the machine will return a positive result. The viral sample will then be sent to the CDC’s own lab in Atlanta, where the positive result will be confirmed.

How long does the test take?

Once a sample arrives at a state lab, test results can be available in as little as 24 hours, according to the Massachusetts Department of Public Health. That’s important, said Hooper, because patients can be kept in isolation while awaiting coronavirus test results.

“When only the CDC was doing [tests] in the US,” he said, “we would wait three days, or four, to get a result, which is obviously problematic if you have a patient in the hospital.”

Individual hospitals are also working to develop their own tests, Hooper said, which “hopefully can be validated by the FDA under their emergency use protocol, and that would add to our capacity and would shorten turnaround time even further, so that we could potentially get a result within a couple of hours.”

What can go wrong?

Because the test looks for viral genetic material in a swab or sputum sample, the quality of a specimen is critical, said Hooper. “How much virus the patient actually is shedding, or is in the site that’s sampled” also matters, he said.

A patient may shed more of the virus later in the infection than earlier, said Hooper, and the virus could have a greater affinity for certain parts of the respiratory tract. If the virus is drawn toward the lower respiratory tract, for example, then a throat swab may be less effective than a sputum sample.

It’s also possible, Hooper said, that some people with the virus haven’t been tested given the CDC’s stringent testing criteria thus far. Coupled with limited testing capacity, clinicians have had to “prioritize the sickest and those in the hospital setting,” he said.

But if enough tests were available, there would be “persons with exposure risks whom we would want to test even if they had few or no symptoms,” said Hooper.

That’s important not only for “public health reasons, but also to understand better what proportion of patients may shed virus before or even without symptoms altogether.”

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