Ask the Lab Scientist – Answers to your questions concerning testing for the novel coronavirus

Dr. Susan Leclair answers your questions concerning testing for the novel coronavirus.

1. Who should be tested for the novel coronavirus?

These directions will probably continue to change as we learn more about the virus and its pattern of spread. But, as of this moment (March 16, 5:00pm EDT), if you have symptoms of COVID19 (fever, dry cough, shortness of breath, and anecdotally a few people have described bone and muscle pain similar to the aftereffects of a strenuous workout), you should contact your physician. Call or email before you visit the office.

Do not wait around to see if things get worse – difficulty in breathing, persistent chest discomfort, confusion or sleepiness, bluish coloration to face or lips, etc. Contact your physician immediately.

2. How do you test for SARS CoV-2?

That depends. China developed a test, based on the ORF1 antibody and the nucleoprotein of the virus. Germany developed a test based on the RdRP,E,N (physical components of the virus). Japan developed a test on the Spike protein (things ticking out when you see the artist’s rendition). The CDC developed a test based on three targets of the nucleoprotein gene in the virus. What all that techie gobbledygook means is that there are multiple versions of the test out there. Some test for all coronaviruses, while others test for certain components of SARS and COVID19, and others test for something else.

What we don’t know about the non-US tests is their false positive/false negative rates, stability when transported from the manufacturing site, required skill level of personnel, and physical environment of the laboratory doing the test.

Having bored you with that, in essence, these tests are similar to the DNA testing one uses for forensic/legal cases.

3. How and from where are the samples collected?

CDC currently calls for the collection of fluids with one nasopharyngeal (nose) swab and an optional oropharyngeal (throat) swab. There is no specific time nor are there any restrictions, such as fasting.

4. Are there special precautions to make sure the sample is collected correctly?

Oh my, yes. The nasopharyngeal swab should be inserted only by someone who has been trained to do so.   For example, the swab cannot touch the side of the nostril. The same is true for the throat swab. For example, the swab cannot touch the tongue, mouth, hard palate and uvula (the thing that hangs down the back of your mouth). If the specimen is poor in quality, then it is possible that the test result might not be correct.

5. What exactly is the test looking for?

If we are talking about the test that was designed by CDC, then we are looking for specific proteins which are products unique to this virus – the N gene.

6. Why is there a delay in getting results?

For the same reason that all genetic tests are “delayed”. The test itself takes time – if done manually, about a full day to a day and a half. The high throughput instruments people are talking about allows you to perform a large number of tests at the same time, but still with that day’s timeframe. Using a very broad brush, the viruses must be removed from the swab and then stimulated to replicate the genetic material until there is a large enough volume to assay. Then, the viral material is combined with compounds that structurally are highly specific to the materials you are seeking. The next step is to separate all of the other compounds from the bound virus material. Once that is done, the material is quantified. Then, finally, the results are interpreted by a clinical laboratory scientist and the results released to your physician.

7. How reliable and sensitive is the test?

In general, a RT transcriptase assay can detect 20 picograms of materials or put another way 1 picogram is 1/1,000,000,000,000 of a gram, and you need 2200 of these grams to make up a pound.  So – really, really sensitive.

These tests are usually extremely reliable. However, since this is an important topic these days, the use of the confirmatory process, with the same or better sensitivity, is key. If both assays result in the same answer, then it is near to impossible for the interpretation to be incorrect.

8. Do the results depend on the source of the specimen? The stage of the illness?

It is the quality of the specimen that matters. If, for example, the “throat” swab was truly a “roof of mouth” swab, then the results might be negative since the swab did not touch the area of the body where the virus is located.  The route for upper respiratory viruses is from the nose/throat to the lungs, so that is the reason both are recommended.

As to stage of illness, this is very much an issue. Supposing a person is infected on Tuesday. On Wednesday, that person has a specimen collected. There has been insufficient time for the virus to increase in number to the point of triggering a positive result in the test.  This then gives the person a false sense of security. They believe that they are not infected when in fact, they will shortly become symptomatic.

9. Will the test tell me when I have recovered?

The test which is currently being used cannot tell you that. In order to prove recovery, you need to test for the presence of antibodies which you have formed. Everyone is concentrating on making, distributing, and using the primary test for the presence of the virus.

I suspect that recovery is now being determined by the change in signs and symptoms.

10. Why is there such a shortage of tests in the USA?

This is a much more complicated question.  According to their website, CDC is responsible for controlling the introduction and spread of infectious diseases and provides consultation and assistance to other nations and international agencies to assist in improving their disease prevention and control, environmental health, and health promotion activities. Again, from their website, CDC laboratory scientists work across the U.S. on a range of critical work, including research, surveillance, and reference diagnostic testing.  By reference, diagnostic testing has typically meant providing more sophisticated testing than what is possible in a hospital laboratory.  They also use laboratory testing in their control of, say, food borne illnesses. For example, they were involved in finding out the source of the recent hepatitis A outbreak in Florida.  Over the years, they have expanded into determining the future possibilities of influenza types in order to prepare future immunizations.

What is important to note here is that they have never been set up for hundreds or thousands of specimens to arrive for the same testing. Most of the food borne illnesses, for example the recent Listeria outbreak, are limited in both number and scope.

In recent years, the CDC has experienced budget cuts and this too has had an impact on the scope of their work. They should be congratulated for the efficiency with which they created the test. That test was subsequently given to test manufacturers for free.

Physician Interactions:

Many physicians have the capability of using telemedicine, opting for the choice of a local laboratory or clinic. This should be the go-to first step. As the professional staff at all facilities become more accustomed to the workload and the changing environment, there may be more opportunities for face to face discussion. But, and this is most important, if you believe that you need clinical attention, contact your physician – first by phone or email.

As a general rule for now, telemedicine would be the preferred option (with local labs if needed). It is important to remember that this is an ever-evolving environment and institutions are actively developing plans to respond to the needs of their patients.