27 March 2020

COVID-19 pathology testing – your questions answered

Communicable Disease pathology

The following is a Q&A with Dr Lynette Waring, the Director of microbiology and immunoserology at Melbourne Pathology.

Q: Can you let us know what your role is in the COVID-19 response?

I am the Microbiologist in Charge of the Microbiology Department at a large private laboratory and I am integrally involved in pathology testing for COVID-19. I regularly interact with requesting doctors, both in the community and in hospitals, as well as with public health officials. Additionally, I Chair the Royal College of Pathologists of Australasia’s (RCPA) Microbiology Advisory Committee.

Q: A lot of GPs and patients really want to know… how accurate is the COVID-19 test? What is the sensitivity – so the true positive rate and what is the specificity, so the true negative rate?

The current tests which are being used in Australia are the PCR (Polymerase Chain Reaction) tests, which are a type of incredibly sensitive and specific molecular tests. The true positive and negative rate in any population, depends on the selection of the population tested and the quality of the samples. Currently, we have largely concentrated on testing individuals who have returned from countries with COVID-19, who present with symptoms of the infection. We have not tested individuals from the broader community, which would be required to understand the true positive rate of infection in our community.

Q: Why is it taking so long for COVID-19 test results to get back to patients?

As this is a new disease, pathology laboratories have introduced these new tests very rapidly. Introducing a new test is not a simple process as validation and quality control processes need to be put in place to ensure the testing is of a high quality. It often takes six to 12 months to introduce a new test, therefore the huge scientific effort that has been required in order to bring testing methods for COVID-19 onto the market has been implemented incredibly fast. For COVID-19, it has been done in a matter of weeks. For speed, quality and efficiency, most laboratories use commercially produced tests.

The Pathologists and Scientists that are involved in testing for COVID-19 are highly skilled and as there is not a huge number of such specialists available, they are an essential workforce. All pathology laboratories around the country are receiving large volumes of tests, which naturally slows the time to get results back to patients.

Laboratories also still need to provide other testing for serious, life threatening conditions other than COVID-19. This is especially increased as the colder winter months bring with them Influenza and pneumonia.

Q: Do you expect the delays in testing to increase or drop over the next few weeks?

Laboratories are working around the clock to effectively deliver high-quality testing within short timeframes as they test for and diagnose COVID-19. Pathologists are doing everything they can to minimise delays in getting results getting back to patients, including streamlining processes and working 24/7. As the numbers of cases increase in our community and therefore the number requiring testing there will be greater pressure placed on pathology laboratories.

Q: So, talk me though what happens once a swab sample is taken from a patient?

As with all pathology tests, sample and request forms have to be adequately labelled, to ensure the sample and request are both correct. These samples are transported to the laboratory and entered into the laboratory computer system. The samples for COVID-19 are separated from all other samples coming into the laboratory. The sample is sent to the Molecular Department where it is batched with other swabs. It is loaded onto the instrument once there is a sufficient number for the run, the test has been adequately assessed by that laboratory, and the viral nucleic acid (genetic material) has been extracted.

The tests use very specific probes to detect if there are any COVID-19 virus specific molecular material in the sample or not. The probes will also assess if the whole test on a particular run was performed satisfactorily.

All NATA/RCPA accredited laboratories have checks and balances in place to ensure the quality of testing is performed to a very high standard. Once a result is available, it is transferred into the laboratories computer system and is also checked to ensure it is correct, and that the whole run was performed successfully. The result is then released as an electronic report which can be sent to the referring doctor.

Q: What kind of test are you doing exactly?

There are a number of tests currently being used for COVID-19. They are PCR tests which detect the presence of the COVID-19 virus genetically. The tests are all very sensitive and highly specific, however, as this is such a new virus, all positive samples are sent for confirmatory testing.

Q: Are any pathology labs doing blood tests for COVID-19 in Australia?

A number of serology and point of Care (POCT)Antigen, IgM/A and or G tests have recently been released into the market in Australia. They are currently un-assessed as to their role in assessing the disease in our population. They may have a role later to determine patients who have had previous infection as they look at the immune response to the virus.

At this stage, we don’t know if patients become are immune from a re-infection. These tests will mainly be used to detect those people who have had the infection and recovered, not to diagnose acute infection. These Antigen tests (or antibody tests) are not able to detect viraemic patients as early as PCR tests, so should not be relied upon, as false negatives would have serious risks of falsely reassuring people and increasing spread of infection.

Q: Are your labs being overloaded?

There has been a huge influx of testing, however, laboratories are doing everything possible to minimise delays. Dedicated laboratory staff, couriers and collectors are all working hard to ensure that laboratories have the support needed for this public health emergency. One of the most important factors is to ensure the health of the staff in the laboratories, as there are only a finite number of appropriately trained staff to do this work.

Q: Are staff working longer hours than normal?

Yes, laboratories are working around the clock, including over the weekends and public holidays to provide accurate, reliable testing within a short time frame.

Q: Have you hired or trained more people to do the tests? Is that possible in this short timeframe? Do you have to be highly trained?

Laboratories are doing everything possible to provide quick results, including hiring additional staff, if available. The Pathologists and Scientists performing these tests are highly skilled and already in short supply, both in Australia and internationally.

Q: What kind of equipment do you need to do the test? Is it expensive? Are there many of these machines in Australia?

The machines are highly specialised, however there is a large range of them. Some can be quite large and expensive, and they differ in terms of availability, capacity and speed, and their ability to transfer results into the laboratory computer system.

Q: Can you comment on the reagents that Australia is low on? Will be be able to re-stock? What is the impact of these shortages?

At present, the Federal Government has been able to source additional test kits for many of the required reagents.

The Royal College of Pathologists of Australasia (RCPA) endorses the strict use of the Communicable Diseases Network Australia (CDNA) National Guidelines when deciding whether to refer a patient for a COVID-19 pathology test. This approach will assist in the effective management of increased demands on pathologists and laboratories, ensuring that resources are allocated appropriately.

The guidelines for COVID-19 testing have been endorsed by the Australian Health Protection Principal Committee and recommend testing only where a patient meets both the current epidemiological and clinical criteria.

Q: How much does the test cost?

The cost of the test alone is just one component of the overall cost. The labour required for all the components involved in testing is often the highest cost, however, some of the instruments and their kits are also very expensive.

Q: Is it possible to scale up your activities? What are the limiting factors?

There were no tests for this newly discovered virus in late January, therefore it is incredible that there are now commercial kits available for wide use by the global population. This is as a vital part of incubating this pandemic. Laboratories have had to upscale on a large scale already, from doing no tests to up to over 1,000 per day, in some cases.

Turn-around times for pathology tests can vary between laboratories and there are two groups of factors to consider. Firstly, there are the factors within each laboratory which can include, workloads, testing methods and staffing levels. Secondly, particularly in a country as sparsely populated as Australia, are those factors outside the laboratory. These include factors, such as, the time taken between specimen collection and delivery of the specimen to the laboratory for testing. Additionally, the overall large volume of testing will also have an impact on turn-around times in both of these areas.

Q: Are you trying to come up with more streamlined processes for getting the results out?

Yes, laboratories are always looking at how they can stream-line processes.

Q: I’ve heard that labs are prioritising sharing results with COVID-19 positive patients. That sort of makes sense. But that leaves negative patients waiting. Can you talk me through the logic of that?

In this current early stage of the pandemic, the vast majority of results are negative. If there is a positive result, laboratories would generally ring the treating doctor as well as the health department to advise the result. This is so they can check if the patient has adequately self-quarantined, and importantly, so contact tracing can commence.

Negative results are predominantly in the majority, therefore, are predominantly returned electronically. The referring physician should advise the patient that if they are at high risk, but have few or no symptoms, a negative result does not rule out COVID-19. The patient should therefore continue any appropriate recommended quarantine.

Q: I saw that some patients were getting test results back via text. Is that coming from the pathology labs?

Some laboratories may be able to offer this service however, this software is not universally available, or quick or easy to set up.

Q: How many labs in NSW are doing the COVID-19 test now? Has that number been increasing?

Initially only the public laboratories were providing testing, however private laboratories are now also offering testing. This is also happening in other states.

I’ve seen some drive-thru COVID-19 testing clinics happening overseas, where the car acts like an isolation unit and the person just winds down their window to get a throat swab. Is that viable in Australia?

These drive through clinics provide collection of the sample only, not the actual testing. This is already being done in some areas of Australia.

Q: What about at-home testing? Is that possible?

At home testing is not available, however, self-collection may be possible for some patients.

Pathologists and Scientists play an incredibly critical role in healthcare, now even more so than ever. Laboratories are working around the clock to effectively deliver high-quality testing within short time frames as they test for and diagnose COVID-19.

Q: How do they know if a person has been cleared of the virus? Are there tests to check for seroconversion as a sign of viral clearance?

No, currently it is a repeat of the original swab, however, due to the limited availability of tests, it is now not recommended.

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