COVID-19


Also known as: Coronavirus
Last Review Date: September 2, 2020


Who is being tested?
The recent increases in community transmission in Victoria and NSW have seen an upsurge in testing in those two states.  Queensland is also running pop-up testing facilities along the road from the NSW border. Across Australia, anyone with symptoms no matter how mild is being urged to get tests and isolate themselves until they have their results.
 
What will happen if I am tested?
Some samples will be collected. This will usually take place in a pop-up testing facility or a special drive-through service, a respiratory or fever clinic, a designated pathology collection centre, or a hospital.

The samples will be:
Nose (nasopharyngeal) swab
This is the most common way of being tested. A swab is carefully inserted into your nose (both sides) to pick up samples of mucus.
 
Throat (oropharyngeal) swab
This will take samples from around the tonsils and the back of your throat.
 
These swabs will be placed in a tube and sent to the lab for testing.
 
Saliva Test
This is being trialled by researchers in Victoria.
 
Sputum
Depending on your situation, you may be asked to rinse out your mouth with clean water and then cough deeply into a sterile container. Sputum comes from the lungs and is not the same as the spit in your mouth.
 
Bronchoalveolar lavage
If you are in hospital, your doctors may decide to take samples from your lower lungs. In some people, the virus cannot be detected from samples taken from the nose or throat, or through sputum. This type of collection is performed using a bronchoscope. This will be done using local anaesthetic.
 
Blood test
A blood test may be taken so that a serology test for COVID-19 can be performed if one is being used in conjunction with your diagnostic test.  A serology test looks for the antibodies that your immune system produces in response to the infection.

Antibody testing
Antibody testing looks for the antibodies your body makes to the virus. They cannot accurately detect infection that has been recently acquired and should only be used in assessing whether someone has previously been infected and has developed an immune response.  Many home test kits are being imported into Australia, mostly from China, and they do not give accurate results. They pose a serious risk to public health.
 
Given the limitations and risks associated with these tests, federal and state government health ministers have issued warnings and some have banned their use as a diagnostic test by everyone including health professionals and for the screening of staff for work purposes.
 
What test is being used?
 The test for SARS-CoV-2 – the virus that causes COVID-19 – detects genetic material from the virus. It uses PCR – a technology that amplifies the genes so that they can be detected.  There are several different types of these tests being used.
 
The test looks for specific SARS-CoV-2 genetic material.  An initial screening test may be positive because of the presence of other, non SARS CoV-2 coronaviruses.  If your sample tests positive a further test for another target gene from the virus will be used to confirm it.  
 
Your samples may also be tested for flu and other respiratory viruses so that your doctors can rule them out.

How long will it take to get the results?
The process for receiving COVID-19 test results differs between states and territories and between public and private laboratories.  See section Accessing your COVID-19 Test Results for details
 
If I think I need to be tested, what should I do?
If you think you need testing call your doctor or phone your state or territory COVID-19 helpline.   If you have any doubts or questions, there is a national hotline at 1800 020 080. 
 
You will be asked to take precautions when you attend for treatment. Follow the instructions you are given.
 
Stay at least 1.5 metres away from other people. Cover your coughs or sneezes with your elbow.
 
Tell the person collecting your sample about:
  • your symptoms
  • any travel history
  • any recent contact with someone who has COVID-19  
 
How much will it cost?
There is a Medicare rebate to cover the cost of COVID-19 testing.

 

The National Coronavirus Helpline

Lab Tests OnlineAU  information partner, Healthdirect Australia, has worked with the Department of Health to establish the National Coronavirus Health Information Line to provide information about COVID-19. 
          
                                        Corona-virus-hotline-(1).jpg                  


The Symptom Checker

The Symptom Checker is an online self-guided tool to help people find out if they need to seek medical help.  It includes questions about travel history, contact with known cases and the clinical symptoms associated with COVID-19, including fever, sore throat, cough and shortness of breath and provides people with advice on what they should do next, such as calling ahead before a visit to a GP, emergency department, or COVID-19 testing clinics.

                                        covid-button2-0746fd.png 

 
COVID-19 testing – what’s happening now and new developments

Around the world the main type of test being used to detect the coronavirus that causes COVID-19 is called RT-PCR – the reverse-transcriptase polymerase chain reaction.  This type of testing for the genetic material of viruses and other microbes has come into common use only in recent years.

Other types of tests are in development and some starting to be used, most notably serology tests. Serology tests detect the antibodies your immune system makes to an infection. Some of these antibodies stay in your blood for months and years. This type of testing is quick to perform, sometimes using just a finger prick blood sample and a small test kit that can be used anywhere. When this type of testing is automated it allows us to test thousands of people. It will be most useful in allowing us to see the true scale of the COVID-19 epidemic.  We will be able to see how many people have had the virus to help us understand how much immunity we have as a community.

RT-PCR testing and how it works
The coronavirus is made up of a genetic material called RNA which is surrounded by proteins and lipids (fats). When the virus enters your cells it uses RNA to replicate itself.

PCR testing detects DNA.  This means that the first step in the testing process is to convert the viral RNA into DNA using the enzyme reverse transcriptase. Once this is done chemicals are used to amplify the DNA so it can be read by the PCR instrument. Hence the name RT-PCR.

The test measures the amount of the virus’s genetic material in the sample.  Usually, the sample will be a nasal and throat swab but can also be sputum or fluids collected from deeper in the lungs.
 
The RT-PCR test can only tell whether the person has live or very recently dead virus in their body at the time of sample collection.

When the person recovers from the infection the results of a RT-PCR test quickly become negative.
 

Serology – a different type of test

Serology tests are different from the RT-PCR test. Instead of measuring genetic material from the actual virus, they measure your body’s response to being infected by the virus.  Serology tests have been used for many years to detect infectious diseases. Serology tests for the coronavirus that causes COVID-19 are being rushed into development with tests already in use in some countries around the world. Several have just been approved for use in Australia and may be available for testing patients in the near future.

How serology testing works

A key step in the human immune system’s response to infection is the production of antibodies to the infection. These antibodies are proteins produced by blood cells called lymphocytes. Antibodies are produced specifically against the virus. They bind very tightly to the virus to help deactivate it so that the body can get rid of it. The body stimulates the lymphocytes to multiply until there are enough of them to produce large quantities of specific antibodies against the virus.

The first type of antibody produced is called IgM and this may appear within days of the initial infection. IgM antibodies typically fade away a few months after the infection but sometimes they persist for longer. Other types of antibodies produced are IgG, and in respiratory infections like coronavirus, IgA.

IgG antibodies usually stay around in the bloodstream much longer after you have recovered – for years or even life-long.
 

What the results can show

The antibody tests recently approved for use in Australia can measure both IgM and IgG anti-coronavirus antibodies. 

If your test results show IgM anti-coronavirus antibodies, it suggests that you have a current or recent infection. If both IgM and IgG are present this means much the same thing. However, if only IgG is present this suggests that you have had an infection at some time in the past and may be immune to further infection by this coronavirus. However, it is not yet certain that people who have been infected will develop immunity to reinfection. This should become clearer in coming months.

The ways that serology testing can be used

Using an antibody test to detect an active infection

Currently, diagnosis of active infection with the virus causing COVID-19 is done with the RT-PCR test. IgM serology tests have the potential to be used to make the diagnosis of a current infection. However, data provided by the companies supplying the new antibody tests show they vary in how soon patients show positive results. This may range between 5 and 10 days after symptoms appear before IgM antibodies can be detected. This means that the currently available serology tests are not really useful for diagnosis in a person with very recent onset of symptoms and the RT-PCR test is required in this case.

Using an antibody test to detect past infection and measure community immunity

IgG serology tests are extremely useful for assessing whether someone has previously been infected and developed an immune response to COVID-19. If this immune response protects someone from being reinfected then this can be used in several ways. If health authorities discover that a large proportion of the population has already developed immunity this can help them predict the likely course of the epidemic. If most schoolchildren are discovered to be IgG positive and hence immune, this could possibly inform decisions on closing or reopening schools.

If a healthcare worker knows that they are now immune to COVID-19 they might be able to be deployed to work in frontline caring positions without risk of becoming infected. It may even be possible to harvest antibodies from people with very high levels and use them as a therapeutic drug to treat critically ill patients.

Quick and easy to perform

These immunoassay antibody tests have some other advantages. They are usually simpler to perform than RT-PCR tests. Some antibody tests in development can be done on a fingerprick blood sample. Currently, tests of this type cannot be sold to consumers at home but could be used in workplaces under supervision. Antibody tests are also likely to be cheaper than RT-PCR tests and large numbers of tests may be automated and thus have a faster turnaround time. The test may require simpler instruments to carry them out so that the testing equipment can be available in more laboratories than those with the required facilities for PCR testing. One concern is the potential for false-positive test results. Many people will have been exposed to other less dangerous coronaviruses . Preliminary data from manufacturers and some labs indicate that this may not be a major problem but we need more data to be certain for each commercially available test.

Different types of tests for COVID-19 are in the pipeline

Many organisations, universities and companies are currently working on developing new tests for the virus causing COVID-19. These will probably include tests that use different methodology from both RT-PCR and serology. Some companies are working on tests that detect viral components such as proteins, nucleic acids or combinations of these in patient samples directly without an amplification step or with newer types of amplification technology that require simpler instruments. This is a rapidly changing area and as data becomes available on these tests LTOAU will try to keep you up to date as more tests become available.

A list of approved COVID-19 tests is available on the TGA website.





 

Testing for SARS-CoV-2 has two main goals.

The first is diagnostic testing in patients with acute symptoms. The question being asked here is: Are the symptoms in this patient due to COVID-19 or something else? This is the most important question in the early stages of this pandemic.

The second type of testing is designed to answer the question: Has this person been exposed to SARS-CoV-2 and developed an immune response? Can they be removed from isolation and permitted to go back to work/school etc? Is the community developing herd immunity? These questions are becoming increasingly important as we move to the next phase of the pandemic. And there is a pressing need for answers.
 
Stage 1: Diagnostic testing
RT-PCR – the reverse-transcriptase polymerase chain reaction. 
In Australia, and around the world, the main type of test being used to detect the coronavirus that causes COVID-19 is called RT-PCR – the reverse-transcriptase polymerase chain reaction. 

This type of testing for the genetic material of viruses and other microbes has come into common use only in recent years. Tests for a wide variety of pathogens are available.

Laboratories around Australia use a number of different RT-PCR testing platforms. However, they require sophisticated instruments and highly trained staff and so are only available in larger labs with the expertise to perform them. They are relatively expensive and take several hours to produce a result.

A significant advantage of RT-PCR tests is that they can be multiplexed – designed to test for several respiratory pathogens at the same time. Typically, these tests use several sets of probes to amplify several different parts of the viral genome and include a positive control set of probes to ensure the sample is adequate and the test performed to specification.

The tests vary in specificity and some require confirmation of positive results by a second more specific test. Very recent data from China suggest that RT-PCR may have a higher fase-negative rate than currently thought mainly due to difficulty in obtaining adequate specimens from the right anatomical sites. When serological tests (see below) become widely available we will be able to see if this is correct.

A new version of RT-PCR test called the Cepheid Xpert® Xpress SARS-CoV-2 has been approved and is being rolled out in sites in Australia. This is both simpler and faster than most other RT-PCR tests and can be used outside main laboratory settings.

There are other types of test that can also be used for diagnostic purposes in people with acute symptoms of COVID-19 but none of these are available in Australia yet.
 
RT-LAMP – reverse transcriptase loop-mediated isothermal amplification.
One of the most advanced of these is another type of amplification technology called RT-LAMP – reverse transcriptase loop-mediated isothermal amplification.

The Abbott ID NOW™ COVID-19 test has been approved for use in the US and some laboratories in Australia already have the ID NOW instruments and are using them for testing for other respiratory pathogens such as influenza and RSV.

These instruments are small, simple to operate and give very rapid test results e.g. COVID-19 positive test results in less than 10 minutes. However, they are not easily multiplexed so they can only assay for one pathogen at a time.

A problem for Australia is going to be that demand for the instruments and test kits in the US will be very high and Abbott may not be able to produce enough to export them at this stage of the pandemic.

Furthermore, the Abbott ID NOW COVID-19 test is not yet on the TGA list of approved tests. Other companies are also developing RT-LAMP tests for COVID-19 but none are available yet for use in Australia.

Other new diagnostic tests on the way
Other types of diagnostic tests are in development. Two companies are in an advanced stage of development of tests that have adapted the CRISPR gene-editing technology to make rapid diagnostic tests that may be suitable for point-of-care use when commercially released.

Another company is developing a rapid antigen test that will identify a unique SARS-CoV-2 protein. We don’t know yet how long it will take to finish development of these tests and get them approved and available in Australia.
 
Stage 2: Exposure testing
Exposure testing relies on standard serology looking for IgM, IgG and possible IgA anti SARS-CoV-2 antibodies. Several point-of-care serology tests have been approved by the TGA for use in Australia.  Since people may not develop a measurable antibody response for 10 or even more days post symptom onset, these rapid point of care tests are unsuitable for diagnosis of acutely symptomatic patients. They are more suited to answering the second type of question posed earlier; Has this person been exposed to SARS-CoV-2 and developed an immune response? Can they be removed from isolation and permitted to go back to work/school etc?

However, the test kits have not yet arrived in volume so at present they are relatively inaccessible, but this should change soon.

The approved tests are all simple plastic cassettes that use lateral flow of the sample by diffusion. These tests can typically give a result in 10-20 minutes and they use a fingerprick or venous blood. They can detect the presence of both IgM and IgG separately by the development of coloured lines in the reading window on the cassette.

They also have a control line that must develop to show that the test has worked properly. These tests have not yet been thoroughly characterised.

However, data supplied by the manufacturers show they vary in their sensitivity. One test claims around 96% sensitivity at five days post-symptom onset and another 81% sensitivity at 4-10 days and 100% sensitivity at 11 days.

They also claim good specificity with close to 100% negative results in unaffected people. This is somewhat surprising since there are a number of other, less dangerous coronaviruses, in circulation in Australia and around the world and many, if not most people will have been exposed to one or more of these. The manufacturers’ figures will need to be confirmed once the tests are in widespread use. 

Pathology laboratories will require automated high-volume tests and until these arrive and are approved for use, it will not be possible to get a handle on the real epidemiology of COVID-19 in our communities. It is likely that high-volume serological tests will become available soon. Once pathology laboratories have access to these serological tests and results are notifiable to state health departments, it will be possible to address another pressing question; Is the community developing herd immunity?
 
For further information
Nature Biotechnology   https://www.nature.com/articles/d41587-020-00010-2

 


You have a sore throat, you might have COVID-19, so you have a test, and when the results come back you will know if you have it -right?  Well it is not quite that simple and doctors have to interpret test results in the light of information about the test and the patient. 

There is no such thing as a perfect test- one which correctly answers the question being asked 100% of the time.  Many factors come into play, not all of them are obvious.  The analytical accuracy and precision of pathology tests are typically very good.  If you do the same test multiple times on the same sample you will generally get the same answer. So why isn’t their diagnostic accuracy the same?

Let’s take the test being used to diagnose COVID-19 in Australia at the moment.  It looks for the virus RNA in a sample taken from the nose or the back of the throat.    The coronavirus is made up of a genetic material called RNA. The test has to have a certain minimum amount of RNA present to record a positive result.  You could tweak the test to find lower levels of virus RNA but in doing so you will increase the likelihood of the test giving a positive result even if there was no RNA in the sample.
 
False negatives and false positives
  • If the test gives a negative result in a person who is actually infected that is called a false negative
  • A person who does not have the infection but whose test gives a positive result is a false positive

We have seen how the number of false positives could increase by trying to push the sensitivity of the test to detect very low viral loads.  Reducing the chance of false positives by reducing the sensitivity will also (very slightly) increase the chance of a false negative.
 
Sensitivity and specificity
The balance of sensitivity (the proportion of patients who have the disease that return a positive test result) and specificity (the proportion of patients without the disease who return a negative test result) is fixed once the test method is set.  But how we interpret a negative or positive result must be made in the light of how likely the patient was to have the virus before we knew the result.

In the general population in Australia or New Zealand you are very unlikely to be infected, so a negative test result is very likely the correct result and you should be reassured you don’t have COVID-19.  If a person returns from New York by plane and two days later develops symptoms consistent with COVID-19, they are much more likely to be infected. A positive result will make it almost certain they are infected but a negative result does not rule it out, it could be a false negative, and isolation with repeat testing on another sample should be considered.
 
When a false negative can occur
So why would the test give a false negative result?  Again, there are many factors in play. 

Getting a good sample
The most important in this case is the sample swab.  Swabs that do not reach a part of the nose or throat where the virus is present will not come back positive.  Repeat testing should always be done on a fresh sample.

Timing
Timing is also important. If the sample was taken too soon after the person was exposed the viral load may not be high enough in the throat to be detected.  On the other hand, doing an RNA test when the patient has recovered will give a negative result and therefore is not useful to know if someone had the virus in the past.

Antibody (serology) tests for COVID-19 look for the antibodies produced by the body in response to the virus. Because this process takes a few days, they are very likely to give a false negative result in the first few days of infection.  The body takes time to produce the antibodies against the virus but they linger for some time – often weeks or months - and so antibody tests are useful to detect past infection and potentially immunity.  But the body also produces antibodies against other similar coronaviruses like the common cold and these may be detected by some of these tests giving false positives. 

Bottom line:  there is no such thing as a perfect diagnostic test, results must always be interpreted with caution and that is best done by a health professional.
 
 
Internal links:
How reliable is pathology testing? 
 
Interpreting coronavirus testing- some things we need to consider.

Readers please note – this is a bit complex and we are going to use some very simple mathematics in our explanation. If you are not comfortable with this then you can read a simple explanation of Bayesian thinking in relation to testing without any maths (How accurate are COVID-19 tests?).

The Reverend Thomas Bayes was an 18th-century Presbyterian minister and mathematician. He developed an important theorem late in his life but it was not published until 1763, two years after his death. It is now known as Bayes theorem. Bayesian probability theory specifies how we should update our belief in the likelihood of something given new evidence or data.  Bayesian probability is not intuitive and is not well understood by many people including some doctors.

Consider the case of medical diagnostic testing.  We start with a patient who we are concerned might have a particular disease.  Our estimate of how likely it is that they have the disease is the “prior probability”. Once we carry out the diagnostic test, we can use Bayes theorem to work out how to use the results of the testing to “update” the probability that the patient has the disease.  This revised estimate is the “posterior” or “post-test probability”.

The prior probability can be hard data e.g. it has been demonstrated by extensive study that in this population the prevalence of tuberculosis is 35%. Alternatively, it can just be an educated estimate based on the clinician’s experience e.g. I have now seen a lot of patients like this in this town with fever, fatigue and dry cough and most have had COVID-19. If they have a known exposure to an infected patient, I would estimate the probability at 95%. If there is no known prior exposure, I would say the probability is 40%.

We then do the test e.g. for tuberculosis or for COVID-19. To accurately interpret a test, it is essential that we have some knowledge of the test performance – how accurate it is. In this context, pathology test performance is measured in terms of sensitivity and specificity.

Sensitivity is the proportion of patients who do have the disease that return a positive test result. It is expressed as a number e.g. 0.95 or as a percentage e.g. 95%.

Specificity is the proportion of patients without the disease who return a negative test result. Again, it is expressed as a number or percentage.

In an ideal world all our diagnostic tests would have 100% sensitivity and specificity. Unfortunately, we don’t live in an ideal world and real diagnostic tests have less than ideal performance and as we will see, this has consequences.

COVID-19 Nucleic Acid Testing
So far almost all the testing that has been done around the world is aimed at detecting viral RNA in swabs taken from the nose and throat of patients. Most of this is RT-PCR nucleic acid testing but other related tests are being introduced. Due to the rapid pace of change in this pandemic we are in the very unusual situation in that none of these tests have received the exhaustive evaluation that new diagnostic tests usually undergo. They have received emergency authorization for use by bodies such as the FDA in the US and the TGA in Australia. Thus, we don’t know the exact sensitivity and specificity of these tests and how they compare to each other in performance. We are not completely in the dark however, as all of the tests have had preliminary evaluations performed and we have a pretty good idea of their sensitivity and specificity and we can use these numbers in our Bayesian estimates.

It has become apparent that for several reasons, but mainly because of difficulties getting good samples of respiratory secretions, that the sensitivity of COVID-19 nucleic acid tests may be as low as 70%. That is, 30% of people who do have the infection may return a negative nucleic acid test result. Specificity of COVID-19 nucleic acid tests is much higher; some tests are estimated to have a specificity of 98%.

Now we can look at the consequences of these test performance figures in two different situations.

Situation 1.

A person returns from New York by plane and two days later develops symptoms consistent with COVID-19. The doctor estimates the probability of COVID-19 in this person as being 90% before the test is done.  This is the “prior” or “pre-test probability”. The test is performed. We can now do a simple calculation to estimate the new probability of the patient having COVID-19 after we get test results. There are online calculators to do these calculations for example this one at MedCalc.

However, to better understand how these calculations are done we can walk through the process.  The best way to do this is to assume that we have 1000 patients just like this.  We can then draw up a table to demonstrate the outcomes for all of these patients (see below).  If we assume a pre-test probability of 90% then of our 1000 patients, 900 will be infected and 100 not. These numbers go down as the bottom line of the table. We then use the test sensitivity and specificity to fill in the rest of the table. Given a sensitivity of 70%, of the 900 infected patients 630 should test positive (0.7 x 900 = 630).  These are the true positives. Given a specificity of 98% of the 100 who are not infected 98 should test negative (0.98 x 100 = 98).  These are the true negatives.  Given these values we can simply calculate the false negative and the false positives by subtracting the true results from the totals at the bottom.  For example, if there are 900 infected and only 630 have a positive test results, then the remaining 900 - 630 = 270 must be false negatives.
 
90% PRE-TEST PROB          INFECTED     NOT INFECTED          TOTALS
TEST POSITIVE 630           TRUE POS 2               FALSE POS 632          TOTAL POS
TEST NEGATIVE 270           FALSE NEG 98             TRUE NEG 368          TOTAL NEG
        TOTALS 900 100 1000
 
We can use these figures to see how we should update our belief in whether the patient has coronavirus or not based on the results of the test.   Firstly, let’s consider the case that the test came back positive.  How likely is it, in this group, that a person with a positive test has coronavirus?  The best way to do this is to calculate what percentage of the total number of positive tests are in fact true positives (true positives/total positive tests).  In this case it is 630/632 = 99.7%.  This is the positive predictive value (PPV).  This means that we can be virtually certain that if a person from this group has a positive result then they have coronavirus (99.7% certain in fact!). 

What about if the test came back negative?  How likely is it, in this group, that a person with a negative test truly doesn’t have coronavirus?  To work this out we need to calculate the negative predictive value (NPV).  This is the percentage of negative tests that are true negatives.  In this case it is 98/368 = 26.6%.  This means that a negative test will only be correct about a quarter of the time!  The result should be disregarded and the patient still considered to be infective.  In these cases, a different type of diagnostic test such as imaging may be useful.

Situation 2.

Another person shared a maxi-taxi with the person above for a short ride the next day. They sat in the front with the window open, the infected person right at the back. They have not developed any symptoms yet. Contact tracers ask them to be tested. The contact tracers estimate the probability of this person being infected with COVD-19 at 5%.  
 
5% PRE-TEST PROB          INFECTED     NOT INFECTED          TOTALS
TEST POSITIVE 35               TRUE POS 19               FALSE POS 54            TOTAL POS
TEST NEGATIVE 15               FALSE NEG 931             TRUE NEG 947          TOTAL NEG
        TOTALS 50 950 1000
 
In this case the PPV = 35/54 = 65%
And NPV = 931/947 = 98.4%

The most likely outcome is a negative result and this will be reassuring, we can be quite confident the person is not infected. A positive result however, is not definitive, a positive result means that they have a 2/3 chance of being truly infected. We should be very suspicious and keep this person isolated for the next couple of weeks and consider repeating the test after 2 or 3 days.

COVID-19 Serology Testing
COVID-19 serology testing is not yet widely available but it will be soon. Depending on how they are used, we will have different requirements of serology tests. Nucleic acid tests have a problem with false-negative test results. Serology tests have the opposite problem, they are subject to false-positive test results. This is because our blood teems with thousands of different antibodies to myriad different antigens that we have been exposed to in our lives. Some of those antigens are closely-related coronaviruses with quite similar structure to SARS-CoV-2. We need to design serological assays that have capture antigens that are unique to SARS-CoV-2 and will not react with antibodies against other coronaviruses and other fortuitously similar antigens. This is not a simple task and assays need extensive evaluation against ideally many hundreds or thousands of SARS-CoV-2 negative samples to prove they have high specificity.

If we are testing someone who has been ill, had a positive nucleic acid test and then recovered, the pre-test probability is 100%. The only reason we would do the test is to assess how strong their immune response was. The only caveat is that we have to be patient. Standard procedure is to take two blood samples for testing, one as early as possible in the first week of the illness and then another several weeks later and to look for a significant rise in the amount of antibodies present (the “titre”). False-positive test results are not a problem in this situation as we don’t expect to see any.

The second very important role for COVID-19 serology tests is to assess exposure in the general population. Most, but not all, authorities expect that people who have seroconverted to SARS-CoV-2 will have some degree of immunity against reinfection, at least in the medium term. Knowing the degree of immunity in the population will be vital information for modellers and help them plan a way out of our current social restrictions. However, evidence to date suggest that although asymptomatic infection with SARS-CoV-2 is not uncommon, it is likely that the prevalence of seroconversion against the virus in the general population will be quite low, especially in Australia where we have succeeded in bringing the infection rate down quite quickly compared with many other countries. This fact compounds the problem of false-positive test results with COVID-19 serology.
Let’s consider a scenario with three different tests.

Scenario 1.
Consider an Australian city or a group of mine workers where 5% of people have had COVID-19 but this is unknown to us. This is the “prior” or “pre-test probability” we use in our calculation. The serological testing is performed with a simple fingerprick blood sample point-of-care (POC) test that can be done at a doctor’s office or a mining site. Its sensitivity and specificity are both 95%. Some POC tests may have better test performance than this, some will have worse. We don’t yet have full independent evaluation data on the POC tests that have received emergency TGA approval in Australia.
 
5% PRE-TEST PROB     SEROCONVERTED NOT SEROCONVERTED          TOTALS
TEST POSITIVE 48               TRUE POS 47               FALSE POS 95              TOTAL POS
TEST NEGATIVE 2                 FALSE NEG 903             TRUE NEG 905            TOTAL NEG
        TOTALS 50 950 1000
 
The first thing to notice is that almost half of our positive test results are false-positive. The positive predictive value or PPV is given by true positives/total positives = 48/95 or 50.5%. A negative result is more helpful, the negative predictive value or NPV is given by true negatives/total negatives = 903/905 or 99.8%. The estimated prevalence of seropositivity in the population is total positives/1000 = 95/1000 or 9.5%. This is almost twice the true prevalence. This test is essentially useless for the modellers and also useless for individuals who receive positive test results.
 
Scenario 2.

Here we have what seems to be a better serology test. The sensitivity of this test is 98% and the specificity is also 98%.
5% PRE-TEST PROB     SEROCONVERTED NOT SEROCONVERTED          TOTALS
TEST POSITIVE 49               TRUE POS 19               FALSE POS 68              TOTAL POS
TEST NEGATIVE 1                 FALSE NEG 931             TRUE NEG 932            TOTAL NEG
        TOTALS 50 950 1000
 
For the modellers this testing might or might not provide useful information depending on how much their calculations are affected by error in the estimated seroprevalence parameter. The positive test rate of 68 positive results out of 1000 people tested (6.8%) is reasonably close to the true underlying prevalence (5%).  This information can be used to estimate the likely transmission dynamics in the population if restrictions were loosened.  However, for any individual who tested positive there is only a 49/68 = 72% chance that they have in fact had COVID-19.  This also means that 19 of the 68 people who tested positive have not had the disease and are therefore susceptible to getting it if they believe themselves immune and expose themselves to infection again. When the prevalence of the condition is low (5% in this case), we need a more specific test to have confidence in the results.

Scenario 3.

Here we have an improved serology test. The sensitivity is the same at 98% but the specificity is better at 99.8%, i.e. we only expect one false positive test result for every 500 people who definitively don’t have the disease. 
5% PRE-TEST PROB     SEROCONVERTED NOT SEROCONVERTED          TOTALS
TEST POSITIVE 49               TRUE POS 2                 FALSE POS 51              TOTAL POS
TEST NEGATIVE 1                 FALSE NEG 948             TRUE NEG 949            TOTAL NEG
        TOTALS 50 950 1000
 
This new test estimates the prevalence of seroconversion in the population as 51 positive tests out of 1000 tested or 5.1% which is almost exactly the true prevalence. Additionally, the problematic false positives have now been reduced to 2 out of 1000 tested but this still means that 2 out of 51 positive tests are false-positives. This increase in the specificity (increasing from 98% to 99.8%) has had a large impact on the usefulness of the test. Since we don’t know the prevalence of seroconversion in the population before we start, it is crucial that the test to be used has adequate sensitivity and very high specificity in particular when we expect the true seroprevalence to be low.

Whoever is using the test has to decide on the utility of the results. The information provided will be very useful for disease modellers. However, we have to decide if it is reasonable that 2 out of every 1000 people tested will be falsely reassured that they have had COVID-19 already.

The current COVID-19 crisis highlights how important it is to correctly interpret diagnostic tests and it is clear that Bayesian thinking is central to this. The Reverend Bayes could never have imagined that his theorem would one day be used to help guide government decisions in the setting of a global pandemic.

External links
TGA list of approved tests
Nature Biotechnology article on types of tests
Annals of Internal Medicine review
 
 
The process for receiving COVID-19 test results differs between states and territories and between public and private laboratories.
 
If you are tested by a private laboratory you will be asked to provide a GP request form and your Medicare card at the time the swab is taken.  Your results will be sent to the doctor who requested the test.  They are responsible for providing your results.
 
If you are tested at a public health facility, a special COVID-19 or respiratory clinic you will be asked to provide contact details so that you can have your result made available to you. Some states provide a phone number so that you can chase up a late result.
 
NSW
 
If you are tested at a NSW Health public hospital, fever clinic, COVID clinic or emergency department and you have a negative result, it will be sent directly to you as an SMS.  If you have a positive result, you will receive a call from public health. Parents, guardians and carers of children will receive results by phone, regardless of whether they are positive or negative. Your local hospital health team will provide you with details on how to register. Results will typically be available 24 to 72 hours after testing. 
 
https://www.health.nsw.gov.au/Infectious/covid-19/Pages/clinics.aspx
 
Victoria

Your doctor or the clinic where you were tested will notify you of your result, either by calling or by SMS, regardless of whether it is positive or negative.  Typically, it takes one to three days for people to get their result after they are tested. Sometimes there can be delays and it can take longer. If you were tested at a mobile drive-through clinic in a retail setting, and have been waiting for more than five days for your test result, you should call the 24-hour coronavirus hotline 1800 675 398.
 
https://www.dhhs.vic.gov.au/getting-tested-coronavirus-covid-19#what-happens-if-i-test-positive-or-negative
 
Queensland

If the test result is negative, you will be contacted by the doctor or the clinic where you were tested, either by a phone call or SMS. If you have been waiting for your result and it has been more than 36-48 hours since your test, you should contact Pathology Queensland on 1800 472 847 to confirm that you have a negative result. This service operates Monday to Friday (excluding public holidays), 8.15am to 5.15pm.  If you have tested positive for COVID-19, you will be contacted immediately for next steps.

https://www.health.qld.gov.au/healthsupport/businesses/pathology-queensland/patients/COVID19-results

https://www.qld.gov.au/health/conditions/health-alerts/coronavirus-covid-19/stay-informed/testing-and-fever-clinics
 
South Australia

SA Pathology has launched a COVID-19 digital health service in partnership with a digital health company. This provides a portal to enable people to access their result. People who have had a recent COVID-19 test will receive an SMS invitation, via their nominated mobile phone number, to register with the portal. 

https://www.sapathology.sa.gov.au/wps/wcm/connect/sa+pathology+internet+content+new/content/news/pinned/covid-19+digital+health+service
  
Western Australia
 
At the time of testing, you will be asked to provide an Australian phone number so that if you return a negative test result you can be informed via SMS. It will take between 2 and 3 days to be notified of your results.  COVID clinics will contact the parents/guardians/carers of children under the age of 16 to provide negative test results. In the event of a positive result a Public Health Unit staff member will phone to discuss your result with you.
 
https://healthywa.wa.gov.au/~/media/Files/Corporate/general%20documents/Infectious%20diseases/PDF/Coronavirus/FAQ%20-%20COVID-19%20Clinics.pdf
 
ACT
 
If the test returns positive for COVID-19, you will usually receive the result within 1–2 days.  If negative, you will usually receive the result in 2–4 days. Depending on where you were tested, a negative result may be sent to you by SMS or a phone call from your doctor.  If you have not received your result within these timeframes, you need to contact the GP who ordered your test or the Respiratory Assessment Clinic that collected the swab. If you were tested at the Weston Creek Walk-in Centre or the EPIC drive-through testing clinic, you can contact (02) 5124 5574 from Monday to Friday, between 9am and 5pm.
If your test result is positive, the Communicable Disease Control (CDC) Section of ACT Health will contact you and give you advice about what you need to do.
 
https://www.covid19.act.gov.au/protecting-yourself-and-others/getting-tested#How-long-do-COVID-19-test-results-take-
 
Tasmania
 
You will be asked to provide contact details at the time of the test. You will be contacted directly with your result. If you have a positive result, you will receive a phone call from the Public Health Service. If your result is negative, you will either receive an SMS or be contacted via the details you provided at the time of testing.
 
https://www.coronavirus.tas.gov.au/keeping-yourself-safe/testing-for-covid19/im-being-tested.-what-should-i-know
 
Northern Territory
 
If your test is positive, the NT Centre for Disease Control will let you know the next steps for isolation and treatment. For general help, you can call 1800 020 080.
 
https://coronavirus.nt.gov.au/stay-safe/testing
 
 
Find the information you need on COVID-19
 
Federal, state and territory governments provide daily updates on COVID-19.  The type of information and the way it is presented varies between them and can include the number of cases, number of tests performed, and those cases being traced for contacts.  There are also some useful global sites. To help you find your way through the great many websites providing information, here are links to pages that are being regularly updated.
 
 
Australia (Australian Government Department of Health)
General information
https://www.health.gov.au/news/health-alerts/novel-coronavirus-2019-ncov-health-alert
 
National Hotline – 1800 020 080
 Number of cases by state and territory, cumulative cases, source of transmission, ages of cases by gender.  Links to weekly epidemiology reports and global figures.
 
https://www.health.gov.au/news/health-alerts/novel-coronavirus-2019-ncov-health-alert/coronavirus-covid-19-current-situation-and-case-numbers#in-australia

COVID resources – series of fact sheets
https://www.health.gov.au/resources/collections/novel-coronavirus-2019-ncov-resources
  
New South Wales (NSW Health)
Latest updates, including new cases, by age and gender, number of tests performed, likely sources, and latest press conference by video.   Links to transmission management advice.
 https://www.health.nsw.gov.au/Infectious/diseases/Pages/covid-19-latest.aspx
 
Queensland (Queensland Health)
Queensland COVID-19 statistics – total cases; case overview by hospital, health service and region; likely source of infection (with maps); age and gender of confirmed cases; testing; self-quarantine notices.
 https://www.qld.gov.au/health/conditions/health-alerts/coronavirus-covid-19/current-status/statistics#testbyhhs
 
General advice
https://www.qld.gov.au/health/conditions/health-alerts/coronavirus-covid-19
 
Victoria  (Victoria Health & Human Services)
 
Daily updates on number of cases and management advice.
 https://www.dhhs.vic.gov.au/coronavirus-covid-19-daily-update
 
General information on management
https://www.dhhs.vic.gov.au/coronavirus
 
 Western Australia (WA Health)
Daily snapshots of number of cases and testing. Links to contact tracing, Australian and state case numbers and overseas information; also, links to clinical updates for GPs and hospitals.
 https://ww2.health.wa.gov.au/Articles/A_E/Coronavirus
 
South Australia
Latest updates with links to confirmed and suspected cases, flights with confirmed cases and transmission  management advice
https://www.sahealth.sa.gov.au/wps/wcm/connect/public+content/sa+health+internet/conditions/infectious+diseases/covid+2019/coronavirus+disease+2019+covid-19 

ACT (Health ACT)
Latest updates with confirmed cases and number of tests. Links to management news.
 
https://www.health.act.gov.au/about-our-health-system/novel-coronavirus-covid-19
 
 Tasmania (Tasmania Department of Health)
General information with daily updates; also, links to transmission management advice
 https://www.dhhs.tas.gov.au/publichealth/communicable_diseases_prevention_unit/infectious_diseases/coronavirus
 
Northern Territory (Northern Territory Department of Health)
 General information with links to border controls, remote communities
 https://coronavirus.nt.gov.au/
 
Global information
 
 Worldometers
Confirmed cases and deaths by country, territory or conveyance
 https://www.worldometers.info/coronavirus/#countries
 
 The World Health Organisation
https://www.who.int/emergencies/diseases/novel-coronavirus-2019
 
Nextstrain
Genomic mapping of cases to establish transmission routes
 https://nextstrain.org/narratives/ncov/sit-rep/en/2020-03-20

Johns Hopkins University
Global information via a map
 
https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Australia’s National Plan for COVID-19

Australia has a world class health system, including a National Plan for Pandemics. This plan includes modelling possible scenarios of COVID-19 spreading through the Australian population, which is informing the actions Australian government and medical experts are taking to slow the spread and prepare our health system. This document outlines scenario modelling undertaken to inform how Australia is preparing our health system, including our intensive care units, for COVID-19.
 
        
                              covid19-icu-modelling-summary-1-(2).jpg   


 

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