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Diagnostic Testing Strategies for COVID-19

Diagnostic Testing Strategies for COVID-19

There are 3 main type of diagnostic tests for COVID-19 
1. Tests to detect the virus
2. Tests to detect antibodies to the virus
3. Imaging modalities

Tests for Viral detection
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The most fool-proof method is sequencing of the viral genome. This is how the virus was identified as a novel and unique entity by the Chinese in Wuhan. Once the sequence was made public, tests to amplify and detect the unique portions of the virus could be designed. These tests called Polymerase Chain Reaction (PCR) or more specifically Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) since it is an RNA virus that needs to be converted to DNA by the enzyme Reverse transcriptase.
Rapid amplification PCR based cartridge platforms, tried and tested extensively for tuberculosis is now available for various virus diseases including SARS-CoV2. This has the potential of being used as a point of care test. 

Advantages of PCR tests:
---------------------------------
The main advantage of PCR is that it is highly specific (Test with 100% specificity means there will be no false positives). The other advantage is that the tests becomes positive in the early phase of the disease and is thus ideal for confirming those with the beginning of symptoms. 

Disadvantages of PCR tests: 
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One disadvantage is that the sensitivity (Ability to pick up the truly infected) maybe as low as 50-70%. One reason is that the number of viral particles may not be very large in some infected people. This test needs sample of the patient's secretions. The best results are obtained from the lungs by broncho-alveolar lavage. This is done in only a few because it is invasive. Nasopharyngeal swabs and sputum are other methods used. 
Specimen collection is very important and any mistake in that will result in false negatives
PCR needs costly equipment and highly trained personnel which limits its use to the advanced laboratories. For highly contagious and deadly viruses this also needs very high safety levels (level 3 or 4). These can be to some extent mitigated by the point of care cartridge tests which are easier to do and which needs only inactivated specimen.
PCR also has the disadvantage that it can become negative in the later phases of disease as the body's immunity builds up. 
The test takes about 4 hours to perform and this the throughput of a laboratory with a single Real time PCR machine may be about 100-120 tests per day. The cartridge based test can be done in 1-2 hours but the throughput is much smaller as many samples cannot be done simultaneously. 
[SEE TABLE ]

Tests to detect antibodies to the virus
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Antibody based detection tests for SARS- CoV2 have been developed. These are mainly of two types. The standard test is ELISA (Enzyme-linked immunosorbent assay) needs a good laboratory and trained personnel. Rapid card tests which have been developed can be done at the point of care without highly trained personnel. 
Two types of antibodies are tested. IgM antibody rises first and is indicative of an active or recent infection. IgG type of antibody rises later and is indicative of a past infection. 
[SEE FIGURE]

Advantages of Antibody based tests: 
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These tests are done on the blood. For rapid card tests, a finger prick is all that is needed. Antibody based tests are cheaper and results are faster; in case of card tests the result takes only a few minutes.
The antibody tests are very sensitive provided it is done at the proper time as recommended. The specificity is also good for a screening test. 
Disadvantages of Antibody based tests: 
-----------------------------------------------------
The main disadvantage limiting its use as the primary diagnostic modality is that it remains negative in the early phase of the disease.  IgM titres start rising only 3-7 days after the onset of symptoms which is about 8-19 days after exposure to the organism. The specificity can also be a problem when it is used primarily as a standalone diagnostic test.

Imaging tests 
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CT scan is very useful in cases of COVID-19 with lung involvement. The findings are fairly specific enough to make a diagnosis in the proper clinical setting even in PCR negative cases.

Which test should we use?
-----------------------------------
A comparison of sensitivities of PCR and antibody based tests according to the day of illness is provided in the table below.

[SEE TABLE 2]

As can be seen from the table, the two tests complement each other and the sensitivity is boosted when used in conjunction. Antibody tests would be eminently suitable for studying incidence and prevalence in the community since even the convalescents and their contacts can be studied for this purpose. 

What strategy to use?
----------------------------
Diagnostic  testing for SARS-CoV-2 is extremely important for its control. It is those countries that have tested the most people that have been able to contain the spread and mortality.    When considering which test to use, we have to take into account the accuracy, cost, infrastructure and human resource available. The following approach may be considered.
1. Use PCR as the primary diagnostic modality
a. Set up testing facilities using Real Time PCR  in as many centres as possible. The tests maybe done in clinical and research laboratories that routinely offer PCR based tests. Machines from universities etc may be borrowed on a temporary basis to boost throughput.
b. Point of care cartridge PCR may be used in centres where it is available. This would be more useful in the peripheral centres like the TB control units
c. Private laboratories may be asked to contribute to the effort by helping to test the pool of patients identified by the public health authorities. They should be supplied reagents free for this purpose.
d. Free market testing may be discouraged as it will mainly be used by hypochondriacs with money to spare and waste resources.
2. Antibody tests need not be used as a primary diagnostic test. 
a. It can however be used sparingly as an adjunct in doubtful cases negative for PCR and to test contacts for epidemiological purposes as needed. 
b. The main use of the antibody test would be to study the incidence and prevalence of disease and local outbreaks by well designed studies setting up surveillance centres.
c. They can be used in a limited manner to screen new arrivals from within or outside the country and those who test poitive may be quarantined.

References
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1. Wang W et al. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020 Mar 11. doi:10.1001/jama.2020.3786. 
2. Drain PK, Garrett NJ. The arrival of a true point-of-care molecular assay-ready for global implementation? Lancet Glob Health. 2015 Nov;3(11):e663-4.
3. Juanjuan Zhao et al. Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019. www.medrxiv.org. March 03, 2020 doi.org/10.1101/2020.03.02.20030189
4. Fatima Amanat et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. www.medrxiv.org. March16,  2020. doi.org/10.1101/2020.03.17.20037713.







Vineesh V
Assistant Professor of Geography,
Directorate of Education,
Government of Kerala.
https://g.page/vineeshvc

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