(The Gist of Science Reporter) Testing Corona

(GIST OF SCIENCE REPORTER) Testing Corona

[October-2020]

Testing Corona

What are the tests for COVID-19?

There are two ways to test for COVID-19: Viral Test and Serology Test.
A viral test is an oral or nasal swab or saliva test that looks for evidence of an active viral infection. Early in the infection, the virus grows in cells at the back of the nose and throat, taking about 5-14 days before symptoms appear. A swab of the nose or throat can be taken and the nucleic acid of the virus can be detected. The virus is detectable several days before symptoms appear and up to eight days after symptoms appear.
However, everything depends on how well the sample was taken and the amount of virus present at the time of swabbing. Once the antibody response begins, the virus is cleared from the body. Once the virus is no longer present in the nose/throat, the test will be negative. And this is where the samples for viral tests are taken from:

Lower respiratory tract: sputum, lavage, aspirate,
Upper respiratory tract: nasopharyngeal and oropharyngeal swabs; nasopharyngeal wash/nasopharyngeal aspirate,
Nasopharyngeal and oropharyngeal swabs.

Samples should be taken within 14 days of the person’s last documented contact with a COVID-19 case. Viral tests do not indicate whether someone was infected in the past. Viral test is further of two major types: RT-PCR test and an antigen test.
RT-PCR test (Reverse Transcription Polymerase Chain Reaction test) looks for the presence of a virus’s genetic material. RT-PCR is a laboratory technique combining reverse transcription of RNA into DNA and amplification of specific DNA targets using Polymerase Chain Reaction (PCR).
The RT-PCR technology is a fairly expensive method. It requires RNA extracting machines, a laboratory and trained technicians. A minimum of 30 samples are needed to make it economically viable. The cost of chemicals and importing elements required for the test is also high.
The antigen tests that have been approved for COVID-19 diagnosis in India give results in 30 minutes. Antigen tests produce results quickly but may be less sensitive. These tests look for the ‘spike protein’ present on the surface of the coronavirus and which facilitates its entry into the human cell. For the antigen test, a nasal swab is collected.
The advantage of using this test is that it reduces the burden of relying on just RT-PCR tests to identify COVID-19 patients. Experts are of the opinion that antigen testing is useful because even if it is less sensitive, it is rapid and the results that are positive will be positive. So, patients who test positive can get into isolation faster.

Serology test/Blood test/Antibody test:

These tests are used to find out the presence of virus in a body. In this method of testing, blood samples are used to find antibodies.
This process also detects the quantity of antibodies that are produced by the immune system. It is an indirect method of testing as it cannot find the virus, but can determine if the immune system has encountered it.
Antibodies can show up between 9-28 days after the infection has set in. By this time, an infected person can spread the disease, if not isolated. This test even looks for evidence of prior infection with the virus. The test provides evidence that someone may have been exposed to the virus in the past, potentially even if they did not have symptoms, by detecting antibodies specific to the virus. The test does not diagnose an active infection or identify who is protected from reinfection.

Storage and Transport of Samples:

For some tests, results may be available at the testing site in less than an hour. For other tests, samples must be sent to a laboratory for analysis, which may take 1-2 days once the sample is received by the lab.
The lab will acquire one of the following samples from you:
Swab test: The lab will take a special cotton swab and collect sample from the inside of the throat or nose.
Nasal aspirate: The lab will inject a saline solution into your nose, then remove the sample with gentle suction.
Tracheal aspirate: A thin, lighted tube called a bronchoscope goes into your lungs, from where the sample is collected.
Sputum test: Sputum is a variation of mucus from your lungs that can be coughed out or sampled from the nose with a swab.
Blood test: The collected sample will be analysed for the virus, either through a blanket test for all variants of the coronavirus or through a specialised gene sequencing test that locates the marker for the novel coronavirus.

Innovations in Testing:

Sample collection: In many countries, saliva is now shown to be as good as swab for testing. This opens up the possibility of self-collection kits that patients can use. Problems in India may be due to paan, supari, etc.
Sample processing: It is now shown by many labs and also confirmed at the Council of Scientific and Industrial Research (CSIR) that it is possible to skip RNA extraction from samples. Such methods can make testing faster and cheaper. This is not possible with the current sample collection method in viral transport media so the entire system needs to be changed.

Testing:

Nucleic acid: There are now methods such as COVID-seq where Next Generation Sequencing (NGS) can be used to test thousands and even tens of thousands of samples daily, using nucleotide barcodes to identify positive samples.
Oxford Nanopore MinIon is a small device about the size of a large stapler that can go from sample to sequence-based diagnosis for a few hundred samples in about 6 hours. The advantage is a low capital investment of only 2 lakhs and greater resistance to mutation-related false negatives than rtPCR.

Microfluidic PCR platform (Fluidigm Biomark) with an assay for SARS-CoV-2 is already in use in many leading global laboratories as a Lab-developed Test (LDT). Advantages of this assay over conventional qPCR assays are very high-throughput with minimal manual labour. With full automation, it can reach a throughput of up to 6000 samples/day.