COVID-19 : Tests

Sl.No.	Topic
1.	RT - PCR
2.	RT-LAMP test
3.	RAPID Antibody Test
4.	ICMR Approved Labs
5.	References

For other laboratory investigations indicated in a COVID 19 suspected or confirmed patient, please refer to the treatment section.

RT - PCR

Laboratory testing for COVID 19 includes methods that detect the presence of virus (RT PCR test) and those that detect antibodies produced in response to infection. Detection of antibodies (serology) can be used both for clinical purposes and population surveillance. RT-PCR: Real time Reverse Transcriptase Polymerase Chain Reaction (rRT PCR) testing is the confirmatory diagnostic test for SARS CoV- 2. Samples: For RT-PCR- for COVID-19, CDC recommends collecting and testing an upper respiratory specimen. Nasopharyngeal specimen is the preferred choice for swab-based SARS-CoV-2 testing. When collection of a nasopharyngeal swab is not possible, the following are acceptable alternatives:

• An oropharyngeal (OP) specimen collected by a healthcare professional, or
• A nasal mid-turbinate (NMT) swab collected by a healthcare professional or by onsite self-collection (using a flocked tapered swab), or
• An anterior nares specimen collected by a healthcare professional or by onsite self-collection (using a round foam swab).

CDC also recommends testing lower respiratory tract specimens, if available. For patients who develop a productive cough, sputum should be collected and tested for SARS-CoV-2. The induction of sputum is not recommended. When it is clinically indicated (e.g., those receiving invasive mechanical ventilation), a lower respiratory tract aspirate or bronchoalveolar lavage sample should be collected and tested as a lower respiratory tract specimen.

Sample collection:

Specimens should be collected as soon as possible once a decision has been made to pursue COVID-19 testing, regardless of the time of symptom onset. Maintain proper infection control when collecting specimens

Nasopharyngeal swab (NP) /oropharyngeal swab (OP)

Use only synthetic fibre swabs with plastic shafts. Do not use calcium alginate swabs or swabs with wooden shafts, as they may contain substances that inactivate some viruses and inhibit PCR testing. Place swabs immediately into sterile tubes containing 2-3 ml of viral transport media. In general CDC is now recommending collecting only the NP swab. If both swabs are used, NP and OP specimens should be combined at collection into a single vial to maximize test sensitivity and limit testing resources. OP swabs remain an acceptable specimen type.

Nasopharyngeal swab:

Insert a swab into nostril parallel to the palate. Swab should reach depth equal to distance from nostrils to outer opening of the ear. Leave swab in place for several seconds to absorb secretions. Slowly remove swab while rotating it.

Oropharyngeal swab (e.g. throat swab):

Swab the posterior pharynx, avoiding the tongue.

Nasopharyngeal wash/aspirate or nasal aspirate

Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

Anterior nares (NS)/ Nasal mid turbinate (NMT) For NS, a single polyester swab with a plastic shaft should be used to sample both nares. NS or NMT swabs should be placed in a transport tube containing either viral transport medium, Amies transport medium, or sterile saline.

Bronchoalveolar lavage, tracheal aspirate

Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

Sputum

Have the patient rinse the mouth with water and then expectorate deep cough sputum directly into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

Store specimens at 2-8°C for up to 72 hours after collection. If a delay in testing or shipping is expected, store specimens at -70°C or below.

Result availability

Results are generally available within a few hours to 2 days.

Guidelines for use of commercial kits for nasal/throat swab based diagnosis of COVID-19 in India, 2 April, 2020

A total of 19 non- US FDA EUA/CE IVD real-time RT-PCR kits have been validated by ICMR-NIV, Pune. Following kits are found suitable for use:

Name of Company	Name of the Kit	Concordance among true negative (%)	Concordance among true positive (%)
Altona Diagnostics	RealStar SARS-CoV-2 RT-PCR kit 1.0	100%	100%
MY LAB	Patho Detect	100%	100%
KILPEST (BLACKBIO)	TRUPCR	100%	100%
Seegene	Allplex 2019-nCoV assay	100%	100%
SD Biosensor	nCoV Real-Time Detection kit	100%	100%

• Central Drugs Standard Control Organization (CDSCO) has been intimated for above listed kits.
• US FDA EUA/CE IVD approved kits can be used directly after due approval from DCGI and intimation to ICMR.

Real time Reverse Transcriptase Polymerase Chain Reaction (rRT PCR) in different countries:

Country	Institute	Gene targets
China	China CDC	ORF1ab and Nucleoprotein (N)
Germany	Charité	RdRP, E, N
Hong Kong	HKU	ORF1b-nsp14, N
Japan	NIID	Pancorona and multiple targets, Spike protein (Peplomer)
Thailand	National Institute of Health	N
United States	US CDC	Three targets in N gene
France	Pasteur Institute	Two targets in RdRP

US commercial labs began testing in early March 2020. As of 5 March 2020 LabCorp announced nationwide availability of COVID-19 testing based on RT-PCR. Quest Diagnostics similarly made nationwide COVID-19 testing available as of 9 March 2020. No quantity limitations were announced; specimen collection and processing must be performed according to CDC requirements.

In Russia, the COVID-19 test was developed and produced by the State Research Center of Virology and Biotechnology VECTOR. On 11 February 2020 the test was registered by the Federal Service for Surveillance in Healthcare.

On 12 March 2020, Mayo Clinic was reported to have developed a test to detect COVID-19 infection.

On 13 March 2020, Roche Diagnostics received FDA approval for a test which could be performed within 3.5 hours, thus allowing one machine to do approximately 4,128 tests in a 24-hour period.

On 19 March 2020, the FDA issued emergency use authorization (EUA) to Abbott Laboratories for a test on Abbott's m2000 system. On 21 March 2020, Cepheid similarly received EUA from the FDA for a test that takes about 45 minutes.

Cost:

Currently, government approved and supported labs are testing for COVID-19 using RT-PCR test and the government has capped the cost for COVID-19 testing at Rs. 4,500.

Sensitivity and Specificity:

The different RT PCR tests in use target different genes.The new COVID -19 -RdRp/Hel assay is highly sensitive and specific compared to the RdRp P2 assay and exhibited no cross-reactivity with other common respiratory pathogens in vitro and in nasopharyngeal aspirates.

RT LAMP TEST:

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The Sree Chitra Tirunal Institute for Medical Sciences and Technology (SCTIMST), Thiruvananthapuram, Kerala has developed a much cheaper and faster diagnostic test kit (Chitra Gene LAMP-N) which is highly confirmatory for the diagnosis of COVID-19. The test kit can detect the "N Gene of SARS COV2 using reverse transcriptase loop-mediated amplification of viral nucleic acid (RT-LAMP)".

This technology is much cheaper, faster, accurate and easy to deploy because of its cost-effectiveness. This is a confirmatory diagnostic test for N gene of SARS-CoV-2 using the RT-LAMP technique. The test kit which is highly specific for SARS-CoV-2 N-gene can detect two regions of the gene which will ensure that the test does not fail even if one region of the viral gene undergoes mutation during its current spread.

The institute has got the approval of Indian Council of Medical Research (ICMR). Using Chitra Gene LAMP-N, the gene detection time is 10 minutes and the sample to result time (from RNA extraction in swab to RT LAMP detection time) will be less than 2 hours. Thirty samples can be tested in a single batch in a single machine and the significantly lower machine waiting time will allow large number of samples to be tested each day in a single machine in multiple shifts.

The new device for LAMP testing costs around Rs 2.5 lakh and the test kit for two regions of N gene( including RNA extraction) will be less than Rs 1000/test, while the RT PCR machine costs around Rs 15 lakh to Rs 40 lakh and the PCR kit cost is Rs 1900-2500/test.

RAPID ANTIBODY TEST:

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Rapid Testing : Latest guidelines - Click here

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These are serological tests done on blood/serum/ plasma. Unlike RT PCR tests that detect the virus itself, this test detects the antibodies – IgM and IgG- produced by the body against the virus.

Advantages:

• Blood/ serum/plasma samples will suffice. Expertise in sample collection not required.
• Results available in 30 minutes
• Results remain positive even weeks after the infection.
• Positive result suggests exposure to SARS CoV-2
• It is useful for screening and epidemiological surveillance.

Disadvantages:

• Test result is positive only after 7-10 days of infection ( the time taken to mount an antibody response)
• Negative result does not rule out COVID 19 infection
• It is not a confirmatory test
• It does not give the quantifiable amount of antibodies in the patient serum, or if these antibodies are able to protect against future infection

List of antibody (IgM, IgG) based rapid tests Antibody based rapid tests validated at NIV, Pune and found to be satisfactory (ICMR approved)

1. SARS-CoV-2 Antibody test (Lateral flow method): Guangzhou Wondfo Biotech, Mylan Laboratories Limited (CE-IVD)
2. COVID-19 IgM IgG Rapid Test: BioMedomics (CE-IVD)
3. COVID-19 IgM/IgG Antibody Rapid Test: ZHUHAI LIVZON DIAGNOSTICS (CEIVD)
4. New Coronavirus (COVID-19) IgG/IgM Rapid Test: Voxtur Bio Ltd, India
5. COVID-19 IgM/IgG Antibody Detection card Test: VANGUARD Diagnostics, India.

Antibody based rapid tests which are CE-IVD approved

1. Onsite COVID-19 IgG/IgM Rapid Test: CTK
2. 2019-nCoV IgG/IgM Rapid Test Cassette: BioMaxima
3. COVID 19 rapid test kit (IgM/IgG): SensingSelf
4. CoV-19 IgG/IgM Rpid Test device: Hangzhou
5. COVID-19 IgG/IgM rapid test: Zhejiang Orient Gene Biotech Co. Ltd
6. SARS-CoV-2 IgG/IgM Antibody Test Kit: eDiagnosis (Wuhan EasyDiagnosis Biomedicine Co. Ltd)
7. One Step Test for Novel Coronavirus (2019-nCoV) IgM/IgG antibody: Getein Biotech
8. COVID-19 IgG/IgM Rapid Test Cassette (Whole Blood/Serum/Plasma): Hangzhou Biotest Biotech Co. Ltd
9. COVID-19 IgM/IgG test kit: AmonMed Biotechnology Co. Ltd
10. COVID-19 Antibody (IgG/IgM) Test Kit: Beijing Abace Biology Co., Ltd

CE-IVD approved kits can be used directly after due approval from DCGI and intimation to ICMR.

Cost:

The different labs (eg. Bione, Abbott ) are offering tests with price ranging from Rs.500 to Rs.3000.

Sensitivity and specificity:

The rapid diagnostic tests available in different countries developed by different agencies vary in their sensitivity and specificity in detecting IgM and IgG antibodies. The sensitivity may range from 87.3% to 100% and specificity may range from 92 % to 100%.

ICMR approved COVID -19 Testing Sites (63) State/UT LIST OF VRDLs

Click to downlod the list