Sunday, July 12, 2020



Dr K Aggarwal
President CMAAO
With inputs from Dr Monica Vasudev

973: IMA-CMAAO Webinar on “Covid testing” 11th June, 2020 4-5pm

Dr KK Aggarwal, President CMAAO
Dr RV Asokan, Hony Secretary General IMA
Dr Ramesh K Datta, Hony Finance Secretary IMA
Dr Jayakrishnan Alapet
Dr Brijendra Prakash
Dr Girdhari Kanuga
Dr Sanchita Sharma


Dr Shalabh Malik
National Head Microbiology
Dr Lal Path Labs

Key points from the discussion

  • The coronavirus is a new virus and with no proven therapy or a vaccine as of date, diagnostic testing becomes an important tool for management of patient with Covid-19.

  • Lab test options available: Molecular, antigen (point of care test, CARD test) and antibody (rapid – not allowed in India so far, CLIA – automated platform, ELISA, IgG/IgM, total (combination of IgG and IgM)

  • Molecular: Conventional (results within 6-8 hours), Automated, which is a closed system – CB-NAAT (gives result in 45 minutes), TruNat (within 2 hours; it first screens for envelope (E) gene, which is common to all coronaviruses and then RdRP [RNA-dependent RNA polymerase] gene, which is specific for Covid-19).

  • The purpose of testing is diagnostic, sero-surveillance, or to know exposure (as around 40-45% of cases are asymptomatic) or immunity levels.

  • Covid testing in India is very regulated, as per ICMR and government guidelines. RT PCR is gold standard investigation; recently Antigen test has been allowed.

  • As per ICMR revised guidelines, patients to be selected for testing include symptomatic international traveler in last 14 days, symptomatic contact of lab confirmed case, symptomatic healthcare worker, hospitalized SARI patient, asymptomatic direct and high risk contact of lab-confirmed cases, asymptomatic healthcare worker in contact with confirmed case without adequate precaution and symptomatic ILI patient in hospital/clusters as identified by the Health ministry.

  • Pre-requisites before testing: As it is a pandemic, every result has to be notified. Doctor’s prescription + Covid-19 ICMR form (patient details, history, clinical features, Govt. ID) is mandatory requirement; infrastructure (BSL-3 or at least BSL-2 facility), trained personnel, waste disposal, judicious training and use of PPE are other testing pre-requisites.

  • Specimen type: nasopharyngeal/oropharyngeal swab; nasopharyngeal has better sensitivity – proper sample collection is crucial. Nylon swabs are used as coronavirus stays longer on synthetic material. Then immediately transfer to VTM (viral transport medium); shipped at 2-8oC with appropriate 3-layer packing. In later stages of infection, bronchoalveolar lavage or endotracheal aspirate is better. Recent studies have shown saliva to be better than nasopharyngeal or oropharyngeal swab.

  • RT PCR: Minimum two gene targets (E gene and RdRP gene) need to be pinpointed to declare as RT PCR positive. More the number of targets better is the sensitivity.

  • If E gene, Rd RP gene and RP gene are positive, this confirms detection of SARS-CoV-2. If one gene is positive and the other is negative, the test is inconclusive; repeat the test or take a fresh sample. If E gene and Rd Rp gene are negative and R P gene is positive, the test is negative for SARS CoV-2 virus.

  • It is a qualitative test as it does not give quantitative assay of viral load. Ct (cycle threshold) can give a clue about the severity of infection. If Ct value is low, this indicates high viral load. If high Ct value, this indicates low viral load. Every lab should report Ct value.

  • All reporting (negative/positive) is done on ICMR website and is highly confidential.

  • Advantages of RT PCR: Speed and sensitivity, early detection and isolation, identification of infected persons which helps in management and implementation of mitigation strategies in containment areas

  • Disadvantages of RT PCR: BSL3 or 2 level facilities are required, PPE training, skilled personnel, false negative test (sampling error, very early disease, incorrect transportation)

  • Rapid antigen test: ICMR recommended (14.6.20), sample collection to reading the result should be done within one hour, prescription/Form 44 are mandatory. If antigen test is negative, but person has symptoms suggestive of Covid-19, then RT PCR is mandatory. Sensitivity is around 50-53%. Specificity is good.

  • Antibody tests: Not used for diagnosis, only for seroprevalence studies; community screening of asymptomatic infections, contact tracing, evaluate results of vaccine trials, immunity. Notification is a must; prescription and form are not mandatory.

  • IgM appears first and then IgG. IgM appears around Day 4, rises to peak around Day 14 and disappears by Day 28. IgG appears around Day 8/9, rises to peak around Day 21 and then stays on. The longevity of IgG is not known. So retesting is done after 3 months.

  • Three types of seroconversion are seen in Covid-19: IgG and IgM may appear at the same time (synchronous seroconversion), IgM seroconversion earlier than IgG, IgM seroconversion later than IgG.

  • There is no advisory yet on IgM testing.

  • Total antibody (IgG + IgM) positive: Exposure to SARS CoV-2 is confirmed and antibodies have developed. If symptomatic, refer to RTPCR; if asymptomatic, then quarantine and repeat IgG x7-10 days.

  • Total antibody (IgG + IgM) negative: Exposure not confirmed, antibodies not developed. If person is symptomatic, do RT PCR; if asymptomatic, then this confirms negative result.

  • Surgical or medical intervention emergency: If antigen negative, antibody positive – is symptomatic, then do PCR; if asymptomatic, then go ahead with surgery.

  • Back to work: If IgG positive, join work (retest after 3 months), if IgG negative and symptomatic, do RT PCR (If positive, quarantine; if negative retest IgG after 14 days), if IgG negative and asymptomatic, join work.

  • Cross reactivity with other viruses like dengue or bacteria like typhoid is being seen.

  • Best test when deciding plasma donor is neutralization test. This requires BSL3+ facility.

  • If PCR positive, antigen negative: low viral load. For antigen test to be positive, high viral load is required. PCR is sensitive for low viral load.

Summary of testing for Covid 19

Ideal time to test from onset of illness
0-14 days
Confirmatory test
High sensitivity
Best for testing symptomatic persons
High cost of infrastructure

Complex sample collection and handling

High TAT 2.5-3 hours for testing 1 patient

Rapid Antigen
0-14 days
Acute and early infection
Faster result
Cost effective
Can be used for mass screening
Relatively low sensitivity vs RT PCR

Complex sample collection and handling

4-21 days
Community screening for detecting active and early infections

Shorter turnaround time
Easy sample collection and transport
Cost effective
High throughput analyzers present across the country
Limited evidence on clinical efficacy of serology based Antibody tests

Can’t be used for detecting early infections esp 0-4 days
≥ 7 days
Assess immunity
Screen potential plasma donors
Assess recovery and past exposure to the virus, return to work

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