Dr Yogesh Gupta
Consultant Microbiologist & Infection Control
Fortis Escort Hospital, Jaipur

Diagnostic testing for SARS-CoV 2

The novel severe acute respiratory syndrome coronavirus 2 (SARS-C0V 2) originated in Wuhan, China, in December 2019. COVID-19 (coronavirus disease 2019) is a respiratory-tract infection, with a newly recognized coronavirus, SARS-CoV-2, thought to have originated as a zoonotic virus that has mutated or otherwise adapted in ways that allow human pathogenicity.

Pathogen is a SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), similar to the agents of SARS (severe acute respiratory syndrome) and MERS (Middle-East respiratory syndrome). Most common complaints are fever (more than 80 percent) and cough, which may or may not be productive, myalgia and fatigue, and alteration in smell and/or taste. Chest imaging in symptomatic patients almost always shows abnormal findings, usually including bilateral infiltrates; laboratory findings are variable but typically include lymphopenia and elevated lactate dehydrogenase and transaminase levels. Viral shedding appears to peak 24 to 48 hours before the symptom onset. In order to suppress COVID-19 transmission, it is important to diagnose COVID-19 patients, which would help in the process of quarantine and isolation of the patients and also in contact tracing.

The current recommendations of testing by the ICMR include all symptomatic (ILI symptoms) individuals, with history of international travel in the last 14 days/contacts of laboratory confirmed cases/health care workers/frontline workers involved in containment and mitigation of COVID19, all patients of severe acute respiratory infection (SARI), asymptomatic direct and high-risk contacts of a confirmed case to be tested once between day 5 and day 10 of coming into contact, all symptomatic ILI within hotspots/containment zones, all hospitalized patients who develop ILI symptoms, all symptomatic ILI among returnees and migrants within 7 days of illness.

Currently, the diagnostic tests for COVID-19 can be categorized into two classes – one is the nucleic acid amplification tests (NAAT) such as RT-PCR/TrueNAT/CBNAAT, and the other is serological test, which detects the presence of antigen or antibodies.

The RT-PCR is still the gold standard for the diagnosis of COVID-19. This test is usually done on respiratory sample like oropharyngeal/nasopharyngeal swab, tracheal section, or BAL. In India, the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) at Pune, adopted a two-step strategy for the diagnosis of COVID-19, using RT-PCR. Primers and probes from two different protocols were combined, and initial screening was performed for E (envelope) gene. Samples positive in the screening test were further subjected to a confirmatory test targeting two genes, one SARS-CoV-2-specific RdRp (RNA-dependent RNA polymerase) gene and other ORF-1b-nsp14 gene3,4. The samples positive for either of the two genes were confirmed as positive for SARSCoV-2.

Serological tests (antibody and antigen) also play an important role in the management of COVID-19. Antibody-based serological tests can be done on blood/serum/plasma samples. Antibodies are generated against the spike (S) and the nucleocapsid (N) protein. IgM and IgG appear mostly at the same time, but IgG can rise earlier than IgM. Antibody levels are not directly correlated with clinical severity.

Recently, ICMR approved antigen based serological test for Covid-19, Standard Q COVID-19 Ag detection, which is a rapid chromatographic immunoassay for qualitative detection of specific antigens to SARS-CoV-2. Standard Q COVID-19 Ag detection kit comes with an inbuilt COVID antigen test device, viral extraction tube with viral lysis buffer, and sterile swab for sample collection. Only nasopharyngeal swab can be used, no other sample (throat swab, broncho-alveolar lavage, or sputum) can be used. This antigen-detection kit has a very high specificity, ranged from 99.3 percent to 100 percent, while sensitivity of the test ranged from 50.6 percent to 84 percent. As per ICMR, suspected individuals who test negative for COVID-19 by rapid antigen test should be definitely tested sequentially by RT-PCR to rule out infection, whereas a positive test should be considered as a true positive, and does not need reconfirmation by RT-PCR test. Thus, diagnostic testing has come in a big way, and will create more facilities for testing and validating new technologies for testing. 

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