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 Table of Contents  
Year : 2020  |  Volume : 64  |  Issue : 6  |  Page : 128-131  

SARS-CoV-2 Laboratory Testing in India's Pandemic Response: A Public Health Perspective

1 Professor, Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
2 Associate Professor, Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India

Date of Submission09-May-2020
Date of Decision11-May-2020
Date of Acceptance12-May-2020
Date of Web Publication2-Jun-2020

Correspondence Address:
Mahesh Moorthy
Department of Clinical Virology, 9th Floor ASHA Building, Christian Medical College, Vellore - 632 004, Tamil Nadu
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijph.IJPH_491_20

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Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted (at the time of writing) in over 3.3 million cases and 233,000 deaths globally and ~33,000 cases and ~1,100 deaths in India. The mainstay of the diagnosis is a reverse-transcription polymerase chain reaction assay to detect SARS-CoV-2 RNA. The accurate diagnosis is contingent on appropriate specimen choice, time of collection, and assay employed. In this commentary, we highlight the role of laboratory diagnostic tests used in the different stages of India's COVID-19 pandemic response.

Keywords: Antibody, COVID-19, laboratory diagnosis, real-time reverse transcription polymerase chain reaction, severe acute respiratory syndrome coronavirus 2

How to cite this article:
Moorthy M, Fletcher J. SARS-CoV-2 Laboratory Testing in India's Pandemic Response: A Public Health Perspective. Indian J Public Health 2020;64, Suppl S2:128-31

How to cite this URL:
Moorthy M, Fletcher J. SARS-CoV-2 Laboratory Testing in India's Pandemic Response: A Public Health Perspective. Indian J Public Health [serial online] 2020 [cited 2022 Aug 19];64, Suppl S2:128-31. Available from:

   Introduction Top

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).[1] SARS-CoV-2 has caused with over 3.3 million cases and ~233,000 deaths globally and ~35,000 cases and over 1,150 deaths reported in India at this time.[2] Although there are several clinical trials ongoing and vaccine targets in the pipeline, there is currently no treatment or vaccine available against SARS-CoV-2.[3] Clinical spectrum ranges from a mild self-limiting illness in majority to severe pneumonia progressing to multi-organ dysfunction requiring critical care (~5%) and resulting in death in a minor proportion (~1%), especially among those with comorbidities. SARS-CoV-2 infection results in either asymptomatic (sub-clinical), presymptomatic, or symptomatic clinical disease [Figure 1]a. Virus transmission occurs through the respiratory route – aerosols, droplets, fomites, and close contact. Although viral loads are similar between asymptomatic and mildly symptomatic cases,[4] symptomatic and presymptomatic modes are likely more relevant for the transmission from a public health standpoint.[5],[6] In this commentary, we discuss the utility of laboratory diagnostic tests in the current pandemic from a public health perspective.
Figure 1: Utility of laboratory assays in the natural history of severe acute respiratory syndrome coronavirus 2 infection. (a) Stages in the time-course of severe acute respiratory syndrome coronavirus 2 infection, infection kinetics, and transmissibility. (b) Utility of laboratory assay in the clinical diagnosis. (c) Utility in a public health setting. Assay utility in the various stages of infection: X – no utility, + minimal utility, ++ utility in most instances, +++ utility in almost all instances, ++++ extremely useful, +/- Use with caution – false negativity common.

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The laboratory diagnosis of SARS-CoV-2 infection follows one of the two broad approaches: (1) direct virus detection and (2) detection of virus-specific immune response. A schematic of kinetics of virus (RNA, infectious virus) and antibody dynamics over the time course of infection is represented in [Figure 1]a. Whether for the purpose of a clinical diagnosis or from a public health standpoint, the accurate diagnosis of SARS-CoV-2 is contingent on appropriate choice and timing of specimen collection and assay employed.[7]

   Direct Detection Top

Direct methods involve the detection of infectious virus and/or viral antigen and/or viral RNA in a respiratory specimen-upper respiratory (nasal, nasopharyngeal, and oropharyngeal swab) and/or lower respiratory tract (endotracheal aspirate, bronchoalveolar lavage) and sputum. Viral RNA detection in the respiratory samples using the real-time reverse-transcription polymerase chain reaction (rRT-PCR) is the gold standard of laboratory diagnosis of SARS-CoV-2. Numerous assay formats targeting the envelope (E), RNA-dependent RNA polymerase, open reading frame 1ab and Spike (S) genes have been developed.[8],[9] While the methodology as such is highly sensitive and specific, false negativity is occasionally seen due to the variability of virus shedding and in late-stage disease.[10],[11] A positive RNA result, however, is not indicative of infectious virus. Virus isolation is performed by the inoculation of the respiratory sample on monolayers of a susceptible cell line (e.g., Vero E6 and Vero CCL81)[12] and quantifies infectious virus. This technique requires a BSL-3 facility and is restricted to reference laboratories in the country, for example, National Institute of Virology, Pune. It is limited in its utility due to the longer turnaround time (TAT) and risk of laboratory infection. Antigen detection kits are not used or available in India, but are being developed with a view to reduce TAT. The assay format is either a rapid diagnostic test (RDT) or ELISA[9] and target the nucleoprotein (N) and Spike (S) antigens.[9] In general, RDTs are only useful when the pretest probability of disease is high. However, follow-on testing with PCR is recommended to confirm the result.

   Detection of Virus-Specific Immune Response Top

The detection of SARS-CoV-2-specific antibodies (IgM, IgG, and IgA) indicates the exposure or immunity and can confirm the late-stage disease (RNA negative). Serologic assays based on a RDT, ELISA, or chemiluminescent assay principle to detect the antibodies (IgM and IgG) against Spike (S), receptor-binding domain (RBD) or N protein of SARS-CoV-2 are relatively simple and cost-effective compared to the molecular assays.[11] Plaque reduction neutralization tests (PRNT) estimate the virus-specific neutralizing antibody which indicate the protection against SARS-CoV-2 re-infection. The assay is low-throughput, requires technical expertise to perform, and requires a BSL-3 facility. Microneutralization assay formats further increase throughput. Attractive alternatives to PRNT including pseudovirion neutralization or surrogate virus neutralization tests that can be performed in BSL-2 laboratories have been developed.[13],[14],[15]

The utility of assays from the clinical management is shown in [Figure 1]b. As the severity of disease increases, a confirmed diagnosis becomes increasingly difficult using direct methods and a combination of PCR and antibody must be used. From a public health standpoint, laboratory assays play an integral role in case identification, assessment of infectivity, and exposure. Further studies are required to identify the correlates of protection in SARS-CoV-2 infection. The utility of assays laboratory assays in public health standpoint is represented in [Figure 1]c.

   Indian Response Top

During the early stage, where cases were primarily among those with travel history, airport screening was initiated at the ports of entry. Symptomatic travelers were quarantined and isolated. In a short time, laboratory testing by rRT-PCR was introduced for the laboratory confirmation but was limited to a few laboratories. Reagents for the laboratory diagnostics were rapidly purchased, disseminated, and deployed in the country and centralized planning and logistics ensured uniformity of testing to some extent. Asymptomatic international travelers were advised home quarantine for 14 days. At the stage of local transmission, symptomatic travelers and contacts were sampled and tested by rRT-PCR. Asymptomatic contacts of confirmed/suspected cases among returning travelers were screened and advised home quarantine. At the stage of community transmission, where no travel history was being reported among cases, testing was done among symptomatic cases and contacts and a larger number of laboratories provided testing. In addition, existing severe acute respiratory infection (SARI)/influenza-like illnesses (ILI) surveillance systems were leveraged, and sample repositories were tested for cryptic community transmission of SARS-CoV-2 by rRT-PCR.[16] This sentinel surveillance strategy was expanded to the areas where SARS-CoV-2 cases have been reported. At the epidemic stage, any symptomatic cases (ILI/SARI) and asymptomatic contacts of confirmed cases were tested. Pool testing in the low prevalence areas and areas involving the community surveillance of asymptomatic individuals is being evaluated. Synchronized nation-wide lockdown was initiated in the country from March 24, 2020, and has now been segregated into color-coded zones (red, orange, and green) based on the transmission hotspots. Symptomatic individuals in hotspots are recommended PCR testing if the date of symptom onset is <7 days and antibody screening if above 7 days.

The overarching national strategy for testing at the different stages of the pandemic has been proactive, with the rational use of available resources enabling some streamlining of laboratory testing response.[17] The strategy has evolved over time in sync with a rapidly changing global situation.[18] PCR assays were rapidly deployed in the country during the early stages and have formed the cornerstone of detection. The central government agencies have also rapidly deployed funding mechanisms for developing novel-testing strategies, and this has led to numerous kits and testing methods being developed in India.

Currently, rRT-PCR remains the frontline and only strategy for testing. However, any detection must be followed up with adequate isolation and quarantine, for effective virus control. Further, over-testing of asymptomatic individuals must be avoided to conserve scarce laboratory resources. Given the inherent variability between the testing systems and level of expertise across the country, quality control remains an important issue. Currently, referral of samples to nodal or reference laboratories is the only mechanism for QA/QC. In addition, periodic shipment of QA/QC panels must be performed to improve the quality.

Antibody assays cannot reliably be used for diagnosing early exposure and acute infection but may be considered the method of choice in late disease (>14 days) and in particular severe disease where direct assays are negative.[11],[19] Currently, assays configurations, particularly RDTs have poor performance (sensitivity and specificity) and are not recommended for stand-alone use to guide decision-making in any setting.[20] ELISA assays employing the S and RBD protein have been developed[21],[22] and various commercial kits (ELISA and RDT) are available in the country. Antibody-based assays are being implemented in a phased manner, particularly in severe cases and as a seroprevalence tool to gauge community transmission While the true extent of virus spread will only be estimated from seroprevalence studies, the immediate focus for containment efforts should be on identification and isolation of cases relevant to public health. Additional public health measures must be put into place in hotspot zones to prevent re-introduction and resurgence of cases in these zones: (a) graded easing of restrictions, (b) sentinel and enhanced SARI surveillance, (d) baseline serosurveys, and (e) assessment of all-cause mortality.

Testing methods are continuing to evolve to address the needs based on clinical or public health utility. Overall, key considerations are the improvements in assay performance (sensitivity and specificity), TAT (on-demand testing in emergency cases), high-throughput batch testing, and expansion of test capacity and ensuring quality control in low-expertise and low-infrastructure settings. The future directions include increased use of rapid NAAT tests, high-throughput antibody formats to cater to the ever-increasing demand for SARS-CoV-2 testing. The most effective way to contain spread continues to be early case identification, isolation, quarantine, physical distancing, and personal hygiene measures.[23]

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

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