Annals of the National Academy of Medical Sciences (India) (Jul 2020)
Molecular Diagnosis of COVID-19: An Update and Review
Abstract
SARS-CoV-2 belongs to genus Betacoronavirus subgenus Sarbecovirus of the family Coronaviridae, which originated as a global public health problem. The disease caused is termed as Coronavirus Disease (COVID-19). The virus spread in more than 213 countries and territories all over the world and disease was declared as a pandemic. SARS-CoV-2 is an enveloped positive-sense single- stranded ribonucleic acid (ssRNA) virus. Severe infection and high-mortality are seen in patients with comorbid conditions like diabetes, hypertension, cancer, old age, malnutrition, children, and pregnancy. In India, strategy for testing of COVID-19 has been framed and revised over the course of time by the Indian Council of Medical Research (ICMR), Department of Health Research (DHR), Ministry of Health and Family Welfare (MOHFW), Government of India. ICMR has created a network of viral research and diagnostic laboratories (VRDLs) all over the country, and COVID-19 testing has also been undertaken by ICMR. AIIMS Jodhpur is a regional level VRDL, mentoring 38 government and private laboratories for molecular diagnosis of COVID-19 in the states of Rajasthan and Gujarat. Currently, real-time reverse transcription polymerase chain reaction (rRT-PCR) assay is used all over the country for diagnosis of COVID-19. It uses the TaqMan fluorogenic probe-based chemistry and 5′- nuclease activity of Taq DNA polymerase. It targets specific genes like the RdRp gene, HKU-Orf1ab gene, E gene, and N gene. Apart from rRT-PCR, other isothermal nucleic acid test (NAT)-like transcription-mediated amplification (TMA), loop-mediated isothermal amplification (LAMP), etc. are emerging diagnostic tools to detect COVID-19. Cepheid Xpert Xpress SARS- CoV-2 test and Truenat betaCoV are point-of-care molecular assays which gives results in less than 1 hour, and helps to provide rapid and accurate results. Automated molecular assays like Cobas SARS-CoV-2 and Multiplex NAAT BioFire Respiratory Panel 2.1 (RP2.1) are newer techniques to curb the disease. Sherlock CRISPR SARS-CoV-2 kit is a highly specific and sensitive assay developed to diagnose COVID-19. rRT-PCR has been combined with techniques like bead hybridization, digital droplet PCR, microarray, etc. for improving the correct diagnosis. Recent molecular assays are the future pillars for containment of COVID-19 outbreaks all over the world.
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