Severe Acute Respiratory Syndrome (SARS) is a respiratory disease caused by a coronavirus that appears to have jumped from horseshoe bats to humans [
1,
2]. SARS outbreak, caused by the SARS-CoV, occurred during 2002–2004 [
3]. A similar respiratory disease caused by another coronavirus, which originated in the Middle East, resulted in an outbreak during the 2012–2013 and was named Middle East Respiratory Syndrome (MERS). MERS is caused by a MERS-CoV, which is believed to have jumped from bats to camels and then infect humans [
4,
5]. Recently, towards the end of 2019 another coronavirus, named SARS-CoV-2 resulted in an outbreak of Coronavirus Disease 2019 (COVID-19). Since the outbreak, COVID-19 pandemic has infected more than 179 million people worldwide resulting in death of about 3.9 million people. Few countries such as Israel and others from the Western Pacific Region have been able control the outbreak significantly (
https://covid19.who.int/). Vaccination, social distancing, general hygiene, contact tracing and most importantly, diagnostic testing for COVID-19 in high numbers, are considered to be important factors in controlling spread of the disease [
6,
7]. Transmissibility of SARS-CoV-2 was found to be about 55% with approximately 30% of individuals remaining asymptomatic [
8]. However, new variants, such as the Delta appears to exhibit prominently higher transmissibility attributed to mutations in the receptor binding domain of spike protein [
9]. This necessitates the testing of as many individuals as possible to diagnose those infected with SARS-CoV-2 and more importantly to identify the asymptomatic carriers who may unknowingly infect a large population. SARS-CoV-2 is a single-stranded positive-sense RNA virus with approximately 29.9 kb genome size [
10]. The capsid outside the genome is formed of nucleocapsid protein (N) which is further enclosed by an envelope. Three types of structural proteins are associated with the envelope: spike protein (S), membrane protein (M) and envelope protein (E). Other than these four structural proteins (N, S, M and E) SARS-CoV-2 genome also encodes sixteen non-structural proteins (NSP1-16). RNA dependent RNA polymerase (RdRp) also known as NSP 12, plays an important role in multiplication of coronavirus [
11]. In late 2020, a fast-spreading B.1.1.7 strain was reported which has mutation in spike protein and 56% more transmissible than the earlier reported strain of SARS-CoV2 [
12]. Another fast-spreading B.1.351 variant of SARS-CoV-2 was reported from South Africa. P.1, P.2 and P3 variants were reported from Brazil. B.1.427/B.1.429 variant was first identified in California. The first case of B.1.525 variant was reported in UK. B.1.526 variant was originated in New York. Recently in India, SARS-CoV-2 variants were reported that belongs to the B.1.617 lineage: B.1.617.1 and B.1.617.2 (
https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/). WHO keeps a close watch on the transmissibility and spreading of new variants of SARS-CoV-2. During late 2020, WHO categorized the emerging variants of SARS-CoV-2 as Variants of interest (VOIs) and Variants of concern (VOCs). The variants with increased transmissibility that can change epidemiology of COVID-19 and/or increased virulence that can reduce the effectiveness of vaccines, diagnosis, therapeutics, etc. are termed as Variants of interest (VOIs) whereas the variants that increase the severity of the disease and results in community transmission/multiple COVID-19 cases/clusters, or has been detected in multiple countries are termed Variants of concern (VOCs). B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) are presently grouped in VOCs, while B.1.427/B.1.429 (Epsilon), P.2 (Zeta), B.1.525 (Eta), P.3 (Theta), B.1.526 (Iota), B.1.617.1 (Kappa) are mentioned as VOIs (
https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/).
Reverse transcription real-time PCR (rt-RT-PCR) employing the Taqman™ chemistry for detection of viral RNA is considered the gold standard for diagnostic testing of individuals for COVID-19 [
17]. A validated rt-RT-PCR assay for COVID-19 diagnosis was designed at Charité Institute of Virology in Berlin, Germany [
18]. Similar assays have been described in many other countries and are commercially available through several companies [
19]. This involves Taqman™ probe based assay for the E gene, followed by a Taqman™ assay for RdRp gene for confirmation. Hong Kong University developed a Taqman™ probe based assay for the N gene followed by a confirmatory assay for Orf1b. United States Centres for Disease Control (US-CDC) has designed Taqman™ rt-RT-PCR using 3 primer–probe assays (N1, N2 and RP), which are assayed separately but simultaneously (
https://www.who.int/docs/default-source/coronaviruse/whoinhouseassays.pdf).
Worldwide, the high demand for Taqman™ assays and other reagents required for the test has resulted in higher prices and shortages, especially for the developing countries with a large population [
20]. Dye based rt-RT-PCR assay using SYBR Green I have been proposed by several research groups for the diagnosis of COVID-19 [
21‐
24]. Next Generation Sequencing (NGS) based assay for testing hundreds to thousands of patient samples in parallel have also been proposed and are under development. Recently, one such NGS based assay for parallel testing of COVID-19 has been cleared for marketing by the United States Food and Drug Administration (US-FDA) under Emergency Use Authorization (EUA) (
https://www.fda.gov/media/146933/download). Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) is also a viable alternative for diagnostic detection of COVID-19 and has been proposed and developed by several researchers. RT-LAMP assays rely on conversion of viral RNA to cDNA, followed by target DNA amplification using a set of four to six primers, at a uniform temperature, without the requirement of temperature cycling. A large amount of target DNA is rapidly amplified in a LAMP reaction and can be detected using DNA binding dyes such as SYBR Green I or through changes in pH, which can be detected visually or colorimetrically by using pH sensitive dyes [
25,
26]. RT-LAMP assays have been described for several human pathogenic viruses, including the Influenza viruses, Zika virus, Chikungunya virus, West Nile virus, etc. [
27‐
30].