**Abstract**

COVID-19 cases were first reported in December 2019, and since then it has spread quickly to create a global pandemic. This respiratory disease is caused by the SARS-CoV-2 virus. A major contributing factor for the fast spread of this virus is that the infectivity by the asymptomatic carriers is similar to symptomatic patients. Thus, to identify the asymptomatic individuals and to provide the essential treatment and care to COVID-19 patients, we rely heavily on diagnostic assays. Efficient, reproducible and accessible diagnostic tests are crucial in combatting a pandemic. Currently, there are few key detection tests which have been successfully employed to field-use. However, there are constant efforts to enhance their efficacy and accessibility. This chapter aims at explaining the basic principles of the current molecular diagnostic tests, which determine the presence of the virus through the detection of its genetic material. This chapter will aid the readers in understanding the basic workings of these molecular diagnostic tests.

**Keywords:** molecular diagnostic tests, PCR assays, SARS-CoV-2, COVID-19, RT-PCR, RPA, LAMP, CRISPR-based assays, LFA

## **1. Introduction**

In December 2019 primary cases of COVID-19 were reported in Wuhan (China), which was later declared as a pandemic by WHO in March 2020 [1]. The COVID-19 is caused by the contagious virus SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2), belonging to the same family as MERS-CoV (Middle East respiratory syndrome coronavirus) and SARS-CoV-1 [2]. Typical symptoms of COVID-19 span a wide range, including fever, dry cough, sore throat and shortness of breath [3]. These symptoms are similar to flu and other respiratory illnesses. In order to provide appropriate care and treatment for COVID-19, it is critical to diagnose SARS-CoV-2 (referred to as CoV-2 hereafter) infections distinctly from other similar diseases. Another complexity to this is that some CoV-2 infected individuals do not exhibit exaggerated symptoms, termed as asymptomatic carriers [4]. It has been shown that the asymptomatic carriers can spread the virus to the same extent as the symptomatic individuals, in the absence of appropriate precautions [4]. Thus, it is imperative to identify all infections efficiently, quarantine and treat appropriately to cease the spread of CoV-2. To achieve this, many diagnostic tests (assays) have been developed and improved by multiple referring (participating) laboratories and CDC (Centers for Disease Control and Prevention). This chapter is focused on simplifying the basic principles of these diagnostic assays. Many scientific review articles which dive deep into the science of CoV-2 diagnostic testing have been

published [1, 3, 5–7]. This chapter, however, aims at explaining the same in nontechnical terms, intended for a general audience.
