The COVID-19 pandemic has created a global storm in the world, and nations worldwide are skirmishing with this unprecedented health crisis. The outbreak of Corona Virus Disease- 19 (COVID-19), caused by Severe Acute Respiratory Syndrome Corona Virus - 2 (SARS- CoV-2), had a significant impact on the healthcare system, especially in the clinical microbiology laboratories worldwide. The choice of a correct anatomical site for good samples collections with the proper precautions is essential for prompt and accurate diagnosis of COVID-19. This review aimed to cover the challenges faced during the choice of appropriate sample collection sites, transport and tests for detection of SARS-CoV-2 infection. The diagnosis tests of COVID-19 can be divided into direct, indirect and complementary tests. In the direct tests, Real-time polymerase chain reaction (RT-PCR) assays are the molecular tests of choice for the diagnosis of COVID-19. The remaining direct tests include GeneXpert and TrueNAT assays. In the indirect testing's; antigen-antibody-based techniques are recommended for surveillance of the disease, which may help to formulate the control measures. These tests not only help in assessing the disease severity, but also they benefit in evaluating the prognosis and management strategies.