Background

The Covid-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is affecting large populations, and has been declared a pandemic by the World Health Organization (WHO).

Mass surveillance of the population and quarantine proved to be effective strategies in dealing with this crisis. The main key for detection is the reverse transcription quantitative polymerase chain reaction (RT-qPCR) test. While this test is effective, it requires professional experience both in sampling and in performing the test. Furthermore, the reagents and lab equipment are expensive (Bruce et al., 2020). Altogether, these created a bottleneck for mass scale testing.

Fortunately, to date, alternative molecular biology methods can overcome such limitations. One of these methods is colorimetric Loop-Mediated Isothermal Amplification (LAMP) (Notomi et al., 2000). LAMP is performed at a single and constant temperature (i.e., isothermal), and allows a one-step reverse transcription. Its results can be visualized by color change with the naked eye. This method is cheap and requires little to no lab equipment (Wang et al., 2016; Yu et al., 2020; Zhang et al., 2020). It can be widely used in points of care such as the workplace and schools, which can increase the number of tested subjects tremendously. We see this method as a surveillance tool to markedly increase the total number of tests per day and identify patients for further tests in hospital settings.

Here we present a protocol for applying one step reverse transcribed LAMP (RT-LAMP) detection method on clinical samples from nasal, throat swabs and from saliva. The primers we used were previously designed by Zhang et al., 2020 on synthetic and purified RNA (Table 1). The protocol we present (Ben-Assa^*, Naddaf^* et al., 2020), while with these same primers, does not require RNA purification steps and can be conducted directly on clinical samples. This protocol requires no professional experience and results can be obtained within an hour. The results of this protocol were compared to the approved RNA purification and quantification RT-qPCR method at the Rambam Health Care Campus (RHCC) hospital. The downside of this method is its detection sensitivity, which is considerably lower than the standard RT-qPCR method (Ben-Assa^*, Naddaf^* et al., 2020). Therefore, it is applicable for a large-scale surveillance tool rather than a replacement of the current gold-standard detection method. While this protocol was validated on SARS-CoV-2, it can be adjusted to other pathogens too (bacteria or viruses).