The pandemic dissemination of the SARS-CoV-2 led, on the one hand, to a worldwide effort to develop mechanistic-based therapeutics and vaccines, and on the other hand, the searching for determining the spreaders and the mechanisms of transmission. Melatonin, a multitask molecule, orchestrates defense responses by allowing the proper mounting, duration, and magnitude of innate immune responses. Melatonin is synthesized on demand by immune-competent cells and constitutively by resident macrophages such as alveolar macrophages. Here we investigated whether the expression of genes relevant to virus invasion and infection varies according to a genic index (MEL-Index) that estimates the capacity of the lung to synthesize melatonin. A COVID-19-Signature composed of 455 genes of 288 human lungs (GTEX, UCSD) was correlated with MEL-Index by Pearson correlation test, gene-set enrichment analysis, and networking tool that integrates the connectivity between the most expressed genes, allowing us to compare the same set of genes under different states. The three independent procedures point to a negative relationship between MEL-Index and SARS-CoV-2 infection. The entry in epithelial AT2 cells should be hampered by a positive correlation TMRPSS2 and a negative correlation with the coding gene for furin, suggesting dysfunctional processing in virus spike. Moreover, MEL-Index also negatively correlates with the genes that codify the proteins of multi-molecular receptor complex CD147, the gateway in macrophages, and other immune cells. In summary, the perspective that lung and respiratory tract melatonin could be a natural protective factor opens new epidemiological and pharmacological perspectives, as high MEL-Index scores could be predictive of asymptomatic carriers, and nasal administrated melatonin could prevent evolution of presymptomatic carriers.