Out of 152 wastewater samples, 76 were from WWTP1 (38 from the affluent and 38 from the effluent) and 76 from WWTP2 (38 from the affluent and 38 from the effluent). In WWTP1, 47.4% (36/76) of the samples presented the E gene (22 in the affluent and 14 in the effluent). The negative samples for the E gene (n = 40) were evaluated for the presence of the N1 gene, where 11.6% (13/40) of the WWTP1 samples presented the N1 gene (5 in the affluent and 8 in the effluent). In WWTP2, only 5.3% (4/76) of the samples presented the SARS-CoV-2 E gene. In contrast, none of the samples presented the N1 gene. Weekly samples from WWTP1 were grouped according to the month of collection to carry out genomic sequencing (Table 1).