A systematic investigation of SARS-CoV-2 genome concentrations in nine Southern California wastewater treatment plants (WWTPs) was carried out. The goal was to compare the variability of the viral concentration among different WWTPs that serve different communities and to correlate the concentration of virus in wastewater with the community level COVID-19 epidemic. The results showed that there were significant differences in viral concentration detected in different plants. However, the variability of SARS-CoV-2 concentration cannot easily be explained by the COVID-19 case reports because a large number of sewer-shed characteristics have important influences on the quantifiable viral concentration in the sewage samples. The results from year-long tracking of SARS-CoV-2 concentration in two large WWTPs, however, matched fairly well with the county level COVID-19 case reports. This suggests continuous monitoring of SARS-CoV-2 in the same treatment plant can offer insights into community level trends of COVID-19 and can serve as an alert for a possible resurgence of the disease. Amplicon-based sequencing targeting two SARS-CoV-2 single nucleotide polymorphism (SNP) mutations was shown as a proof-of-concept for identifying SARS-CoV-2 variants in wastewater. The outcomes of this research contribute to the advancement of wastewater-based epidemiology for COVID-19 and other infectious diseases.