Genomic surveillance of SARS - CoV-2 basically relied on the sequencing of clinical Corona Virus Disease 2019 ( COVID-19 ) samples . However , clinical genomic surveillance is expensive , inefficient , lacks community representation and has sampling bias due to testing of only symptomatic individuals and to systemic healthcare disparities , particularly in poor and underserved communities ( Kaplan et al . , 2021;Karthikeyan et al . , 2021;Peccia et al . , 2020;Smith et al . , 2021;Wolfe et al . , 2022 ) . Variants of SARS - CoV-2 can also be tracked in community wastewater ( wastewater genomic surveillance ) which offers cost - effective , unbiased and real - time capture of virus spread and dynamic ( Ahmed et al . , 2022a;Karthikeyan et al . , 2021;Michael - Kordatou et al . , 2020;Smith et al . , 2021 ) . In addition , wastewater genomic surveillance tracks existing and new emerging variants , for which targeted assays do not exist as yet . These data are valuable for transmission network analysis and interpretation , as well as an emerging technology for tracing viral evolution ( Karthikeyan et al . , 2021;Vo et al . , 2022 ) . However , wastewater genomic surveillance remains a challenge , since low viral loads , matrix effect , heavily fragmented RNA , poor enrichment or amplification of SARS - CoV-2 genome and PCR inhibitors could lead to poor sequencing quality ( Karthikeyan et al . , 2021;Wolfe et al . , 2022 ( Heijnen et al . , 2021 ) while Lee et al . applied RT - qPCR assays that detect mutations present in Alpha to wastewater samples ( Lee et al . , 2021 ) . Jahn et al . used wastewater genome sequencing to detect Alpha , Beta and Gamma variants ( Jahn et al . , 2021 ) . Yaniv et al . developed RT - qPCR assays for Alpha , Beta , Gamma and Delta ( Yaniv et al . , 2021a(Yaniv et al . , , 2021b . In addition , in our previous studies ( Avgeris et al . , 2021;Galani et al . , 2022 ) , we showed that wastewaterbased epidemiology ( WBE ) can predict hospitalizations and ICP admissions , whereas using our novel Nested - Seq assay for SARS - CoV-2 mutation / variant analysis we provided real - time monitoring of SARS - CoV-2 variants and identified those strains with selective advantage to become dominant in community / population level .