SRX22417249 WSLH-707759001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448924 707759001 WSLH-707759001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417250 WSLH-707521001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448925 707521001 WSLH-707521001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417251 WSLH-707274001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448926 707274001 WSLH-707274001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417252 WSLH-707800001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448927 707800001 WSLH-707800001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417253 WSLH-708024001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448928 708024001 WSLH-708024001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417254 WSLH-708163001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448929 708163001 WSLH-708163001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417255 WSLH-708171001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448930 708171001 WSLH-708171001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417256 WSLH-708167001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448931 708167001 WSLH-708167001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417257 WSLH-708028001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448932 708028001 WSLH-708028001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417258 WSLH-708026001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448933 708026001 WSLH-708026001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417259 WSLH-707522001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448934 707522001 WSLH-707522001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417260 WSLH-708169001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448935 708169001 WSLH-708169001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417261 WSLH-708179001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448936 708179001 WSLH-708179001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417262 WSLH-708032001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448937 708032001 WSLH-708032001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417263 WSLH-4566 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448938 4566 WSLH-4566 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417264 WSLH-4567 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448939 4567 WSLH-4567 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417265 WSLH-707260001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448940 707260001 WSLH-707260001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417266 WSLH-708160001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448941 708160001 WSLH-708160001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417267 WSLH-707527001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448942 707527001 WSLH-707527001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417268 WSLH-707769001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448943 707769001 WSLH-707769001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417269 WSLH-4559 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448944 4559 WSLH-4559 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417270 WSLH-4571 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448945 4571 WSLH-4571 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417271 WSLH-707773001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448946 707773001 WSLH-707773001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417272 WSLH-707783001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448947 707783001 WSLH-707783001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417273 WSLH-708172001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448948 708172001 WSLH-708172001 WGS METAGENOMIC RT-PCR Illumina MiSeq SRX22417274 WSLH-707789001 SRP402434 PRJNA889839 A total of 10 mL of wastewater were concentrated using Nanotrap Magnetic Virus Particles (Ceres Nano) and total nucleic acids were extracted using Maxwell(R) HT Environmental TNA kits (Promega). Both steps were performed on a KingFisher Apex and Flex (ThermoFisher Scientic), respectively. The sequencing library was generated using QIAseq DIRECT SARS-CoV-2 Enhanced kits with the primer Booster (Qiagen) following manufacturer's instructions. Briefly, single-stranded viral RNA molecules were reverse transcribed into cDNA using hexaprimers. SARS-CoV-2 genome was then specifically enriched using a SARS-CoV-2 primer panel. The panel consists of approximately 550 primers for creating 425 amplicons, covering the entire SARS-CoV-2 viral genome. The second PCR was performed using seven cycles. The library preparation was fully automated using the Biomek i5 Automated Workstation (Beckman Coulter). Prior to sequencing, the library was quantified using the Qubit (ThermoFisher Scientic) and the quality was assessed using the QIAxcel Advanced System (Qiagen). The library was sequenced on an Illumina MiSeq platform using MiSeq Reagent v2 (300 cycles) kits. SRS19448949 707789001 WSLH-707789001 WGS METAGENOMIC RT-PCR Illumina MiSeq