SRX22328100 CAP222_2020_008WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378153 CAP222_2020 CAP222_2020_008WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328101 CAP222_3120_038WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378156 CAP222_3120 CAP222_3120_038WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328102 CAP244_4370_332WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378161 CAP244_4370 CAP244_4370_332WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328103 CAP244_4390_359WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378157 CAP244_4390 CAP244_4390_359WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328104 CAP244_4400_372WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378155 CAP244_4400 CAP244_4400_372WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328105 CAP268_2000_008WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378158 CAP268_2000 CAP268_2000_008WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328106 CAP268_3100_032WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378160 CAP268_3100 CAP268_3100_032WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328107 CAP222_4190_095WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378154 CAP222_4190 CAP222_4190_095WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328108 CAP268_3160_058WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378159 CAP268_3160 CAP268_3160_058WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328109 CAP268_4180_086WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378164 CAP268_4180 CAP268_4180_086WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328110 CAP268_4220_137WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378165 CAP268_4220 CAP268_4220_137WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328111 CAP268_4240_163WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378172 CAP268_4240 CAP268_4240_163WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328112 CAP268_4260_189WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378162 CAP268_4260 CAP268_4260_189WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328113 CAP268_4280_217WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378163 CAP268_4280 CAP268_4280_217WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328114 CAP277_2000_008WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378184 CAP277_2000 CAP277_2000_008WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328115 CAP277_3090_030WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378183 CAP277_3090 CAP277_3090_030WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328116 CAP277_3160_058WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378166 CAP277_3160 CAP277_3160_058WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328117 CAP277_4180_085WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378167 CAP277_4180 CAP277_4180_085WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328118 CAP280_4270_209WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378170 CAP280_4270 CAP280_4270_209WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328119 CAP280_4280_222WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378168 CAP280_4280 CAP280_4280_222WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328120 CAP280_4310_256WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378191 CAP280_4310 CAP280_4310_256WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328121 CAP280_4340_296WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378169 CAP280_4340 CAP280_4340_296WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328122 CAP333_2000_004WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378171 CAP333_2000 CAP333_2000_004WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328123 CAP333_3110_033WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378173 CAP333_3110 CAP333_3110_033WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328124 CAP222_4250_174WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378176 CAP222_4250 CAP222_4250_174WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328125 CAP333_4170_068WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378174 CAP333_4170 CAP333_4170_068WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328126 CAP333_4180_082WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378178 CAP333_4180 CAP333_4180_082WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328127 CAP333_4200_109WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378175 CAP333_4200 CAP333_4200_109WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328128 CAP333_4220_133WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378177 CAP333_4220 CAP333_4220_133WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328129 CAP333_4240_156WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378181 CAP333_4240 CAP333_4240_156WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328130 CAP337_2000_009WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378182 CAP337_2000 CAP337_2000_009WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328131 CAP337_3090_029WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378179 CAP337_3090 CAP337_3090_029WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328132 CAP337_3160_059WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378180 CAP337_3160 CAP337_3160_059WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328133 CAP337_4180_087WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378186 CAP337_4180 CAP337_4180_087WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328134 CAP337_4200_111WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378185 CAP337_4200 CAP337_4200_111WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328135 CAP222_4270_200WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378188 CAP222_4270 CAP222_4270_200WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328136 CAP337_4230_151WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378192 CAP337_4230 CAP337_4230_151WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328137 CAP337_4240_163WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378187 CAP337_4240 CAP337_4240_163WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328138 CAP372_2000_003WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378189 CAP372_2000 CAP372_2000_003WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328139 CAP372_3100_027WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378190 CAP372_3100 CAP372_3100_027WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328140 CAP372_3160_053WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378195 CAP372_3160 CAP372_3160_053WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328141 CAP372_4180_081WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378196 CAP372_4180 CAP372_4180_081WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328142 CAP372_4200_106WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378193 CAP372_4200 CAP372_4200_106WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328143 CAP372_4220_132WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378197 CAP372_4220 CAP372_4220_132WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328144 CAP372_4240_161WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378194 CAP372_4240 CAP372_4240_161WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328145 CAP372_4250_172WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378198 CAP372_4250 CAP372_4250_172WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328146 CAP222_4290_224WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378199 CAP222_4290 CAP222_4290_224WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328147 CAP372_9999_182WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378200 CAP372_9999 CAP372_9999_182WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328148 CAP380_2000_008WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378203 CAP380_2000 CAP380_2000_008WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328149 CAP380_3110_037WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378201 CAP380_3110 CAP380_3110_037WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328150 CAP222_4330_278WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378202 CAP222_4330 CAP222_4330_278WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328151 CAP222_4350_304WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378204 CAP222_4350 CAP222_4350_304WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328152 CAP222_4360_313WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378205 CAP222_4360 CAP222_4360_313WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328153 CAP244_2000_009WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378212 CAP244_2000 CAP244_2000_009WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328154 CAP244_3100_033WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378206 CAP244_3100 CAP244_3100_033WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328155 CAP244_3160_056WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378214 CAP244_3160 CAP244_3160_056WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328156 CAP244_4180_081WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378208 CAP244_4180 CAP244_4180_081WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328157 CAP244_4200_107WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378209 CAP244_4200 CAP244_4200_107WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328158 CAP244_4220_137WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378213 CAP244_4220 CAP244_4220_137WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328159 CAP244_4230_150WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378207 CAP244_4230 CAP244_4230_150WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328160 CAP222_4170_070WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378211 CAP222_4170 CAP222_4170_070WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328161 CAP244_4260_191WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378210 CAP244_4260 CAP244_4260_191WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328162 CAP244_4290_230WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378216 CAP244_4290 CAP244_4290_230WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328163 CAP244_4310_255WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378215 CAP244_4310 CAP244_4310_255WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328164 CAP244_4330_282WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378223 CAP244_4330 CAP244_4330_282WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328165 CAP244_4350_307WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378221 CAP244_4350 CAP244_4350_307WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328166 CAP380_3160_059WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378217 CAP380_3160 CAP380_3160_059WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328167 CAP380_4180_085WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378220 CAP380_4180 CAP380_4180_085WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328168 CAP380_4200_110WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378222 CAP380_4200 CAP380_4200_110WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328169 CAP380_4210_125WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378219 CAP380_4210 CAP380_4210_125WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328170 CAP217_4180_087WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378218 CAP217_4180 CAP217_4180_087WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328171 CAP316_2000_012WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378224 CAP316_2000 CAP316_2000_012WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328172 CAP316_3100_036WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378226 CAP316_3100 CAP316_3100_036WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328173 CAP222_4310_251WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378227 CAP222_4310 CAP222_4310_251WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328174 CAP316_3140_053WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378225 CAP316_3140 CAP316_3140_053WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328175 CAP316_4180_090WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378232 CAP316_4180 CAP316_4180_090WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328176 CAP316_4200_114WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378228 CAP316_4200 CAP316_4200_114WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328177 CAP316_4220_141WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378230 CAP316_4220 CAP316_4220_141WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328178 CAP316_4240_166WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378229 CAP316_4240 CAP316_4240_166WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328179 CAP316_4260_192WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378233 CAP316_4260 CAP316_4260_192WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328180 CAP316_4270_205WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378235 CAP316_4270 CAP316_4270_205WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328181 CAP222_4210_122WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378234 CAP222_4210 CAP222_4210_122WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328182 CAP277_4200_110WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378231 CAP277_4200 CAP277_4200_110WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328183 CAP277_4220_137WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378237 CAP277_4220 CAP277_4220_137WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328184 CAP277_4240_163WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378236 CAP277_4240 CAP277_4240_163WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328185 CAP277_4260_189WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378241 CAP277_4260 CAP277_4260_189WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328186 CAP277_4280_215WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378242 CAP277_4280 CAP277_4280_215WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328187 CAP277_4300_243WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378238 CAP277_4300 CAP277_4300_243WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328188 CAP277_4310_254WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378239 CAP277_4310 CAP277_4310_254WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328189 CAP280_2000_012WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378243 CAP280_2000 CAP280_2000_012WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328190 CAP280_3100_036WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378240 CAP280_3100 CAP280_3100_036WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328191 CAP280_3160_063WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378244 CAP280_3160 CAP280_3160_063WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328192 CAP222_4230_148WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378245 CAP222_4230 CAP222_4230_148WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328193 CAP280_4180_090WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378247 CAP280_4180 CAP280_4180_090WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328194 CAP280_4200_117WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378248 CAP280_4200 CAP280_4200_117WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328195 CAP280_4230_156WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378246 CAP280_4230 CAP280_4230_156WPI AMPLICON VIRAL RNA PCR Illumina MiSeq SRX22328196 CAP280_4250_184WPI SRP469636 bp0 Viral RNA was reverse transcribed to cDNA using Superscript IV Reverse Transcriptase (Invitrogen). Multiple cDNA primers (with PrimerIDs) were multiplexed to generate cDNA templates corresponding to multiple regions of the genome. A first round PCR was performed using the KAPA2G Fast Multiplex Mix (Kapa Biosystems), followed by a second round PCR using the Expand High Fidelity PCR System (Roche) to incorporate Illumina MiSeq version 3 indexes and adapters. PCR products were purified using AMPureXP beads (Beckman Coulter). SRS19378249 CAP280_4250 CAP280_4250_184WPI AMPLICON VIRAL RNA PCR Illumina MiSeq