SRX18001135 K045856 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510079 K045856 K045856 AMPLICON VIRAL RNA RT-PCR GridION SRX18001136 K045857 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510080 K045857 K045857 AMPLICON VIRAL RNA RT-PCR GridION SRX18001137 K045866 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510081 K045866 K045866 AMPLICON VIRAL RNA RT-PCR GridION SRX18001138 K048202 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510082 K048202 K048202 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001139 K048203 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510083 K048203 K048203 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001140 K048204 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510084 K048204 K048204 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001141 K048205 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510085 K048205 K048205 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001142 K048206 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510086 K048206 K048206 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001143 K048207 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510088 K048207 K048207 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001144 K048210 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510087 K048210 K048210 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001145 K048211 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510089 K048211 K048211 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001146 K048212 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510091 K048212 K048212 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001147 K048213 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510090 K048213 K048213 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001148 K045867 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510092 K045867 K045867 AMPLICON VIRAL RNA RT-PCR GridION SRX18001149 K048214 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510093 K048214 K048214 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001150 K048215 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510094 K048215 K048215 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001151 K048216 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510095 K048216 K048216 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001152 K048217 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510096 K048217 K048217 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001153 K048218 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510097 K048218 K048218 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001154 K048219 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510098 K048219 K048219 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001155 K048220 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510099 K048220 K048220 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001156 K048222 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510100 K048222 K048222 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001157 K048223 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510101 K048223 K048223 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001158 K048224 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510102 K048224 K048224 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001159 K045868 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510103 K045868 K045868 AMPLICON VIRAL RNA RT-PCR GridION SRX18001160 K048225 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510104 K048225 K048225 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001161 K048226 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510106 K048226 K048226 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001162 K048252 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510105 K048252 K048252 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001163 K048253 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510107 K048253 K048253 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001164 K048254 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510108 K048254 K048254 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001165 K048255 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510109 K048255 K048255 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001166 K045871 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510110 K045871 K045871 AMPLICON VIRAL RNA RT-PCR GridION SRX18001167 K048256 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510111 K048256 K048256 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001168 K048257 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510112 K048257 K048257 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001169 K048259 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510113 K048259 K048259 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001170 K048260 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510114 K048260 K048260 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001171 K048261 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510115 K048261 K048261 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001172 K048262 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510116 K048262 K048262 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001173 K048263 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510118 K048263 K048263 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001174 K048264 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510117 K048264 K048264 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001175 K048265 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510119 K048265 K048265 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001176 K048266 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510120 K048266 K048266 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001177 K045872 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510121 K045872 K045872 AMPLICON VIRAL RNA RT-PCR GridION SRX18001178 K048267 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510122 K048267 K048267 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001179 K048268 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510124 K048268 K048268 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001180 K048269 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510123 K048269 K048269 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001181 K048270 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510125 K048270 K048270 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001182 K048271 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510126 K048271 K048271 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001183 K048272 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510127 K048272 K048272 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001184 K048273 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510128 K048273 K048273 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001185 K048274 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510129 K048274 K048274 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001186 K048275 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510130 K048275 K048275 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001187 K048276 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510131 K048276 K048276 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001188 K047362 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510132 K047362 K047362 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001189 K047363 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510133 K047363 K047363 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001190 K047364 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510134 K047364 K047364 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001191 K047365 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510137 K047365 K047365 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001192 K047366 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510135 K047366 K047366 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001193 K047367 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510136 K047367 K047367 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001194 K047368 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510138 K047368 K047368 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001195 K047369 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510139 K047369 K047369 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001196 K045861 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510141 K045861 K045861 AMPLICON VIRAL RNA RT-PCR GridION SRX18001197 K047370 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510140 K047370 K047370 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001198 K047371 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510142 K047371 K047371 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001199 K047372 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510143 K047372 K047372 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001200 K047373 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510144 K047373 K047373 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001201 K047374 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510145 K047374 K047374 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001202 K047375 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510146 K047375 K047375 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001203 K047376 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510147 K047376 K047376 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001204 K047377 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510148 K047377 K047377 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001205 K047378 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510149 K047378 K047378 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001206 K047379 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510150 K047379 K047379 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001207 K045862 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510151 K045862 K045862 AMPLICON VIRAL RNA RT-PCR GridION SRX18001208 K047380 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510152 K047380 K047380 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001209 K047381 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510153 K047381 K047381 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001210 K047382 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510154 K047382 K047382 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001211 K047383 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510155 K047383 K047383 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001212 K048166 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510156 K048166 K048166 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001213 K048167 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510157 K048167 K048167 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001214 K048227 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510158 K048227 K048227 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001215 K048228 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510159 K048228 K048228 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001216 K048229 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510161 K048229 K048229 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001217 K048230 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510160 K048230 K048230 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001218 K048231 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510162 K048231 K048231 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001219 K048232 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510163 K048232 K048232 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001220 K048234 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510164 K048234 K048234 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001221 K048235 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510165 K048235 K048235 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001222 K045869 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510166 K045869 K045869 AMPLICON VIRAL RNA RT-PCR GridION SRX18001223 K048236 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510167 K048236 K048236 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001224 K048237 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510168 K048237 K048237 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001225 K048238 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510169 K048238 K048238 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001226 K048239 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510170 K048239 K048239 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001227 K048240 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510171 K048240 K048240 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001228 K048241 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510172 K048241 K048241 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001229 K048242 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510173 K048242 K048242 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001230 K048243 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510174 K048243 K048243 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001231 K048244 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510175 K048244 K048244 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001232 K048245 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510176 K048245 K048245 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001233 K045870 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510177 K045870 K045870 AMPLICON VIRAL RNA RT-PCR GridION SRX18001234 K048246 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510178 K048246 K048246 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001235 K048247 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510179 K048247 K048247 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001236 K048248 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510180 K048248 K048248 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001237 K048249 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510181 K048249 K048249 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001238 K048250 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510182 K048250 K048250 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001239 K048251 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510183 K048251 K048251 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001240 K048301 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510184 K048301 K048301 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001241 K048302 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510185 K048302 K048302 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001242 K045858 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510188 K045858 K045858 AMPLICON VIRAL RNA RT-PCR GridION SRX18001243 K045876 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510186 K045876 K045876 AMPLICON VIRAL RNA RT-PCR GridION SRX18001244 K045877 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510187 K045877 K045877 AMPLICON VIRAL RNA RT-PCR GridION SRX18001245 K045878 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510189 K045878 K045878 AMPLICON VIRAL RNA RT-PCR GridION SRX18001246 K045879 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510190 K045879 K045879 AMPLICON VIRAL RNA RT-PCR GridION SRX18001247 K045880 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510191 K045880 K045880 AMPLICON VIRAL RNA RT-PCR GridION SRX18001248 K045881 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510192 K045881 K045881 AMPLICON VIRAL RNA RT-PCR GridION SRX18001249 K045882 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510193 K045882 K045882 AMPLICON VIRAL RNA RT-PCR GridION SRX18001250 K045883 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510194 K045883 K045883 AMPLICON VIRAL RNA RT-PCR GridION SRX18001251 K045884 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510195 K045884 K045884 AMPLICON VIRAL RNA RT-PCR GridION SRX18001252 K045885 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510196 K045885 K045885 AMPLICON VIRAL RNA RT-PCR GridION SRX18001253 K045859 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510197 K045859 K045859 AMPLICON VIRAL RNA RT-PCR GridION SRX18001254 K047350 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510198 K047350 K047350 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001255 K047351 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510199 K047351 K047351 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001256 K047352 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510200 K047352 K047352 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001257 K047353 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510201 K047353 K047353 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001258 K047354 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510202 K047354 K047354 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001259 K047355 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510203 K047355 K047355 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001260 K047356 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510204 K047356 K047356 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001261 K047357 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510205 K047357 K047357 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001262 K047358 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510206 K047358 K047358 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001263 K047359 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510207 K047359 K047359 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001264 K045860 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510208 K045860 K045860 AMPLICON VIRAL RNA RT-PCR GridION SRX18001265 K047360 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510209 K047360 K047360 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001266 K047361 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510210 K047361 K047361 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001267 K045865 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510211 K045865 K045865 AMPLICON VIRAL RNA RT-PCR GridION SRX18001268 K048192 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510212 K048192 K048192 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001269 K048193 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510213 K048193 K048193 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001270 K048194 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510214 K048194 K048194 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001271 K048195 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510216 K048195 K048195 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001272 K048196 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510215 K048196 K048196 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001273 K048197 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510217 K048197 K048197 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001274 K048198 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510218 K048198 K048198 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001275 K048199 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510219 K048199 K048199 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001276 K048200 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510220 K048200 K048200 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001277 K048201 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510221 K048201 K048201 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001278 K045873 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510222 K045873 K045873 AMPLICON VIRAL RNA RT-PCR GridION SRX18001279 K048277 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510223 K048277 K048277 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001280 K048278 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510224 K048278 K048278 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001281 K048279 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510225 K048279 K048279 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001282 K048280 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510226 K048280 K048280 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001283 K048281 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510227 K048281 K048281 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001284 K048282 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510228 K048282 K048282 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001285 K048283 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510229 K048283 K048283 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001286 K048284 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510230 K048284 K048284 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001287 K048285 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510231 K048285 K048285 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001288 K048286 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510232 K048286 K048286 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001289 K045874 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510233 K045874 K045874 AMPLICON VIRAL RNA RT-PCR GridION SRX18001290 K048287 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510235 K048287 K048287 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001291 K048288 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510234 K048288 K048288 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001292 K048289 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510236 K048289 K048289 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001293 K048290 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510237 K048290 K048290 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001294 K048291 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510238 K048291 K048291 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001295 K048292 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510239 K048292 K048292 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001296 K048293 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510240 K048293 K048293 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001297 K048294 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510241 K048294 K048294 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001298 K048295 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510242 K048295 K048295 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001299 K048296 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510243 K048296 K048296 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001300 K045875 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510245 K045875 K045875 AMPLICON VIRAL RNA RT-PCR GridION SRX18001301 K048297 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510244 K048297 K048297 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001302 K048298 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510246 K048298 K048298 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001303 K048299 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510247 K048299 K048299 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001304 K048300 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510248 K048300 K048300 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001305 K048168 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510249 K048168 K048168 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001306 K048169 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510251 K048169 K048169 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001307 K048170 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510250 K048170 K048170 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001308 K048171 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510252 K048171 K048171 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001309 K045863 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510253 K045863 K045863 AMPLICON VIRAL RNA RT-PCR GridION SRX18001310 K048172 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510254 K048172 K048172 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001311 K048173 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510255 K048173 K048173 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001312 K048174 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510256 K048174 K048174 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001313 K048175 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510257 K048175 K048175 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001314 K048176 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510259 K048176 K048176 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001315 K048177 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510258 K048177 K048177 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001316 K048178 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510261 K048178 K048178 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001317 K048179 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510260 K048179 K048179 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001318 K048180 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510262 K048180 K048180 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001319 K048181 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510263 K048181 K048181 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001320 K045864 SRP265610 PRJNA636748 Amplicons were generated using the ARTIC PCR tiling method. Libraries were prepared using the Ligation Sequencing kit and method using the 96 plate barcodes. Libraries were run on the Oxford Nanopore GridION. SRS15510264 K045864 K045864 AMPLICON VIRAL RNA RT-PCR GridION SRX18001321 K048182 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510265 K048182 K048182 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001322 K048183 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510266 K048183 K048183 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001323 K048184 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510267 K048184 K048184 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001324 K048185 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510268 K048185 K048185 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001325 K048186 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510269 K048186 K048186 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001326 K048187 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510270 K048187 K048187 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001327 K048188 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510271 K048188 K048188 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001328 K048189 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510273 K048189 K048189 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001329 K048190 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510272 K048190 K048190 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq SRX18001330 K048191 SRP265610 PRJNA636748 Amplicons were generated using the COVIDseq assay. Libraries were prepared according to the manufacturer's instructions using the Illumina Nextera UD indexes. Libraries were run on the Illumina MiSeq. SRS15510274 K048191 K048191 AMPLICON VIRAL RNA RT-PCR Illumina MiSeq