RNA was extracted from SARS-CoV-2 positive saliva and nasopharyngeal swab samples. SARS-CoV-2 genomes were amplified using Qiagen OneStep Ahead RT-PCR kit and two sets of tiled amplicon primers. Libraries were constructed using Illumina Nextera XT (cat FC-131-1096) at 0.25x the volume described in the protocol. Libraries were pooled equimolarly and sequenced on the Illumina NextSeq500 and NextSeq2000 using the 2  150 bp paired end protocol.