Virus sequencing of patients infected with COVID-19 from Southern California, Tijuana, New Orleans and Jordan by the SEARCH Alliance along with a large number of partners. The virus sequence data will be used to to gain insights into the emergence and spread of SARS-CoV-2. The sequencing is being performed using an amplicon-based sequencing scheme using PrimalSeq with artic nCoV-2019 scheme. Nanopore data was processed using the artic-nCoV019 pipeline with minimap2 and medaka. Illumina data was processed using iVar (Grubaguh et al. Genome Biology 2019) with bwa. Methodology is available at https://github.com/andersen-lab/HCoV-19-Genomics