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Peculiar among human RNA viruses, coronaviruses have large genomes containing accessory genes that are not required for replication [1]. Here, we report two large deletions in ORF7a, both of which produce new open reading frames (ORFs) through the fusion of the N-terminus of ORF7a and a downstream ORF. We recovered genomes from the SARS-CoV-2 isolates from two separate patients as part of an ongoing University of Washington IRB-approved genomic surveillance project [2, 3]. Sequencing libraries were generated from double-stranded cDNA [4] using Swift Biosciences’ SARS-CoV-2 Normalase Amplicon Sequencing kit or the Nextera DNA Flex Pre-Enrichment kit (Illumina) followed by enrichment using a SARS-CoV-2 xGen enrichment panel (NC_045512; IDT). Sequence reads were trimmed using Trimommatic v0. 38 [5], aligned to the SARS-CoV-2 reference genome (NC_045512. 2) using …