key: cord-0046163-6xn9swsq
authors: Addetia, Amin; Xie, Hong; Roychoudhury, Pavitra; Shrestha, Lasata; Loprieno, Michelle; Huang, Meei-Li; Jerome, Keith R.; Greninger, Alexander L.
title: Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates
date: 2020-06-23
journal: J Clin Virol
DOI: 10.1016/j.jcv.2020.104523
sha: 6000095a173661729fac7a5fbe70983268bb23e6
doc_id: 46163
cord_uid: 6xn9swsq

nan

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 BBMap (https://sourceforge.net/projects/bbmap/), trimmed of synthetic PCR primers using Primerclip (https://github.com/swiftbiosciences/primerclip) if appropriate, and visualized in Geneious v11.1.4 (6) . Sequencing reads and consensus genomes are available under NCBI BioProject PRJNA610428. ORF7a of SARS-CoV-2 interacts with the ribosomal transport proteins HEATDR3 and MDN1 (10) , and has been demonstrated to inhibit cellular translation in SARS-CoV (11) . Based on the size of the deletions recovered and structure of ORF7a, we hypothesize that most biochemical functions of ORF7a would be inactivated by these deletions. Interestingly, ORF6 of SARS-CoV-2 interacts with the mRNA export proteins NUP98 and RAE1, and may inhibit cellular translation (10) . This redundancy may partially explain the ORF7a deletions observed in our isolates. We predict global sequencing projects may yield additional clinical SARS-CoV-2 isolates with deletions in ORF6 or ORF7a, but not both. 

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An 81 nucleotide deletion in SARS-CoV

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WA-UW-4570 and resulted in the fusion of ORF7a and ORF8. A 227-nucleotide deletion beginning at nt 27,524 was identified in b) WA-UW-5812 and resulted in the fusion of ORF7a and ORF7b. The deletions in c) WA-UW-4570 and d) WA-UW-5812 were confirmed by RT-PCR. An 826-bp product is expected for strains with an intact ORF7a. 434-bp and 599-bp amplicons were obtained for WA-UW-4570 and WA-UW-5812, respectively. The deletions in e) WA-UW-4570 and f) WA-UW-5812 severely truncate the 

Residues retained are highlighted in purple, while those lost are highlighted in gold