Author: Gage Kahl Moreno; Katarina M Braun; Peter J Halfmann; Trent M Prall; Kasen K Riemersma; Amelia K Haj; Joseph Lalli; Kelsey R Florek; Thomas C Friedrich; Yoshihiro Kawaoka; David H O'Connor
Title: Limited SARS-CoV-2 diversity within hosts and following passage in cell culture Document date: 2020_4_20
ID: izu5x2d4_1
Snippet: No deletion in spike gene after passaging in cell culture 117 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.051011 doi: bioRxiv preprint To understand how serial passaging SARS-CoV-2 affects genomic variation, we sequenced 118 virus populations after each passage using the same SISPA metagenomics approac.....
Document: No deletion in spike gene after passaging in cell culture 117 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.051011 doi: bioRxiv preprint To understand how serial passaging SARS-CoV-2 affects genomic variation, we sequenced 118 virus populations after each passage using the same SISPA metagenomics approach we used 119 to characterize the original biological specimen. Passaged sample names and cell lines are 120 described in the methods. An in-house pipeline (available at: 121 https://github.com/katarinabraun/SARSCoV2_passage_MS) was applied to trim out primer 122 sequences, bioinformatically deplete host reads, and generate alignment files, which contained 123 all reads mapping to the SARS-CoV-2 Madison reference genome (MT039887.1). At the 124 consensus level, SARS-CoV-2 does not accumulate genetic variation after two passages on 125
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