title: Longitudinal Whole-genome Sequence Characterization of a Persistent SARS-CoV-2 BA.5 Infection in Immunocompromised Patient receiving Sotrovimab
design: We used 11 L of RNA as template for reverse transcription using Invitrogen SuperScript IV reverse transcription and random hexamers (both ThermoFisher Scientific). We performed whole-genome amplification of the coronavirus with an Artic_nCov-2019_V3 panel of primers (Integrated DNA Technologies, Inc., https://www.idtdna.comExternal Link) (https://artic.network/ncov-2019) and Q5 Hot Start DNA polymerase (New England Biolabs, https://www.neb.comExternal Link). We prepared libraries by using the Nextera DNA Flex Library Preparation Kit (Illumina, https://www.illumina.comExternal Link), following the manufacturers instructions. Libraries were quantified with a Quantus Fluorometer (Promega, https://www.promega.comExternal Link) before being pooled at equimolar concentrations (4 nM). We then sequenced them in pools of <17 libraries on the Miseq system (Illumina Inc.) with the MiSeq Reagent Micro kit version 2 (2151 bp) or in pools of <96 libraries with the MiSeq Reagent (2201 bp).