This protocol describes step-by-step instructions for building long (~2kb) amplicon libraries to recover SARS-CoV-2 genomes using the nanopore sequencing.It can be applied for sequencing on the MinION or GridION. This protocol was developed in collaboration with the Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Brazil and the two sequencing facilities at Pathogen Genomic Unit (PGU) and UCL Genomics, University College London (UCL), United Kingdom. This document describes the manual steps to perform the protocol, but for further information about the automation of the protocol, please, contact PGU-UCL. Manager: Rachel Williams https:\/\/www.ucl.ac.uk\/infection-immunity\/pathogen-genomics-unitThis protocol is based in the amplicon tiling strategy described previously by Quick J et al 2017. However, we have applied this strategy to recover long reads (2kb), then some adjustments were performed in the protocol.